TY - JOUR A1 - Glückler, Ramesh A1 - Herzschuh, Ulrike A1 - Kruse, Stefan A1 - Andreev, Andrei A1 - Vyse, Stuart Andrew A1 - Winkler, Bettina A1 - Biskaborn, Boris A1 - Pestryakova, Luidmila Agafyevna A1 - Dietze, Elisabeth T1 - Wildfire history of the boreal forest of south-western Yakutia (Siberia) over the last two millennia documented by a lake-sediment charcoal record JF - Biogeosciences : BG / European Geosciences Union N2 - Wildfires, as a key disturbance in forest ecosystems, are shaping the world's boreal landscapes. Changes in fire regimes are closely linked to a wide array of environmental factors, such as vegetation composition, climate change, and human activity. Arctic and boreal regions and, in particular, Siberian boreal forests are experiencing rising air and ground temperatures with the subsequent degradation of permafrost soils leading to shifts in tree cover and species composition. Compared to the boreal zones of North America or Europe, little is known about how such environmental changes might influence long-term fire regimes in Russia. The larch-dominated eastern Siberian deciduous boreal forests differ markedly from the composition of other boreal forests, yet data about past fire regimes remain sparse. Here, we present a high-resolution macroscopic charcoal record from lacustrine sediments of Lake Khamra (southwest Yakutia, Siberia) spanning the last ca. 2200 years, including information about charcoal particle sizes and morphotypes. Our results reveal a phase of increased charcoal accumulation between 600 and 900 CE, indicative of relatively high amounts of burnt biomass and high fire frequencies. This is followed by an almost 900-year-long period of low charcoal accumulation without significant peaks likely corresponding to cooler climate conditions. After 1750 CE fire frequencies and the relative amount of biomass burnt start to increase again, coinciding with a warming climate and increased anthropogenic land development after Russian colonization. In the 20th century, total charcoal accumulation decreases again to very low levels despite higher fire frequency, potentially reflecting a change in fire management strategies and/or a shift of the fire regime towards more frequent but smaller fires. A similar pattern for different charcoal morphotypes and comparison to a pollen and non-pollen palynomorph (NPP) record from the same sediment core indicate that broad-scale changes in vegetation composition were probably not a major driver of recorded fire regime changes. Instead, the fire regime of the last two millennia at Lake Khamra seems to be controlled mainly by a combination of short-term climate variability and anthropogenic fire ignition and suppression. Y1 - 2021 U6 - https://doi.org/10.5194/bg-18-4185-2021 SN - 1726-4170 SN - 1726-4189 VL - 18 IS - 13 SP - 4185 EP - 4209 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Raatz, Larissa A1 - Pirhofer-Walzl, Karin A1 - Müller, Marina E.H. A1 - Scherber, Christoph A1 - Joshi, Jasmin Radha T1 - Who is the culprit: Is pest infestation responsible for crop yield losses close to semi-natural habitats? JF - Ecology and Evolution N2 - Semi-natural habitats (SNHs) are becoming increasingly scarce in modern agricultural landscapes. This may reduce natural ecosystem services such as pest control with its putatively positive effect on crop production. In agreement with other studies, we recently reported wheat yield reductions at field borders which were linked to the type of SNH and the distance to the border. In this experimental landscape-wide study, we asked whether these yield losses have a biotic origin while analyzing fungal seed and fungal leaf pathogens, herbivory of cereal leaf beetles, and weed cover as hypothesized mediators between SNHs and yield. We established experimental winter wheat plots of a single variety within conventionally managed wheat fields at fixed distances either to a hedgerow or to an in-field kettle hole. For each plot, we recorded the fungal infection rate on seeds, fungal infection and herbivory rates on leaves, and weed cover. Using several generalized linear mixed-effects models as well as a structural equation model, we tested the effects of SNHs at a field scale (SNH type and distance to SNH) and at a landscape scale (percentage and diversity of SNHs within a 1000-m radius). In the dry year of 2016, we detected one putative biotic culprit: Weed cover was negatively associated with yield values at a 1-m and 5-m distance from the field border with a SNH. None of the fungal and insect pests, however, significantly affected yield, neither solely nor depending on type of or distance to a SNH. However, the pest groups themselves responded differently to SNH at the field scale and at the landscape scale. Our findings highlight that crop losses at field borders may be caused by biotic culprits; however, their negative impact seems weak and is putatively reduced by conventional farming practices. KW - arable weeds KW - cereal leaf beetle KW - fungal pathogens KW - herbivory KW - structural equation model KW - wheat Y1 - 2021 U6 - https://doi.org/10.1002/ece3.8046 SN - 1467-6435 VL - 11 SP - 13232 EP - 13246 PB - Wiley-Blackwell CY - Oxford ET - 19 ER - TY - JOUR A1 - Raatz, Larissa A1 - Pirhofer-Walzl, Karin A1 - Müller, Marina E.H. A1 - Scherber, Christoph A1 - Joshi, Jasmin Radha T1 - Who is the culprit: Is pest infestation responsible for crop yield losses close to semi-natural habitats? JF - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Semi-natural habitats (SNHs) are becoming increasingly scarce in modern agricultural landscapes. This may reduce natural ecosystem services such as pest control with its putatively positive effect on crop production. In agreement with other studies, we recently reported wheat yield reductions at field borders which were linked to the type of SNH and the distance to the border. In this experimental landscape-wide study, we asked whether these yield losses have a biotic origin while analyzing fungal seed and fungal leaf pathogens, herbivory of cereal leaf beetles, and weed cover as hypothesized mediators between SNHs and yield. We established experimental winter wheat plots of a single variety within conventionally managed wheat fields at fixed distances either to a hedgerow or to an in-field kettle hole. For each plot, we recorded the fungal infection rate on seeds, fungal infection and herbivory rates on leaves, and weed cover. Using several generalized linear mixed-effects models as well as a structural equation model, we tested the effects of SNHs at a field scale (SNH type and distance to SNH) and at a landscape scale (percentage and diversity of SNHs within a 1000-m radius). In the dry year of 2016, we detected one putative biotic culprit: Weed cover was negatively associated with yield values at a 1-m and 5-m distance from the field border with a SNH. None of the fungal and insect pests, however, significantly affected yield, neither solely nor depending on type of or distance to a SNH. However, the pest groups themselves responded differently to SNH at the field scale and at the landscape scale. Our findings highlight that crop losses at field borders may be caused by biotic culprits; however, their negative impact seems weak and is putatively reduced by conventional farming practices. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1240 KW - arable weeds KW - cereal leaf beetle KW - fungal pathogens KW - herbivory KW - structural equation model KW - wheat Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-549622 SN - 1866-8372 SP - 13232 EP - 13246 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Boeker, Sonja A1 - Hermanussen, Michael A1 - Scheffler, Christiane ED - Scheffler, Christiane ED - Koziel, Slawomir ED - Hermanussen, Michael ED - Bogin, Barry T1 - Westernization of self-perception in modern affluent Indonesian school children T2 - Human Biology and Public Health N2 - Background Subjective Social Status is used as an important predictor for psychological and physiological findings, most commonly measured with the MacArthur Scale (Ladder Test). Previous studies have shown that this test fits better in Western cultures. The idea of a social ladder itself and ranking oneself “higher” or “lower” is a concept that accords to the Western thinking. Objectives We hypothesize that in a culture where only the elites have adapted to a Western lifestyle, the test results reflect a higher level of accuracy for this stratum. We also expect that self-perception differs per sex. Sample and Methods We implemented the Ladder Test in a study of Indonesian schoolchildren aged between 5 and 13 years (boys N = 369, girls N= 364) from non-private and private schools in Kupang in 2020. Results Our analysis showed that the Ladder Test results were according to the Western expectations only for the private school, as the Ladder Scores significantly decreased with age (LM: p = 0.04). The Ladder Test results are best explained by “Education Father” for the non-private school pupils (p = 0.01) and all boys (p = 0.04), by “School Grades” for the private school cohort (p = 0.06) and by “Household Score” for girls (p =0.09). Conclusion This finding indicates that the concept of ranking oneself “high” or “low” on a social ladder is strongly implicated with Western ideas. A ladder implies social movement by “climbing” up or down. According to that, reflection of self-perception is influenced by culture. KW - self-perception KW - social status KW - westernization KW - cultural dependence Y1 - 2021 U6 - https://doi.org/10.52905/hbph.v1.4 SN - 2748-9957 VL - 2021 IS - 1 SP - 1 EP - 13 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Yan, Jiawei A1 - Frøkjær, Emil Egede A1 - Engelbrekt, Christian A1 - Leimkühler, Silke A1 - Ulstrup, Jens A1 - Wollenberger, Ulla A1 - Xiao, Xinxin A1 - Zhang, Jingdong T1 - Voltammetry and single-molecule in situ scanning tunnelling microscopy of the redox metalloenzyme human sulfite oxidase JF - ChemElectroChem N2 - Human sulfite oxidase (hSO) is a homodimeric two-domain enzyme central in the biological sulfur cycle. A pyranopterin molybdenum cofactor (Moco) is the catalytic site and a heme b(5) group located in the N-terminal domain. The two domains are connected by a flexible linker region. Electrons produced at the Moco in sulfite oxidation, are relayed via heme b(5) to electron acceptors or an electrode surface. Inter-domain conformational changes between an open and a closed enzyme conformation, allowing "gated" electron transfer has been suggested. We first recorded cyclic voltammetry (CV) of hSO on single-crystal Au(111)-electrode surfaces modified by self-assembled monolayers (SAMs) both of a short rigid thiol, cysteamine and of a longer structurally flexible thiol, omega-amino-octanethiol (AOT). hSO on cysteamine SAMs displays a well-defined pair of voltammetric peaks around -0.207 V vs. SCE in the absence of sulfite substrate, but no electrocatalysis. hSO on AOT SAMs displays well-defined electrocatalysis, but only "fair" quality voltammetry in the absence of sulfite. We recorded next in situ scanning tunnelling spectroscopy (STS) of hSO on AOT modified Au(111)-electrodes, disclosing, a 2-5 % surface coverage of strong molecular scale contrasts, assigned to single hSO molecules, notably with no contrast difference in the absence and presence of sulfite. In situ STS corroborated this observation with a sigmoidal tunnelling current/overpotential correlation. KW - cyclic voltammetry KW - human sulfite oxidase KW - in  situ scanning KW - tunnelling spectroscopy KW - self-assembled molecular monolayers KW - single-crystal gold electrodes Y1 - 2021 U6 - https://doi.org/10.1002/celc.202001258 SN - 2196-0216 VL - 8 IS - 1 SP - 164 EP - 171 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Scheffler, Christiane A1 - Nguyen, Thi Hong A1 - Hermanussen, Michael T1 - Vietnamese migrants are as tall as they want to be JF - Human biology and public health N2 - Background: Members of the same social group tent to have the same body height. Migrants tend to adjust in height to their host communities. Objectives: Social-Economic-Political-Emotional (SEPE) factors influence growth. We hypothesized that Vietnamese young adult migrants in Germany (1) are taller than their parents, (2) are as tall as their German peers, and (3) are as tall as predicted by height expectation at age 13 years. Sample: The study was conducted in 30 male and 54 female Vietnamese migrants (mean age 26.23 years. SD=4.96) in Germany in 2020. Methods: Information on age, sex, body height, school and education, job, height and ethnicity of best friend, migration history and cultural identification, parental height and education, and recalled information on their personal height expectations at age 13 years were obtained by questionnaire. The data were analyzed by St. Nicolas House Analysis (SNHA) and multiple regression. Results: Vietnamese young adults are taller than their parents (females 3.85cm, males 7.44cm), but do not fully attain height of their German peers. The body height is positively associated with the height of best friend (p < 0.001), the height expectation at age 13 year (p < 0.001), and father’s height (p=0.001). Conclusion: Body height of Vietnamese migrants in Germany reflects competitive growth and strategic growth adjustments. The magnitude of this intergenerational trend supports the concept that human growth depends on SEPE factors. KW - body height KW - regulation of growth KW - migrants KW - Social-Economic-Political-Emotional (SEPE) factors Y1 - 2021 U6 - https://doi.org/10.52905/hbph.v2.12 SN - 2748-9957 IS - 2 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Günther, Kerstin A1 - Schmidt, Marcus A1 - Quitt, Heinz A1 - Heinken, Thilo T1 - Veränderungen der Waldvegetation im Elbe-Havelwinkel von 1960 bis 2015 JF - Tuexenia : Mitteilungen der Floristisch-Soziologischen Arbeitsgemeinschaft N2 - Forest ecosystems are subject to a variety of influences such as forest management, nitrogen deposition, changes in the groundwater level or the immigration of invasive species. The repetition of historical releves is an important means of documenting the resulting changes in plant communities and determining their main drivers. In 2015, we examined the vegetation change in 140 semi-permanent plots in managed forests in the Elbe valley in the NE German lowlands (Saxony-Anhalt, Brandenburg). The first survey took place from 1956 to 1963. The releves cover an almost uniquely broad spectrum of different site conditions, ranging from wet forests (alluvial, swamp and bog forests of Alnion incanae, Alnion glutinosae and Betulion pubescentis) to acidic mixed oak forests (Quercion roboris) up to acidic, mostly dry pine forests with different nutrient status (Dicrano-Pinion). We analyzed the changes in the vegetation with the help of forest stand data, winner and loser species, alpha- and beta-diversity as well as the Ellenberg indicator values for nitrogen, reaction, moisture and light. In contrast to previous resurvey studies, areas were also taken into account on which a complete change of forest stand had taken place before the second survey. Particularly in the wet forests and acidic forests with a moderately good nutrient supply, changes in the main tree species have been recorded, and many pine stands have been newly established in the meantime. The species richness has decreased overall and in almost all forest types, but the beta-diversity has remained unchanged or has increased. The Ellenberg values indicate a decrease in soil moisture in the wet forests, while the acidic pine forests in particular have become darker, richer in nutrients and more humid. The number of loser species is more than twice as high as that of the winner species, but with different developments in the individual forest types. In particular, the wet forests, the acidic mixed oak forests and the lichen-pine forests have lost most of their characteristic species. The resurvey after more than 50 years shows a different development of the individual forest types. Vegetation changes in the wet forests are mainly due to local groundwater level drawdown and the resulting increased availability of nutrients. The alluvial forests were also strongly influenced by forest interventions. The reasons for the trend towards more humid and more nutrient-rich conditions in formerly dry acidic pine and oak forests are nitrogen depositions and a succession after the abandonment of historical forms of forest use (litter raking, forest pasture). Although the individual forest types have developed differently, eutrophication, falling groundwater levels and silviculture are the most important causes for the changes in vegetation. Silvicultural interventions such as clear cutting and stand conversion with a change of tree species are at the same time the main reason why the vegetation has not been homogenized despite the leveling of the site gradient as measured by the beta-diversity. N2 - Waldökosysteme unterliegen vielfältigen Einflüssen wie forstlicher Bewirtschaftung, Stickstoffdeposition, Veränderung des Grundwasserspiegels oder der Einwanderung invasiver Arten. Die Wiederholung historischer Vegetationsaufnahmen ist ein wichtiges Mittel, um Veränderungen der Pflanzengesellschaften zu dokumentieren und mögliche Hauptursachen (Treiber) zu bestimmen. Wir haben 2015 den Vegetationswandel auf 140 semi-permanenten Plots in Wirtschaftswäldern der Elbtalniederung im Nordostdeutschen Tiefland (Sachsen-Anhalt, Brandenburg) untersucht. Die Erstaufnahme erfolgte von 1956 bis 1963. Die Vegetationsaufnahmen decken ein fast einzigartig breites Spektrum unterschiedlicher Waldstandorte ab, das von Feuchtwäldern (Au-, Bruch- und Moorwäldern des Alnion incanae, Alnion glutinosae und Betulion pubescentis) über bodensaure Eichen-Mischwälder (Quercion roboris) bis hin zu bodensauren, meist trockenen Kiefernwäldern mit unterschiedlicher Nährstoffausstattung (Dicrano-Pinion) reicht. Die Veränderungen der Vegetation haben wir mit Hilfe von Bestandesdaten, Gewinner- und Verliererarten, der α- und β -Diversität sowie der Ellenberg-Zeigerwerte für Stickstoff, Reaktion, Feuchte und Licht analysiert. Dabei wurden, anders als in den meisten bisherigen Wiederholungsuntersuchungen, auch Flächen berücksichtigt, auf denen bis zur Zweitaufnahme ein vollständiger Bestandeswechsel stattgefunden hatte. Insbesondere in den Feuchtwäldern und den bodensauren Wäldern mit mäßig guter Nährstoffversorgung sind Wechsel der Hauptbaumarten zu verzeichnen; außerdem wurden viele Kiefernbestände zwischenzeitlich neu begründet. Die Artenzahl hat insgesamt und in fast allen Waldtypen abgenommen, die β-Diversität ist jedoch unverändert geblieben bzw. hat sich erhöht. Die Zeigerwerte deuten auf eine Abnahme der Bodenfeuchte in den Au-, Bruch-, und Moorwäldern hin, während insbesondere die bodensauren Kiefernwälder dunkler, nährstoffreicher und feuchter geworden sind. Die Anzahl der Verlierer-Arten ist mehr als doppelt so hoch wie die der Gewinner-Arten, jedoch mit unterschiedlicher Entwicklung in den einzelnen Waldtypen. Insbesondere die nassen und feuchten Wälder, die bodensauren Eichen-Mischwälder und die Flechten-Kiefernwälder haben die meisten ihrer charakteristischen Arten verloren. Veränderungen der Vegetation in den Feuchtwäldern gehen v. a. auf lokal gesunkene Grundwasserspiegel und eine dadurch gestiegene Nährstoffverfügbarkeit zurück; die Artenzusammensetzung der Auwälder wurde zudem sehr stark durch forstliche Eingriffe beeinflusst. Ursachen für den Trend zu feuchteren und nährstoffreicheren Bedingungen in ehemals trockenen bodensauren Kiefern- und Eichenwäldern sind Stickstoffeinträge sowie eine Sukzession nach Aufgabe historischer Waldnutzungs-formen (Streunutzung, Waldweide). Obwohl sich die einzelnen Waldtypen unterschiedlich entwickelt haben, sind Eutrophierung, sinkende Grundwasserspiegel und Waldbaumaßnahmen insgesamt die wichtigsten Ursachen für die beobachteten Vegetationsveränderungen. Forstliche Eingriffe wie Kahlschlag und Bestandesumbau mit Baumartenwechsel sind zugleich die Hauptursache dafür, dass es trotz Nivellierung des Standortsgradienten, gemessen an der β-Diversität, nicht zu einer Homogenisierung der Vegetation gekommen ist. T2 - Vegetation change in the forests between the Elbe and Havel rivers (NE Germany) from 1960 to 2015 KW - environmental gradient KW - eutrophication KW - falling groundwater level KW - homogenisation KW - phytodiversity KW - silviculture KW - vegetation change Y1 - 2021 U6 - https://doi.org/10.14471/2021.41.005 SN - 0722-494X IS - 41 SP - 53 EP - 85 PB - Floristisch-Soziologische Arbeitsgemeinschaft CY - Göttingen ER - TY - JOUR A1 - de Oliveira-Silva, Anna Elizabeth A1 - Piratelli, Augusto João A1 - Zurell, Damaris A1 - da Silva, Fernando Rodrigues T1 - Vegetation cover restricts habitat suitability predictions of endemic Brazilian Atlantic Forest birds JF - Perspectives in Ecology and Conservation N2 - Ecological niche models (ENMs) are often used to investigate how climatic variables from known occurrence records can estimate potential species range distribution. Although climate-based ENMs provide critical baseline information, the inclusion of non-climatic predictors related to vegetation cover might generate more realistic scenarios. This assumption is particularly relevant for species with life-history traits related to forest habitats and sensitive to habitat loss and fragmentation. Here, we developed ENMs for 36 Atlantic Forest endemic birds considering two sets of predictor variables: (i) climatic variables only and (ii) climatic variables combined with the percentage of remaining native vegetation. We hypothesized that the inclusion of native vegetation data would decrease the potential range distribution of forest-dependent species by limiting their occurrence in regions harboring small areas of native vegetation habitats, despite otherwise favorable climatic conditions. We also expected that habitat restriction in the climate-vegetation models would be more pronounced for highly forest-dependent birds. The inclusion of vegetation data in the modeling procedures restricted the final distribution ranges of 22 out of 36 modeled species, while the 14 remaining presented an expansion of their ranges. We observed that species with high and medium forest dependency showed higher restriction in range size predictions between predictor sets than species with low forest dependency, which showed no alteration or range expansion. Overall, our results suggest that ENMs based on climatic and landscape variables may be a useful tool for conservationists to better understand the dynamic of bird species distributions in threatened and highly fragmented regions such as the Atlantic Forest hotspot.(c) 2021 Associacao Brasileira de Cie circumflex accent ncia Ecol ogica e Conservacao. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/ ). KW - Conservation KW - Ecological niche modeling KW - Forest dependency KW - Fragmentation KW - Habitat loss KW - Landscape KW - Life-history traits Y1 - 2021 U6 - https://doi.org/10.1016/j.pecon.2021.09.002 SN - 2530-0644 VL - 20 IS - 1 SP - 1 EP - 8 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Courtin, Jérémy A1 - Andreev, Andrei A1 - Raschke, Elena A1 - Bala, Sarah A1 - Biskaborn, Boris A1 - Liu, Sisi A1 - Zimmermann, Heike A1 - Diekmann, Bernhard A1 - Stoof-Leichsenring, Kathleen R. A1 - Pestryakova, Luidmila Agafyevna A1 - Herzschuh, Ulrike T1 - Vegetation changes in Southeastern Siberia during the late pleistocene and the holocene JF - Frontiers in Ecology and Evolution N2 - Relationships between climate, species composition, and species richness are of particular importance for understanding how boreal ecosystems will respond to ongoing climate change. This study aims to reconstruct changes in terrestrial vegetation composition and taxa richness during the glacial Late Pleistocene and the interglacial Holocene in the sparsely studied southeastern Yakutia (Siberia) by using pollen and sedimentary ancient DNA (sedaDNA) records. Pollen and sedaDNA metabarcoding data using the trnL g and h markers were obtained from a sediment core from Lake Bolshoe Toko. Both proxies were used to reconstruct the vegetation composition, while metabarcoding data were also used to investigate changes in plant taxa richness. The combination of pollen and sedaDNA approaches allows a robust estimation of regional and local past terrestrial vegetation composition around Bolshoe Toko during the last similar to 35,000 years. Both proxies suggest that during the Late Pleistocene, southeastern Siberia was covered by open steppe-tundra dominated by graminoids and forbs with patches of shrubs, confirming that steppe-tundra extended far south in Siberia. Both proxies show disturbance at the transition between the Late Pleistocene and the Holocene suggesting a period with scarce vegetation, changes in the hydrochemical conditions in the lake, and in sedimentation rates. Both proxies document drastic changes in vegetation composition in the early Holocene with an increased number of trees and shrubs and the appearance of new tree taxa in the lake's vicinity. The sedaDNA method suggests that the Late Pleistocene steppe-tundra vegetation supported a higher number of terrestrial plant taxa than the forested Holocene. This could be explained, for example, by the "keystone herbivore" hypothesis, which suggests that Late Pleistocene megaherbivores were able to maintain a high plant diversity. This is discussed in the light of the data with the broadly accepted species-area hypothesis as steppe-tundra covered such an extensive area during the Late Pleistocene. KW - last glacial KW - Holocene KW - Lake Bolshoe Toko KW - paleoenvironments KW - sedimentary ancient DNA KW - metabarcoding KW - trnL KW - pollen Y1 - 2021 U6 - https://doi.org/10.3389/fevo.2021.625096 SN - 2296-701X VL - 9 PB - Frontiers Media CY - Lausanne ER - TY - GEN A1 - Drago, Claudia A1 - Weithoff, Guntram T1 - Variable Fitness Response of Two Rotifer Species Exposed to Microplastics Particles BT - The Role of Food Quantity and Quality T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Plastic pollution is an increasing environmental problem, but a comprehensive understanding of its effect in the environment is still missing. The wide variety of size, shape, and polymer composition of plastics impedes an adequate risk assessment. We investigated the effect of differently sized polystyrene beads (1-, 3-, 6-µm; PS) and polyamide fragments (5–25 µm, PA) and non-plastics items such as silica beads (3-µm, SiO2) on the population growth, reproduction (egg ratio), and survival of two common aquatic micro invertebrates: the rotifer species Brachionus calyciflorus and Brachionus fernandoi. The MPs were combined with food quantity, limiting and saturating food concentration, and with food of different quality. We found variable fitness responses with a significant effect of 3-µm PS on the population growth rate in both rotifer species with respect to food quantity. An interaction between the food quality and the MPs treatments was found in the reproduction of B. calyciflorus. PA and SiO2 beads had no effect on fitness response. This study provides further evidence of the indirect effect of MPs in planktonic rotifers and the importance of testing different environmental conditions that could influence the effect of MPs. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1248 KW - microplastics KW - population growth rate KW - polystyrene KW - polyamide KW - silica beads KW - fitness response KW - rotifers KW - Brachionus fernandoi KW - Brachionus calyciflorus KW - egg ratio Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-552615 SN - 1866-8372 IS - 1248 ER - TY - JOUR A1 - Drago, Claudia A1 - Weithoff, Guntram T1 - Variable Fitness Response of Two Rotifer Species Exposed to Microplastics Particles BT - The Role of Food Quantity and Quality JF - Toxics N2 - Plastic pollution is an increasing environmental problem, but a comprehensive understanding of its effect in the environment is still missing. The wide variety of size, shape, and polymer composition of plastics impedes an adequate risk assessment. We investigated the effect of differently sized polystyrene beads (1-, 3-, 6-µm; PS) and polyamide fragments (5–25 µm, PA) and non-plastics items such as silica beads (3-µm, SiO2) on the population growth, reproduction (egg ratio), and survival of two common aquatic micro invertebrates: the rotifer species Brachionus calyciflorus and Brachionus fernandoi. The MPs were combined with food quantity, limiting and saturating food concentration, and with food of different quality. We found variable fitness responses with a significant effect of 3-µm PS on the population growth rate in both rotifer species with respect to food quantity. An interaction between the food quality and the MPs treatments was found in the reproduction of B. calyciflorus. PA and SiO2 beads had no effect on fitness response. This study provides further evidence of the indirect effect of MPs in planktonic rotifers and the importance of testing different environmental conditions that could influence the effect of MPs. KW - microplastics KW - population growth rate KW - polystyrene KW - polyamide KW - silica beads KW - fitness response KW - rotifers KW - Brachionus fernandoi KW - Brachionus calyciflorus KW - egg ratio Y1 - 2021 U6 - https://doi.org/10.3390/toxics9110305 SN - 2305-6304 VL - 9 IS - 11 PB - MDPI CY - Basel ER - TY - JOUR A1 - Warmt, Christian A1 - Fenzel, Carolin Kornelia A1 - Henkel, Jörg A1 - Bier, Frank Fabian T1 - Using Cy5-dUTP labelling of RPA-amplicons with downstream microarray analysis for the detection of antibiotic resistance genes JF - Scientific reports N2 - In this report we describe Cy5-dUTP labelling of recombinase-polymerase-amplification (RPA) products directly during the amplification process for the first time. Nucleic acid amplification techniques, especially polymerase-chain-reaction as well as various isothermal amplification methods such as RPA, becomes a promising tool in the detection of pathogens and target specific genes. Actually, RPA even provides more advantages. This isothermal method got popular in point of care diagnostics because of its speed and sensitivity but requires pre-labelled primer or probes for a following detection of the amplicons. To overcome this disadvantages, we performed an labelling of RPA-amplicons with Cy5-dUTP without the need of pre-labelled primers. The amplification results of various multiple antibiotic resistance genes indicating great potential as a flexible and promising tool with high specific and sensitive detection capabilities of the target genes. After the determination of an appropriate rate of 1% Cy5-dUTP and 99% unlabelled dTTP we were able to detect the bla(CTX-M15) gene in less than 1.6E-03 ng genomic DNA corresponding to approximately 200 cfu of Escherichia coli cells in only 40 min amplification time. Y1 - 2021 U6 - https://doi.org/10.1038/s41598-021-99774-z SN - 2045-2322 VL - 11 IS - 1 PB - Macmillan Publishers Limited, part of Springer Nature CY - [London] ER - TY - JOUR A1 - Yildiz, Tugba A1 - Leimkühler, Silke T1 - TusA is a versatile protein that links translation efficiency to cell division in Escherichia coli JF - Journal of bacteriology N2 - To enable accurate and efficient translation, sulfur modifications are introduced posttranscriptionally into nucleosides in tRNAs. The biosynthesis of tRNA sulfur modifications involves unique sulfur trafficking systems for the incorporation of sulfur atoms in different nucleosides of tRNA. One of the proteins that is involved in inserting the sulfur for 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U34) modifications in tRNAs is the TusA protein. TusA, however, is a versatile protein that is also involved in numerous other cellular pathways. Despite its role as a sulfur transfer protein for the 2-thiouridine formation in tRNA, a fundamental role of TusA in the general physiology of Escherichia coli has also been discovered. Poor viability, a defect in cell division, and a filamentous cell morphology have been described previously for tusA-deficient cells. In this report, we aimed to dissect the role of TusA for cell viability. We were able to show that the lack of the thiolation status of wobble uridine (U-34) nucleotides present on Lys, Gln, or Glu in tRNAs has a major consequence on the translation efficiency of proteins; among the affected targets are the proteins RpoS and Fis. Both proteins are major regulatory factors, and the deregulation of their abundance consequently has a major effect on the cellular regulatory network, with one consequence being a defect in cell division by regulating the FtsZ ring formation.
IMPORTANCE More than 100 different modifications are found in RNAs. One of these modifications is the mnm(5)s(2)U modification at the wobble position 34 of tRNAs for Lys, Gln, and Glu. The functional significance of U34 modifications is substantial since it restricts the conformational flexibility of the anticodon, thus providing translational fidelity. We show that in an Escherichia coli TusA mutant strain, involved in sulfur transfer for the mnm(5)s(2)U34 thio modifications, the translation efficiency of RpoS and Fis, two major cellular regulatory proteins, is altered. Therefore, in addition to the transcriptional regulation and the factors that influence protein stability, tRNA modifications that ensure the translational efficiency provide an additional crucial regulatory factor for protein synthesis. KW - iron-sulfur clusters KW - tRNA thio modifications KW - FtsZ ring formation KW - cell KW - division KW - TusA KW - RpoS KW - Fis KW - FtsZ Y1 - 2021 U6 - https://doi.org/10.1128/JB.00659-20 SN - 1098-5530 VL - 203 IS - 7 PB - American Society for Microbiology CY - Washington ER - TY - JOUR A1 - Kaech, Heidi A1 - Dennis, Alice B. A1 - Vorburger, Christoph T1 - Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa JF - BMC genomics N2 - Background Secondary endosymbionts of aphids provide benefits to their hosts, but also impose costs such as reduced lifespan and reproductive output. The aphid Aphis fabae is host to different strains of the secondary endosymbiont Hamiltonella defensa, which encode different putative toxins. These strains have very different phenotypes: They reach different densities in the host, and the costs and benefits (protection against parasitoid wasps) they confer to the host vary strongly. Results We used RNA-Seq to generate hypotheses on why four of these strains inflict such different costs to A. fabae. We found different H. defensa strains to cause strain-specific changes in aphid gene expression, but little effect of H. defensa on gene expression of the primary endosymbiont, Buchnera aphidicola. The highly costly and over-replicating H. defensa strain H85 was associated with strongly reduced aphid expression of hemocytin, a marker of hemocytes in Drosophila. The closely related strain H15 was associated with downregulation of ubiquitin-related modifier 1, which is related to nutrient-sensing and oxidative stress in other organisms. Strain H402 was associated with strong differential regulation of a set of hypothetical proteins, the majority of which were only differentially regulated in presence of H402. Conclusions Overall, our results suggest that costs of different strains of H. defensa are likely caused by different mechanisms, and that these costs are imposed by interacting with the host rather than the host's obligatory endosymbiont B. aphidicola. KW - Aphis fabae KW - Buchnera KW - Cost of resistance KW - Hamiltonella KW - Host-symbiont interaction KW - RNA-Seq KW - Symbiosis Y1 - 2021 U6 - https://doi.org/10.1186/s12864-021-07742-8 SN - 1471-2164 VL - 22 IS - 1 PB - BioMed Central CY - London ER - TY - JOUR A1 - Leimkühler, Silke T1 - Transition metals in catalysis BT - the functional relationship of Fe-S clusters and molybdenum or tungsten cofactor-containing enzyme systems JF - Inorganics : open access journal Y1 - 2021 U6 - https://doi.org/10.3390/inorganics9010006 SN - 2304-6740 VL - 9 IS - 1 PB - MDPI CY - Basel ER - TY - GEN A1 - Bergholz, Kolja A1 - Kober, Klarissa A1 - Jeltsch, Florian A1 - Schmidt, Kristina A1 - Weiß, Lina T1 - Trait means or variance BT - What determines plant species' local and regional occurrence in fragmented dry grasslands? T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - One of the few laws in ecology is that communities consist of few common and many rare taxa. Functional traits may help to identify the underlying mechanisms of this community pattern, since they correlate with different niche dimensions. However, comprehensive studies are missing that investigate the effects of species mean traits (niche position) and intraspecific trait variability (ITV, niche width) on species abundance. In this study, we investigated fragmented dry grasslands to reveal trait-occurrence relationships in plants at local and regional scales. We predicted that (a) at the local scale, species occurrence is highest for species with intermediate traits, (b) at the regional scale, habitat specialists have a lower species occurrence than generalists, and thus, traits associated with stress-tolerance have a negative effect on species occurrence, and (c) ITV increases species occurrence irrespective of the scale. We measured three plant functional traits (SLA = specific leaf area, LDMC = leaf dry matter content, plant height) at 21 local dry grassland communities (10 m × 10 m) and analyzed the effect of these traits and their variation on species occurrence. At the local scale, mean LDMC had a positive effect on species occurrence, indicating that stress-tolerant species are the most abundant rather than species with intermediate traits (hypothesis 1). We found limited support for lower specialist occurrence at the regional scale (hypothesis 2). Further, ITV of LDMC and plant height had a positive effect on local occurrence supporting hypothesis 3. In contrast, at the regional scale, plants with a higher ITV of plant height were less frequent. We found no evidence that the consideration of phylogenetic relationships in our analyses influenced our findings. In conclusion, both species mean traits (in particular LDMC) and ITV were differently related to species occurrence with respect to spatial scale. Therefore, our study underlines the strong scale-dependency of trait-abundance relationships. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1151 KW - LMA KW - niche width KW - plant functional trait KW - scale-dependency KW - species abundance KW - trait-environment relationship Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-519905 SN - 1866-8372 SP - 3357 EP - 3365 ER - TY - JOUR A1 - Bergholz, Kolja A1 - Kober, Klarissa A1 - Jeltsch, Florian A1 - Schmidt, Kristina A1 - Weiß, Lina T1 - Trait means or variance BT - What determines plant species' local and regional occurrence in fragmented dry grasslands? JF - Ecology and evolution N2 - One of the few laws in ecology is that communities consist of few common and many rare taxa. Functional traits may help to identify the underlying mechanisms of this community pattern, since they correlate with different niche dimensions. However, comprehensive studies are missing that investigate the effects of species mean traits (niche position) and intraspecific trait variability (ITV, niche width) on species abundance. In this study, we investigated fragmented dry grasslands to reveal trait-occurrence relationships in plants at local and regional scales. We predicted that (a) at the local scale, species occurrence is highest for species with intermediate traits, (b) at the regional scale, habitat specialists have a lower species occurrence than generalists, and thus, traits associated with stress-tolerance have a negative effect on species occurrence, and (c) ITV increases species occurrence irrespective of the scale. We measured three plant functional traits (SLA = specific leaf area, LDMC = leaf dry matter content, plant height) at 21 local dry grassland communities (10 m × 10 m) and analyzed the effect of these traits and their variation on species occurrence. At the local scale, mean LDMC had a positive effect on species occurrence, indicating that stress-tolerant species are the most abundant rather than species with intermediate traits (hypothesis 1). We found limited support for lower specialist occurrence at the regional scale (hypothesis 2). Further, ITV of LDMC and plant height had a positive effect on local occurrence supporting hypothesis 3. In contrast, at the regional scale, plants with a higher ITV of plant height were less frequent. We found no evidence that the consideration of phylogenetic relationships in our analyses influenced our findings. In conclusion, both species mean traits (in particular LDMC) and ITV were differently related to species occurrence with respect to spatial scale. Therefore, our study underlines the strong scale-dependency of trait-abundance relationships. KW - LMA KW - niche width KW - plant functional trait KW - scale-dependency KW - species abundance KW - trait-environment relationship Y1 - 2020 U6 - https://doi.org/10.1002/ece3.7287 SN - 2045-7758 VL - 11 IS - 7 SP - 3357 EP - 3365 PB - John Wiley & Sons, Inc. ER - TY - THES A1 - Knox-Brown, Patrick Frank T1 - Towards understanding the sequence-structure-function relationship of intrinsically disordered LEA_4 proteins from Arabidopsis thaliana N2 - Water-deficits can cause lethal damage to organisms, which is rooted in cellular dehydration. Many plant species, but also other organisms have developed mechanisms to tolerate such stresses, such as the expression of LEA proteins. Many studies report on physiological protective functions of LEA proteins but lack information about their precise mechanisms on a molecular level. Most LEA proteins are intrinsically disordered in dilute solution but may adopt a distinct secondary structure upon changes in solvent conditions. Understanding the molecular mechanism of how LEA proteins contribute to the counteraction of cellular damage during water-deficits may in the long-term pave the way for breeding crops that are resistant to the effects of global warming. The objective of the work at hand is to improve the biophysical understanding of the sequencestructure-function relationship of LEA proteins as membrane stabilizers, based on the LEA_4 family of the model plant A. thaliana. This is pursued by using a combination of spectroscopic and scattering techniques, supported by bioinformatics and computational analyses. Eight out of the 18 LEA_4 proteins are experimentally assessed revealing that a coil-helix transition in response to water-deficit is a common feature, as predicted for the entire family. In addition, they all stabilize simple membrane models during a freeze/ thaw cycle. Three-dimensional structure prediction of representative members suggests that their completely folded states are represented by a sequential arrangement of alpha-helical segments connected by unstructured linkers, which is experimentally verified for the LEA_4 protein COR15A. The unstructured linker region of COR15A represents a conserved motif among its closest homologs and is, therefore, of particular interest. Facilitating a set of seven designed and investigated COR15A mutants uncovers a complex interplay of transient interactions between the amphipathic alpha-helical segments, mediated by the linker, which fine-tunes folding transitions and structural ensembles upon reduced water-availability. Finally, alpha-helicity is also induced in COR15A upon temperature decrease, which is enhanced in the presence of osmolytes. In addition, high solution osmolarity induced secondary structure is followed by oligomerization of COR15A. Interestingly, the functionality of COR15A, in terms of liposome stabilization, strongly correlates with its alpha-helix ratio in the folded state. The present work significantly improves the understanding of the sequence-structure-function relationship for LEA_4 proteins and offers novel findings on folding mechanisms and oligomerization of COR15A. N2 - Wasserdefizite können zu letalem Schaden von Organismen führen, der letztendlich aus zellulärer Dehydrierung resultiert. Viele Pflanzen, aber auch andere Organismen haben Mechanismen entwickelt, um solche Stressfaktoren zu tolerieren, z.B. die Expression von LEAProteinen. Diverse Studien beschreiben deren physiologische Schutzfunktionen, es fehlen jedoch Informationen ihrer präzisen Mechanismen auf molekularer Ebene. Die meisten LEA-Proteine sind in wässriger Lösung intrinsisch unstrukturiert, können jedoch in Reaktion auf veränderte Lösungsmittelbedingungen geordnete Strukturen ausbilden. Ein solides Verständnis ihrer molekularen Mechanismen führt daher über die Entschlüsselung ihrer Sequenz-StrukturFunktions-Beziehungen, welche langfristig den Weg zur Entwicklung von Pflanzen ebnen, die Resistenzen gegen die Auswirkungen der globalen Erwärmung aufweisen.. Ziel der vorliegenden Arbeit ist, das Verständnis der Sequenz-Struktur-Funktions-Beziehung der LEA_4-Familie aus der Modellpflanze A. thaliana zu verbessern. Dazu wird eine Kombination von Spektroskopie- und Streutechniken (unterstützt durch prädiktive Computeranalysen) verwendet. Alle acht experimentell untersuchten der insgesamt 18 LEA_4-Proteine zeigen einen Coil-Helix-Übergang in Reaktion auf Wasserdefizit als gemeinsames Merkmal und stabilisieren einfache Membranmodelle während eines Gefrier-/ Tau-Vorgang. Die dreidimensionale Strukturvorhersage repräsentativer LEA_4-Proteine deutet an, dass der gefaltete Zustand einer Abfolge alpha-helikaler Segmente unterbrochen durch unstrukturierte Domänen entspricht, was für das LEA_4-Protein COR15A experimentell belegt wird. Der unstrukturierte Linker, der die beiden alpha-helikalen Segmente von COR15A verbindet, stellt ein Motiv dar, das innerhalb der nächsten Homologen konserviert ist und ist daher von besonderem Interesse. Mithilfe von sieben entworfenen und untersuchten COR15A-Mutanten kann der komplexe Zusammenhang transienter Wechselwirkungen zwischen den amphipathischen, alpha-helikalen Segmenten, vermittelt durch den Linker, gezeigt werden. Dieser spielt eine zentrale Rolle in der Feinabstimmung von Faltungsübergängen und strukturellen Ensembles bei verringerter Wasserverfügbarkeit. Ferner wird gezeigt, dass alpha-helikale Struktur auch durch Temperaturerniedrigung induziert werden kann, was in Gegenwart von Osmolyten stärker ausgeprägt ist. Hohe Osmolaritäten induzieren außerdem eine Oligomerisierung von COR15A. Interessanterweise korreliert die Funktionalität von COR15A (die Stabilisierung von Liposomen) stark mit dem relativen alpha-Helix-Anteil im gefalteten Zustand. Die vorliegende Arbeit verbessert erheblich das Verständnis für eine Sequenz-StrukturFunktions-Beziehung für LEA_4-Proteine und bietet neue Erkenntnisse zu Faltungsmechanismen und Oligomerisierung von COR15A. KW - IDPs KW - alpha-helix KW - coil-helix KW - linker KW - structure-function KW - protein-folding KW - LEA Y1 - 2021 ER - TY - JOUR A1 - Ceulemans, Ruben A1 - Guill, Christian A1 - Gaedke, Ursula T1 - Top predators govern multitrophic diversity effects in tritrophic food webs JF - Ecology : a publication of the Ecological Society of America N2 - It is well known that functional diversity strongly affects ecosystem functioning. However, even in rather simple model communities consisting of only two or, at best, three trophic levels, the relationship between multitrophic functional diversity and ecosystem functioning appears difficult to generalize, because of its high contextuality. In this study, we considered several differently structured tritrophic food webs, in which the amount of functional diversity was varied independently on each trophic level. To achieve generalizable results, largely independent of parametrization, we examined the outcomes of 128,000 parameter combinations sampled from ecologically plausible intervals, with each tested for 200 randomly sampled initial conditions. Analysis of our data was done by training a random forest model. This method enables the identification of complex patterns in the data through partial dependence graphs, and the comparison of the relative influence of model parameters, including the degree of diversity, on food-web properties. We found that bottom-up and top-down effects cascade simultaneously throughout the food web, intimately linking the effects of functional diversity of any trophic level to the amount of diversity of other trophic levels, which may explain the difficulty in unifying results from previous studies. Strikingly, only with high diversity throughout the whole food web, different interactions synergize to ensure efficient exploitation of the available nutrients and efficient biomass transfer to higher trophic levels, ultimately leading to a high biomass and production on the top level. The temporal variation of biomass showed a more complex pattern with increasing multitrophic diversity: while the system initially became less variable, eventually the temporal variation rose again because of the increasingly complex dynamical patterns. Importantly, top predator diversity and food-web parameters affecting the top trophic level were of highest importance to determine the biomass and temporal variability of any trophic level. Overall, our study reveals that the mechanisms by which diversity influences ecosystem functioning are affected by every part of the food web, hampering the extrapolation of insights from simple monotrophic or bitrophic systems to complex natural food webs. KW - food-web efficiency KW - functional diversity KW - machine learning KW - nutrient KW - exploitation KW - production KW - random forest KW - temporal variability KW - top KW - predator KW - trait diversity Y1 - 2021 U6 - https://doi.org/10.1002/ecy.3379 SN - 0012-9658 SN - 1939-9170 VL - 102 IS - 7 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Kim, Shin Woong A1 - Leifheit, Eva F. A1 - Maaß, Stefanie A1 - Rillig, Matthias C. T1 - Time-dependent toxicity of tire particles on soil nematodes JF - Frontiers in Environmental Science N2 - Tire-wear particles (TWPs) are being released into the environment by wearing down during car driving, and are considered an important microplastic pollution source. The chemical additive leaching from these polymer-based materials and its potential effects are likely temporally dynamic, since amounts of potentially toxic compounds can gradually increase with contact time of plastic particles with surrounding media. In the present study, we conducted soil toxicity tests using the soil nematode Caenorhabditis elegans with different soil pre-incubation (30 and 75 days) and exposure (short-term exposure, 2 days; lifetime exposure, 10 days) times. Soil pre-incubation increased toxicity of TWPs, and the effective concentrations after the pre-incubation were much lower than environmentally relevant concentrations. The lifetime of C. elegans was reduced faster in the TWP treatment groups, and the effective concentration for lifetime exposure tests were 100- to 1,000-fold lower than those of short-term exposure tests. Water-extractable metal concentrations (Cr, Cu, Ni, Pb, and Zn) in the TWP-soils showed no correlation with nominal TWP concentrations or pre-incubation times, and the incorporated metals in the TWPs may be not the main reason of toxicity in this study. Our results show that toxic effects of TWPs can be time-dependent, both in terms of the microplastic particles themselves and their interactions in the soil matrix, but also because of susceptibility of target organisms depending on developmental stage. It is vital that future works consider these aspects, since otherwise effects of microplastics and TWPs could be underestimated. KW - Caenorhabditis elegans KW - exposure time KW - lifetime KW - microplastics KW - soil KW - incubation Y1 - 2021 U6 - https://doi.org/10.3389/fenvs.2021.744668 SN - 2296-665X VL - 9 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Rutschmann, Sereina A1 - Chen, Ping A1 - Zhou, Changfa A1 - Monaghan, Michael T. T1 - Three mitochondrial genomes of early-winged insects (Ephemeroptera: Baetidae and Leptophlebiidae) JF - Mitochondrial DNA Part B N2 - Mayflies (Ephemeroptera) are a semi-aquatic insect order with comparatively few genomic data available despite their phylogenetic position at the root of the winged-insects and possession of ancestral traits. Here, we provide three mitochondrial genomes (mtgenomes) from representatives of the two most species-rich families, Baetis rutilocylindratus and Cloeon dipterum (Baetidae), and Habrophlebiodes zijinensis (Leptophlebiidae). All mtgenomes had a complete set of 13 protein-coding genes and a conserved orientation except for two inverted tRNAs in H. zijinensis. Phylogenetic reconstructions using 21 mayfly mtgenomes and representatives of seven additional orders recovered both Baetidae and Leptophlebiidae as well supported monophyletic clades, with Ephemeroptera as the sister-taxon to all other winged insects (i.e. Odonata and Neoptera). KW - Baetis KW - Cloeon KW - Habrophlebiodes KW - mayfly KW - mitochondrial phylogeny Y1 - 2021 U6 - https://doi.org/10.1080/23802359.2021.1974966 SN - 2380-2359 VL - 6 IS - 10 SP - 2969 EP - 2971 PB - Routledge, Taylor & Francis Group CY - Abingdon ER - TY - JOUR A1 - Nie, Yan A1 - Wang, Weiwei A1 - Xu, Xun A1 - Ma, Nan A1 - Lendlein, Andreas T1 - The response of human induced pluripotent stem cells to cyclic temperature changes explored by BIO-AFM JF - MRS advances : a journal of the Materials Research Society (MRS) N2 - Human induced pluripotent stem cells (hiPSCs) are highly sensitive to extrinsic physical and biochemical signals from their extracellular microenvironments. In this study, we analyzed the effect of cyclic temperature changes on hiPSCs behaviors, especially by means of scanning force microscopy (BIO-AFM). The alternation in cellular mechanics, as well as the secretion and pattern of deposition of extracellular matrix (ECM) protein in hiPSCs were evaluated. The arrangement of the actin cytoskeleton changed with the variation of the temperature. The rearranged cytoskeleton architecture led to the subsequent changes in cell mechanics (Young's modulus of hiPSCs). With the exposure to the cyclic cold stimuli, an increase in the average surface roughness (Ra) and roughness mean square (RMS) was detected. This observation might be at least in part due to the upregulated secretion of Laminin alpha 5 during repeated temporary cooling. The expression of pluripotent markers, NANOG and SOX2, was not impaired in hiPSCs, when exposed to the cyclic cold stimuli for 24 h. Our findings provide an insight into the effect of temperature on the hiPSC behaviors, which may contribute to a better understanding of the application of locally controlled therapeutic hypothermia. Y1 - 2021 U6 - https://doi.org/10.1557/s43580-021-00110-4 SN - 2059-8521 VL - 6 IS - 31 SP - 745 EP - 749 PB - Springer CY - Cham ER - TY - CHAP A1 - Inäbnit, Thomas A1 - Dennis, Alice T1 - The mitochondrial genome of Melampus bidentatus (Panpulmonata, Ellobioidea) T2 - Integrative and comparative biology / Society of Integrative and Comparative Biology Y1 - 2021 SN - 1540-7063 SN - 1557-7023 VL - 61 IS - Supplement 1 SP - E405 EP - E405 PB - Oxford University Press CY - Oxford ER - TY - THES A1 - Kaptur, Joanna Alexandra T1 - The LEUNIG regulatory complex BT - how does it control shoot apical meristem formation and its postembryonic activity? N2 - Patterning along the apical-basal (A-B) axis is a crucial step during the early stages of plant embryogenesis and leads to the establishment of two poles of which each will develop their own stem cell niches. The activity of these meristems is responsible for post-embryonic growth, with the shoot apical meristem (SAM) generating the above-ground organs and the root apical meristem (RAM) producing the subterranean structures of the plant. While several transcriptional regulators governing A-B patterning have been identified, precisely how their regulatory function is orchestrated remains elusive. This study focuses on transcriptional co-regulators LEUNIG (LUG) and closely related LEUNIG_HOMOLOG (LUH) and their role in the formation of A-B patterning during embryogenesis as well as their post-embryonic maintenance. A link between the LUG regulatory complex and SAM formation and maintenance comes from the observation that lug mutants heterozygous for the luh allele (lug luh+/-) often have enlarged SAMs resulting from misregulated cell divisions. A more severe phenotype is observed in lug luh double mutants which are embryonically lethal. In this study, a detailed characterisation of lug luh embryo phenotype reveals that these mutants display aberrant cell divisions along the A-B axis, which correlates with defects in auxin distribution, complete loss of apical identity, and altered expression of transcription factors determining basal fate. Like other co-regulators, LUG and LUH lack intrinsic DNA-binding domains and instead must interact with DNA-binding cofactors to ensure recruitment to regulatory elements of target genes. This either involves direct contact between the co-regulators and transcription factors (TFs) or the formation of higher-order complexes with adaptor proteins such as SEUSS (SEU) or related SEUSS-LIKEs (SLKs), which facilitate binding to specific TFs. Results presented in this study provide insight into the molecular framework for the LUG regulatory complex activity during embryogenesis. Both yeast and in planta assays showed that LUG/LUH and SEU/SLKs physically associate with a variety of WUSCHEL-RELATED HOMEOBOX (WOX) TFs including members of the WOX2-module. Furthermore, genetic interactions between members of the WOX2-module and the LUG regulatory complex, support their mutual action during embryogenesis. Based on the reduced activity of HOMEODOMAIN LEUCINE-ZIPPER CLASS III (HD-ZIPIII) promoters in lug luh embryos, a model is proposed in which the LUG regulatory complex functions together with WOX2-module to promote apical identity and subsequent SAM initiation through regulation of the HD-ZIPIIIs. The activity of the LUG complex in promoting basal embryo identity through positive regulation of microRNA165/166 suggests that this complex also has functions that are independent of the WOX2-module. Preliminary work reported in this study further uncovered the role of the LUG regulatory complex in post-embryonic development. While the fasciated inflorescence meristems of lug luh+/- plants displayed defects in auxin transport and altered activity of stem cell markers, embryonically rescued lug luh mutants formed flat and differentiated SAMs. In addition, rescued lug luh mutants exhibited severely disorganised RAM and defects in quiescent center (QC) specification, supporting the involvement of the LUG complex in post-embryonic RAM maintenance. KW - LEUNIG LEUNIG_HOMOLOG SEUSS SEUSS-LIKEs Arabidopsis embryogenesis WOX2-module HD-ZIPIII Y1 - 2021 ER - TY - JOUR A1 - Baunach, Martin A1 - Chowdhury, Somak A1 - Stallforth, Pierre A1 - Dittmann-Thünemann, Elke T1 - The landscape of recombination events that create nonribosomal peptide diversity JF - Molecular biology and evolution : MBE N2 - Nonribosomal peptides (NRP) are crucial molecular mediators in microbial ecology and provide indispensable drugs. Nevertheless, the evolution of the flexible biosynthetic machineries that correlates with the stunning structural diversity of NRPs is poorly understood. Here, we show that recombination is a key driver in the evolution of bacterial NRP synthetase (NRPS) genes across distant bacterial phyla, which has guided structural diversification in a plethora of NRP families by extensive mixing andmatching of biosynthesis genes. The systematic dissection of a large number of individual recombination events did not only unveil a striking plurality in the nature and origin of the exchange units but allowed the deduction of overarching principles that enable the efficient exchange of adenylation (A) domain substrates while keeping the functionality of the dynamic multienzyme complexes. In the majority of cases, recombination events have targeted variable portions of the A(core) domains, yet domain interfaces and the flexible A(sub) domain remained untapped. Our results strongly contradict the widespread assumption that adenylation and condensation (C) domains coevolve and significantly challenge the attributed role of C domains as stringent selectivity filter during NRP synthesis. Moreover, they teach valuable lessons on the choice of natural exchange units in the evolution of NRPS diversity, which may guide future engineering approaches. KW - evolution KW - recombination KW - structural diversity KW - natural products KW - nonribosomal peptide synthetases KW - microbial ecology Y1 - 2021 U6 - https://doi.org/10.1093/molbev/msab015 SN - 0737-4038 SN - 1537-1719 VL - 38 IS - 5 SP - 2116 EP - 2130 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Garrido, Claudia A1 - Leimkühler, Silke T1 - The inactivation of human aldehyde oxidase 1 by hydrogen peroxide and superoxide JF - Drug metabolism and disposition / American Society for Pharmacology and Experimental Therapeutics N2 - Mammalian aldehyde oxidases (AOX) are molybdo-flavoenzymes of pharmacological and pathophysiologic relevance that are involved in phase I drug metabolism and, as a product of their enzymatic activity, are also involved in the generation of reactive oxygen species. So far, the physiologic role of aldehyde oxidase 1 in the human body remains unknown. The human enzyme hAOX1 is characterized by a broad substrate specificity, oxidizing aromatic/aliphatic aldehydes into their corresponding carboxylic acids, and hydroxylating various heteroaromatic rings. The enzyme uses oxygen as terminal electron acceptor to produce hydrogen peroxide and superoxide during turnover. Since hAOX1 and, in particular, some natural variants produce not only H2O2 but also high amounts of superoxide, we investigated the effect of both ROS molecules on the enzymatic activity of hAOX1 in more detail. We compared hAOX1 to the high-O-2(.-)-producing natural variant L438V for their time-dependent inactivation with H2O2/O-2(.-) during substrate turnover. We show that the inactivation of the hAOX1 wild-type enzyme is mainly based on the production of hydrogen peroxide, whereas for the variant L438V, both hydrogen peroxide and superoxide contribute to the time-dependent inactivation of the enzyme during turnover. Further, the level of inactivation was revealed to be substrate-dependent: using substrates with higher turnover numbers resulted in a faster inactivation of the enzymes. Analysis of the inactivation site of the enzyme identified a loss of the terminal sulfido ligand at the molybdenum active site by the produced ROS during turnover. Y1 - 2021 U6 - https://doi.org/10.1124/dmd.121.000549 SN - 1521-009X SN - 0090-9556 VL - 49 IS - 9 SP - 729 EP - 735 PB - American Society for Pharmacology and Experimental Therapeutics CY - Bethesda ER - TY - JOUR A1 - Gräf, Ralph A1 - Grafe, Marianne A1 - Meyer, Irene A1 - Mitic, Kristina A1 - Pitzen, Valentin T1 - The dictyostelium centrosome JF - Cells : open access journal N2 - The centrosome of Dictyostelium amoebae contains no centrioles and consists of a cylindrical layered core structure surrounded by a corona harboring microtubule-nucleating gamma-tubulin complexes. It is the major centrosomal model beyond animals and yeasts. Proteomics, protein interaction studies by BioID and superresolution microscopy methods led to considerable progress in our understanding of the composition, structure and function of this centrosome type. We discuss all currently known components of the Dictyostelium centrosome in comparison to other centrosomes of animals and yeasts. KW - microtubule-organizing center KW - microtubule-organization KW - centrosome KW - Dictyostelium KW - mitosis Y1 - 2021 U6 - https://doi.org/10.3390/cells10102657 SN - 2073-4409 VL - 10 IS - 10 PB - MDPI CY - Basel ER - TY - JOUR A1 - Soeriyadi, Angela H. A1 - Ongley, Sarah E. A1 - Kehr, Jan-Christoph A1 - Pickford, Russel A1 - Dittmann, Elke A1 - Neilan, Brett A. T1 - Tailoring enzyme stringency masks the multispecificity of a lyngbyatoxin (indolactam alkaloid) nonribosomal peptide synthetase JF - ChemBioChem N2 - Indolactam alkaloids are activators of protein kinase C (PKC) and are of pharmacological interest for the treatment of pathologies involving PKC dysregulation. The marine cyanobacterial nonribosomal peptide synthetase (NRPS) pathway for lyngbyatoxin biosynthesis, which we previously expressed in E. coli, was studied for its amenability towards the biosynthesis of indolactam variants. Modification of culture conditions for our E. coli heterologous expression host and analysis of pathway products suggested the native lyngbyatoxin pathway NRPS does possess a degree of relaxed specificity. Site-directed mutagenesis of two positions within the adenylation domain (A-domain) substrate-binding pocket was performed, resulting in an alteration of substrate preference between valine, isoleucine, and leucine. We observed relative congruence of in vitro substrate activation by the LtxA NRPS to in vivo product formation. While there was a preference for isoleucine over leucine, the substitution of alternative tailoring domains may unveil the true in vivo effects of the mutations introduced herein. KW - a domain KW - indolactams KW - MbtH KW - natural products KW - teleocidin Y1 - 2021 U6 - https://doi.org/10.1002/cbic.202100574 SN - 1439-4227 SN - 1439-7633 VL - 23 IS - 3 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Scheffler, Christiane A1 - Hermanussen, Michael T1 - Stunting does not impair physical fitness in Indonesian school children JF - Human biology and public health N2 - Background: Physical fitness is decreased in malnourished children and adults. Poor appearance and muscular flaccidity are among the first signs of malnutrition. Malnutrition is often associated with stunting. Objectives: We test the hypotheses that stunted children of low social strata are physically less fit than children of high social strata. Sample: We investigated 354 school girls and 369 school boys aged 5.83 to 13.83 (mean 9.54) years from three different social strata in Kupang (West-Timor, Indonesia) in 2020. Methods: We measured height, weight, and elbow breadth, calculated standard deviation (SDS) of height and weight according to CDC references, and the Frame index as an indicator of long-term physical fitness, and we tested physical fitness in standing long jump and hand grip strength. Results: Children of low social strata are physically fittest. They jump longer distances, and they have higher values in the Frame index. No association exists between height SDS and physical fitness, neither in respect to standing long jump, nor to hand grip strength. Conclusion: Stunting does not impair physical fitness in Indonesian school children. Our results support the concept that SEPE (social-economic-political-emotional) factors are involved in the regulation of human growth. KW - stunting KW - standing long jump KW - handgrip strength KW - SEPE KW - frame index Y1 - 2021 U6 - https://doi.org/10.52905/hbph.v2.19 SN - 2748-9957 IS - 2 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Scheffler, Christiane A1 - Hermanussen, Michael A1 - Rogol, Alan D. T1 - Stunting BT - historical lessons that catch-up growth tells us for mapping growth restoration JF - Archives of disease in childhood : a peer review journal for health professionals and researchers covering conception to adolescence Y1 - 2020 U6 - https://doi.org/10.1136/archdischild-2020-319240 SN - 0003-9888 SN - 1468-2044 VL - 106 IS - 8 SP - 819 EP - 820 PB - BMJ Publishing Group CY - London ER - TY - JOUR A1 - Tung, Wing Tai A1 - Sun, Xianlei A1 - Wang, Weiwei A1 - Xu, Xun A1 - Ma, Nan A1 - Lendlein, Andreas T1 - Structure, mechanical properties and degradation behavior of electrospun PEEU fiber meshes and films JF - MRS advances : a journal of the Materials Research Society (MRS) N2 - The capability of a degradable implant to provide mechanical support depends on its degradation behavior. Hydrolytic degradation was studied for a polyesteretherurethane (PEEU70), which consists of poly(p-dioxanone) (PPDO) and poly(epsilon-caprolactone) (PCL) segments with a weight ratio of 70:30 linked by diurethane junction units. PEEU70 samples prepared in the form of meshes with average fiber diameters of 1.5 mu m (mesh1.5) and 1.2 mu m (mesh1.2), and films were sterilized and incubated in PBS at 37 degrees C with 5 vol% CO2 supply for 1 to 6 weeks. Degradation features, such as cracks or wrinkles, became apparent from week 4 for all samples. Mass loss was found to be 11 wt%, 6 wt%, and 4 wt% for mesh1.2, mesh1.5, and films at week 6. The elongation at break decreased to under 20% in two weeks for mesh1.2. In case of the other two samples, this level of degradation was achieved after 4 weeks. The weight average molecular weight of both PEEU70 mesh and film samples decreased to below 30 kg/mol when elongation at break dropped below 20%. The time period of sustained mechanical stability of PEEU70-based meshes depends on the fiber diameter and molecular weight. Y1 - 2021 U6 - https://doi.org/10.1557/s43580-020-00001-0 SN - 2059-8521 VL - 6 IS - 10 SP - 276 EP - 282 PB - Springer Nature Switzerland AG CY - Cham ER - TY - GEN A1 - Bornhorst, Dorothee A1 - Abdelilah-Seyfried, Salim T1 - Strong as a Hippo’s Heart: Biomechanical Hippo Signaling During Zebrafish Cardiac Development T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The heart is comprised of multiple tissues that contribute to its physiological functions. During development, the growth of myocardium and endocardium is coupled and morphogenetic processes within these separate tissue layers are integrated. Here, we discuss the roles of mechanosensitive Hippo signaling in growth and morphogenesis of the zebrafish heart. Hippo signaling is involved in defining numbers of cardiac progenitor cells derived from the secondary heart field, in restricting the growth of the epicardium, and in guiding trabeculation and outflow tract formation. Recent work also shows that myocardial chamber dimensions serve as a blueprint for Hippo signaling-dependent growth of the endocardium. Evidently, Hippo pathway components act at the crossroads of various signaling pathways involved in embryonic zebrafish heart development. Elucidating how biomechanical Hippo signaling guides heart morphogenesis has direct implications for our understanding of cardiac physiology and pathophysiology. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1236 KW - Hippo signaling KW - Yap1/Wwtr1 (Taz) KW - cardiac development KW - mechanobiology KW - endocardium KW - myocardium KW - zebrafish KW - intra-organ-communication Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-548731 SN - 1866-8372 SP - 1 EP - 10 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Bornhorst, Dorothee A1 - Abdelilah-Seyfried, Salim T1 - Strong as a Hippo’s Heart: Biomechanical Hippo Signaling During Zebrafish Cardiac Development JF - Frontiers in Cell and Developmental Biology N2 - The heart is comprised of multiple tissues that contribute to its physiological functions. During development, the growth of myocardium and endocardium is coupled and morphogenetic processes within these separate tissue layers are integrated. Here, we discuss the roles of mechanosensitive Hippo signaling in growth and morphogenesis of the zebrafish heart. Hippo signaling is involved in defining numbers of cardiac progenitor cells derived from the secondary heart field, in restricting the growth of the epicardium, and in guiding trabeculation and outflow tract formation. Recent work also shows that myocardial chamber dimensions serve as a blueprint for Hippo signaling-dependent growth of the endocardium. Evidently, Hippo pathway components act at the crossroads of various signaling pathways involved in embryonic zebrafish heart development. Elucidating how biomechanical Hippo signaling guides heart morphogenesis has direct implications for our understanding of cardiac physiology and pathophysiology. KW - Hippo signaling KW - Yap1/Wwtr1 (Taz) KW - cardiac development KW - mechanobiology KW - endocardium KW - myocardium KW - zebrafish KW - intra-organ-communication Y1 - 2021 U6 - https://doi.org/10.3389/fcell.2021.731101 SN - 2296-634X VL - 9 SP - 1 EP - 10 PB - Frontiers Media CY - Lausanne, Schweiz ER - TY - JOUR A1 - Compart, Julia A1 - Li, Xiaoping A1 - Fettke, Jörg T1 - Starch-A complex and undeciphered biopolymer JF - Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants N2 - Starch is a natural storage carbohydrate in plants and algae. It consists of two relatively simple homo-biopolymers, amylopectin and amylose, with only alpha-1,4 and alpha-1,6 linked glucosyl units. Starch is an essential source of nutrition and animal food, as well as an important raw material for industry. However, despite increasing knowledge, detailed information about its structure and turnover are largely lacking. In the last decades, most data were generated using bulk experiments, a method which obviously presents limitations regarding a deeper understanding of the starch metabolism. Here, we discuss some unavoidable questions arising from the existing data. We focus on a few examples related to starch biosynthesis, degradation, and structure where these limitations strongly emerge. Closing these knowledge gaps will also be extremely important for taking the necessary steps in order to set up starch-providing crops for the challenges of the ongoing climate changes, as well as for increasing the usability of starches for industrial applications by biotechnology. KW - Starch KW - Starch structure KW - Organization model KW - Starch metabolism KW - Analytical limitations Y1 - 2021 U6 - https://doi.org/10.1016/j.jplph.2021.153389 SN - 0176-1617 SN - 1618-1328 VL - 258 SP - 258 EP - 259 PB - Elsevier CY - München ER - TY - JOUR A1 - Liu, Qingting A1 - Li, Xiaoping A1 - Fettke, Jörg T1 - Starch granules in Arabidopsis thaliana mesophyll and guard cells show similar morphology but differences in size and number JF - International journal of molecular sciences N2 - Transitory starch granules result from complex carbon turnover and display specific situations during starch synthesis and degradation. The fundamental mechanisms that specify starch granule characteristics, such as granule size, morphology, and the number per chloroplast, are largely unknown. However, transitory starch is found in the various cells of the leaves of Arabidopsis thaliana, but comparative analyses are lacking. Here, we adopted a fast method of laser confocal scanning microscopy to analyze the starch granules in a series of Arabidopsis mutants with altered starch metabolism. This allowed us to separately analyze the starch particles in the mesophyll and in guard cells. In all mutants, the guard cells were always found to contain more but smaller plastidial starch granules than mesophyll cells. The morphological properties of the starch granules, however, were indiscernible or identical in both types of leaf cells. KW - starch granules KW - starch granule number per chloroplast KW - starch morphology KW - mesophyll cell KW - guard cell KW - LCSM KW - Arabidopsis thaliana KW - starch granule initiation KW - starch metabolism Y1 - 2021 U6 - https://doi.org/10.3390/ijms22115666 SN - 1422-0067 SN - 1661-6596 VL - 22 IS - 11 PB - Molecular Diversity Preservation International CY - Basel ER - TY - GEN A1 - Liu, Qingting A1 - Li, Xiaoping A1 - Fettke, Jörg T1 - Starch granules in Arabidopsis thaliana mesophyll and guard cells show similar morphology but differences in size and number T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Transitory starch granules result from complex carbon turnover and display specific situations during starch synthesis and degradation. The fundamental mechanisms that specify starch granule characteristics, such as granule size, morphology, and the number per chloroplast, are largely unknown. However, transitory starch is found in the various cells of the leaves of Arabidopsis thaliana, but comparative analyses are lacking. Here, we adopted a fast method of laser confocal scanning microscopy to analyze the starch granules in a series of Arabidopsis mutants with altered starch metabolism. This allowed us to separately analyze the starch particles in the mesophyll and in guard cells. In all mutants, the guard cells were always found to contain more but smaller plastidial starch granules than mesophyll cells. The morphological properties of the starch granules, however, were indiscernible or identical in both types of leaf cells. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1143 KW - starch granules KW - starch metabolism KW - starch granule initiation KW - starch granule number per chloroplast KW - starch morphology KW - mesophyll cell KW - guard cell KW - LCSM KW - Arabidopsis thaliana Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-511067 SN - 1866-8372 IS - 1143 ER - TY - GEN A1 - Liu, Qingting A1 - Zhou, Yuan A1 - Fettke, Jörg T1 - Starch granule size and morphology of Arabidopsis thaliana starch-related mutants analyzed during diurnal rhythm and development T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Transitory starch plays a central role in the life cycle of plants. Many aspects of this important metabolism remain unknown; however, starch granules provide insight into this persistent metabolic process. Therefore, monitoring alterations in starch granules with high temporal resolution provides one significant avenue to improve understanding. Here, a previously established method that combines LCSM and safranin-O staining for in vivo imaging of transitory starch granules in leaves of Arabidopsis thaliana was employed to demonstrate, for the first time, the alterations in starch granule size and morphology that occur both throughout the day and during leaf aging. Several starch-related mutants were included, which revealed differences among the generated granules. In ptst2 and sex1-8, the starch granules in old leaves were much larger than those in young leaves; however, the typical flattened discoid morphology was maintained. In ss4 and dpe2/phs1/ss4, the morphology of starch granules in young leaves was altered, with a more rounded shape observed. With leaf development, the starch granules became spherical exclusively in dpe2/phs1/ss4. Thus, the presented data provide new insights to contribute to the understanding of starch granule morphogenesis. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1245 KW - starch metabolism KW - starch granule KW - starch granule size KW - starch granule morphology KW - LCSM KW - Arabidopsis thaliana Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-550291 SN - 1866-8372 VL - 26 SP - 1 EP - 9 PB - Universitätsverlag Potsdam CY - Potsdam ET - 19 ER - TY - JOUR A1 - Liu, Qingting A1 - Zhou, Yuan A1 - Fettke, Jörg T1 - Starch granule size and morphology of Arabidopsis thaliana starch-related mutants analyzed during diurnal rhythm and development JF - Molecules : a journal of synthetic chemistry and natural product chemistry / Molecular Diversity Preservation International N2 - Transitory starch plays a central role in the life cycle of plants. Many aspects of this important metabolism remain unknown; however, starch granules provide insight into this persistent metabolic process. Therefore, monitoring alterations in starch granules with high temporal resolution provides one significant avenue to improve understanding. Here, a previously established method that combines LCSM and safranin-O staining for in vivo imaging of transitory starch granules in leaves of Arabidopsis thaliana was employed to demonstrate, for the first time, the alterations in starch granule size and morphology that occur both throughout the day and during leaf aging. Several starch-related mutants were included, which revealed differences among the generated granules. In ptst2 and sex1-8, the starch granules in old leaves were much larger than those in young leaves; however, the typical flattened discoid morphology was maintained. In ss4 and dpe2/phs1/ss4, the morphology of starch granules in young leaves was altered, with a more rounded shape observed. With leaf development, the starch granules became spherical exclusively in dpe2/phs1/ss4. Thus, the presented data provide new insights to contribute to the understanding of starch granule morphogenesis. KW - starch metabolism KW - starch granule KW - starch granule size KW - starch granule morphology KW - LCSM KW - Arabidopsis thaliana Y1 - 2021 U6 - https://doi.org/10.3390/molecules26195859 SN - 1420-3049 VL - 26 SP - 1 EP - 9 PB - MDPI CY - Basel, Schweiz ET - 19 ER - TY - JOUR A1 - Merida, Angel A1 - Fettke, Jörg T1 - Starch granule initiation in Arabidopsis thaliana chloroplasts JF - The plant journal N2 - The initiation of starch granule formation and the mechanism controlling the number of granules per plastid have been some of the most elusive aspects of starch metabolism. This review covers the advances made in the study of these processes. The analyses presented herein depict a scenario in which starch synthase isoform 4 (SS4) provides the elongating activity necessary for the initiation of starch granule formation. However, this protein does not act alone; other polypeptides are required for the initiation of an appropriate number of starch granules per chloroplast. The functions of this group of polypeptides include providing suitable substrates (maltooligosaccharides) to SS4, the localization of the starch initiation machinery to the thylakoid membranes, and facilitating the correct folding of SS4. The number of starch granules per chloroplast is tightly regulated and depends on the developmental stage of the leaves and their metabolic status. Plastidial phosphorylase (PHS1) and other enzymes play an essential role in this process since they are necessary for the synthesis of the substrates used by the initiation machinery. The mechanism of starch granule formation initiation in Arabidopsis seems to be generalizable to other plants and also to the synthesis of long-term storage starch. The latter, however, shows specific features due to the presence of more isoforms, the absence of constantly recurring starch synthesis and degradation, and the metabolic characteristics of the storage sink organs. KW - starch granules KW - starch metabolism KW - starch granule initiation KW - starch KW - granule number per chloroplast KW - starch morphology KW - Arabidopsis thaliana Y1 - 2021 U6 - https://doi.org/10.1111/tpj.15359 SN - 0960-7412 SN - 1365-313X VL - 107 IS - 3 SP - 688 EP - 697 PB - Wiley CY - Hoboken ER - TY - THES A1 - Egli, Lukas T1 - Stabilizing agricultural systems through diversity N2 - In the light of climate change, rising demands for agricultural products and the intensification and specialization of agricultural systems, ensuring an adequate and reliable supply of food is fundamental for food security. Maintaining diversity and redundancy has been postulated as one generic principle to increase the resilience of agricultural production and other ecosystem services. For example, if one crop fails due to climate instability and extreme events, others can compensate the losses. Crop diversity might be particularly important if different crops show asynchronous production trends. Furthermore, spatial heterogeneity has been suggested to increase stability at larger scales as production losses in some areas can be buffered by surpluses in undisturbed ones. Besides systematically investigating the mechanisms underlying stability, identifying transformative pathways that foster them is important. In my thesis, I aim at answering the following questions: (i) How does yield stability differ between nations, regions and farms, and what is the effect of crop diversity on yield stability in relation to agricultural inputs, climate heterogeneity, climate instability and time at the national, regional or farm level? (ii) Is asynchrony between crops a better predictor of production stability than crop diversity? (iii) What is the effect of asynchrony between and within crops on stability and how is it related to crop diversity and space, respectively? (iv) What is the state of the art and what are knowledge gaps in exploring resilience and its multidimensionality in ecological and social-ecological systems with agent-based models and what are potential ways forward? In the first chapter, I provide the theoretical background for the subsequent analyses. I stress the need to better understand the resilience of social-ecological systems and particularly the stability of agricultural production. Moreover, I introduce diversity and spatial heterogeneity as two prominently discussed resilience mechanisms and describe approaches to assess resilience. In the second chapter, I combined agriculture and climate data at three levels of organization and spatial extents to investigate yield stability patterns and their relation to crop diversity, fertilizer, irrigation, climate heterogeneity and instability and time of nations globally, regions in Europe and farms in Germany using statistical analyses. Yield stability decreased from the national to the farm level. Several nations and regions substantially contributed to larger-scale stability. Crop diversity was positively associated with yield stability across all three levels of organization. This effect was typically more profound at smaller scales and in variable climates. In addition to crop diversity, climate heterogeneity was an important stabilizing mechanism especially at larger scales. These results confirm the stabilizing effect of crop diversity and spatial heterogeneity, yet their importance depends on the scale and agricultural management. Building on the findings of the second chapter, I deepened in the third chapter my research on the effect of crop diversity at the national level. In particular, I tested if asynchrony between crops, i.e. between the temporal production patterns of different crops, better predicts agricultural production stability than crop diversity. The stabilizing effect of asynchrony was multiple times higher than the effect of crop diversity, i.e. asynchrony is one important property that can explain why a higher diversity supports the stability of national food production. Therefore, strategies to stabilize agricultural production through crop diversification also need to account for the asynchrony of the crops considered. The previous chapters suggest that both asynchrony between crops and spatial heterogeneity are important stabilizing mechanisms. In the fourth chapter, I therefore aimed at better understanding the relative importance of asynchrony between and within crops, i.e. between the temporal production patterns of different crops and between the temporal production patterns of different cultivation areas of the same crop. Better understanding their relative importance is important to inform agricultural management decisions, but so far this has been hardly assessed. To address this, I used crop production data to study the effect of asynchrony between and within crops on the stability of agricultural production in regions in Germany and nations in Europe. Both asynchrony between and within crops consistently stabilized agricultural production. Adding crops increased asynchrony between crops, yet this effect levelled off after eight crops in regions in Germany and after four crops in nations in Europe. Combining already ten farms within a region led to high asynchrony within crops, indicating distinct production patters, while this effect was weaker when combining multiple regions within a nation. The results suggest, that both mechanisms need to be considered in agricultural management strategies that strive for more resilient farming systems. The analyses in the foregoing chapters focused at different levels of organization, scales and factors potentially influencing agricultural stability. However, these statistical analyses are restricted by data availability and investigate correlative relationships, thus they cannot provide a mechanistic understanding of the actual processes underlying resilience. In this regard, agent-based models (ABM) are a promising tool. Besides their ability to measure different properties and to integrate multiple situations through extensive manipulation in a fully controlled system, they can capture the emergence of system resilience from individual interactions and feedbacks across different levels of organization. In the fifth chapter, I therefore reviewed the state of the art and potential knowledge gaps in exploring resilience and its multidimensionality in ecological and social-ecological systems with ABMs. Next, I derived recommendations for a more effective use of ABMs in resilience research. The review suggests that the potential of ABMs is not utilized in most models as they typically focus on a single dimension of resilience and are mostly limited to one reference state, disturbance type and scale. Moreover, only few studies explicitly test the ability of different mechanisms to support resilience. To solve real-world problems related to the resilience of complex systems, ABMs need to assess multiple stability properties for different situations and under consideration of the mechanisms that are hypothesized to render a system resilient. In the sixth chapter, I discuss the major conclusions that can be drawn from the previous chapters. Moreover, I showcase the use of simulation models to identify management strategies to enhance asynchrony and thus stability, and the potential of ABMs to identify pathways to implement such strategies. The results of my thesis confirm the stabilizing effect of crop diversity, yet its importance depends on the scale, agricultural management and climate. Moreover, strategies to stabilize agricultural production through crop diversification also need to account for the asynchrony of the crops considered. As spatial heterogeneity and particularly asynchrony within crops strongly enhances stability, integrated management approaches are needed that simultaneously address multiple resilience mechanisms at different levels of organization, scales and time horizons. For example, the simulation suggests that only increasing the number of crops at both the pixel and landscape level avoids trade-offs between asynchrony between and within crops. If their potential is better exploited, agent-based models have the capacity to systematically assess resilience and to identify comprehensive pathways towards resilient farming systems. N2 - In Anbetracht des Klimawandels, steigender Nachfrage nach landwirtschaftlichen Produkten und der weitgehenden Intensivierung und Spezialisierung landwirtschaftlicher Systeme ist eine ausreichende und zuverlässige Nahrungsmittelproduktion zentral für die Ernährungssicherheit. Eine hohe Nutzpflanzenvielfalt und räumliche Heterogenität können helfen, die Resilienz bzw. Widerstandsfähigkeit der landwirtschaftlichen Produktion zu stärken. Fällt zum Beispiel die Ernte einer Nutzpflanze aufgrund einer Dürre aus, können andere die Verluste ausgleichen. Außerdem können Produktionsverluste in einigen Gebieten durch Überschüsse in anderen Gebieten kompensiert werden. In meiner Arbeit habe ich mittels umfassender Landwirtschafts- und Klimadaten und statistischer Analysen untersucht, wie sich insbesondere Nutzpflanzenvielfalt und Klimaheterogenität auf zeitliche Ertragsstabilität auswirken. Zudem habe ich evaluiert, ob asynchrone Produktionstrends unterschiedlicher Nutzpflanzen den stabilisierenden Effekt einer hohen Nutpflanzenvielfalt erklären können. Außerdem habe ich den Effekt asynchroner Produktionstrends unterschiedlicher Nutzpflanzen und von unterschiedlichen Anbaugebieten derselben Nutzpflanze in Bezug auf Produktionsstabilität verglichen und mit einer Computersimulation eruiert, wie diese Mechanismen durch Diversifizierung verändert werden. Zum Schluss habe ich untersucht, wie umfassend die Resilienz ökologischer und sozioökologischer Systeme mittels agentenbasierter Modelle bislang erforscht wurde. Die Untersuchungen dieser Arbeit zeigen, dass Nutzpflanzenvielfalt die landwirtschaftliche Produktion auf sämtlichen untersuchten Organisationsebenen stabilisiert. Asynchrone Produktionstrends unterschiedlicher Nutzpflanzen können erklären, warum eine höhere Diversität die Produktion stabilisiert. Daneben sind asynchrone Produktionstrends unterschiedlicher Anbaugebiete besonders wichtig. Meine Simulation zeigt, dass nur eine Diversifizierung auf Feld- und Landschaftsebene asynchrone Produktionsmuster zwischen Nutpflanzen und Anbaugebieten gleichzeitig erhöht oder zumindest keine der beiden Mechanismen verringert. Agentenbasierte Modelle bieten die Möglichkeit, Resilienz systematisch zu untersuchen und Wege aufzuzeigen, die zu resilienteren Anbausystemen führen. Meine Ergebnisse unterstreichen die Notwendigkeit umfassenderer Ansätze um eine resiliente, produktive und nachhaltige landwirtschaftliche Produktion in Zeiten globaler Veränderungsprozesse zu erreichen. Dies beinhaltet insbesondere eine Diversifizierung der Nutzpflanzen auf unterschiedlichen Ebenen unter Berücksichtigung der zeitlichen Produktionstrends sowie eine nachhaltige Nutzung landwirtschaftlicher Betriebsmittel. T2 - Stabilisierung landwirtschaftlicher Systeme durch Diversität KW - Agent-based models KW - Agroecology KW - Resilience KW - Social-ecological systems KW - Sustainability KW - Agentenbasierte Modelle KW - Agrarökologie KW - Resilienz KW - Sozialökologische Systeme KW - Nachhaltigkeit Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-496848 ER - TY - CHAP A1 - Dunsing, Valentin A1 - Petrich, Annett A1 - Chiantia, Salvatore T1 - Spectral detection enables multi-color fluorescence fluctuation spectroscopy studies in living cells BT - Meeting abstract: 65th Annual Meeting of the Biophysical Society (BPS), Feb. 22-26, 2021 T2 - Biophysical journal : BJ / ed. by the Biophysical Society Y1 - 2021 U6 - https://doi.org/10.1016/j.bpj.2020.11.2206 SN - 0006-3495 SN - 1542-0086 VL - 120 IS - 3, Suppl. 1 SP - 356A EP - 356A PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Nwosu, Ebuka Canisius A1 - Roeser, Patricia Angelika A1 - Yang, Sizhong A1 - Pinkerneil, Sylvia A1 - Ganzert, Lars A1 - Dittmann, Elke A1 - Brauer, Achim A1 - Wagner, Dirk A1 - Liebner, Susanne T1 - Species-level spatio-temporal dynamics of cyanobacteria in a hard-water temperate lake in the Southern Baltics JF - Frontiers in microbiology N2 - Cyanobacteria are important primary producers in temperate freshwater ecosystems. However, studies on the seasonal and spatial distribution of cyanobacteria in deep lakes based on high-throughput DNA sequencing are still rare. In this study, we combined monthly water sampling and monitoring in 2019, amplicon sequence variants analysis (ASVs; a proxy for different species) and quantitative PCR targeting overall cyanobacteria abundance to describe the seasonal and spatial dynamics of cyanobacteria in the deep hard-water oligo-mesotrophic Lake Tiefer See, NE Germany. We observed significant seasonal variation in the cyanobacterial community composition (p < 0.05) in the epi- and metalimnion layers, but not in the hypolimnion. In winter-when the water column is mixed-picocyanobacteria (Synechococcus and Cyanobium) were dominant. With the onset of stratification in late spring, we observed potential niche specialization and coexistence among the cyanobacteria taxa driven mainly by light and nutrient dynamics. Specifically, ASVs assigned to picocyanobacteria and the genus Planktothrix were the main contributors to the formation of deep chlorophyll maxima along a light gradient. While Synechococcus and different Cyanobium ASVs were abundant in the epilimnion up to the base of the euphotic zone from spring to fall, Planktothrix mainly occurred in the metalimnetic layer below the euphotic zone where also overall cyanobacteria abundance was highest in summer. Our data revealed two potentially psychrotolerant (cold-adapted) Cyanobium species that appear to cope well under conditions of lower hypolimnetic water temperature and light as well as increasing sediment-released phosphate in the deeper waters in summer. The potential cold-adapted Cyanobium species were also dominant throughout the water column in fall and winter. Furthermore, Snowella and Microcystis-related ASVs were abundant in the water column during the onset of fall turnover. Altogether, these findings suggest previously unascertained and considerable spatiotemporal changes in the community of cyanobacteria on the species level especially within the genus Cyanobium in deep hard-water temperate lakes. KW - Cyanobium KW - picocyanobacteria diversity KW - amplicon sequencing KW - lake monitoring KW - ecological succession KW - lake stratification KW - psychrotolerant Y1 - 2021 U6 - https://doi.org/10.3389/fmicb.2021.761259 SN - 1664-302X VL - 12 PB - Frontiers Media CY - Lausanne ER - TY - GEN A1 - Zurell, Damaris A1 - König, Christian A1 - Malchow, Anne-Kathleen A1 - Kapitza, Simon A1 - Bocedi, Greta A1 - Travis, Justin M. J. A1 - Fandos, Guillermo T1 - Spatially explicit models for decision-making in animal conservation and restoration T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Models are useful tools for understanding and predicting ecological patterns and processes. Under ongoing climate and biodiversity change, they can greatly facilitate decision-making in conservation and restoration and help designing adequate management strategies for an uncertain future. Here, we review the use of spatially explicit models for decision support and to identify key gaps in current modelling in conservation and restoration. Of 650 reviewed publications, 217 publications had a clear management application and were included in our quantitative analyses. Overall, modelling studies were biased towards static models (79%), towards the species and population level (80%) and towards conservation (rather than restoration) applications (71%). Correlative niche models were the most widely used model type. Dynamic models as well as the gene-to-individual level and the community-to-ecosystem level were underrepresented, and explicit cost optimisation approaches were only used in 10% of the studies. We present a new model typology for selecting models for animal conservation and restoration, characterising model types according to organisational levels, biological processes of interest and desired management applications. This typology will help to more closely link models to management goals. Additionally, future efforts need to overcome important challenges related to data integration, model integration and decision-making. We conclude with five key recommendations, suggesting that wider usage of spatially explicit models for decision support can be achieved by 1) developing a toolbox with multiple, easier-to-use methods, 2) improving calibration and validation of dynamic modelling approaches and 3) developing best-practise guidelines for applying these models. Further, more robust decision-making can be achieved by 4) combining multiple modelling approaches to assess uncertainty, and 5) placing models at the core of adaptive management. These efforts must be accompanied by long-term funding for modelling and monitoring, and improved communication between research and practise to ensure optimal conservation and restoration outcomes. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1243 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-549915 SN - 1866-8372 VL - 2022 SP - 1 EP - 16 PB - Universitätsverlag Potsdam CY - Potsdam ET - 4 ER - TY - GEN A1 - Cahsan, Binia De A1 - Kiemel, Katrin A1 - Westbury, Michael V. A1 - Lauritsen, Maike A1 - Autenrieth, Marijke A1 - Gollmann, Günter A1 - Schweiger, Silke A1 - Stenberg, Marika A1 - Nyström, Per A1 - Drews, Hauke A1 - Tiedemann, Ralph T1 - Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Northern range margin populations of the European fire-bellied toad (Bombina bombina) have rapidly declined during recent decades. Extensive agricultural land use has fragmented the landscape, leading to habitat disruption and loss, as well as eutrophication of ponds. In Northern Germany (Schleswig-Holstein) and Southern Sweden (Skåne), this population decline resulted in decreased gene flow from surrounding populations, low genetic diversity, and a putative reduction in adaptive potential, leaving populations vulnerable to future environmental and climatic changes. Previous studies using mitochondrial control region and nuclear transcriptome-wide SNP data detected introgressive hybridization in multiple northern B. bombina populations after unreported release of toads from Austria. Here, we determine the impact of this introgression by comparing the body conditions (proxy for fitness) of introgressed and nonintrogressed populations and the genetic consequences in two candidate genes for putative local adaptation (the MHC II gene as part of the adaptive immune system and the stress response gene HSP70 kDa). We detected regional differences in body condition and observed significantly elevated levels of within individual MHC allele counts in introgressed Swedish populations, associated with a tendency toward higher body weight, relative to regional nonintrogressed populations. These differences were not observed among introgressed and nonintrogressed German populations. Genetic diversity in both MHC and HSP was generally lower in northern than Austrian populations. Our study sheds light on the potential benefits of translocations of more distantly related conspecifics as a means to increase adaptive genetic variability and fitness of genetically depauperate range margin populations without distortion of local adaptation. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1177 KW - Bombina bombina KW - heat shock protein KW - introgression KW - major histocompatibility complex KW - scaled mass index Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523883 SN - 1866-8372 IS - 14 ER - TY - JOUR A1 - Cahsan, Binia De A1 - Kiemel, Katrin A1 - Westbury, Michael V. A1 - Lauritsen, Maike A1 - Autenrieth, Marijke A1 - Gollmann, Günter A1 - Schweiger, Silke A1 - Stenberg, Marika A1 - Nyström, Per A1 - Drews, Hauke A1 - Tiedemann, Ralph T1 - Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad JF - Ecology and Evolution N2 - Northern range margin populations of the European fire-bellied toad (Bombina bombina) have rapidly declined during recent decades. Extensive agricultural land use has fragmented the landscape, leading to habitat disruption and loss, as well as eutrophication of ponds. In Northern Germany (Schleswig-Holstein) and Southern Sweden (Skåne), this population decline resulted in decreased gene flow from surrounding populations, low genetic diversity, and a putative reduction in adaptive potential, leaving populations vulnerable to future environmental and climatic changes. Previous studies using mitochondrial control region and nuclear transcriptome-wide SNP data detected introgressive hybridization in multiple northern B. bombina populations after unreported release of toads from Austria. Here, we determine the impact of this introgression by comparing the body conditions (proxy for fitness) of introgressed and nonintrogressed populations and the genetic consequences in two candidate genes for putative local adaptation (the MHC II gene as part of the adaptive immune system and the stress response gene HSP70 kDa). We detected regional differences in body condition and observed significantly elevated levels of within individual MHC allele counts in introgressed Swedish populations, associated with a tendency toward higher body weight, relative to regional nonintrogressed populations. These differences were not observed among introgressed and nonintrogressed German populations. Genetic diversity in both MHC and HSP was generally lower in northern than Austrian populations. Our study sheds light on the potential benefits of translocations of more distantly related conspecifics as a means to increase adaptive genetic variability and fitness of genetically depauperate range margin populations without distortion of local adaptation. KW - Bombina bombina KW - heat shock protein KW - introgression KW - major histocompatibility complex KW - scaled mass index Y1 - 2021 SN - 2045-7758 VL - 11 IS - 14 PB - John Wiley & Sons, Inc. CY - New Jersey ER - TY - JOUR A1 - Bogin, Barry ED - Scheffler, Christiane ED - Koziel, Slawomir ED - Hermanussen, Michael ED - Bogin, Barry T1 - Social-Economic-Political-Emotional (SEPE) factors regulate human growth T2 - Human Biology and Public Health N2 - Background There is a recurring and seamless interaction between the biology of human development and the social-economic-political-emotional (SEPE) environment. The SEPE environment influences the quality of the material conditions for human biology and, simultaneously, human growth in height and other dimensions provide social and moral signals that provide information to community networks. Objectives This article reviews the role of SEPE factors in human growth, especially skeletal growth. Sample and Methods The meaning of SEPE is defined and shown to be related to individual and group prestige, to social identity, and to ego and task motivation. These influence dominance or subordination of communities and the material and moral conditions of societies. Historical and contemporary examples of SEPE effects on skeletal size are presented. Results Membership in a SEPE community impacts skeletal size in height and breadth. Higher SEPE classes are taller, lower SEPE classes are broader. In elite level sport the winners have more growth stimulation via the hormone IGF-1 even before the contest. These findings are explained in terms of dominance versus subordination and the Community Effect in Height hypothesis. Conclusions SEPE factor regulation of human growth is shown to be a more comprehensive explanation for plasticity in height than traditional concepts such as socioeconomic status and simple-minded genetic determinism. People belonging to upper SEPE class communities, the elites, know that they are superior and are treated as such by the non-elites. The material and moral condition for life operating through these community social networks provide positive stimulation for the elites and negative stimulation for the lower SEPE classes. These differences maintain the gradients in height between SEPE communities in human societies. KW - prestige KW - dominance-subordination KW - social identity KW - ego motivation KW - material and moral conditions KW - community effects Y1 - 2021 U6 - https://doi.org/10.52905/hbph.v1.10 SN - 2748-9957 VL - 2021 IS - 1 SP - 1 EP - 20 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Carpio Arias, Tannia Valeria A1 - Arias Mogrovejo, Diana Carolina A1 - Nicolalde Cifuentes, Tomás Marcelo A1 - Tapia Veloz, Estephany Carolina A1 - Zeeuw, Chris I. de A1 - Vinueza Veloz, Maria Fernanda T1 - Sleep quality does not mediate the negative effects of chronodisruption on body composition and metabolic syndrome in healthcare workers in Ecuador JF - Diabetes & metabolic syndrome : clinical research & reviews ; the official journal of DiabetesIndia N2 - Background and aims: The objective of the present work was to determine to what extent sleep quality may mediate the association between chronodisruption (CD) and metabolic syndrome (MS), and between CD and body composition (BC). Methodology: Cross-sectional study which included 300 adult health workers, 150 of whom were night shift workers and thereby exposed to CD. Diagnosis of MS was made based on Adult Treatment Panel III criteria. Sleep quality was measured using the Pittsburgh Sleep Quality Index. Body mass index (BMI), fat mass percentage, and visceral fat percentage were measured as indicators of body composition (BC). Data were analyzed using logistic, linear regression and structural equation models. Results: The odds of health workers exposed to CD to suffer MS was 22.13 (IC95 8.68-66.07) when the model was adjusted for age, gender, physical activity and energy consumption. CD was also significantly associated with an increase in fat mass and visceral fat percentages, but not to BMI. Surprisingly, there was not enough evidence supporting the hypothesis that sleep quality contributes to the association between CD and MS or between CD and BC. Conclusions: Sleep quality does not mediate the negative effects of CD on MS nor on BC. KW - Shift work KW - Metabolic syndrome KW - Sleep quality KW - Chronodisruption KW - Body composition Y1 - 2021 U6 - https://doi.org/10.1016/j.dsx.2021.01.017 SN - 1871-4021 SN - 1878-0334 VL - 15 IS - 1 SP - 397 EP - 402 PB - Elsevier CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Yarman, Aysu A1 - Kurbanoğlu, Sevinç A1 - Zebger, Ingo A1 - Scheller, Frieder W. T1 - Simple and robust BT - the claims of protein sensing by molecularly imprinted polymers JF - Sensors and actuators : B, Chemical : an international journal devoted to research and development of chemical transducers N2 - A spectrum of 7562 publications on Molecularly Imprinted Polymers (MIPs) has been presented in literature within the last ten years (Scopus, September 7, 2020). Around 10 % of the papers published on MIPs describe the recognition of proteins. The straightforward synthesis of MIPs is a significant advantage as compared with the preparation of enzymes or antibodies. MIPs have been synthesized from only one up to six functional monomers while proteins are made up of 20 natural amino acids. Furthermore, they can be synthesized against structures of low immunogenicity and allow multi-analyte measurements via multi-target synthesis. Electrochemical methods allow simple polymer synthesis, removal of the template and readout. Among the different sensor configurations electrochemical MIP-sensors provide the broadest spectrum of protein analytes. The sensitivity of MIP-sensors is sufficiently high for biomarkers in the sub-nanomolar region, nevertheless the cross-reactivity of highly abundant proteins in human serum is still a challenge. MIPs for proteins offer innovative tools not only for clinical and environmental analysis, but also for bioimaging, therapy and protein engineering. KW - Molecularly imprinted polymer KW - Plastibodies KW - Functional scaffolds KW - Biomimetic sensors KW - Proteins Y1 - 2021 U6 - https://doi.org/10.1016/j.snb.2020.129369 SN - 0925-4005 SN - 1873-3077 VL - 330 PB - Elsevier Science CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Rogol, Alan D. ED - Scheffler, Christiane ED - Koziel, Slawomir ED - Hermanussen, Michael ED - Bogin, Barry T1 - Settings Perspective BT - Bridging the Gap between Human Biology and Public Health T2 - Human Biology and Public Health KW - growth KW - maturation KW - populations KW - secular change Y1 - 2021 U6 - https://doi.org/10.52905/hbph.v1.2 SN - 2748-9957 VL - 2021 IS - 1 SP - 1 EP - 2 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - GEN A1 - Münch, Juliane A1 - Abdelilah-Seyfried, Salim T1 - Sensing and Responding of Cardiomyocytes to Changes of Tissue Stiffness in the Diseased Heart T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Cardiomyocytes are permanently exposed to mechanical stimulation due to cardiac contractility. Passive myocardial stiffness is a crucial factor, which defines the physiological ventricular compliance and volume of diastolic filling with blood. Heart diseases often present with increased myocardial stiffness, for instance when fibrotic changes modify the composition of the cardiac extracellular matrix (ECM). Consequently, the ventricle loses its compliance, and the diastolic blood volume is reduced. Recent advances in the field of cardiac mechanobiology revealed that disease-related environmental stiffness changes cause severe alterations in cardiomyocyte cellular behavior and function. Here, we review the molecular mechanotransduction pathways that enable cardiomyocytes to sense stiffness changes and translate those into an altered gene expression. We will also summarize current knowledge about when myocardial stiffness increases in the diseased heart. Sophisticated in vitro studies revealed functional changes, when cardiomyocytes faced a stiffer matrix. Finally, we will highlight recent studies that described modulations of cardiac stiffness and thus myocardial performance in vivo. Mechanobiology research is just at the cusp of systematic investigations related to mechanical changes in the diseased heart but what is known already makes way for new therapeutic approaches in regenerative biology. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1234 KW - mechanobiology KW - tissue stiffness KW - cardiomyocyte KW - heart regeneration KW - titin KW - collagen KW - agrin KW - extracellular matrix Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-545805 SN - 1866-8372 ER - TY - JOUR A1 - Münch, Juliane A1 - Abdelilah-Seyfried, Salim T1 - Sensing and responding of cardiomyocytes to changes of tissue stiffness in the diseased heart JF - Frontiers in cell developmental biology N2 - Cardiomyocytes are permanently exposed to mechanical stimulation due to cardiac contractility. Passive myocardial stiffness is a crucial factor, which defines the physiological ventricular compliance and volume of diastolic filling with blood. Heart diseases often present with increased myocardial stiffness, for instance when fibrotic changes modify the composition of the cardiac extracellular matrix (ECM). Consequently, the ventricle loses its compliance, and the diastolic blood volume is reduced. Recent advances in the field of cardiac mechanobiology revealed that disease-related environmental stiffness changes cause severe alterations in cardiomyocyte cellular behavior and function. Here, we review the molecular mechanotransduction pathways that enable cardiomyocytes to sense stiffness changes and translate those into an altered gene expression. We will also summarize current knowledge about when myocardial stiffness increases in the diseased heart. Sophisticated in vitro studies revealed functional changes, when cardiomyocytes faced a stiffer matrix. Finally, we will highlight recent studies that described modulations of cardiac stiffness and thus myocardial performance in vivo. Mechanobiology research is just at the cusp of systematic investigations related to mechanical changes in the diseased heart but what is known already makes way for new therapeutic approaches in regenerative biology. KW - mechanobiology KW - tissue stiffness KW - cardiomyocyte KW - heart regeneration KW - titin KW - collagen KW - agrin KW - extracellular matrix Y1 - 2020 U6 - https://doi.org/10.3389/fcell.2021.642840 SN - 2296-634X VL - 9 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Guill, Christian A1 - Hülsemann, Janne A1 - Klauschies, Toni T1 - Self-organised pattern formation increases local diversity in metacommunities JF - Ecology letters N2 - Self-organised formation of spatial patterns is known from a variety of different ecosystems, yet little is known about how these patterns affect the diversity of communities. Here, we use a food chain model in which autotroph diversity is described by a continuous distribution of a trait that affects both growth and defence against heterotrophs. On isolated patches, diversity is always lost over time due to stabilising selection, and the local communities settle on one of two alternative stable community states that are characterised by a dominance of either defended or undefended species. In a metacommunity context, dispersal can destabilise these states and complex spatio-temporal patterns in the species' abundances emerge. The resulting biomass-trait feedback increases local diversity by an order of magnitude compared to scenarios without self-organised pattern formation, thereby maintaining the ability of communities to adapt to potential future changes in biotic or abiotic environmental conditions. KW - biomass-trait feedback KW - fitness gradient KW - food chain KW - functional KW - diversity KW - metacommunity KW - self-organisation KW - source-sink dynamics KW - spatio-temporal pattern KW - trait-based aggregate model KW - Turing instability Y1 - 2021 U6 - https://doi.org/10.1111/ele.13880 SN - 1461-023X SN - 1461-0248 VL - 24 IS - 12 SP - 2624 EP - 2634 PB - Wiley-Blackwell CY - Oxford ER - TY - GEN A1 - Stiegler, Jonas A1 - Kiemel, Katrin A1 - Eccard, Jana A1 - Fischer, Christina A1 - Hering, Robert A1 - Ortmann, Sylvia A1 - Strigl, Lea A1 - Tiedemann, Ralph T1 - Seed traits matter BT - Endozoochoric dispersal through a pervasive mobile linker T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Although many plants are dispersed by wind and seeds can travel long distances across unsuitable matrix areas, a large proportion relies on co-evolved zoochorous seed dispersal to connect populations in isolated habitat islands. Particularly in agricultural landscapes, where remaining habitat patches are often very small and highly isolated, mobile linkers as zoochorous seed dispersers are critical for the population dynamics of numerous plant species. However, knowledge about the quali- or quantification of such mobile link processes, especially in agricultural landscapes, is still limited. In a controlled feeding experiment, we recorded the seed intake and germination success after complete digestion by the European brown hare (Lepus europaeus) and explored its mobile link potential as an endozoochoric seed disperser. Utilizing a suite of common, rare, and potentially invasive plant species, we disentangled the effects of seed morphological traits on germination success while controlling for phylogenetic relatedness. Further, we measured the landscape connectivity via hares in two contrasting agricultural landscapes (simple: few natural and semi-natural structures, large fields; complex: high amount of natural and semi-natural structures, small fields) using GPS-based movement data. With 34,710 seeds of 44 plant species fed, one of 200 seeds (0.51%) with seedlings of 33 species germinated from feces. Germination after complete digestion was positively related to denser seeds with comparatively small surface area and a relatively slender and elongated shape, suggesting that, for hares, the most critical seed characteristics for successful endozoochorous seed dispersal minimize exposure of the seed to the stomach and the associated digestive system. Furthermore, we could show that a hare's retention time is long enough to interconnect different habitats, especially grasslands and fields. Thus, besides other seed dispersal mechanisms, this most likely allows hares to act as effective mobile linkers contributing to ecosystem stability in times of agricultural intensification, not only in complex but also in simple landscapes. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1229 KW - agricultural landscapes KW - endozoochory KW - Lepus europaeus KW - mobile links KW - seed dispersal KW - seed dispersal syndrome Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-544265 SN - 1866-8372 SP - 18477 EP - 18491 ER - TY - JOUR A1 - Stiegler, Jonas A1 - Kiemel, Katrin A1 - Eccard, Jana A1 - Fischer, Christina A1 - Hering, Robert A1 - Ortmann, Sylvia A1 - Strigl, Lea A1 - Tiedemann, Ralph A1 - Ullmann, Wiebke A1 - Blaum, Niels T1 - Seed traits matter BT - endozoochoric dispersal through a pervasive mobile linker JF - Ecology and evolution N2 - Although many plants are dispersed by wind and seeds can travel long distances across unsuitable matrix areas, a large proportion relies on co-evolved zoochorous seed dispersal to connect populations in isolated habitat islands. Particularly in agricultural landscapes, where remaining habitat patches are often very small and highly isolated, mobile linkers as zoochorous seed dispersers are critical for the population dynamics of numerous plant species. However, knowledge about the quali- or quantification of such mobile link processes, especially in agricultural landscapes, is still limited. In a controlled feeding experiment, we recorded the seed intake and germination success after complete digestion by the European brown hare (Lepus europaeus) and explored its mobile link potential as an endozoochoric seed disperser. Utilizing a suite of common, rare, and potentially invasive plant species, we disentangled the effects of seed morphological traits on germination success while controlling for phylogenetic relatedness. Further, we measured the landscape connectivity via hares in two contrasting agricultural landscapes (simple: few natural and semi-natural structures, large fields; complex: high amount of natural and semi-natural structures, small fields) using GPS-based movement data. With 34,710 seeds of 44 plant species fed, one of 200 seeds (0.51%) with seedlings of 33 species germinated from feces. Germination after complete digestion was positively related to denser seeds with comparatively small surface area and a relatively slender and elongated shape, suggesting that, for hares, the most critical seed characteristics for successful endozoochorous seed dispersal minimize exposure of the seed to the stomach and the associated digestive system. Furthermore, we could show that a hare's retention time is long enough to interconnect different habitats, especially grasslands and fields. Thus, besides other seed dispersal mechanisms, this most likely allows hares to act as effective mobile linkers contributing to ecosystem stability in times of agricultural intensification, not only in complex but also in simple landscapes. KW - agricultural landscapes KW - endozoochory KW - Lepus europaeus KW - mobile links KW - seed dispersal KW - seed dispersal syndrome Y1 - 2021 U6 - https://doi.org/10.1002/ece3.8440 SN - 2045-7758 VL - 11 IS - 24 SP - 18477 EP - 18491 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Stiegler, Jonas A1 - Kiemel, Katrin A1 - Eccard, Jana A1 - Fischer, Christina A1 - Hering, Robert A1 - Ortmann, Sylvia A1 - Strigl, Lea A1 - Tiedemann, Ralph T1 - Seed traits matter BT - Endozoochoric dispersal through a pervasive mobile linker JF - Ecology and Evolution N2 - Although many plants are dispersed by wind and seeds can travel long distances across unsuitable matrix areas, a large proportion relies on co-evolved zoochorous seed dispersal to connect populations in isolated habitat islands. Particularly in agricultural landscapes, where remaining habitat patches are often very small and highly isolated, mobile linkers as zoochorous seed dispersers are critical for the population dynamics of numerous plant species. However, knowledge about the quali- or quantification of such mobile link processes, especially in agricultural landscapes, is still limited. In a controlled feeding experiment, we recorded the seed intake and germination success after complete digestion by the European brown hare (Lepus europaeus) and explored its mobile link potential as an endozoochoric seed disperser. Utilizing a suite of common, rare, and potentially invasive plant species, we disentangled the effects of seed morphological traits on germination success while controlling for phylogenetic relatedness. Further, we measured the landscape connectivity via hares in two contrasting agricultural landscapes (simple: few natural and semi-natural structures, large fields; complex: high amount of natural and semi-natural structures, small fields) using GPS-based movement data. With 34,710 seeds of 44 plant species fed, one of 200 seeds (0.51%) with seedlings of 33 species germinated from feces. Germination after complete digestion was positively related to denser seeds with comparatively small surface area and a relatively slender and elongated shape, suggesting that, for hares, the most critical seed characteristics for successful endozoochorous seed dispersal minimize exposure of the seed to the stomach and the associated digestive system. Furthermore, we could show that a hare's retention time is long enough to interconnect different habitats, especially grasslands and fields. Thus, besides other seed dispersal mechanisms, this most likely allows hares to act as effective mobile linkers contributing to ecosystem stability in times of agricultural intensification, not only in complex but also in simple landscapes. KW - agricultural landscapes KW - endozoochory KW - Lepus europaeus KW - mobile links KW - seed dispersal KW - seed dispersal syndrome Y1 - 2021 U6 - https://doi.org/10.1002/ece3.8440 SN - 2045-7758 VL - 11 IS - 24 SP - 18477 EP - 18491 PB - John Wiley & Sons, Inc. ER - TY - JOUR A1 - Ouédraogo, Karim A1 - Zaré, Alhassane A1 - Korbéogo, Gabin A1 - Ouédraogo, Oumarou A1 - Linstädter, Anja T1 - Resilience strategies of West African pastoralists in response to scarce forage resources JF - Pastoralism : research, policy and practice N2 - Finding sufficient natural fodder resources to feed livestock has become a challenge for herders in the Sahel zone of Burkina Faso. Despite the existence of pastoral reserves, the issue of fodder shortage remains unsolved. This article highlights the changes in behaviour and the evolution of pastoral practices caused by the scarcity of forage resources. These changes are defined and classified as resilience strategies. Thus, this paper aims to analyse these strategies using new semantics that calls for other forms of perceptions or approach to the questions of pastoralists' resilience strategies. Interviews (semi-structured and casual conversations), ethnographic observations and ethnobotanical surveys were used to collect data. In rangelands, such high value fodder species as Andropogon gayanus, Pennisetum pedicellatum and Dactyloctenium aegyptium that were abundant herbaceous plants during the last decades are disappearing. Concomitantly, species with lower forage value, such as Senna obtusifolia, which are more resilient to ecological disturbance factors, are colonizing rangelands. Faced with these ecological changes, pastoralists are trying to redefine and reconfigure their practices, and this implies a redefinition of their identity. They use resilience strategies such as mowing grasses, building up fodder bundles, conserving crop residues, exploiting Senna obtusifolia (a previously neglected species), using woody fodder and adapting the type of livestock and the size of the herds to the ability of pastoralists to feed them. Strategies that are older than these are the integration of agriculture with livestock and decollectivized transhumance. It is these resilience strategies that this article exposes and analyses as defence mechanisms of Sahelian pastoralists in the face of the depletion of forage resources in their environments. KW - Pastoralism KW - Forage values KW - Burkina Faso KW - Ecological changes Y1 - 2021 U6 - https://doi.org/10.1186/s13570-021-00210-8 SN - 2041-7136 VL - 11 IS - 1 PB - SpringerOpen CY - Heidelberg ER - TY - JOUR A1 - John, Sheeba A1 - Olas, Justyna Jadwiga A1 - Müller-Röber, Bernd T1 - Regulation of alternative splicing in response to temperature variation in plants JF - Journal of experimental botany N2 - Plants have evolved numerous molecular strategies to cope with perturbations in environmental temperature, and to adjust growth and physiology to limit the negative effects of extreme temperature. One of the strategies involves alternative splicing of primary transcripts to encode alternative protein products or transcript variants destined for degradation by nonsense-mediated decay. Here, we review how changes in environmental temperature-cold, heat, and moderate alterations in temperature-affect alternative splicing in plants, including crops. We present examples of the mode of action of various temperature-induced splice variants and discuss how these alternative splicing events enable favourable plant responses to altered temperatures. Finally, we point out unanswered questions that should be addressed to fully utilize the endogenous mechanisms in plants to adjust their growth to environmental temperature. We also indicate how this knowledge might be used to enhance crop productivity in the future. KW - alternative splicing KW - ambient temperature KW - cold KW - heat KW - plants KW - stress KW - adaptation Y1 - 2021 U6 - https://doi.org/10.1093/jxb/erab232 SN - 0022-0957 SN - 1460-2431 VL - 72 IS - 18 SP - 6150 EP - 6163 PB - Oxford Univ. Press CY - Oxford ER - TY - THES A1 - Moga, Akanksha T1 - Reconstitution of molybdenum cofactor biosynthesis in giant vesicles N2 - Bottom-up synthetic biology is used for the understanding of how a cell works. It is achieved through developing techniques to produce lipid-based vesicular structures as cellular mimics. The most common techniques used to produce cellular mimics or synthetic cells is through electroformation and swelling method. However, the abovementioned techniques cannot efficiently encapsulate macromolecules such as proteins, enzymes, DNA and even liposomes as synthetic organelles. This urges the need to develop new techniques that can circumvent this issue and make the artificial cell a reality where it is possible to imitate a eukaryotic cell through encapsulating macromolecules. In this thesis, the aim to construct a cell system using giant unilamellar vesicles (GUVs) to reconstitute the mitochondrial molybdenum cofactor biosynthetic pathway. This pathway is highly conserved among all life forms, and therefore is known for its biological significance in disorders induced through its malfunctioning. Furthermore, the pathway itself is a multi-step enzymatic reaction that takes place in different compartments. Initially, GTP in the mitochondrial matrix is converted to cPMP in the presence of cPMP synthase. Further, produced cPMP is transported across the membrane to the cytosol, to be converted by MPT synthase into MPT. This pathway provides a possibility to address the general challenges faced in the development of a synthetic cell, to encapsulate large biomolecules with good efficiency and greater control and to evaluate the enzymatic reactions involved in the process. For this purpose, the emulsion-based technique was developed and optimised to allow rapid production of GUVs (~18 min) with high encapsulation efficiency (80%). This was made possible by optimizing various parameters such as density, type of oil, the impact of centrifugation speed/time, lipid concentration, pH, temperature, and emulsion droplet volume. Furthermore, the method was optimised in microtiter plates for direct experimentation and visualization after the GUV formation. Using this technique, the two steps - formation of cPMP from GTP and the formation of MPT from cPMP were encapsulated in different sets of GUVs to mimic the two compartments. Two independent fluorescence-based detection systems were established to confirm the successful encapsulation and conversion of the reactants. Alternatively, the enzymes produced using bacterial expression and measured. Following the successful encapsulation and evaluation of enzymatic reactions, cPMP transport across mitochondrial membrane has been mimicked using GUVs using a complex mitochondrial lipid composition. It was found that the cPMP interaction with the lipid bilayer results in transient pore-formation and leakage of internal contents. Overall, it can be concluded that in this thesis a novel technique has been optimised for fast production of functional synthetic cells. The individual enzymatic steps of the Moco biosynthetic pathway have successfully implemented and quantified within these cellular mimics. N2 - Die synthetische Biologie wird in der von unten-nach-oben-Methode eingesetzt, um zu verstehen, wie eine Zelle funktioniert. Dafür werden Techniken zur Herstellung lipidbasierter vesikul rer Strukturen als zellul re Nachahmungen entwickelt. Die gebräuchlichste Technik zur Herstellung von Zellnachahmungen oder synthetischen Zellen ist die Elektroformations- und Schwellmethode. Diese Techniken können jedoch Makromoleküle wie Proteine, Enzyme, DNA und sogar Liposomen nicht effizient als synthetische Organellen einkapseln. Daher ist es dringend erforderlich, neue Techniken zu entwickeln, die dieses Problem umgehen und die künstliche Zelle zu einer Realität machen, in der es möglich ist, eine eukaryotische Zelle durch Einkapselung von Makromolekülen zu imitieren. Das Ziel dieser Arbeit war es, ein komplexes Zellensystemmodel zu konstruieren, bei dem riesige unilamellare Vesikel (GUVs) zur Rekonstruktion des mitochondrialen Molybd n-Kofaktor-Biosynthesewegs verwendet werden. Dieser Stoffwechselweg ist bei allen Lebensformen hoch konserviert und daher aufgrund von St rungen, die durch Fehlfunktionen hervorgerufen werden, für seine biologische Bedeutung relevant. Darüber hinaus ist die Biosynthese selbst eine mehrstufige enzymatische Reaktion, die in verschiedenen Kompartimenten abläuft. Zunächst wird GTP in der mitochondrialen Matrix in Gegenwart von cPMP-Synthase zu cPMP umgewandelt. Anschlie end wird das produzierte cPMP über die Membran zum Zytosol transportiert, wo es von der MPT-Synthase in MPT umgewandelt wird. Dieser Biosyntheseweg bietet eine M glichkeit, den allgemeinen Herausforderungen bei der Entwicklung einer synthetischen Zelle zu begegnen, um große Biomoleküle mit guter Effizienz und Kontrolle zu verkapseln und die am Prozess beteiligten enzymatischen Reaktionen zu bewerten. Zu diesem Zweck wurde die emulsionsbasierte Technik entwickelt und optimiert, die eine schnelle Produktion von GUVs (~18 min) mit hoher Verkapselungseffizienz (80%) ermöglicht. M glich wurde dies durch die Optimierung verschiedener Parameter wie Dichte,  ltyp, Einfluss von Zentrifugationsgeschwindigkeit/-zeit, Lipidkonzentration, pH-Wert, Temperatur und Emulsionstropfenvolumen. Darüber hinaus wurde die Methode in Mikrotiterplatten für das direkte Experimentieren und die Visualisierung nach der GUV-Bildung optimiert. Mit dieser Technik wurden die beiden Schritte, die Bildung von cPMP aus GTP und die Bildung von MPT aus cPMP, in verschiedenen GUVs eingekapselt, um die beiden Kompartimente nachzuahmen. Zwei unabhängige fluoreszenzbasierte Detektionssysteme wurden eingerichtet, um die erfolgreiche Einkapselung und Umwandlung der Reaktanten zu best tigen. Alternativ wurden die Enzyme mittels bakterieller Expression produziert und gemessen. Nach der erfolgreichen Einkapselung und Auswertung der enzymatischen Reaktionen wurde der cPMP-Transport durch die mitochondriale Membran mit Hilfe von GUVs unter Verwendung einer komplexen mitochondrialen Lipidzusammensetzung nachgeahmt. Es wurde festgestellt, dass die cPMP-Wechselwirkung mit der Lipiddoppelschicht zu einer transienten Porenbildung und zum Auslaufen des inneren Inhalts führt. Insgesamt kann der Schluss gezogen werden, dass in dieser Arbeit eine neuartige Technik für die schnelle Herstellung funktioneller synthetischer Zellen optimiert wurde. Einzelne enzymatische Schritte des Moco-Biosynthesewegs wurden in diesen zellul ren Mimiken erfolgreich implementiert und quantifiziert. KW - GUVs KW - Molybdenum cofactor biosynthetic KW - Microscopy KW - Inverted emulsion-based method KW - Mikroskop KW - Biochemie Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-510167 ER - TY - JOUR A1 - Seep, Lea A1 - Razaghi-Moghadam, Zahra A1 - Nikoloski, Zoran T1 - Reaction lumping in metabolic networks for application with thermodynamic metabolic flux analysis JF - Scientific reports N2 - Thermodynamic metabolic flux analysis (TMFA) can narrow down the space of steady-state flux distributions, but requires knowledge of the standard Gibbs free energy for the modelled reactions. The latter are often not available due to unknown Gibbs free energy change of formation ,Delta fG0, of metabolites. To optimize the usage of data on thermodynamics in constraining a model, reaction lumping has been proposed to eliminate metabolites with unknown Delta fG0. However, the lumping procedure has not been formalized nor implemented for systematic identification of lumped reactions. Here, we propose, implement, and test a combined procedure for reaction lumping, applicable to genome-scale metabolic models. It is based on identification of groups of metabolites with unknown Delta fG0 whose elimination can be conducted independently of the others via: (1) group implementation, aiming to eliminate an entire such group, and, if this is infeasible, (2) a sequential implementation to ensure that a maximal number of metabolites with unknown Delta fG0 are eliminated. Our comparative analysis with genome-scale metabolic models of Escherichia coli, Bacillus subtilis, and Homo sapiens shows that the combined procedure provides an efficient means for systematic identification of lumped reactions. We also demonstrate that TMFA applied to models with reactions lumped according to the proposed procedure lead to more precise predictions in comparison to the original models. The provided implementation thus ensures the reproducibility of the findings and their application with standard TMFA. Y1 - 2021 U6 - https://doi.org/10.1038/s41598-021-87643-8 SN - 2045-2322 VL - 11 IS - 1 PB - Macmillan Publishers Limited, part of Springer Nature CY - London ER - TY - JOUR A1 - Steppert, Isabel A1 - Schönfelder, Jessy A1 - Schultz, Carolyn A1 - Kuhlmeier, Dirk T1 - Rapid in vitro differentiation of bacteria by ion mobility spectrometry JF - Applied Microbiology and Biotechnology N2 - Rapid screening of infected people plays a crucial role in interrupting infection chains. However, the current methods for identification of bacteria are very tedious and labor intense. Fast on-site screening for pathogens based on volatile organic compounds (VOCs) by ion mobility spectrometry (IMS) could help to differentiate between healthy and potentially infected subjects. As a first step towards this, the feasibility of differentiating between seven different bacteria including resistant strains was assessed using IMS coupled to multicapillary columns (MCC-IMS). The headspace above bacterial cultures was directly drawn and analyzed by MCC-IMS after 90 min of incubation. A cluster analysis software and statistical methods were applied to select discriminative VOC clusters. As a result, 63 VOC clusters were identified, enabling the differentiation between all investigated bacterial strains using canonical discriminant analysis. These 63 clusters were reduced to 7 discriminative VOC clusters by constructing a hierarchical classification tree. Using this tree, all bacteria including resistant strains could be classified with an AUC of 1.0 by receiver-operating characteristic analysis. In conclusion, MCC-IMS is able to differentiate the tested bacterial species, even the non-resistant and their corresponding resistant strains, based on VOC patterns after 90 min of cultivation. Although this result is very promising, in vivo studies need to be performed to investigate if this technology is able to also classify clinical samples. With a short analysis time of 5 min, MCC-IMS is quite attractive for a rapid screening for possible infections in various locations from hospitals to airports. Key Points center dot Differentiation of bacteria by MCC-IMS is shown after 90-min cultivation. center dot Non-resistant and resistant strains can be distinguished. center dot Classification of bacteria is possible based on metabolic features. KW - Bacteria identification KW - Volatile organic compounds (VOC) KW - Ion mobility KW - spectrometry (IMS) KW - Antibiotic resistance KW - Infection KW - Diagnostic Y1 - 2021 U6 - https://doi.org/10.1007/s00253-021-11315-w SN - 0175-7598 SN - 1432-0614 VL - 105 IS - 10 SP - 4297 EP - 4307 PB - Springer CY - New York ER - TY - JOUR A1 - Steppert, Claus A1 - Steppert, Isabel A1 - Sterlacci, William A1 - Bollinger, Thomas T1 - Rapid detection of SARS-CoV-2 infection by multicapillary column coupled ion mobility spectrometry (MCC-IMS) of breath BT - a proof of concept study JF - Journal of breath research : volatiles for medical diagnosis ; official journal of the International Association for Breath Research (IABR) and the International Society for Breath Odor Research (ISBOR) N2 - There is an urgent need for screening of patients with a communicable viral disease to cut infection chains. Recently, we demonstrated that ion mobility spectrometry coupled with a multicapillary column (MCC-IMS) is able to identify influenza-A infections in patients' breath. With a decreasing influenza epidemic and upcoming SARS-CoV-2 infections we proceeded further and analyzed patients with suspected SARS-CoV-2 infections. In this study, the nasal breath of 75 patients (34 male, 41 female, aged 64.4 +/- 15.4 years) was investigated by MCC-IMS for viral infections. Fourteen were positively diagnosed with influenza-A infection and sixteen with SARS-CoV-2 by reverse transcription polymerase chain reaction (RT-PCR) of nasopharyngeal swabs. In one patient RT-PCR was highly suspicious of SARS-CoV-2 but initially inconclusive. The remaining 44 patients served as controls. Breath fingerprints for specific infections were assessed by a combination of cluster analysis and multivariate statistics. There were no significant differences in gender or age according to the groups. In the cross validation of the discriminant analysis 72 of the 74 clearly defined patients could be correctly classified to the respective group. Even the inconclusive patient could be mapped to the SARS-CoV-2 group by applying the discrimination functions. Conclusion: SARS-CoV-2 infection and influenza-A infection can be detected with the help of MCC-IMS in breath in this pilot study. As this method provides a fast non-invasive diagnosis it should be further developed in a larger cohort for screening of communicable viral diseases. A validation study is ongoing during the second wave of COVID-19. Trial registration: ClinicalTrial.gov, NCT04282135 Registered 20 February 2020-Retrospectively registered, KW - breath analysis KW - ion mobility spectrometry KW - COVID-19 KW - influenza-A Y1 - 2021 U6 - https://doi.org/10.1088/1752-7163/abe5ca SN - 1752-7163 VL - 15 IS - 2 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Malchow, Anne-Kathleen A1 - Bocedi, Greta A1 - Palmer, Stephen C. F. A1 - Travis, Justin M. J. A1 - Zurell, Damaris T1 - RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and speciesu0027 responses to environmental changes JF - Ecography N2 - Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models. KW - connectivity KW - conservation KW - dispersal KW - evolution KW - population dynamics KW - range dynamics Y1 - 2021 SN - 1600-0587 VL - 44 IS - 10 PB - John Wiley & Sons, Inc. CY - New Jersey ER - TY - GEN A1 - Malchow, Anne-Kathleen A1 - Bocedi, Greta A1 - Palmer, Stephen C. F. A1 - Travis, Justin M. J. A1 - Zurell, Damaris T1 - RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and speciesu0027 responses to environmental changes T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1178 KW - connectivity KW - conservation KW - dispersal KW - evolution KW - population dynamics KW - range dynamics Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523979 SN - 1866-8372 IS - 10 ER - TY - JOUR A1 - Malchow, Anne-Kathleen A1 - Bocedi, Greta A1 - Palmer, Stephen C. F. A1 - Travis, Justin M. J. A1 - Zurell, Damaris T1 - RangeShiftR BT - an R package for individual-based simulation of spatial changes JF - Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos N2 - Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models. KW - connectivity KW - conservation KW - dispersal KW - evolution KW - population dynamics KW - range dynamics Y1 - 2021 U6 - https://doi.org/10.1111/ecog.05689 SN - 1600-0587 VL - 44 IS - 10 SP - 1443 EP - 1452 PB - Wiley-Blackwell CY - Oxford [u.a.] ER - TY - JOUR A1 - Li, Xiaoxiao A1 - Yang, Wei A1 - Sun, Tao A1 - Gaedke, Ursula T1 - Quantitative food web structure and ecosystem functions in a warm-temperate seagrass bed JF - Marine biology : international journal on life in oceans and coastal waters N2 - Seagrass beds are important habitats in coastal areas but increasingly decline in area and quality, thus conservation measures are urgently needed. Quantitative food webs, describing the biomass distribution and energy fluxes among trophic groups, reveal structural and functional aspects of ecosystems. Their knowledge can improve ecological conservation. For the recently discovered large warm-temperate seagrass (Zostera japonica) habitat in China's Yellow River Delta wetland, we used delta C-13 and delta N-15 measurements and a Bayesian isotope mixing model to construct its food web diagram with quantitative estimations of consumer diet compositions, comprising detritus and 14 living trophic groups from primary producers to fish. We then estimated the quantitative food web fluxes based on biomass measurements and calculated corresponding ecosystem functions. Pelagic producers were significantly C-13-depleted compared to benthic sources. Consumers (except zooplankton) were increasingly C-13-depleted with increasing trophic positions even though the consumed benthic production surpassed the pelagic one. Bivalves dominated consumer biomasses and fluxes and were the first to connect the pelagic and benthic pathways, whereas zooplankton and gastropods were specialized on the two pathways, respectively. We found flat biomass and production pyramids indicating low trophic transfer efficiencies. Generally, the energetic structure of the quantitative food web was consistent with the stable isotope analysis, and the estimated net primary production and most estimated production to biomass ratios of the trophic groups fell within literature ranges. This study provides a systematical understanding of the quantitative trophic ecology of a seagrass bed and facilitates synergistic knowledge on management, conservation, and restoration. Y1 - 2021 U6 - https://doi.org/10.1007/s00227-021-03878-z SN - 0025-3162 SN - 1432-1793 VL - 168 IS - 5 PB - Springer CY - Berlin ; Heidelberg ER - TY - JOUR A1 - Fudickar, Werner A1 - Roder, Phillip A1 - Listek, Martin A1 - Hanack, Katja A1 - Linker, Torsten T1 - Pyridinium alkynylanthracenes as sensitizers for photodynamic therapy JF - Photochemistry and photobiology N2 - Photodynamic therapy (PDT) is a mild but effective method to treat certain types of cancer upon irradiation with visible light. Here, three isomeric methylpyridinium alkynylanthracenes 1op were evaluated as sensitizers for PDT. Upon irradiation with blue or green light, all three compounds show the ability to initiate strand breaks of plasmid DNA. The mayor species responsible for cleavage is singlet oxygen (O-1(2)) as confirmed by scavenging reagents. Only isomers 1m and 1p can be incorporated into HeLa cells, whereas isomer 1o cannot permeate through the membrane. While isomer 1m targets the cell nucleus, isomer 1p assembles in the cellular cytoplasm and impacts the cellular integrity. This is in accordance with a moderate toxicity of 1p in the dark, whereas 1m exhibits no dark toxicity. Both isomers are suitable as PDT reagents, with a CC50 of 3 mu m and 75 nm, for 1p and 1m, respectively. Thus, derivative 1m, which can be easily synthesized, becomes an interesting candidate for cancer therapy. Y1 - 2021 U6 - https://doi.org/10.1111/php.13554 SN - 0031-8655 SN - 1751-1097 VL - 98 IS - 1 SP - 193 EP - 201 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Calderan-Rodrigues, Maria Juliana A1 - Luzarowski, Marcin A1 - Monte-Bello, Carolina Cassano A1 - Minen, Romina Ines A1 - Zühlke, Boris M. A1 - Nikoloski, Zoran A1 - Skirycz, Aleksandra A1 - Caldana, Camila T1 - Proteogenic dipeptides are characterized by diel fluctuations and target of rapamycin complex-signaling dependency in the model plant Arabidopsis thaliana JF - Frontiers in plant science : FPLS N2 - As autotrophic organisms, plants capture light energy to convert carbon dioxide into ATP, nicotinamide adenine dinucleotide phosphate (NADPH), and sugars, which are essential for the biosynthesis of building blocks, storage, and growth. At night, metabolism and growth can be sustained by mobilizing carbon (C) reserves. In response to changing environmental conditions, such as light-dark cycles, the small-molecule regulation of enzymatic activities is critical for reprogramming cellular metabolism. We have recently demonstrated that proteogenic dipeptides, protein degradation products, act as metabolic switches at the interface of proteostasis and central metabolism in both plants and yeast. Dipeptides accumulate in response to the environmental changes and act via direct binding and regulation of critical enzymatic activities, enabling C flux distribution. Here, we provide evidence pointing to the involvement of dipeptides in the metabolic rewiring characteristics for the day-night cycle in plants. Specifically, we measured the abundance of 13 amino acids and 179 dipeptides over short- (SD) and long-day (LD) diel cycles, each with different light intensities. Of the measured dipeptides, 38 and eight were characterized by day-night oscillation in SD and LD, respectively, reaching maximum accumulation at the end of the day and then gradually falling in the night. Not only the number of dipeptides, but also the amplitude of the oscillation was higher in SD compared with LD conditions. Notably, rhythmic dipeptides were enriched in the glucogenic amino acids that can be converted into glucose. Considering the known role of Target of Rapamycin (TOR) signaling in regulating both autophagy and metabolism, we subsequently investigated whether diurnal fluctuations of dipeptides levels are dependent on the TOR Complex (TORC). The Raptor1b mutant (raptor1b), known for the substantial reduction of TOR kinase activity, was characterized by the augmented accumulation of dipeptides, which is especially pronounced under LD conditions. We were particularly intrigued by the group of 16 dipeptides, which, based on their oscillation under SD conditions and accumulation in raptor1b, can be associated with limited C availability or photoperiod. By mining existing protein-metabolite interaction data, we delineated putative protein interactors for a representative dipeptide Pro-Gln. The obtained list included enzymes of C and amino acid metabolism, which are also linked to the TORC-mediated metabolic network. Based on the obtained results, we speculate that the diurnal accumulation of dipeptides contributes to its metabolic adaptation in response to changes in C availability. We hypothesize that dipeptides would act as alternative respiratory substrates and by directly modulating the activity of the focal enzymes. KW - dipeptide KW - diel cycle KW - metabolism KW - TOR signaling KW - protein-metabolite KW - interactions KW - carbon limitation KW - amino acid Y1 - 2021 U6 - https://doi.org/10.3389/fpls.2021.758933 SN - 1664-462X VL - 12 PB - Frontiers Media CY - Lausanne ER - TY - THES A1 - Spinti, Daniela T1 - Proteasomal protein turnover during defense priming in Arabidopsis T1 - Proteasomaler Proteinabbau während der erworbenen Immunantwort in Arabidopsis N2 - The ubiquitin-proteasome-system (UPS) is a cellular cascade involving three enzymatic steps for protein ubiquitination to target them to the 26S proteasome for proteolytic degradation. Several components of the UPS have been shown to be central for regulation of defense responses during infections with phytopathogenic bacteria. Upon recognition of the pathogen, local defense is induced which also primes the plant to acquire systemic resistance (SAR) for enhanced immune responses upon challenging infections. Here, ubiquitinated proteins were shown to accumulate locally and systemically during infections with Psm and after treatment with the SAR-inducing metabolites salicylic acid (SA) and pipecolic acid (Pip). The role of the 26S proteasome in local defense has been described in several studies, but the potential role during SAR remains elusive and was therefore investigated in this project by characterizing the Arabidopsis proteasome mutants rpt2a-2 and rpn12a-1 during priming and infections with Pseudomonas. Bacterial replication assays reveal decreased basal and systemic immunity in both mutants which was verified on molecular level showing impaired activation of defense- and SAR-genes. rpt2a-2 and rpn12a-1 accumulate wild type like levels of camalexin but less SA. Endogenous SA treatment restores local PR gene expression but does not rescue the SAR-phenotype. An RNAseq experiment of Col-0 and rpt2a-2 reveal weak or absent induction of defense genes in the proteasome mutant during priming. Thus, a functional 26S proteasome was found to be required for induction of SAR while compensatory mechanisms can still be initiated. E3-ubiquitin ligases conduct the last step of substrate ubiquitination and thereby convey specificity to proteasomal protein turnover. Using RNAseq, 11 E3-ligases were found to be differentially expressed during priming in Col-0 of which plant U-box 54 (PUB54) and ariadne 12 (ARI12) were further investigated to gain deeper understanding of their potential role during priming. PUB54 was shown to be expressed during priming and /or triggering with virulent Pseudomonas. pub54 I and pub54-II mutants display local and systemic defense comparable to Col-0. The heavy-metal associated protein 35 (HMP35) was identified as potential substrate of PUB54 in yeast which was verified in vitro and in vivo. PUB54 was shown to be an active E3-ligase exhibiting auto-ubiquitination activity and performing ubiquitination of HMP35. Proteasomal turnover of HMP35 was observed indicating that PUB54 targets HMP35 for ubiquitination and subsequent proteasomal degradation. Furthermore, hmp35-I benefits from increased resistance in bacterial replication assays. Thus, HMP35 is potentially a negative regulator of defense which is targeted and ubiquitinated by PUB54 to regulate downstream defense signaling. ARI12 is transcriptionally activated during priming or triggering and hyperinduced during priming and triggering. Gene expression is not inducible by the defense related hormone salicylic acid (SA) and is dampened in npr1 and fmo1 mutants consequently depending on functional SA- and Pip-pathways, respectively. ARI12 accumulates systemically after priming with SA, Pip or Pseudomonas. ari12 mutants are not altered in resistance but stable overexpression leads to increased resistance in local and systemic tissue. During priming and triggering, unbalanced ARI12 levels (i.e. knock out or overexpression) leads to enhanced FMO1 activation indicating a role of ARI12 in Pip-mediated SAR. ARI12 was shown to be an active E3-ligase with auto-ubiquitination activity likely required for activation with an identified ubiquitination site at K474. Mass spectrometrically identified potential substrates were not verified by additional experiments yet but suggest involvement of ARI12 in regulation of ROS in turn regulating Pip-dependent SAR pathways. Thus, data from this project provide strong indications about the involvement of the 26S proteasome in SAR and identified a central role of the two so far barely described E3-ubiquitin ligases PUB54 and ARI12 as novel components of plant defense. N2 - Das Ubiquitin-Proteasom-System (UPS) ist ein in drei Schritten enzymatisch ablaufender Prozess zur Ubiquitinierung von Proteinen, wodurch diese zum proteolytischen Abbau an das 26S Proteasom geschickt werden. Verschiedene Komponenten des UPS sind zentral an der Regulation von Immunantworten während der Infektion mit phytopathogenen Bakterien beteiligt. Beim Erkennen einer Infektion werden lokale Abwehrreaktionen initiiert, wobei auch mobile Signale in distalen Pflanzenteilen verteilt werden, welche die Pflanze primen (vorbereiten). Mit dem Erwerb der systemischen Resistenz (SAR) kann die Immunantwort bei einer zweiten Infektion verstärkt aktiviert werden. Es wurde hier gezeigt, dass ubiquitinierte Proteine in lokalem und systemischem Gewebe akkumulieren, wenn Arabidopsis mit Pseudomonas infiziert oder mit SAR-induzierender Salizylsäure (SA) oder Pipecolinsäure (Pip) behandelt wird. Die genaue Rolle des 26S Proteasoms in der systemischen Immunantwort ist bisher unklar und wurde daher in diesem Projekt mithilfe der Charakterisierung der Proteasommutanten rpt2a-2 und rpn12a-1 während des Primings genauer untersucht. In Bakterienwachstumsversuchen zeigte sich eine lokal und systemisch erhöhte Suszeptibilität der Proteasommutanten, welche auf molekularer Ebene durch ausbleibende Aktivierung von Abwehrgenen verifiziert wurde. Beide Mutanten akkumulieren ähnliche Mengen Camalexin während einer Infektion, sind aber in der Biosynthese von SA gestört. Die endogene Applikation von SA löst lokale PR-Gen Expression aus, kann aber nicht das SAR-Defizit ausgleichen. In einem RNAseq Experiment wurde das Transkriptom von Col-0 und rpt2a-2 während des Primings analysiert und zeigte, dass zentrale Abwehr- und SAR-Gene nicht oder nur schwach induziert werden. Es konnte somit gezeigt werden, dass ein funktionales 26S Proteasom zur vollen Induktion aller Teile der lokalen und systemischen Immunantwort benötigt wird, während ausgleichende Prozesse weiterhin aktiviert werden können. E3-Ubiquitin Ligasen führen den letzten Schritt der Substratubiquitinierung durch und vermitteln dadurch die Spezifität des proteasomalen Proteinabbaus. Mithilfe des RNAseq Experiments konnten 11 differentiell exprimierte Transkripte, annotiert als E3-Ligasen, identifiziert werden. Von diesen wurden PLANT U-BOX 54 (PUB54) und ARIADNE 12 (ARI12) weiter analysiert, um ein tiefergehendes Verständnis ihres Einflusses auf die systemische Immunantwort zu erhalten. PUB54 wird während des Primings und bei Infektionen mit virulenten Pseudomonas exprimiert. Die pub54 I und pub54-II Mutanten zeigen lokal und systemisch eine wildtyp-ähnliche Resistenz. Das „heavy-metal associated protein 35” (HMP35) wurde in Hefe als potentielles Substrat von PUB54 identifiziert und in vitro und in vivo verifiziert. PUB54 ist eine aktive E3-Ligase mit Autoubiquitinierungsaktivität, welche HMP35 ubiquitiniert. HMP35 wird außerdem in planta proteasomal abgebaut, wodurch eine Ubiquitinierung von HMP35 durch PUB54 zum proteasomalen Abbau nahegelegt wird. Des Weiteren wurde gezeigt, dass hmp35 Mutanten von erhöhter Resistenz profitieren. HMP35 agiert möglicherweise als negativer Regulator der Immunantwort und wird zur Aktivierung von Abwehrreaktionen durch PUB54 für den proteasomalen Abbau markiert. ARI12 wird nach Priming oder Infektion mit Pseudomonas transkriptionell aktiviert und nach sekundärer Infektion hyperinduziert, wobei die Behandlung mit SA keine Expression induziert. ARI12 ist jedoch reduziert in npr1 und fmo1 Mutanten, wodurch eine Abhängigkeit der Genexpression von funktionalen SA- und Pip-Signalwegen angedeutet wird. ARI12 akkumuliert in systemischem Gewebe nach lokaler Behandlung mit SA, Pip, oder Pseudomonas. Die ari12 Mutante zeigt wildtypähnliche Resistenz gegenüber bakteriellen Infektionen, wohingegen die Überexpression zu einer verstärkten Resistenz in lokalem und systemischem Gewebe führt. Unausgewogene Level von ARI12 (d.h. knockout oder Überexpression) führen zur erhöhten Expression von FMO1, sodass ARI12 potentiell eine regulatorische Rolle in der Pip-vermittelten systemischen Immunantwort übernimmt. Es konnte gezeigt werden, dass ARI12 eine aktive E3-Ligase mit Autoubiquitinierungsaktivität an Lys474 ist, welche vermutlich für die Aktivierung benötigt wird. Massenspektrometrisch identifizierte, mögliche Substrate von ARI12 konnten noch nicht experimentell bestätigt werden, deuten aber auf eine Rolle von ARI12 in der Regulation von reaktiven Oxygen Spezies (ROS) hin, welche wiederum Pip-anhängige Signalwege regulieren. Zusammengenommen deuten die Daten aus diesem Projekt darauf hin, dass das 26S Proteasom durch den regulierten Proteinabbau zentral ist für die systemische erworbene Resistenz und dass die bisher wenig untersuchten E3-Ligasen PUB54 und ARI12 neue regulatorische Komponenten der pflanzlichen Immunabwehr darstellen. KW - defense priming KW - Arabidopsis KW - Ubiquitin-proteasome-system KW - E3-ubiquitin ligases KW - Arabidopsis KW - E3-Ubiquitin Ligasen KW - Ubiquitin-Proteasom-System KW - erworbene Immunantwort Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-505909 ER - TY - THES A1 - Liu, Yue T1 - Polymeric objects switchable between two shapes N2 - As the ongoing trend of developing smart materials that can reversibly switch geometry stimulated by environmental control addressed increasing attention in many research fields, especially for biomedical or soft robotic applications. Shape-memory polymers (SMPs), which can change shape, stiffness, size, and structure when exposed to an external stimulus, are intensively explored as encouraging material candidates for achieving multifunctionality, and for miniaturizing into micro-components to expand the applications. Besides, the geometrical design has gained growing attention for creating engineering applications, such as bi-stable mechanisms, and has the potential to be explored by implementing SMP for new functions. In this context, this thesis aimed to develop smart micro-/nano-objects based on SMP and explore new functions by geometrical design using SMP. Here, two types of stimuli-responsive objects capable of one-way temperature-memory effect (TME) or free-standing reversible actuation e.g., micro/nanofibers (i) and microcuboids (ii) at different aspects were explored. At first, it was hypothesized that the advanced atomic force microscopy (AFM) platform can be established to study individual polymeric micro-/nanofibers (i) in terms of incorporation and characterization of a reversible shape-memory actuation capability. Crystallizable material was chosen for preparing the fibers and the molecular alignment within the fibers among different diameters will influence the crystallization-induced elongation during cooling that determined the reversible effect. For the second type, microcuboids (ii), it was hypothesized that a programming and quantification approach can be developed to enable the realization and characterization of a one-way micro-TME and micro-shape-memory polymer actuation (SMPA) in microcuboids. The responsive temperature of one-way shape transformation can be tuned by programming temperature (Tp) and the separation temperature (Tsep) for post-programming can influence the actuation. Finally, a geometrical design with bi-stability was combined with SME to create new functions of shape actuation. It was hypothesized that the predicted bi-stable or mono-stable structures can be achieved with the aid of digital fabrication methods. Using shape-memory effect (SME), the alteration of bi-stable and mono-stable can initiate shape transformation with a larger magnitude and higher energy output. In the first part, the method to quantify the reversible SMPA of a single micro/nano crystallizable fiber with geometry change during the actuation was explored. Electrospinning was used to prepare poly (ε-caprolactone) (PCL) micro/nanofiber with different diameters, which were fixed by UV glue and crosslinked on the structured silicon wafer. Using AFM, the programming, as well as the observation of recovery and reversible displacement of the fiber, were performed by vertical three-point bending at the free suspended part. A plateau tip was chosen to achieve stable contact and longer working distance for performing larger deformation, enabling intensified reversible SMPA of single fibers. In this way, programming strains of 39 ± 1% or 46 ± 1% were realized for fiber with a diameter of 1 ± 0.2 µm and 300 ± 50 nm, which were bent at 80 °C and fixed at 10 °C. Values for the reversible elongation of εrev = 3.4 ± 0.1% and 10.5 ± 0.1% were obtained for a single micro and nanofiber respectively between 10 and 60 °C. The higher actuation effect observed for nanofiber demonstrated that the highly compact and oriented crystallites in nanofibers, which determined the pronounced εrev compared to the thick microfibers. Besides, a stable reversible actuation of a nanofiber can be tracked by AFM tip up to 10 cycles, indicating a sustainable application can be achieved on the fiber actuators. The findings obtained for cPCL micro-/nano-fibers will help design and evaluate the next generation polymeric microactuators or micromanipulators. The second part of the thesis studies the shape-memory effect (SME) of a single individual SMP micro-object by controlling deformation temperatures during programming and actuation temperatures during reversible change. In this work, microcuboids of crosslinked poly[ethylene-co-(vinyl acetate)] (cPEVA) elastomers with 18 wt% vinyl acetate (VA) contents were successfully prepared by template-based replication from polydimethylsiloxane (PDMS) mold. The micro-TME and micro-SMPA were observed and studied based on micro-geometry change using optical microscopy (OM) and AFM. Different switching temperatures of shape recovery were achieved from 55 °C to 86 °C by tuning Tp from 55 °C to 100 °C, indicating a successful implementation of micro-TME on individual microcuboid. For micro-SMPA functionalization, microcuboids were deformed by compression at 100 °C and the change in single particle height was monitored during cyclic heating and cooling between various Tseps from 60 °C to 85 °C and 20 °C. The micro-SMPA on a single microcuboid was achieved with a reversible strain in the range of 2 to 7%, whereby higher compression ratio CR and Tsep induced prominent reversible strain. The results achieved in this work demonstrated the successful functionalization of microcuboids with different SMEs by controlling temperatures during programming and actuation processes. Based on these achievements, such micro-objects can be further designed as on demand switchable microactuators or release systems with adjustable working temperatures. In the last part of the work, a new function of shape-memory polymeric bi-stable 3D structured film was designed and fabricated. The SME and geometrical design of compliant mechanics were merged to enable switching between bi-stable and mono-stable states, which generate snap movement that mimics the Venus flytrap. A truncated tetrahedron structure with a slope angle as a tunable parameter to alter the bi-stability was chosen for the study to combine with SME. It was anticipated that the structured film designed with a slope angle of 30° exhibited mono-stable behavior, and such a structure with a slope angle of 45° exhibited bi-stable behavior. Then the structured SMP film of designed mono-stable shape was successfully fabricated using soft lithography based on 3D printed master molds supported from digital manufacturing. The structured mold was also used in programming the SMP film into the structure with a higher slope angle to attain bi-stability. Finally, the switching between bi-stable and mono-stable states was successfully realized using SME, which introduces snapping movement triggered by heat. The implementation of compliant mechanisms by the SME increased the magnitude of thermally induced reconfiguration without additional external force. To sum up, the results of the thesis support the development of smart objects capable of one-way micro-TME, free-standing reversible actuation, or bi-stability mediated shape-memory reconfiguration. Electrospinning and template-based method were used for fabrication with good control of geometry and low size dispersity. Microscopy methods especially the AFM platform with decent sensitivity was developed for implementation as well as characterization of SME on individual micro-/nanoobjects. Implementation of bi-stability improves the shape transformation amplitude of thermally triggered SMP. These findings can give novel insights for designing polymer-based actuators or soft robotics. KW - shape-memory polymer KW - compliant mechanism KW - atomic force microscopy Y1 - 2021 ER - TY - THES A1 - Tung, Wing Tai T1 - Polymeric fibrous scaffold on macro/microscale towards tissue regeneration Y1 - 2021 ER - TY - JOUR A1 - Sauer, Michael A1 - Grebe, Markus T1 - Plant cell biology BT - PIN polarity maintained JF - Current biology : CB N2 - PIN-FORMED (PIN) polar protein localization directs transport of the growth and developmental regulator auxin in plants. Once established after cytokinesis, PIN polarity requires maintenance. Now, direct interactions between PIN, MAB4/MEL and PID proteins suggest self-reinforced maintenance of PIN polarity through limiting lateral diffusion. Y1 - 2021 U6 - https://doi.org/10.1016/j.cub.2021.03.070 SN - 0960-9822 SN - 1879-0445 VL - 31 IS - 9 SP - R449 EP - R451 PB - Cell Press CY - Cambridge ER - TY - CHAP A1 - Dennis, Alice B. A1 - Inäbnit, Thomas T1 - Physiological and genomic variation among cryptic species of a marsh snail (Melampus bidentatus) T2 - Integrative and comparative biology / Society of Integrative and Comparative Biology Y1 - 2021 U6 - https://doi.org/10.1093/icb/icab001 SN - 1540-7063 SN - 1557-7023 VL - 61 SP - E195 EP - E196 PB - Oxford University Press CY - Oxford ER - TY - GEN A1 - Kahl, Sandra A1 - Kappel, Christian A1 - Joshi, Jasmin Radha A1 - Lenhard, Michael T1 - Phylogeography of a widely distributed plant species reveals cryptic genetic lineages with parallel phenotypic responses to warming and drought conditions T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - To predict how widely distributed species will perform under future climate change, it is crucial to understand and reveal their underlying phylogenetics. However, detailed information about plant adaptation and its genetic basis and history remains scarce and especially widely distributed species receive little attention despite their putatively high adaptability. To examine the adaptation potential of a widely distributed species, we sampled the model plant Silene vulgaris across Europe. In a greenhouse experiment, we exposed the offspring of these populations to a climate change scenario for central Europe and revealed the population structure through whole-genome sequencing. Plants were grown under two temperatures (18°C and 21°C) and three precipitation regimes (65, 75, and 90 mm) to measure their response in biomass and fecundity-related traits. To reveal the population genetic structure, ddRAD sequencing was employed for a whole-genome approach. We found three major genetic clusters in S. vulgaris from Europe: one cluster comprising Southern European populations, one cluster of Western European populations, and another cluster containing central European populations. Population genetic diversity decreased with increasing latitude, and a Mantel test revealed significant correlations between FST and geographic distances as well as between genetic and environmental distances. Our trait analysis showed that the genetic clusters significantly differed in biomass-related traits and in the days to flowering. However, half of the traits showed parallel response patterns to the experimental climate change scenario. Due to the differentiated but parallel response patterns, we assume that phenotypic plasticity plays an important role for the adaptation of the widely distributed species S. vulgaris and its intraspecific genetic lineages. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1218 KW - climate adaptation KW - ddRAD KW - Silene vulgaris Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-530035 SN - 1866-8372 SP - 13986 EP - 14002 ER - TY - JOUR A1 - Kahl, Sandra A1 - Kappel, Christian A1 - Joshi, Jasmin Radha A1 - Lenhard, Michael T1 - Phylogeography of a widely distributed plant species reveals cryptic genetic lineages with parallel phenotypic responses to warming and drought conditions JF - Ecology and Evolution N2 - To predict how widely distributed species will perform under future climate change, it is crucial to understand and reveal their underlying phylogenetics. However, detailed information about plant adaptation and its genetic basis and history remains scarce and especially widely distributed species receive little attention despite their putatively high adaptability. To examine the adaptation potential of a widely distributed species, we sampled the model plant Silene vulgaris across Europe. In a greenhouse experiment, we exposed the offspring of these populations to a climate change scenario for central Europe and revealed the population structure through whole-genome sequencing. Plants were grown under two temperatures (18°C and 21°C) and three precipitation regimes (65, 75, and 90 mm) to measure their response in biomass and fecundity-related traits. To reveal the population genetic structure, ddRAD sequencing was employed for a whole-genome approach. We found three major genetic clusters in S. vulgaris from Europe: one cluster comprising Southern European populations, one cluster of Western European populations, and another cluster containing central European populations. Population genetic diversity decreased with increasing latitude, and a Mantel test revealed significant correlations between FST and geographic distances as well as between genetic and environmental distances. Our trait analysis showed that the genetic clusters significantly differed in biomass-related traits and in the days to flowering. However, half of the traits showed parallel response patterns to the experimental climate change scenario. Due to the differentiated but parallel response patterns, we assume that phenotypic plasticity plays an important role for the adaptation of the widely distributed species S. vulgaris and its intraspecific genetic lineages. KW - climate adaptation KW - ddRAD KW - Silene vulgaris Y1 - 2021 U6 - https://doi.org/10.1002/ece3.8103 SN - 2045-7758 VL - 11 IS - 20 SP - 13986 EP - 14002 PB - John Wiley & Sons, Inc. CY - Hoboken ER - TY - GEN A1 - Clegg, Mark R. A1 - Wacker, Alexander A1 - Spijkerman, Elly T1 - Phenotypic Diversity and Plasticity of Photoresponse Across an Environmentally Contrasting Family of Phytoflagellates T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Organisms often employ ecophysiological strategies to exploit environmental conditions and ensure bio-energetic success. However, the many complexities involved in the differential expression and flexibility of these strategies are rarely fully understood. Therefore, for the first time, using a three-part cross-disciplinary laboratory experimental analysis, we investigated the diversity and plasticity of photoresponsive traits employed by one family of environmentally contrasting, ecologically important phytoflagellates. The results demonstrated an extensive inter-species phenotypic diversity of behavioural, physiological, and compositional photoresponse across the Chlamydomonadaceae, and a multifaceted intra-species phenotypic plasticity, involving a broad range of beneficial photoacclimation strategies, often attributable to environmental predisposition and phylogenetic differentiation. Deceptively diverse and sophisticated strong (population and individual cell) behavioural photoresponses were observed, with divergence from a general preference for low light (and flexibility) dictated by intra-familial differences in typical habitat (salinity and trophy) and phylogeny. Notably, contrasting lower, narrow, and flexible compared with higher, broad, and stable preferences were observed in freshwater vs. brackish and marine species. Complex diversity and plasticity in physiological and compositional photoresponses were also discovered. Metabolic characteristics (such as growth rates, respiratory costs and photosynthetic capacity, efficiency, compensation and saturation points) varied elaborately with species, typical habitat (often varying more in eutrophic species, such as Chlamydomonas reinhardtii), and culture irradiance (adjusting to optimise energy acquisition and suggesting some propensity for low light). Considerable variations in intracellular pigment and biochemical composition were also recorded. Photosynthetic and accessory pigments (such as chlorophyll a, xanthophyll-cycle components, chlorophyll a:b and chlorophyll a:carotenoid ratios, fatty acid content and saturation ratios) varied with phylogeny and typical habitat (to attune photosystem ratios in different trophic conditions and to optimise shade adaptation, photoprotection, and thylakoid architecture, particularly in freshwater environments), and changed with irradiance (as reaction and harvesting centres adjusted to modulate absorption and quantum yield). The complex, concomitant nature of the results also advocated an integrative approach in future investigations. Overall, these nuanced, diverse, and flexible photoresponsive traits will greatly contribute to the functional ecology of these organisms, addressing environmental heterogeneity and potentially shaping individual fitness, spatial and temporal distribution, prevalence, and ecosystem dynamics. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1219 KW - photoresponse KW - behaviour KW - physiology KW - composition KW - photosynthesis KW - acclimation KW - Chlamydomonas KW - ecophysiology Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-536174 SN - 1866-8372 IS - 1219 ER - TY - JOUR A1 - Clegg, Mark R. A1 - Wacker, Alexander A1 - Spijkerman, Elly T1 - Phenotypic Diversity and Plasticity of Photoresponse Across an Environmentally Contrasting Family of Phytoflagellates JF - Frontiers in plant science : FPLS N2 - Organisms often employ ecophysiological strategies to exploit environmental conditions and ensure bio-energetic success. However, the many complexities involved in the differential expression and flexibility of these strategies are rarely fully understood. Therefore, for the first time, using a three-part cross-disciplinary laboratory experimental analysis, we investigated the diversity and plasticity of photoresponsive traits employed by one family of environmentally contrasting, ecologically important phytoflagellates. The results demonstrated an extensive inter-species phenotypic diversity of behavioural, physiological, and compositional photoresponse across the Chlamydomonadaceae, and a multifaceted intra-species phenotypic plasticity, involving a broad range of beneficial photoacclimation strategies, often attributable to environmental predisposition and phylogenetic differentiation. Deceptively diverse and sophisticated strong (population and individual cell) behavioural photoresponses were observed, with divergence from a general preference for low light (and flexibility) dictated by intra-familial differences in typical habitat (salinity and trophy) and phylogeny. Notably, contrasting lower, narrow, and flexible compared with higher, broad, and stable preferences were observed in freshwater vs. brackish and marine species. Complex diversity and plasticity in physiological and compositional photoresponses were also discovered. Metabolic characteristics (such as growth rates, respiratory costs and photosynthetic capacity, efficiency, compensation and saturation points) varied elaborately with species, typical habitat (often varying more in eutrophic species, such as Chlamydomonas reinhardtii), and culture irradiance (adjusting to optimise energy acquisition and suggesting some propensity for low light). Considerable variations in intracellular pigment and biochemical composition were also recorded. Photosynthetic and accessory pigments (such as chlorophyll a, xanthophyll-cycle components, chlorophyll a:b and chlorophyll a:carotenoid ratios, fatty acid content and saturation ratios) varied with phylogeny and typical habitat (to attune photosystem ratios in different trophic conditions and to optimise shade adaptation, photoprotection, and thylakoid architecture, particularly in freshwater environments), and changed with irradiance (as reaction and harvesting centres adjusted to modulate absorption and quantum yield). The complex, concomitant nature of the results also advocated an integrative approach in future investigations. Overall, these nuanced, diverse, and flexible photoresponsive traits will greatly contribute to the functional ecology of these organisms, addressing environmental heterogeneity and potentially shaping individual fitness, spatial and temporal distribution, prevalence, and ecosystem dynamics. KW - photoresponse KW - behaviour KW - physiology KW - composition KW - photosynthesis KW - acclimation KW - Chlamydomonas KW - ecophysiology Y1 - 2021 U6 - https://doi.org/10.3389/fpls.2021.707541 SN - 1664-462X IS - 12 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Omranian, Sara A1 - Angeleska, Angela A1 - Nikoloski, Zoran T1 - PC2P BT - parameter-free network-based prediction of protein complexes JF - Bioinformatics N2 - Motivation: Prediction of protein complexes from protein-protein interaction (PPI) networks is an important problem in systems biology, as they control different cellular functions. The existing solutions employ algorithms for network community detection that identify dense subgraphs in PPI networks. However, gold standards in yeast and human indicate that protein complexes can also induce sparse subgraphs, introducing further challenges in protein complex prediction. Results: To address this issue, we formalize protein complexes as biclique spanned subgraphs, which include both sparse and dense subgraphs. We then cast the problem of protein complex prediction as a network partitioning into biclique spanned subgraphs with removal of minimum number of edges, called coherent partition. Since finding a coherent partition is a computationally intractable problem, we devise a parameter-free greedy approximation algorithm, termed Protein Complexes from Coherent Partition (PC2P), based on key properties of biclique spanned subgraphs. Through comparison with nine contenders, we demonstrate that PC2P: (i) successfully identifies modular structure in networks, as a prerequisite for protein complex prediction, (ii) outperforms the existing solutions with respect to a composite score of five performance measures on 75% and 100% of the analyzed PPI networks and gold standards in yeast and human, respectively, and (iii,iv) does not compromise GO semantic similarity and enrichment score of the predicted protein complexes. Therefore, our study demonstrates that clustering of networks in terms of biclique spanned subgraphs is a promising framework for detection of complexes in PPI networks. Y1 - 2021 U6 - https://doi.org/10.1093/bioinformatics/btaa1089 SN - 1367-4803 SN - 1460-2059 VL - 37 IS - 1 SP - 73 EP - 81 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Stark, Markus A1 - Bach, Moritz A1 - Guill, Christian T1 - Patch isolation and periodic environmental disturbances have idiosyncratic effects on local and regional population variabilities in meta-food chains JF - Theoretical ecology N2 - While habitat loss is a known key driver of biodiversity decline, the impact of other landscape properties, such as patch isolation, is far less clear. When patch isolation is low, species may benefit from a broader range of foraging opportunities, but are at the same time adversely affected by higher predation pressure from mobile predators. Although previous approaches have successfully linked such effects to biodiversity, their impact on local and metapopulation dynamics has largely been ignored. Since population dynamics may also be affected by environmental disturbances that temporally change the degree of patch isolation, such as periodic changes in habitat availability, accurate assessment of its link with isolation is highly challenging. To analyze the effect of patch isolation on the population dynamics on different spatial scales, we simulate a three-species meta-food chain on complex networks of habitat patches and assess the average variability of local populations and metapopulations, as well as the level of synchronization among patches. To evaluate the impact of periodic environmental disturbances, we contrast simulations of static landscapes with simulations of dynamic landscapes in which 30 percent of the patches periodically become unavailable as habitat. We find that increasing mean patch isolation often leads to more asynchronous population dynamics, depending on the parameterization of the food chain. However, local population variability also increases due to indirect effects of increased dispersal mortality at high mean patch isolation, consequently destabilizing metapopulation dynamics and increasing extinction risk. In dynamic landscapes, periodic changes of patch availability on a timescale much slower than ecological interactions often fully synchronize the dynamics. Further, these changes not only increase the variability of local populations and metapopulations, but also mostly overrule the effects of mean patch isolation. This may explain the often small and inconclusive impact of mean patch isolation in natural ecosystems. KW - Metacommunity dynamics KW - Dispersal KW - Patch isolation KW - Stability KW - Synchronization KW - Disturbance Y1 - 2021 U6 - https://doi.org/10.1007/s12080-021-00510-0 SN - 1874-1738 SN - 1874-1746 VL - 14 IS - 3 SP - 489 EP - 500 PB - Springer CY - Dordrecht ER - TY - THES A1 - Huang, Sichao T1 - Past and present biodiversity in northeastern Siberia inferred from sedimentary DNA metabarcoding N2 - The arctic-boreal treeline is a transition zone from taiga to tundra covering a vast area in Siberia. It often features large environmental gradients and reacts sensitively to changes in the environment. For example, the expansion of shrubs and a northward movement of the treeline are observable in Siberia as a response to the warming climate. The changes in vegetation across the treeline are known to influence the water chemistry in the lakes. This causes further alteration to the composition and diversity of sensitive aquatic organisms such as diatoms and macrophytes. Despite the rising awareness of the complex climate-feedback mechanisms of terrestrial plants, the understanding of their assembly rules and about responses of aquatic biomes in the surrounding treeline lakes is still limited. The goal of this thesis is to examine the previous and present biodiversity of terrestrial and freshwater biomes from the Siberian treeline ecotone, as well as their reactions to environmental changes. In particular, this thesis attempts to examine the performance of applying sedimentary DNA metabarcoding in terrestrial plants, aquatic macrophytes and diatoms, their spatial patterns along the environmental gradients and their temporal patterns throughout the climate transition from the late Pleistocene to Holocene. Sedimentary DNA metabarcoding combined with next-generation sequencing is applied as a primary tool to explore the composition and diversity of terrestrial plants, diatoms and aquatic macrophytes. The main study area is located in Chukotka of northeastern Siberia in the Arctic, a biodiversity hotspot due to its continental location and the diverse habitats of the glacial refugium. The modern diatom diversity was assessed with a specific diatom metabarcoding marker and morphological identification. Both approaches agree to a dominance of Fragilariaceae and Aulacoseiraceae, as well as on the environmental influential indicators of the diatom community. The high diversity of Fragilariaceae identified in the thermokarst lakes is found to follow the vegetation gradient along the treeline, suggesting that diatom metabarcoding can decipher relationships between diatom assemblage shifts and the relevant environmental changes. In particular, the metabarcoding approach detects diversification of fragilarioids in glacial lakes which is not visible using morphology. Sedimentary ancient DNA records indicate a vegetation mosaic of forb-dominated steppe-tundra during 28-19 ka, followed by a shift to dwarf-shrub tundra during 19-14 ka. During the most recent 14 thousand years, the vegetation consists of deciduous shrublands, then a change to boreal forest is observed. Investigations on the alpha diversity of the vegetation show that species richness is unexpectedly highest during pre-LGM, which is likely related to the extensive area that allows for more taxa. The optimum Holocene warming during 9-6 ka is not accompanied by a high richness as widely believed, but with an evenly distributed community by the fulfilment of erect shrubs. Furthermore, changes in taxonomic and phylogenetic diversity show complementary results in understanding community diversity. The composition and richness in the modern macrophytes community from Siberian Arctic and Chinese alpine are best co-influenced by July temperature and electrical conductivity.. Past macrophyte turnover during the late Pleistocene-Holocene is less noticeable in Siberia, whereas a pronounced community change from emergent to submerged plants is detected from Chinese alpine regions at about 14 ka due to increasing temperature and varying water conductivity. Finally, sedimentary DNA metabarcoding is a cost-effective and powerful proxy for ecological application, whereas completeness of the reference library, coverage and resolution of the metabarcoding marker are the major limitations of sedimentary DNA based diversity monitoring. The composition and richness in modern vegetation and macrophytes across broad spatial gradients is constrained by environmental variables, suggesting a potential usage for environmental monitoring. Diatom distributions are driven by different water variables along the treeline. Past records indicate that the shrub coverage has a noticeable influence on the assemblies of both terrestrial plants and aquatic macrophytes, though the shift in macrophyte community is relatively minor in the past 28 thousand years. In the long-term, the shrub expansion may eventually result in a genetically more diverse vegetation community but reduced species richness. When exceeding the optimal temperatures, further warming may lead to a decrease and putative loss of macrophytes and diatoms. N2 - Die arktisch-boreale Baumgrenze ist eine Übergangszone von Taiga zu Tundra, die ein weites Gebiet in Sibirien abdeckt. Es weist häufig große Umweltgradienten auf und reagiert empfindlich auf Änderungen in der Umwelt. Beispielsweise sind in Sibirien als Reaktion auf das sich erwärmende Klima die Ausdehnung von Sträuchern und eine Bewegung der Baumgrenze nach Norden zu beobachten. Es ist bekannt, dass die Veränderungen der Vegetation entlang der Baumgrenze die Wasserchemie in den Seen beeinflussen. Dies führt zu einer weiteren Veränderung der Zusammensetzung und Vielfalt empfindlicher Wasserorganismen wie Kieselalgen und Makrophyten. Trotz des zunehmenden Bewusstseins für die komplexen Klimarückkopplungsmechanismen von Landpflanzen ist das Verständnis ihrer Zusammensetzung und der Reaktionen aquatischer Biome in den umliegenden Baumseen immer noch begrenzt. Ziel dieser Arbeit ist es, die bisherige und gegenwärtige Artenvielfalt von Land- und Süßwasserbiomen aus dem sibirischen Baumlinien-Ökoton sowie deren Reaktionen auf Umweltveränderungen zu untersuchen. In dieser Arbeit wird insbesondere versucht, die Leistung der Anwendung der sedimentären DNA-Metabarkodierung in Landpflanzen, aquatischen Makrophyten und Kieselalgen, ihre räumlichen Muster entlang der Umweltgradienten und ihre zeitlichen Muster während des Klimaübergangs vom späten Pleistozän zum Holozän zu untersuchen. Die metabolische DNA-Metabarkodierung in Kombination mit der “Next generation Sequencing” wird als primäres Instrument zur Untersuchung der Zusammensetzung und Vielfalt von Landpflanzen, Kieselalgen und aquatischen Makrophyten eingesetzt. Das Hauptuntersuchungsgebiet befindet sich in Chukotka im Nordosten Sibiriens in der Arktis, einem Hotspot für Artenvielfalt aufgrund seiner kontinentalen Lage und der vielfältigen Lebensräume des Gletscher-Refugiums. Die moderne Diatomeendiversität wurde mit einem spezifischen Diatom-Metabarcoding Marker und einer morphologischen Identifizierung bewertet. Beide Ansätze stimmen mit einer Dominanz von Fragilariaceae und Aulacoseiraceae sowie mit den umweltbeeinflussenden Indikatoren der Kieselalgengemeinschaft überein. Die hohe Vielfalt der in den Thermokarstseen identifizierten Fragilariaceae folgt dem Vegetationsgradienten entlang der Baumgrenze, was darauf hindeutet, dass die Metabarkodierung von Kieselalgen Beziehungen zwischen Verschiebungen der Kieselalgenassemblage und den relevanten Umweltveränderungen entschlüsseln kann. Insbesondere erkennt der Metabarcoding-Ansatz eine Diversifikation von Fragilarioiden in Gletscherseen, die unter Verwendung der Morphologie nicht sichtbar ist. Sedimentäre alte DNA-Aufzeichnungen weisen auf ein Vegetationsmosaik der von Forb dominierten Steppentundra zwischen 28 und 19 ka hin, gefolgt von einer Verschiebung in die Zwergstrauch-Tundra zwischen 19 und 14 ka. In den letzten 14.000 Jahren besteht die Vegetation aus Laubbäumen, dann wird eine Veränderung des borealen Waldes beobachtet. Untersuchungen zur Alpha-Diversität der Vegetation zeigen, dass der Artenreichtum vor der LGM unerwartet am höchsten ist, was wahrscheinlich mit dem ausgedehnten Gebiet zusammenhängt, das mehr Taxa zulässt. Die optimale Erwärmung des Holozäns während 9-6 ka geht nicht mit einem hohen Reichtum einher, wie allgemein angenommen wird, sondern mit einer gleichmäßig verteilten Gemeinschaft durch die Erfüllung aufrecht stehender Sträucher. Darüber hinaus zeigen Änderungen der taxonomischen und phylogenetischen Vielfalt komplementäre Ergebnisse für das Verständnis der Vielfalt in der Gemeinschaft. Die Zusammensetzung und der Reichtum der modernen Makrophytengemeinschaft aus der sibirischen Arktis und den chinesischen Alpen werden am besten von der Temperatur im Juli und der elektrischen Leitfähigkeit beeinflusst. Der vergangene Makrophytenumsatz während des späten Pleistozän-Holozäns ist in Sibirien weniger auffällig, während in chinesischen Alpenregionen bei etwa 14 ka aufgrund der steigenden Temperatur und der unterschiedlichen Wasserleitfähigkeit ein ausgeprägter Wechsel der Gemeinschaft von emergenten zu untergetauchten Pflanzen festgestellt wird. Schließlich ist die Sediment-DNA-Metabarkodierung ein kostengünstiger und leistungsfähiger Proxy für die ökologische Anwendung, während die Vollständigkeit der Referenzbibliothek, die Abdeckung und die Auflösung des Metabarkodierungsmarkers die Hauptbeschränkungen der auf Sediment-DNA basierenden Diversitätsüberwachung darstellen. Die Zusammensetzung und der Reichtum an moderner Vegetation und Makrophyten über breite räumliche Gradienten hinweg werden durch Umgebungsvariablen eingeschränkt, was auf eine mögliche Verwendung für die Umweltüberwachung hindeutet. Die Verteilung der Kieselalgen wird durch verschiedene Wasservariablen entlang der Baumgrenze gesteuert. Frühere Aufzeichnungen zeigen, dass die Strauchbedeckung einen spürbaren Einfluss auf die Ansammlungen von Landpflanzen und Wassermakrophyten hat, obwohl die Verschiebung der Makrophytengemeinschaft in den letzten 28.000 Jahren relativ gering ist. Langfristig kann die Strauchausdehnung letztendlich zu einer genetisch vielfältigeren Vegetationsgemeinschaft führen, die jedoch den Artenreichtum verringert. Wenn die optimalen Temperaturen überschritten werden, kann eine weitere Erwärmung zu einer Abnahme und einem mutmaßlichen Verlust von Makrophyten und Kieselalgen führen. KW - metabarcoding KW - plant diversity KW - iatom diversity KW - phylogenetic diversity KW - ancient DNA Y1 - 2021 ER - TY - GEN A1 - Perkins, Anita A1 - Rose, Andrew A1 - Grossart, Hans-Peter A1 - Rojas-Jimenez, Keilor Osvaldo A1 - Barroso Prescott, Selva Kiri A1 - Oakes, Joanne M. T1 - Oxic and Anoxic Organic Polymer Degradation Potential of Endophytic Fungi From the Marine Macroalga, Ecklonia radiata T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Cellulose and chitin are the most abundant polymeric, organic carbon source globally. Thus, microbes degrading these polymers significantly influence global carbon cycling and greenhouse gas production. Fungi are recognized as important for cellulose decomposition in terrestrial environments, but are far less studied in marine environments, where bacterial organic matter degradation pathways tend to receive more attention. In this study, we investigated the potential of fungi to degrade kelp detritus, which is a major source of cellulose in marine systems. Given that kelp detritus can be transported considerable distances in the marine environment, we were specifically interested in the capability of endophytic fungi, which are transported with detritus, to ultimately contribute to kelp detritus degradation. We isolated 10 species and two strains of endophytic fungi from the kelp Ecklonia radiata. We then used a dye decolorization assay to assess their ability to degrade organic polymers (lignin, cellulose, and hemicellulose) under both oxic and anoxic conditions and compared their degradation ability with common terrestrial fungi. Under oxic conditions, there was evidence that Ascomycota isolates produced cellulose-degrading extracellular enzymes (associated with manganese peroxidase and sulfur-containing lignin peroxidase), while Mucoromycota isolates appeared to produce both lignin and cellulose-degrading extracellular enzymes, and all Basidiomycota isolates produced lignin-degrading enzymes (associated with laccase and lignin peroxidase). Under anoxic conditions, only three kelp endophytes degraded cellulose. We concluded that kelp fungal endophytes can contribute to cellulose degradation in both oxic and anoxic environments. Thus, endophytic kelp fungi may play a significant role in marine carbon cycling via polymeric organic matter degradation. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1246 KW - kelp KW - fungi KW - endophytes KW - carbon cycling KW - extracellular enzymes KW - cellulose polymeric organic matter Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-550520 SN - 1866-8372 VL - 12 SP - 1 EP - 13 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Perkins, Anita A1 - Rose, Andrew A1 - Grossart, Hans-Peter A1 - Rojas-Jimenez, Keilor Osvaldo A1 - Barroso Prescott, Selva Kiri A1 - Oakes, Joanne M. T1 - Oxic and Anoxic Organic Polymer Degradation Potential of Endophytic Fungi From the Marine Macroalga, Ecklonia radiata JF - Frontiers in Microbiology N2 - Cellulose and chitin are the most abundant polymeric, organic carbon source globally. Thus, microbes degrading these polymers significantly influence global carbon cycling and greenhouse gas production. Fungi are recognized as important for cellulose decomposition in terrestrial environments, but are far less studied in marine environments, where bacterial organic matter degradation pathways tend to receive more attention. In this study, we investigated the potential of fungi to degrade kelp detritus, which is a major source of cellulose in marine systems. Given that kelp detritus can be transported considerable distances in the marine environment, we were specifically interested in the capability of endophytic fungi, which are transported with detritus, to ultimately contribute to kelp detritus degradation. We isolated 10 species and two strains of endophytic fungi from the kelp Ecklonia radiata. We then used a dye decolorization assay to assess their ability to degrade organic polymers (lignin, cellulose, and hemicellulose) under both oxic and anoxic conditions and compared their degradation ability with common terrestrial fungi. Under oxic conditions, there was evidence that Ascomycota isolates produced cellulose-degrading extracellular enzymes (associated with manganese peroxidase and sulfur-containing lignin peroxidase), while Mucoromycota isolates appeared to produce both lignin and cellulose-degrading extracellular enzymes, and all Basidiomycota isolates produced lignin-degrading enzymes (associated with laccase and lignin peroxidase). Under anoxic conditions, only three kelp endophytes degraded cellulose. We concluded that kelp fungal endophytes can contribute to cellulose degradation in both oxic and anoxic environments. Thus, endophytic kelp fungi may play a significant role in marine carbon cycling via polymeric organic matter degradation. KW - kelp KW - fungi KW - endophytes KW - carbon cycling KW - extracellular enzymes KW - cellulose polymeric organic matter Y1 - 2021 U6 - https://doi.org/10.3389/fmicb.2021.726138 SN - 1664-302X VL - 12 SP - 1 EP - 13 PB - Frontiers in microbiology CY - Lausanne, Schweiz ER - TY - THES A1 - Brunacci, Nadia T1 - Oligodepsipeptides as matrix for drug delivery systems and submicron particulate carriers Y1 - 2021 ER - TY - JOUR A1 - Tran, V. Phuong A1 - Tamura, Yui A1 - Pham, Van-Cuong A1 - Elhussiny, Mohamed Z. A1 - Han, Guofeng A1 - Sur Chowdhury, Vishwajit A1 - Furuse, Mitsuhiro T1 - Neuropeptide Y modifies a part of diencephalic catecholamine but not indolamine metabolism in chicks depending on feeding status JF - Neuropeptides N2 - The role of the monoaminergic system in the feeding behavior of neonatal chicks has been reported, but the functional relationship between the metabolism of monoamines and appetite-related neuropeptides is still unclear. This study aimed to investigate the changes in catecholamine and indolamine metabolism in response to the central action of neuropeptide Y (NPY) in different feeding statuses and the underlying mechanisms. In Experiment 1, the diencephalic concentrations of amino acids and monoamines following the intracerebroventricular (ICV) injection of NPY (375 pmol/10 mu l/chick), saline solution under ad libitum, and fasting conditions for 30 min were determined. Central NPY significantly decreased L-tyrosine concentration, the precursor of catecholamines under feeding condition, but not under fasting condition. Central NPY significantly increased dopamine metabolites, including 3,4-dihydroxyphenylacetic acid and homovanillic acid (HVA). The concentration of 3-methoxy-4-hydroxyphenylglycol was significantly reduced under feeding condition, but did not change under fasting condition by NPY. However, no effects of NPY on indolamine metabolism were found in either feeding status. Therefore, the mechanism of action of catecholamines with central NPY under feeding condition was elucidated in Experiment 2. Central NPY significantly attenuated diencephalic gene expression of catecholaminergic synthetic enzymes, such as tyrosine hydroxylase, L-aromatic amino acid decarboxylase, and GTP cyclohydrolase I after 30 min of feeding. In Experiment 3, co-injection of alpha-methyl-L-tyrosine, an inhibitor of tyrosine hydroxylase with NPY, moderately attenuated the orexigenic effect of NPY, accompanied by a significant positive correlation between food intake and HVA levels. In Experiment 4, there was a significant interaction between NPY and clorgyline, an inhibitor of monoamine oxidase A with ICV co-injection which implies that co-existence of NPY and clorgyline enhances the orexigenic effect of NPY. In conclusion, central NPY modifies a part of catecholamine metabolism, which is illustrated by the involvement of dopamine transmission and metabolism under feeding but not fasting conditions. KW - Neuropeptide Y KW - Feeding behavior KW - Neonatal chick KW - CNS KW - Catecholamines Y1 - 2021 U6 - https://doi.org/10.1016/j.npep.2021.102169 SN - 0143-4179 SN - 1532-2785 VL - 89 PB - Elsevier CY - New York, NY ER - TY - JOUR A1 - Dunsing, Valentin A1 - Petrich, Annett A1 - Chiantia, Salvatore T1 - Multicolor fluorescence fluctuation spectroscopy in living cells via spectral detection JF - eLife N2 - Signaling pathways in biological systems rely on specific interactions between multiple biomolecules. Fluorescence fluctuation spectroscopy provides a powerful toolbox to quantify such interactions directly in living cells. Cross-correlation analysis of spectrally separated fluctuations provides information about intermolecular interactions but is usually limited to two fluorophore species. Here, we present scanning fluorescence spectral correlation spectroscopy (SFSCS), a versatile approach that can be implemented on commercial confocal microscopes, allowing the investigation of interactions between multiple protein species at the plasma membrane. We demonstrate that SFSCS enables cross-talk-free cross-correlation, diffusion, and oligomerization analysis of up to four protein species labeled with strongly overlapping fluorophores. As an example, we investigate the interactions of influenza A virus (IAV) matrix protein 2 with two cellular host factors simultaneously. We furthermore apply raster spectral image correlation spectroscopy for the simultaneous analysis of up to four species and determine the stoichiometry of ternary IAV polymerase complexes in the cell nucleus. KW - fluorescence KW - optical microscopy KW - virus assembly KW - protein-protein KW - interactions KW - diffusion KW - Viruses Y1 - 2021 U6 - https://doi.org/10.7554/eLife.69687 SN - 2050-084X VL - 10 PB - eLife Sciences Publications CY - Cambridge ER - TY - JOUR A1 - Kürschner, Tobias A1 - Scherer, Cédric A1 - Radchuk, Viktoriia A1 - Blaum, Niels A1 - Kramer-Schadt, Stephanie T1 - Movement can mediate temporal mismatches between resource availability and biological events in host-pathogen interactions JF - Ecology and evolution N2 - Global change is shifting the timing of biological events, leading to temporal mismatches between biological events and resource availability. These temporal mismatches can threaten species' populations. Importantly, temporal mismatches not only exert strong pressures on the population dynamics of the focal species, but can also lead to substantial changes in pairwise species interactions such as host-pathogen systems. We adapted an established individual-based model of host-pathogen dynamics. The model describes a viral agent in a social host, while accounting for the host's explicit movement decisions. We aimed to investigate how temporal mismatches between seasonal resource availability and host life-history events affect host-pathogen coexistence, that is, disease persistence. Seasonal resource fluctuations only increased coexistence probability when in synchrony with the hosts' biological events. However, a temporal mismatch reduced host-pathogen coexistence, but only marginally. In tandem with an increasing temporal mismatch, our model showed a shift in the spatial distribution of infected hosts. It shifted from an even distribution under synchronous conditions toward the formation of disease hotspots, when host life history and resource availability mismatched completely. The spatial restriction of infected hosts to small hotspots in the landscape initially suggested a lower coexistence probability due to the critical loss of susceptible host individuals within those hotspots. However, the surrounding landscape facilitated demographic rescue through habitat-dependent movement. Our work demonstrates that the negative effects of temporal mismatches between host resource availability and host life history on host-pathogen coexistence can be reduced through the formation of temporary disease hotspots and host movement decisions, with implications for disease management under disturbances and global change. KW - classical swine fever KW - dynamic landscapes KW - global change KW - host– pathogen dynamics KW - individual‐ based model KW - movement ecology Y1 - 2021 U6 - https://doi.org/10.1002/ece3.7478 SN - 2045-7758 VL - 11 IS - 10 SP - 5728 EP - 5741 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Hu, Ting-Li A1 - Cheng, Feng A1 - Xu, Zhen A1 - Chen, Zhong-Zheng A1 - Yu, Lei A1 - Ban, Qian A1 - Li, Chun-Lin A1 - Pan, Tao A1 - Zhang, Bao-Wei T1 - Molecular and morphological evidence for a new species of the genus Typhlomys (Rodentia: Platacanthomyidae) JF - Zoological research : ZR = Dongwuxue-yanjiu : jikan / published by Kunming Institute of Zoology, Chinese Academy of Sciences, Zhongguo Kexueyuan Kunming Dongwu Yanjiusuo zhuban, Dongwuxue-yanjiu Bianji Weiyuanhui bianji N2 - In this study, we reassessed the taxonomic position of Typhlomys (Rodentia: Platacanthomyidae) from Huangshan, Anhui, China, based on morphological and molecular evidence. Results suggested that Typhlomys is comprised of up to six species, including four currently recognized species ( Typhlomys cinereus, T. chapensis, T. daloushanensis, and T. nanus), one unconfirmed candidate species, and one new species ( Typhlomys huangshanensis sp. nov.). Morphological analyses further supported the designation of the Huangshan specimens found at mid-elevations in the southern Huangshan Mountains (600 m to 1 200 m a.s.l.) as a new species. KW - Morphology KW - Phylogenetics KW - Species delimitation KW - Taxonomy Y1 - 2021 U6 - https://doi.org/10.24272/j.issn.2095-8137.2020.132 SN - 2095-8137 VL - 42 IS - 1 SP - 100 EP - 107 PB - Yunnan Renmin Chubanshe CY - Kunming ER - TY - THES A1 - Möser, Christin T1 - Modular DNA constructs for oligovalent bio-enhancement and functional screening T1 - Modulare DNA-Konstrukte für oligovalente Bio-Verstärkung und funktionelles Screening N2 - Deoxyribonucleic acid (DNA) nanostructures enable the attachment of functional molecules to nearly any unique location on their underlying structure. Due to their single-base-pair structural resolution, several ligands can be spatially arranged and closely controlled according to the geometry of their desired target, resulting in optimized binding and/or signaling interactions. This dissertation covers three main projects. All of them use variations of functionalized DNA nanostructures that act as platform for oligovalent presentation of ligands. The purpose of this work was to evaluate the ability of DNA nanostructures to precisely display different types of functional molecules and to consequently enhance their efficacy according to the concept of multivalency. Moreover, functionalized DNA structures were examined for their suitability in functional screening assays. The developed DNA-based compound ligands were used to target structures in different biological systems. One part of this dissertation attempted to bind pathogens with small modified DNA nanostructures. Pathogens like viruses and bacteria are known for their multivalent attachment to host cells membranes. By blocking their receptors for recognition and/or fusion with their targeted host in an oligovalent manner, the objective was to impede their ability to adhere to and invade cells. For influenza A, only enhanced binding of oligovalent peptide-DNA constructs compared to the monovalent peptide could be observed, whereas in the case of respiratory syncytial virus (RSV), binding as well as blocking of the target receptors led to an increased inhibition of infection in vitro. In the final part, the ability of chimeric DNA-peptide constructs to bind to and activate signaling receptors on the surface of cells was investigated. Specific binding of DNA trimers, conjugated with up to three peptides, to EphA2 receptor expressing cells was evaluated in flow cytometry experiments. Subsequently, their ability to activate these receptors via phosphorylation was assessed. EphA2 phosphorylation was significantly increased by DNA trimers carrying three peptides compared to monovalent peptide. As a result of activation, cells underwent characteristic morphological changes, where they "round up" and retract their periphery. The results obtained in this work comprehensively prove the capability of DNA nanostructures to serve as stable, biocompatible, controllable platforms for the oligovalent presentation of functional ligands. Functionalized DNA nanostructures were used to enhance biological effects and as tool for functional screening of bio-activity. This work demonstrates that modified DNA structures have the potential to improve drug development and to unravel the activation of signaling pathways. N2 - Desoxyribonukleinsäure (DNS, engl. DNA) - Nanostrukturen ermöglichen die Anbringung funktioneller Moleküle an nahezu jede einzigartige Stelle der zugrunde liegenden Struktur. Aufgrund der Basenpaar-Strukturauflösung von DNA können mehrere Moleküle (z.B. Liganden) entsprechend der Geometrie ihres gewünschten Ziels räumlich angeordnet und genau kontrolliert werden, was zu optimierten Bindungs- und/oder Signalwechselwirkungen führt. Diese Dissertation umfasst drei Hauptprojekte. Alle Projekte verwenden Varianten von funktionalisierten DNA-Nanostrukturen, die als Plattform für die oligovalente Präsentation von Liganden dienen. Ziel der vorliegenden Arbeit war es, die Fähigkeit von DNA-Nanostrukturen zur präzisen Positionierung verschiedener Arten von funktionellen Molekülen zu evaluieren und folglich die Wirksamkeit der Moleküle gemäß dem Konzept der Multivalenz zu erhöhen. Außerdem wurde untersucht, wie funktionalisierte DNA-Strukturen in verschiedenen Verfahren zur Erforschung von biologischen Interaktionen eingesetzt werden können. Die entwickelten DNA-basierten Liganden wurden verwendet, um Strukturen auf verschiedenen biologischen Systemen gezielt zu binden. In einem Teil dieser Dissertation wurde versucht, Krankheitserreger mit kleinen modifizierten DNA-Nanostrukturen zu binden. Pathogene, wie Viren und Bakterien, sind für ihre multivalente Anheftung an Wirtszellmembranen bekannt. Durch die oligovalente Blockierung ihrer Rezeptoren für die Erkennung und/oder Fusion mit ihrem Wirt sollte ihre Fähigkeit, sich an Zielzellen anzuheften und in diese einzudringen, beeinträchtigt werden. Bei Influenza A Viren konnte nur eine verstärkte Bindung von oligovalenten Peptid-DNA-Konstrukten im Vergleich zu monovalenten Peptiden beobachtet werden, wohingegen bei Respiratorischen Synzytial-Viren (RSV) sowohl die Bindung als auch die Blockierung der Zielrezeptoren zu einer verstärkten Hemmung der Infektion in vitro führte. Im letzten Teil wurden chimäre DNA-Peptidkonstrukte auf ihre Fähigkeit, an Signalrezeptoren auf der Oberfläche von Zellen zu binden und diese zu aktivieren, getestet. Die spezifische Bindung von mit bis zu drei Peptiden konjugierten DNA-Trimeren an EphA2-Rezeptor-exprimierende Zellen wurde in Durchflusszytometrie-Experimenten untersucht. Anschließend wurde ihre Fähigkeit, diese Rezeptoren durch Phosphorylierung zu aktivieren, beurteilt. Die Phosphorylierung von EphA2 war durch DNA-Trimere, die drei Peptide trugen, im Vergleich zu monovalenten Peptiden signifikant erhöht. Infolge der Aktivierung kommt es zu charakteristischen morphologischen Veränderungen der Zellen, bei denen diese ihre Peripherie "abrunden" und zurückziehen. Die in dieser Arbeit erzielten Ergebnisse beweisen umfassend die Fähigkeit von DNA-Nanostrukturen, als stabile, biokompatible, kontrollierbare Plattformen für die oligovalente Präsentation funktioneller Liganden zu fungieren. Funktionalisierte DNA-Nanostrukturen wurden zur Verstärkung biologischer Effekte und als Werkzeug für das funktionelle Screening von biologischen Interaktionen verwendet. Diese Arbeit zeigt, dass modifizierte DNA-Strukturen das Potenzial haben, die Medikamentenentwicklung zu verbessern und die Aktivierung von Signalwegen zu entschlüsseln. KW - DNA KW - multivalency KW - influenza KW - respiratory syncytial virus KW - nanostructure KW - ephrin KW - DNA KW - Ephrin KW - Influenza KW - Multivalenz KW - Nanostruktur KW - Respiratorisches Synzytial-Virus KW - DNS Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-507289 ER - TY - JOUR A1 - Straube, Nicolas A1 - Preick, Michaela A1 - Naylor, Gavin J. P. A1 - Hofreiter, Michael T1 - Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for lantern shark taxonomy (Chondrichthyes: Etmopteridae) JF - Royal Society Open Science N2 - After initial detection of target archival DNA of a 116-year-old syntype specimen of the smooth lantern shark, Etmopterus pusillus, in a single-stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has 12 times coverage and a length of 16 741 bp. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple E. pusillus samples from various distant localities as well as sequences from a morphological similar species, the shortfin smooth lantern shark Etmopterus joungi. Results confirm the almost global distribution of E. pusillus and suggest E. joungi to be a junior synonym of E. pusillus. As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet collection type specimen for taxonomy. KW - museum specimens KW - archival DNA KW - deep-sea sharks KW - Etmopterus pusillus KW - Etmopterus joungi KW - taxonomy Y1 - 2021 U6 - https://doi.org/10.1098/rsos.210474 SN - 2054-5703 VL - 8 IS - 9 PB - Royal Society CY - London ER - TY - JOUR A1 - Wang, Meng A1 - Li, Panpan A1 - Ma, Yao A1 - Nie, Xiang A1 - Grebe, Markus A1 - Men, Shuzhen T1 - Membrane sterol composition in Arabidopsis thaliana affects root elongation via auxin biosynthesis JF - International journal of molecular sciences N2 - Plant membrane sterol composition has been reported to affect growth and gravitropism via polar auxin transport and auxin signaling. However, as to whether sterols influence auxin biosynthesis has received little attention. Here, by using the sterol biosynthesis mutant cyclopropylsterol isomerase1-1 (cpi1-1) and sterol application, we reveal that cycloeucalenol, a CPI1 substrate, and sitosterol, an end-product of sterol biosynthesis, antagonistically affect auxin biosynthesis. The short root phenotype of cpi1-1 was associated with a markedly enhanced auxin response in the root tip. Both were neither suppressed by mutations in polar auxin transport (PAT) proteins nor by treatment with a PAT inhibitor and responded to an auxin signaling inhibitor. However, expression of several auxin biosynthesis genes TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 (TAA1) was upregulated in cpi1-1. Functionally, TAA1 mutation reduced the auxin response in cpi1-1 and partially rescued its short root phenotype. In support of this genetic evidence, application of cycloeucalenol upregulated expression of the auxin responsive reporter DR5:GUS (beta-glucuronidase) and of several auxin biosynthesis genes, while sitosterol repressed their expression. Hence, our combined genetic, pharmacological, and sterol application studies reveal a hitherto unexplored sterol-dependent modulation of auxin biosynthesis during Arabidopsis root elongation. KW - Arabidopsis thaliana KW - auxin KW - auxin biosynthesis KW - cycloeucalenol KW - CPI1 KW - sitosterol KW - sterol Y1 - 2021 U6 - https://doi.org/10.3390/ijms22010437 SN - 1422-0067 VL - 22 IS - 1 PB - MDPI CY - Basel ER - TY - JOUR A1 - Paolini, Alessio A1 - Fontana, Federica A1 - Van-Cuong Pham, A1 - Rödel, Claudia Jasmin A1 - Seyfried, Salim T1 - Mechanosensitive Notch-Dll4 and Klf2-Wnt9 signaling pathways intersect in guiding valvulogenesis in zebrafish JF - Cell reports N2 - In the zebrafish embryo, the onset of blood flow generates fluid shear stress on endocardial cells, which are specialized endothelial cells that line the interior of the heart. High levels of fluid shear stress activate both Notch and Klf2 signaling, which play crucial roles in atrioventricular valvulogenesis. However, it remains unclear why only individual endocardial cells ingress into the cardiac jelly and initiate valvulogenesis. Here, we show that lateral inhibition between endocardial cells, mediated by Notch, singles out Delta-like-4-positive endocardial cells. These cells ingress into the cardiac jelly, where they form an abluminal cell population. Delta-like-4-positive cells ingress in response to Wnt9a, which is produced in parallel through an Erk5Klf2-Wnt9a signaling cascade also activated by blood flow. Hence, mechanical stimulation activates parallel mechanosensitive signaling pathways that produce binary effects by driving endocardial cells toward either luminal or abluminal fates. Ultimately, these cell fate decisions sculpt cardiac valve leaflets. Y1 - 2021 U6 - https://doi.org/10.1016/j.celrep.2021.109782 SN - 2211-1247 VL - 37 IS - 1 PB - Cell Press CY - Maryland Heights, MO ER - TY - JOUR A1 - Xu, Rudan A1 - Razaghi-Moghadam, Zahra A1 - Nikoloski, Zoran T1 - Maximization of non-idle enzymes improves the coverage of the estimated maximal in vivo enzyme catalytic rates in Escherichia coli JF - Bioinformatics N2 - Motivation: Constraint-based modeling approaches allow the estimation of maximal in vivo enzyme catalytic rates that can serve as proxies for enzyme turnover numbers. Yet, genome-scale flux profiling remains a challenge in deploying these approaches to catalogue proxies for enzyme catalytic rates across organisms. Results: Here, we formulate a constraint-based approach, termed NIDLE-flux, to estimate fluxes at a genome-scale level by using the principle of efficient usage of expressed enzymes. Using proteomics data from Escherichia coli, we show that the fluxes estimated by NIDLE-flux and the existing approaches are in excellent qualitative agreement (Pearson correlation > 0.9). We also find that the maximal in vivo catalytic rates estimated by NIDLE-flux exhibits a Pearson correlation of 0.74 with in vitro enzyme turnover numbers. However, NIDLE-flux results in a 1.4-fold increase in the size of the estimated maximal in vivo catalytic rates in comparison to the contenders. Integration of the maximum in vivo catalytic rates with publically available proteomics and metabolomics data provide a better match to fluxes estimated by NIDLE-flux. Therefore, NIDLE-flux facilitates more effective usage of proteomics data to estimate proxies for kcatomes. Y1 - 2021 U6 - https://doi.org/10.1093/bioinformatics/btab575 SN - 1367-4803 SN - 1460-2059 VL - 37 IS - 21 SP - 3848 EP - 3855 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Fedders, Ronja A1 - Muenzner, Matthias A1 - Weber, Pamela A1 - Sommerfeld, Manuela A1 - Knauer, Miriam A1 - Kedziora, Sarah A1 - Kast, Naomi A1 - Heidenreich, Steffi A1 - Raila, Jens A1 - Weger, Stefan A1 - Henze, Andrea A1 - Schupp, Michael T1 - Liver-secreted RBP4 does not impair glucose homeostasis in mice JF - The journal of biological chemistry N2 - Retinol-binding protein 4 (RBP4) is the major transport protein for retinol in blood. Recent evidence from genetic mouse models shows that circulating RBP4 derives exclusively from hepatocytes. Because RBP4 is elevated in obesity and associates with the development of glucose intolerance and insulin resistance, we tested whether a liver-specific overexpression of RBP4 in mice impairs glucose homeostasis. We used adeno-associated viruses (AAV) that contain a highly liver-specific promoter to drive expression of murine RBP4 in livers of adult mice. The resulting increase in serum RBP4 levels in these mice was comparable with elevated levels that were reported in obesity. Surprisingly, we found that increasing circulating RBP4 had no effect on glucose homeostasis. Also during a high-fat diet challenge, elevated levels of RBP4 in the circulation failed to aggravate the worsening of systemic parameters of glucose and energy homeostasis. These findings show that liver-secreted RBP4 does not impair glucose homeostasis. We conclude that a modest increase of its circulating levels in mice, as observed in the obese, insulin-resistant state, is unlikely to be a causative factor for impaired glucose homeostasis. KW - liver KW - retinoid-binding protein KW - glucose metabolism KW - insulin resistance KW - mouse KW - TTR Y1 - 2018 U6 - https://doi.org/10.1074/jbc.RA118.004294 SN - 1083-351X VL - 293 IS - 39 SP - 15269 EP - 15276 PB - American Society for Biochemistry and Molecular Biology CY - Bethesda ER - TY - JOUR A1 - Trindade, Inês T1 - License to flower BT - LEAFY has pioneer activity JF - Molecular plant Y1 - 2021 U6 - https://doi.org/10.1016/j.molp.2021.04.007 SN - 1674-2052 SN - 1752-9867 VL - 14 IS - 5 SP - 719 EP - 720 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Andreev, Andrei A1 - Raschke, Elena A1 - Biskaborn, Boris A1 - Vyse, Stuart Andrew A1 - Courtin, Jérémy A1 - Böhmer, Thomas A1 - Stoof-Leichsenring, Kathleen R. A1 - Kruse, Stefan A1 - Pestryakova, Luidmila Agafyevna A1 - Herzschuh, Ulrike T1 - Late Pleistocene to Holocene vegetation and climate changes in northwestern Chukotka (Far East Russia) deduced from lakes Ilirney and Rauchuagytgyn pollen records JF - Boreas : an international journal of quaternary research N2 - This paper presents two new pollen records and quantitative climate reconstructions from northern Chukotka documenting environmental changes over the last 27.9 ka. Open tundra- and steppe-like habitats dominated between 27.9 and 18.7 cal. ka BP. Betula and Alnus shrubs might have grown in sheltered microhabitats but disappeared after 18.7 cal. ka BP. Although the climate was rather harsh, local herb-dominated communities supported herbivores as is evident by the presence of coprophilous spores in the sediments. The increase in Salix and Cyperaceae similar to 16.1 cal. ka BP suggests climate amelioration. Shrub Betula appeared similar to 15.9 cal. ka BP, and became dominant after similar to 15.52 cal. ka BP, whilst typical steppe communities drastically reduced. Very high presence of Botryococcus in the Lateglacial sediments reflects widespread shallow habitats, probably due to lake level increase. Shrub Alnus became common after similar to 13 cal. ka BP reflecting further climate amelioration. Simultaneously, herb communities gradually decreased in the vegetation reaching a minimum similar to 11.8 cal. ka BP. A gradual decrease of algae remains suggests a reduction of shallow-water habitats. Shrubby and graminoid tundra was dominant similar to 11.8-11.1 cal. ka BP, later Salix stands significantly decreased. The forest-tundra ecotone established in the Early Holocene, shortly after 11.1 cal. ka BP. Low contents of green algae in the Early Holocene sediments likely reflect deeper aquatic conditions. The most favourable climate conditions were between similar to 10.6 and 7 cal. ka BP. Vegetation became similar to the modern after similar to 7 cal. ka BP but Pinus pumila came to the Ilirney area at about 1.2 cal. ka BP. It is important to emphasize that the study area provided refugia for Betula and Alnus during MIS 2. It is also notable that our records do not reflect evidence of Younger Dryas cooling, which is inconsistent with some regional environmental records but in good accordance with some others. Y1 - 2021 U6 - https://doi.org/10.1111/bor.12521 SN - 0300-9483 SN - 1502-3885 VL - 50 IS - 3 SP - 652 EP - 670 PB - Wiley-Blackwell CY - Oxford [u.a.] ER - TY - JOUR A1 - Mbebi, Alain J. A1 - Tong, Hao A1 - Nikoloski, Zoran T1 - L-2,L-1-norm regularized multivariate regression model with applications to genomic prediction JF - Bioinformatics N2 - Motivation: Genomic selection (GS) is currently deemed the most effective approach to speed up breeding of agricultural varieties. It has been recognized that consideration of multiple traits in GS can improve accuracy of prediction for traits of low heritability. However, since GS forgoes statistical testing with the idea of improving predictions, it does not facilitate mechanistic understanding of the contribution of particular single nucleotide polymorphisms (SNP). Results: Here, we propose a L-2,L-1-norm regularized multivariate regression model and devise a fast and efficient iterative optimization algorithm, called L-2,L-1-joint, applicable in multi-trait GS. The usage of the L-2,L-1-norm facilitates variable selection in a penalized multivariate regression that considers the relation between individuals, when the number of SNPs is much larger than the number of individuals. The capacity for variable selection allows us to define master regulators that can be used in a multi-trait GS setting to dissect the genetic architecture of the analyzed traits. Our comparative analyses demonstrate that the proposed model is a favorable candidate compared to existing state-of-the-art approaches. Prediction and variable selection with datasets from Brassica napus, wheat and Arabidopsis thaliana diversity panels are conducted to further showcase the performance of the proposed model. Y1 - 2021 U6 - https://doi.org/10.1093/bioinformatics/btab212 SN - 1367-4803 SN - 1460-2059 VL - 37 IS - 18 SP - 2896 EP - 2904 PB - Oxford Univ. Press CY - Oxford ER - TY - THES A1 - Novakovic, Lazar T1 - Investigating DEFECTIVE KERNEL 1 regulation of primary cell wall biosynthesis and mechanical properties during plant growth in Arabidopsis thaliana N2 - Plants possess cell wall, a polysaccharide exoskeleton which encompasses all plant cells. Cell wall gives plant cells mechanical support, defines their shape, enables growth and water transport through a plant. It also has important role in communication with the external environment. Regulation of plant cell wall biosynthesis and cell and organ morphogenesis depends on cell’s ability to detect mechanical signals originating both from the external environment and from internal plant tissues. Thanks to the presence of the cell wall, all living plant cells develop constant internal pressure generated by the active water uptake, known as turgor pressure, which enables them to grow. Thus, actively growing cells in the tissue are exerting mechanical stress to each other. In order to properly coordinate cell growth, tissue morphogenesis and maintain cell-to-cell adhesion, plant cell have to detect these mechanical signals. That is performed by a group of still not well enough characterized plant mechanosensitive proteins. Mechanosensors are proteins capable of detecting changes in mechanical stress patterns and translating them into physiological and developmental outputs. One of plant mechanosensitive proteins, DEFECTIVE KERNEL1 (DEK1) has shown to be a very important in proper plant development. DEK1 bears similarity with animal cysteine proteases of Calpain superfamily. DEK1 is very important for plant development since all null alleles are embryo lethal. During the last 20 years of DEK1 studies, this protein has proven to be a very difficult for different molecular and biochemical manipulations. As a consequence, very little is known about its direct target proteins. Wang and co-workers (2003) and Johnson and co-workers (2008) have given a valuable contribution to biochemical understanding of DEK1 by determining that it functions as Cys-protease in similar way as animal calpains. However, a lot of indirect knowledge was gathered about the effects of disruption and modulation of DEK1 activity. DEK1 is important for proper organ development, epidermal specification, and maintenance. However, some studies have inferred that DEK1 affects expression of different cell wall related genes, and it regulates cell-to-cell adhesion in epidermal cells. This led to two extensive studies (Amanda et al., 2016, 2017) which demonstrated importance of DEK1 in regulation leaf epidermal cell walls in A. thaliana mature leaves and inflorescence stems. These studies demonstrated that DEK1 also influences cell wall thickness and cell-to-cell adhesion and that it could potentially regulate cell growth and expansion. Building up on this research, we decided to try to further characterize molecular and biomechanical aspects of DEK1 mediated cell wall regulation, with special emphasis on regulation of cellulose synthesis. We used two mutant lines, with modulated DEK1 activity, a constitutive overexpressor for DEK1 CALPAIN domain and a point mutant in CALPAIN domain, dek1-4. In Chapter 3 we demonstrated that DEK1 regulates dynamics of Cellulose Synthase Complexes (CSCs). Both lines showed decreased crystalline cellulose contents. This led us to investigate if velocity of CSCs in cotyledons, was affected, since it is known that changes in cellulose contents are often caused by defects in CSC. We found that bothDEK1 modulated lines we used have significantly decreased velocity of CSCs. We have also examined plasma membrane turnover rates of CSCs and found out that after photo-bleaching OE CALPAIN has much faster recovery rates compared to Col-0 wild type, while dek1-4 has lower exocytotic rates of CSCs, and much longer life-time of CSCs inserted into the plasma membrane. These results suggested that DEK1 regulates different aspects of CSC dynamics, possibly through interaction with different regulatory proteins. Decrease in cellulose contents we observed in DEK1 modulated lines, prompted us to investigate how this reflects biomechanics and structural properties of epidermal cotyledon cell walls of DEK1 modulated lines, which is described in Chapter 4. To achieve this, we developed a novel microdissection method for isolation and mechanical and structural characterization of native epidermal cell wall monolayers using atomic force microscopy (AFM). AFM force spectroscopy assays showed that both DEK1 modulated lines had stiffer cell walls compared to Col-0. This was awkward since we initially detected decrease in crystalline cellulose which implied decrease in cell wall stiffness. However, subsequent high-resolution AFM imaging has revealed that DEK1 modulate lines cells walls have their cellulose microfibrils organized in thicker bundles than Col-0. Also, polysaccharide composition analysis has revealed that DEK1 modulated lines have increased abundance of pectins, which could also be responsible for the observed increase in cell wall stiffness. Previous work has shown that different dek1 mutants and modulated lines have defects in cell-to-cell adhesion. This implied that DEK1 may be involved in sensing and/or maintaining cell wall integrity (CWI). We performed several growth assays to determine role of DEK1 in CWI, which is described in Chapter 5. We performed cellulose synthesis perturbation assays with cellulose synthesis inhibitor Isoxaben and obtained very interesting results. While OE CALPAIN plants were hypersensitive to Isoxaben, dek1-4 has shown complete insensitivity. Furthermore, a regular CWI maintenance response, reported in A. thaliana as result of compromised CWI, ectopic lignification in seedlings’ roots was absent in both DEK1 modulated lines we examined. We detected interesting growth response of DEK1 lines to NaCl and mannitol treatments as well. Although these findings are pointing out that DEK1 could be part of CWI signalling pathways, more experiments are necessary to fully elucidate possible role of DEK1 in CWI sensing and/or maintenance pathways, especially to check if DEK1 is interacting with Catharanthus roseus Receptor Like Kinase group of CWI sensors. Studies on 4-month old short day grown DEK1 modulated lines, have shown defects in branching, with development of fasciated stem branches in a DEK1 modulated line overexpressing CALPAIN domain (Amanda et al., 2017). This result pointed out to a possibility that DEK1 may regulate organ morphogenesis and patterning at the level of shoot apical meristem (SAM). Work towards elucidating role of DEK1 in SAM maintenance and organ patterning is detailed in Chapter 6. We determined that OE CALPAIN had significantly larger central zone of SAM as well as larger individual SAM cells in central zone, as well as higher distribution of cell sizes, implying possible cell expansion defects. dek1-4 did not exhibited changes in SAM central zone size or individual stem cell size, but it seemed that it had increased number of stem cells in SAM central zone. Both DEK1 lines had perturbation of phyllotaxis on SAM level, with disturbed divergence angles between floral primordia. Disturbed phyllotaxis was also observed between siliques, in mature plants. In addition to this, OE CALPAIN has exhibited occurrence of multiple (up to four) siliques growing from a single stem node. All this is pointing out that DEK1 might participate in hormone-signalling in the SAM.. DEK1 is a highly intriguing protein. However, since it is a unigene, and in addition to that, a regulatory protease, it probably participates in multiple signalling pathways, which makes understanding its function much more complicated. KW - DEK1 KW - atomic force microscopy KW - cellulose microfibrils KW - shoot apical meristem KW - phyllotaxis KW - biomechanics KW - cellulose synthase complex KW - cell wall Y1 - 2021 ER - TY - JOUR A1 - Flöder, Sabine A1 - Yong, Joanne A1 - Klauschies, Toni A1 - Gaedke, Ursula A1 - Poprick, Tobias A1 - Brinkhoff, Thorsten A1 - Moorthi, Stefanie T1 - Intraspecific trait variation alters the outcome of competition in freshwater ciliates JF - Ecology and evolution N2 - Trait variation among heterospecific and conspecific organisms may substantially affect community and food web dynamics. While the relevance of competition and feeding traits have been widely studied for different consumer species, studies on intraspecific differences are more scarce, partly owing to difficulties in distinguishing different clones of the same species. Here, we investigate how intraspecific trait variation affects the competition between the freshwater ciliates Euplotes octocarinatus and Coleps hirtus in a nitrogen-limited chemostat system. The ciliates competed for the microalgae Cryptomonas sp. (Cry) and Navicula pelliculosa (Nav), and the bacteria present in the cultures over a period of 33 days. We used monoclonal Euplotes and three different Coleps clones (Col 1, Col 2, and Col 3) in the experiment that could be distinguished by a newly developed rDNA-based molecular assay based on the internal transcribed spacer (ITS) regions. While Euplotes feeds on Cry and on bacteria, the Coleps clones cannot survive on bacteria alone but feed on both Cry and Nav with clone-specific rates. Experimental treatments comprised two-species mixtures of Euplotes and one or all of the three different Coleps clones, respectively. We found intraspecific variation in the traits "selectivity" and "maximum ingestion rate" for the different algae to significantly affect the competitive outcome between the two ciliate species. As Nav quickly escaped top-down control and likely reached a state of low food quality, ciliate competition was strongly determined by the preference of different Coleps clones for Cry as opposed to feeding on Nav. In addition, the ability of Euplotes to use bacteria as an alternative food source strengthened its persistence once Cry was depleted. Hence, trait variation at both trophic levels codetermined the population dynamics and the outcome of species competition. KW - ciliate predators KW - intraspecific trait variation KW - microalgal resource KW - predator trait variation KW - predator-prey systems KW - resource competition Y1 - 2021 U6 - https://doi.org/10.1002/ece3.7828 SN - 2045-7758 VL - 11 IS - 15 SP - 10225 EP - 10243 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Scharnweber, Inga Kristin A1 - Andersson, Matilda L. A1 - Chaguaceda, Fernando A1 - Eklöv, Peter T1 - Intraspecific differences in metabolic rates shape carbon stable isotope trophic discrimination factors of muscle tissue in the common teleost Eurasian perch (Perca fluviatilis) JF - Ecology and evolution N2 - Stable isotopes represent a unique approach to provide insights into the ecology of organisms. δ13C and δ15N have specifically been used to obtain information on the trophic ecology and food-web interactions. Trophic discrimination factors (TDF, Δ13C and Δ15N) describe the isotopic fractionation occurring from diet to consumer tissue, and these factors are critical for obtaining precise estimates within any application of δ13C and δ15N values. It is widely acknowledged that metabolism influences TDF, being responsible for different TDF between tissues of variable metabolic activity (e.g., liver vs. muscle tissue) or species body size (small vs. large). However, the connection between the variation of metabolism occurring within a single species during its ontogeny and TDF has rarely been considered. Here, we conducted a 9-month feeding experiment to report Δ13C and Δ15N of muscle and liver tissues for several weight classes of Eurasian perch (Perca fluviatilis), a widespread teleost often studied using stable isotopes, but without established TDF for feeding on a natural diet. In addition, we assessed the relationship between the standard metabolic rate (SMR) and TDF by measuring the oxygen consumption of the individuals. Our results showed a significant negative relationship of SMR with Δ13C, and a significant positive relationship of SMR with Δ15N of muscle tissue, but not with TDF of liver tissue. SMR varies inversely with size, which translated into a significantly different TDF of muscle tissue between size classes. In summary, our results emphasize the role of metabolism in shaping-specific TDF (i.e., Δ13C and Δ15N of muscle tissue) and especially highlight the substantial differences between individuals of different ontogenetic stages within a species. Our findings thus have direct implications for the use of stable isotope data and the applications of stable isotopes in food-web studies. KW - fractionation factors KW - metabolism KW - ontogeny KW - standard metabolic rate KW - tissue types KW - δ13C KW - δ15N Y1 - 2021 SN - 2045-7758 VL - 11 IS - 14 SP - 9804 EP - 9814 PB - John Wiley & Sons, Inc. CY - New Jersey ER - TY - GEN A1 - Scharnweber, Inga Kristin A1 - Andersson, Matilda L. A1 - Chaguaceda, Fernando A1 - Eklöv, Peter T1 - Intra-specific differences in metabolic rates shape carbon stable isotope trophic discrimination factors of muscle tissue in the common teleost Eurasian perch (Perca fluviatilis) T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Stable isotopes represent a unique approach to provide insights into the ecology of organisms. δ13C and δ15N have specifically been used to obtain information on the trophic ecology and food-web interactions. Trophic discrimination factors (TDF, Δ13C and Δ15N) describe the isotopic fractionation occurring from diet to consumer tissue, and these factors are critical for obtaining precise estimates within any application of δ13C and δ15N values. It is widely acknowledged that metabolism influences TDF, being responsible for different TDF between tissues of variable metabolic activity (e.g., liver vs. muscle tissue) or species body size (small vs. large). However, the connection between the variation of metabolism occurring within a single species during its ontogeny and TDF has rarely been considered. Here, we conducted a 9-month feeding experiment to report Δ13C and Δ15N of muscle and liver tissues for several weight classes of Eurasian perch (Perca fluviatilis), a widespread teleost often studied using stable isotopes, but without established TDF for feeding on a natural diet. In addition, we assessed the relationship between the standard metabolic rate (SMR) and TDF by measuring the oxygen consumption of the individuals. Our results showed a significant negative relationship of SMR with Δ13C, and a significant positive relationship of SMR with Δ15N of muscle tissue, but not with TDF of liver tissue. SMR varies inversely with size, which translated into a significantly different TDF of muscle tissue between size classes. In summary, our results emphasize the role of metabolism in shaping-specific TDF (i.e., Δ13C and Δ15N of muscle tissue) and especially highlight the substantial differences between individuals of different ontogenetic stages within a species. Our findings thus have direct implications for the use of stable isotope data and the applications of stable isotopes in food-web studies. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1179 KW - fractionation factors KW - metabolism KW - ontogeny KW - standard metabolic rate KW - tissue types KW - δ13C KW - δ15N Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-524015 SN - 1866-8372 IS - 14 ER - TY - JOUR A1 - De Sousa Mota, Cristiano A1 - Diniz, Ana A1 - Coelho, Catarina A1 - Santos-Silva, Teresa A1 - Esmaeeli Moghaddam Tabalvandani, Mariam A1 - Leimkühler, Silke A1 - Cabrita, Eurico J. A1 - Marcelo, Filipa A1 - Romão, Maria João T1 - Interrogating the inhibition mechanisms of human aldehyde oxidase by X-ray crystallography and NMR spectroscopy BT - the raloxifene case JF - Journal of medicinal chemistry / American Chemical Society N2 - Human aldehyde oxidase (hAOX1) is mainly present in the liver and has an emerging role in drug metabolism, since it accepts a wide range of molecules as substrates and inhibitors. Herein, we employed an integrative approach by combining NMR, X-ray crystallography, and enzyme inhibition kinetics to understand the inhibition modes of three hAOX1 inhibitors-thioridazine, benzamidine, and raloxifene. These integrative data indicate that thioridazine is a noncompetitive inhibitor, while benzamidine presents a mixed type of inhibition. Additionally, we describe the first crystal structure of hAOX1 in complex with raloxifene. Raloxifene binds tightly at the entrance of the substrate tunnel, stabilizing the flexible entrance gates and elucidating an unusual substrate-dependent mechanism of inhibition with potential impact on drug-drug interactions. This study can be considered as a proof-of-concept for an efficient experimental screening of prospective substrates and inhibitors of hAOX1 relevant in drug discovery. Y1 - 2021 U6 - https://doi.org/10.1021/acs.jmedchem.1c01125 SN - 0022-2623 SN - 1520-4804 VL - 64 IS - 17 SP - 13025 EP - 13037 PB - American Chemical Society CY - Washington ER -