TY - GEN A1 - Noonan, Michael J. A1 - Fleming, Christen H. A1 - Tucker, Marlee A. A1 - Kays, Roland A1 - Harrison, Autumn-Lynn A1 - Crofoot, Margaret C. A1 - Abrahms, Briana A1 - Alberts, Susan C. A1 - Ali, Abdullahi H. A1 - Blaum, Niels T1 - Effects of body size on estimation of mammalian area requirements T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Accurately quantifying species' area requirements is a prerequisite for effective area-based conservation. This typically involves collecting tracking data on species of interest and then conducting home-range analyses. Problematically, autocorrelation in tracking data can result in space needs being severely underestimated. Based on the previous work, we hypothesized the magnitude of underestimation varies with body mass, a relationship that could have serious conservation implications. To evaluate this hypothesis for terrestrial mammals, we estimated home-range areas with global positioning system (GPS) locations from 757 individuals across 61 globally distributed mammalian species with body masses ranging from 0.4 to 4000 kg. We then applied block cross-validation to quantify bias in empirical home-range estimates. Area requirements of mammals <10 kg were underestimated by a mean approximately15%, and species weighing approximately100 kg were underestimated by approximately50% on average. Thus, we found area estimation was subject to autocorrelation-induced bias that was worse for large species. Combined with the fact that extinction risk increases as body mass increases, the allometric scaling of bias we observed suggests the most threatened species are also likely to be those with the least accurate home-range estimates. As a correction, we tested whether data thinning or autocorrelation-informed home-range estimation minimized the scaling effect of autocorrelation on area estimates. Data thinning required an approximately93% data loss to achieve statistical independence with 95% confidence and was, therefore, not a viable solution. In contrast, autocorrelation-informed home-range estimation resulted in consistently accurate estimates irrespective of mass. When relating body mass to home range size, we detected that correcting for autocorrelation resulted in a scaling exponent significantly >1, meaning the scaling of the relationship changed substantially at the upper end of the mass spectrum. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1206 KW - allometry KW - animal movement KW - area-based conservation KW - autocorrelation KW - home range KW - kernel density estimation KW - reserve design KW - scaling Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-526824 SN - 1866-8372 IS - 4 ER - TY - GEN A1 - Tzoneva, Rumiana A1 - Stoyanova, Tihomira A1 - Petrich, Annett A1 - Popova, Desislava A1 - Uzunova, Veselina A1 - Albena, Momchilova A1 - Chiantia, Salvatore T1 - Effect of Erufosine on Membrane Lipid Order in Breast Cancer Cell Models T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Alkylphospholipids are a novel class of antineoplastic drugs showing remarkable therapeutic potential. Among them, erufosine (EPC3) is a promising drug for the treatment of several types of tumors. While EPC3 is supposed to exert its function by interacting with lipid membranes, the exact molecular mechanisms involved are not known yet. In this work, we applied a combination of several fluorescence microscopy and analytical chemistry approaches (i.e., scanning fluorescence correlation spectroscopy, line-scan fluorescence correlation spectroscopy, generalized polarization imaging, as well as thin layer and gas chromatography) to quantify the effect of EPC3 in biophysical models of the plasma membrane, as well as in cancer cell lines. Our results indicate that EPC3 affects lipid–lipid interactions in cellular membranes by decreasing lipid packing and increasing membrane disorder and fluidity. As a consequence of these alterations in the lateral organization of lipid bilayers, the diffusive dynamics of membrane proteins are also significantly increased. Taken together, these findings suggest that the mechanism of action of EPC3 could be linked to its effects on fundamental biophysical properties of lipid membranes, as well as on lipid metabolism in cancer cells. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1000 KW - alkylphospholipids KW - fluorescence microscopy KW - fluorescence correlation spectroscopy KW - lipids KW - plasma membrane KW - cancer KW - lipid–lipid interactions KW - membrane microdomains KW - membrane biophysics Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-477056 SN - 1866-8372 IS - 1000 ER - TY - GEN A1 - Hentrich, Doreen A1 - Tauer, Klaus A1 - Espanol, Montserrat A1 - Ginebra, Maria-Pau A1 - Taubert, Andreas T1 - EDTA and NTA effectively tune the mineralization of calcium phosphate from bulk aqueous solution T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - This study describes the effects of nitrilotriacetic acid (NTA) and ethylenediaminotetraacetic acid (EDTA) on themineralization of calciumphosphate from bulk aqueous solution. Mineralization was performed between pH 6 and 9 and with NTA or EDTA concentrations of 0, 5, 10, and 15 mM. X-ray diffraction and infrared spectroscopy show that at low pH, mainly brushite precipitates and at higher pH, mostly hydroxyapatite forms. Both additives alter the morphology of the precipitates. Without additive, brushite precipitates as large plates. With NTA, the morphology changes to an unusual rod-like shape. With EDTA, the edges of the particles are rounded and disk-like particles form. Conductivity and pH measurements suggest that the final products form through several intermediate steps. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1095 KW - biomineralization KW - biomimetic mineralization KW - calcium phosphate KW - NTA KW - EDTA KW - precipitation KW - brushite KW - hydroxyapatite Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-469186 SN - 1866-8372 IS - 1095 ER - TY - GEN A1 - Pajoro, Alice A1 - Madrigal, Pedro A1 - Muiño, Jose M. A1 - Matus, José Tomás A1 - Jin, Jian A1 - Mecchia, Martin A. A1 - Debernardi, Juan M. A1 - Palatnik, Javier F. A1 - Balazadeh, Salma A1 - Arif, Muhammad A1 - Ó’Maoiléidigh, Diarmuid S. A1 - Wellmer, Frank A1 - Krajewski, Pawel A1 - Riechmann, José-Luis A1 - Angenent, Gerco C. A1 - Kaufmann, Kerstin T1 - Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Results: We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Conclusions: Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1327 KW - flower development KW - floral organ KW - floral meristem KW - chromatin accessibility KW - growth regulate factor Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431139 SN - 1866-8372 VL - 15 ER - TY - GEN A1 - Li, Xiaoping A1 - Apriyanto, Ardha A1 - Flores Castellanos, Junio A1 - Compart, Julia A1 - Muntaha, Sidratul Nur A1 - Fettke, Jörg T1 - Dpe2/phs1 revealed unique starch metabolism with three distinct phases characterized by different starch granule numbers per chloroplast, allowing insights into the control mechanism of granule number regulation by gene co-regulation and metabolic profiling T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - An Arabidopsis mutant lacking both the cytosolic Disproportionating enzyme 2 (DPE2) and the plastidial glucan Phosphorylase 1 (PHS1) revealed a unique starch metabolism. Dpe2/phs1 has been reported to have only one starch granule number per chloroplast when grown under diurnal rhythm. For this study, we analyzed dpe2/phs1 in details following the mutant development, and found that it showed three distinct periods of granule numbers per chloroplast, while there was no obvious change observed in Col-0. In young plants, the starch granule number was similar to that in Col-0 at first, and then decreased significantly, down to one or no granule per chloroplast, followed by an increase in the granule number. Thus, in dpe2/phs1, control over the starch granule number is impaired, but it is not defective in starch granule initiation. The data also indicate that the granule number is not fixed, and is regulated throughout plant growth. Furthermore, the chloroplasts revealed alterations during these three periods, with a partially strong aberrant morphology in the middle phase. Interestingly, the unique metabolism was perpetuated when starch degradation was further impaired through an additional lack of Isoamylase 3 (ISA3) or Starch excess 4 (SEX4). Transcriptomic studies and metabolic profiling revealed the co-regulation of starch metabolism-related genes and a clear metabolic separation between the periods. Most senescence-induced genes were found to be up-regulated more than twice in the starch-less mature leaves. Thus, dpe2/phs1 is a unique plant material source, with which we may study starch granule number regulation to obtain a more detailed understanding. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1286 KW - LCSM KW - RNA-Seq KW - metabolic-profiling KW - starch granule number regulation KW - starch initiation KW - starch degradation Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-571250 SN - 1866-8372 IS - 1286 ER - TY - GEN A1 - Hering, Robert A1 - Hauptfleisch, Morgan A1 - Jago, Mark A1 - Smith, Taylor A1 - Kramer-Schadt, Stephanie A1 - Stiegler, Jonas A1 - Blaum, Niels T1 - Don't stop me now: Managed fence gaps could allow migratory ungulates to track dynamic resources and reduce fence related energy loss T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - In semi-arid environments characterized by erratic rainfall and scattered primary production, migratory movements are a key survival strategy of large herbivores to track resources over vast areas. Veterinary Cordon Fences (VCFs), intended to reduce wildlife-livestock disease transmission, fragment large parts of southern Africa and have limited the movements of large wild mammals for over 60 years. Consequently, wildlife-fence interactions are frequent and often result in perforations of the fence, mainly caused by elephants. Yet, we lack knowledge about at which times fences act as barriers, how fences directly alter the energy expenditure of native herbivores, and what the consequences of impermeability are. We studied 2-year ungulate movements in three common antelopes (springbok, kudu, eland) across a perforated part of Namibia's VCF separating a wildlife reserve and Etosha National Park using GPS telemetry, accelerometer measurements, and satellite imagery. We identified 2905 fence interaction events which we used to evaluate critical times of encounters and direct fence effects on energy expenditure. Using vegetation type-specific greenness dynamics, we quantified what animals gained in terms of high quality food resources from crossing the VCF. Our results show that the perforation of the VCF sustains herbivore-vegetation interactions in the savanna with its scattered resources. Fence permeability led to peaks in crossing numbers during the first flush of woody plants before the rain started. Kudu and eland often showed increased energy expenditure when crossing the fence. Energy expenditure was lowered during the frequent interactions of ungulates standing at the fence. We found no alteration of energy expenditure when springbok immediately found and crossed fence breaches. Our results indicate that constantly open gaps did not affect energy expenditure, while gaps with obstacles increased motion. Closing gaps may have confused ungulates and modified their intended movements. While browsing, sedentary kudu's use of space was less affected by the VCF; migratory, mixed-feeding springbok, and eland benefited from gaps by gaining forage quality and quantity after crossing. This highlights the importance of access to vast areas to allow ungulates to track vital vegetation patches. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1278 KW - veterinary cordon fence KW - ungulate KW - fence ecology KW - resource-tracking KW - energy expenditure KW - accelerometer KW - GPS KW - wildlife and habitat management Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-570087 SN - 1866-8372 IS - 1278 ER - TY - GEN A1 - Kowalski, Gabriele Joanna A1 - Grimm, Volker A1 - Herde, Antje A1 - Guenther, Anja A1 - Eccard, Jana T1 - Does Animal Personality Affect Movement in Habitat Corridors? BT - Experiments with Common Voles (Microtus arvalis) Using Different Corridor Widths T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Animal personality may affect an animal’s mobility in a given landscape, influencing its propensity to take risks in an unknown environment. We investigated the mobility of translocated common voles in two corridor systems 60 m in length and differing in width (1 m and 3 m). Voles were behaviorally phenotyped in repeated open field and barrier tests. Observed behavioral traits were highly repeatable and described by a continuous personality score. Subsequently, animals were tracked via an automated very high frequency (VHF) telemetry radio tracking system to monitor their movement patterns in the corridor system. Although personality did not explain movement patterns, corridor width determined the amount of time spent in the habitat corridor. Voles in the narrow corridor system entered the corridor faster and spent less time in the corridor than animals in the wide corridor. Thus, landscape features seem to affect movement patterns more strongly than personality. Meanwhile, site characteristics, such as corridor width, could prove to be highly important when designing corridors for conservation, with narrow corridors facilitating faster movement through landscapes than wider corridors. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 747 KW - activity KW - animal personality KW - wildlife corridors KW - habitat connectivity KW - individual differences KW - rodents Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-435770 SN - 1866-8372 IS - 747 ER - TY - GEN A1 - Heinken, Thilo A1 - Raudnitschka, Dorit T1 - Do wild ungulates contribute to the dispersal of vascular plants in central European forests by epizoochory? BT - A case study in NE Germany BT - Eine Fallstudie aus Nordostdeutschland N2 - The external dispersal ("epizoochory") of vascular plant diaspores (seeds and fruits) by roe deer and wild boar, i.e. the most common wild large mammals with a large home range in central Europe, was investigated in a 6.5-km² forest area in NE Germany dominated by mesic deciduous forests. The study involved brushing out the diaspores from the coats and hooves of 25 shot roe deer and nine wild boar. The results were compared with the forest vegetation of the study area. Whilst wild boar transported large amounts of various diaspores in the coat, the significance of roe deer for epizoochory was low due to their sleek fur and different behaviour compared to wild boar. Altogether, 55 vascular plant species were transported externally. Since only a limited number of seeds came from woodland habitats, the open landscape was at least as important as a source of attached seeds as the forest vegetation. Thus, most plant species occurring in the studied forest area, especially characteristic woodland herbs, showed no adaptations to epizoochorous dispersal, although being very abundant in the herb layer. We conclude that hoofed game play a particular role concerning the dispersal of ruderal and grassland species in the agricultural landscape of central Europe. However, the actual spread of some herb species in forests of northern Germany, e.g. Agrostis capillaris, Brachypodium sylvaticum, Deschampsia flexuosa, Galium aparine and Urtica dioica, may be mainly facilitated by wild ungulates. Though dispersal by large mammals is an important mechanism for long-distance dispersal of plants in general, our results suggest that most of the characteristic herb species of mesic deciduous forests have only low epizoochorous dispersal potentials. The implications for nature conservation and silviculture are discussed. N2 - Die Ausbreitung von Gefäßpflanzen-Diasporen (Samen und Früchte) durch äußerliche Anhaftung ("Epizoochorie") an Rehen und Wildschweinen, den beiden häufigsten Schalenwild-Arten in Mitteleuropa, wurde im 6,5 km² großen Forst Brieselang bei Berlin (Bundesland Brandenburg) untersucht, in dem mesophile Laubwälder vorherrschen. Dazu wurden die Felle und Hufe von 25 geschossenen Rehen und neun Wildschweinen ausgekämmt und die Diasporen anschließend bestimmt. Die Ergebnisse wurden mit der Waldvegetation verglichen. Während Wildschweine große Mengen verschiedener Diasporentypen transportierten, war die Bedeutung von Rehen für die Ausbreitung von Pflanzen auf Grund des glatten Fells und der im Vergleich zum Wildschwein unterschiedlichen Verhaltensweisen wesentlich geringer. Insgesamt wurden 55 Phanerogamenarten epizoochor transportiert. Da nur ein kleiner Teil der ausgebreiteten Pflanzen Waldhabitate bevorzugt, war das Offenland eine mindestens ebenso wichtige Quelle anhaftender Diasporen wie die Waldvegetation. Die meisten Waldpflanzenarten wurden nicht ausgebreitet; insbesondere solche Arten, die ausschließlich in Wäldern wachsen, wurden nicht nachgewiesen. Viele Pflanzenarten sind – vermutlich auf Grund ihrer Diasporenmorphologie – weitgehend vom Transport ausgeschlossen, obwohl sie sehr häufig in der Krautschicht des untersuchten Waldes vorkommen. Daher ist Schalenwild in der Agrarlandschaft Mitteleuropas vermutlich vor allem für die Ausbreitung von Ruderal-, Segetal- und Grünlandpflanzen von Bedeutung. Die Ausbreitung einiger Pflanzenarten der Krautschicht in norddeutschen Wäldern z.B. Agrostis capillaris, Brachypodium sylvaticum, Deschampsia flexuosa, Galium aparine und Urtica dioica, könnte jedoch wesentlich auf Schalenwild zurückgehen. Obwohl Großsäuger insgesamt ein wichtiger Vektor für die Fernausbreitung von Pflanzen sind, zeigt unsere Studie, dass die meisten charakteristischen Waldbodenpflanzen mesophiler Laubwälder kaum ausgebreitet werden, also nur ein geringes epizoochores Ausbreitungspotenzial aufweisen. Die Bedeutung der Ergebnisse für den Waldnaturschutz und den Waldbau wird diskutiert. T2 - Trägt Schalenwild durch Epizoochorie zur Ausbreitung von Gefäßpflanzen in mitteleuropäischen Wäldern bei? KW - Diasporenmorphologie KW - Epizoochorie KW - Brandenburg KW - Reh KW - Waldbodenpflanzen KW - Wildschwein KW - diaspore morphology KW - epizoochory KW - forest plant species KW - NE Germany KW - roe deer KW - wild boar Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-5850 ER - TY - GEN A1 - Breitenstein, Michael A1 - Nielsen, Peter E. A1 - Hölzel, Ralph A1 - Bier, Frank Fabian T1 - DNA-nanostructure-assembly by sequential spotting T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background: The ability to create nanostructures with biomolecules is one of the key elements in nanobiotechnology. One of the problems is the expensive and mostly custom made equipment which is needed for their development. We intended to reduce material costs and aimed at miniaturization of the necessary tools that are essential for nanofabrication. Thus we combined the capabilities of molecular ink lithography with DNA-self-assembling capabilities to arrange DNA in an independent array which allows addressing molecules in nanoscale dimensions. Results: For the construction of DNA based nanostructures a method is presented that allows an arrangement of DNA strands in such a way that they can form a grid that only depends on the spotted pattern of the anchor molecules. An atomic force microscope (AFM) has been used for molecular ink lithography to generate small spots. The sequential spotting process allows the immobilization of several different functional biomolecules with a single AFM-tip. This grid which delivers specific addresses for the prepared DNA-strand serves as a two-dimensional anchor to arrange the sequence according to the pattern. Once the DNA-nanoarray has been formed, it can be functionalized by PNA (peptide nucleic acid) to incorporate advanced structures. Conclusions: The production of DNA-nanoarrays is a promising task for nanobiotechnology. The described method allows convenient and low cost preparation of nanoarrays. PNA can be used for complex functionalization purposes as well as a structural element. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1027 KW - atomic force microscope KW - peptide nucleic acid KW - persistence length KW - adapter oligonucleotide KW - high fluorescence signal Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431108 SN - 1866-8372 IS - 1027 ER - TY - GEN A1 - Sicard, Adrien A1 - Kappel, Christian A1 - Josephs, Emily B. A1 - Wha Lee, Young A1 - Marona, Cindy A1 - Stinchcombe, John R. A1 - Wright, Stephen I. A1 - Lenhard, Michael T1 - Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella N2 - In the Bateson–Dobzhansky–Muller model of genetic incompatibilities post-zygotic gene-flow barriers arise by fixation of novel alleles at interacting loci in separated populations. Many such incompatibilities are polymorphic in plants, implying an important role for genetic drift or balancing selection in their origin and evolution. Here we show that NPR1 and RPP5 loci cause a genetic incompatibility between the incipient species Capsella grandiflora and C. rubella, and the more distantly related C. rubella and C. orientalis. The incompatible RPP5 allele results from a mutation in C. rubella, while the incompatible NPR1 allele is frequent in the ancestral C. grandiflora. Compatible and incompatible NPR1 haplotypes are maintained by balancing selection in C. grandiflora, and were divergently sorted into the derived C. rubella and C. orientalis. Thus, by maintaining differentiated alleles at high frequencies, balancing selection on ancestral polymorphisms can facilitate establishing gene-flow barriers between derived populations through lineage sorting of the alternative alleles. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 231 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-93568 ER - TY - GEN A1 - Bareither, Nils A1 - Scheffel, André A1 - Metz, Johannes T1 - Distribution of polyploid plants in the common annual Brachypodium distachyon (s.l.) in Israel is not linearly correlated with aridity N2 - The ecological benefits of polyploidy are intensely debated. Some authors argue that plants with duplicated chromosome sets (polyploids) are more stress-resistant and superior colonizers and may thus outnumber their low ploidy conspecifics in more extreme habitats. Brachypodium distachyon (sensu lato), for example, a common annual grass in Israel and the entire Mediterranean basin, comprises three cytotypes of differing chromosome numbers that were recently proposed as distinct species. It was suggested that increased aridity increases the occurrence of its polyploid cytotype. Here, we tested at two spatial scales whether polyploid plants of B. distachyon s.l. are more frequently found in drier habitats in Israel. We collected a total of 430 specimens (i) along a largescale climatic gradient with 15 thoroughly selected sites (spanning 114–954 mm annual rainfall), and (ii) from corresponding Northern (more mesic) and Southern (more arid) hill slopes to assess the micro-climatic difference between contrasting exposures. Cytotypes were then determined via flow cytometry. Polyploid plants comprised 90% of all specimens and their proportion ranged between 0% and 100% per site. However, this proportion was not correlated with aridity along the large-scale gradient, nor were polyploids more frequently found on Southern exposures. Our results show for both spatial scales that increasing aridity is not the principal driver for the distribution of polyploids in B. distachyon s.l. in Israel. Notably, though, diploid plants were restricted essentially to four intermediate sites, while polyploids dominated the most arid and the most mesic sites. This, to some degree, clustered pattern suggests that the distribution of cytotypes is not entirely random and calls for future studies to assess further potential drivers. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 334 KW - Aridity KW - Brachypodium distachyon KW - Brachypodium hybridum KW - Brachypodium stacei KW - cytotype KW - exposition KW - Israel KW - Mediterranean grass species KW - polyploidization KW - rainfall gradient KW - slope aspect Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-395293 ER - TY - GEN A1 - Baumann, Tobias A1 - Arndt, Katja Maren A1 - Müller, Kristian M. T1 - Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background: DNA fragments carrying internal recognition sites for the restriction endonucleases intended for cloning into a target plasmid pose a challenge for conventional cloning. Results: A method for directional insertion of DNA fragments into plasmid vectors has been developed. The target sequence is amplified from a template DNA sample by PCR using two oligonucleotides each containing a single deoxyinosine base at the third position from the 5' end. Treatment of such PCR products with endonuclease V generates 3' protruding ends suitable for ligation with vector fragments created by conventional restriction endonuclease reactions. Conclusions: The developed approach generates terminal cohesive ends without the use of Type II restriction endonucleases, and is thus independent from the DNA sequence. Due to PCR amplification, minimal amounts of template DNA are required. Using the robust Taq enzyme or a proofreading Pfu DNA polymerase mutant, the method is applicable to a broad range of insert sequences. Appropriate primer design enables direct incorporation of terminal DNA sequence modifications such as tag addition, insertions, deletions and mutations into the cloning strategy. Further, the restriction sites of the target plasmid can be either retained or removed. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 983 KW - cohesive ends KW - DNA cleavage KW - genetic vectors KW - modified primers KW - molecular methods KW - polymerase chain reaction KW - recombinant Escherichia coli KW - restriction enzymes Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431085 SN - 1866-8372 IS - 983 ER - TY - GEN A1 - Olmer, Ruth A1 - Engels, Lena A1 - Usman, Abdulai A1 - Menke, Sandra A1 - Malik, Muhammad Nasir Hayat A1 - Pessler, Frank A1 - Göhring, Gudrun A1 - Bornhorst, Dorothee A1 - Bolten, Svenja A1 - Abdelilah-Seyfried, Salim A1 - Scheper, Thomas A1 - Kempf, Henning A1 - Zweigerdt, Robert A1 - Martin, Ulrich T1 - Differentiation of Human Pluripotent Stem Cells into Functional Endothelial Cells in Scalable Suspension Culture T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Endothelial cells (ECs) are involved in a variety of cellular responses. As multifunctional components of vascular structures, endothelial (progenitor) cells have been utilized in cellular therapies and are required as an important cellular component of engineered tissue constructs and in vitro disease models. Although primary ECs from different sources are readily isolated and expanded, cell quantity and quality in terms of functionality and karyotype stability is limited. ECs derived from human induced pluripotent stem cells (hiPSCs) represent an alternative and potentially superior cell source, but traditional culture approaches and 2D differentiation protocols hardly allow for production of large cell numbers. Aiming at the production of ECs, we have developed a robust approach for efficient endothelial differentiation of hiPSCs in scalable suspension culture. The established protocol results in relevant numbers of ECs for regenerative approaches and industrial applications that show in vitro proliferation capacity and a high degree of chromosomal stability. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1182 KW - virus infection KW - progenitor cells KW - in vitro KW - telomere dysfunction KW - cord blood KW - cardiomyogenic differentiation KW - angiogenesis KW - efficient KW - aberrations KW - expression Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-427095 SN - 1866-8372 IS - 5 ER - TY - GEN A1 - Kolyvushko, Oleksandr A1 - Latzke, Juliane A1 - Dahmani, Ismail A1 - Osterrieder, Nikolaus A1 - Chiantia, Salvatore A1 - Azab, Walid T1 - Differentially-charged liposomes interact with alphaherpesviruses and interfere with virus entry T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Exposure of phosphatidylserine (PS) in the outer leaflet of the plasma membrane is induced by infection with several members of the Alphaherpesvirinae subfamily. There is evidence that PS is used by the equine herpesvirus type 1 (EHV-1) during entry, but the exact role of PS and other phospholipids in the entry process remains unknown. Here, we investigated the interaction of differently charged phospholipids with virus particles and determined their influence on infection. Our data show that liposomes containing negatively charged PS or positively charged DOTAP (N-[1-(2,3-Dioleoyloxy)propyl]-N,N,N-trimethylammonium) inhibited EHV-1 infection, while neutral phosphatidylcholine (PC) had no effect. Inhibition of infection with PS was transient, decreased with time, and was dose dependent. Our findings indicate that both cationic and anionic phospholipids can interact with the virus and reduce infectivity, while, presumably, acting through different mechanisms. Charged phospholipids were found to have antiviral effects and may be used to inhibit EHV-1 infection. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1088 KW - alphaherpesvirus KW - EHV-1 KW - phosphatidylserine KW - inhibition KW - pathogen host interaction Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-471895 SN - 1866-8372 IS - 1088 ER - TY - GEN A1 - Liesenjohann, Monique A1 - Liesenjohann, Thilo A1 - Palme, Rupert A1 - Eccard, Jana T1 - Differential behavioural and endocrine responses of common voles (Microtus arvalis) to nest predators and resource competitors N2 - Background: Adaptive behavioural strategies promoting co-occurrence of competing species are known to result from a sympatric evolutionary past. Strategies should be different for indirect resource competition (exploitation, e.g., foraging and avoidance behaviour) than for direct interspecific interference (e.g., aggression, vigilance, and nest guarding). We studied the effects of resource competition and nest predation in sympatric small mammal species using semi-fossorial voles and shrews, which prey on vole offspring during their sensitive nestling phase. Experiments were conducted in caged outdoor enclosures. Focus common vole mothers (Microtus arvalis) were either caged with a greater white-toothed shrew (Crocidura russula) as a potential nest predator, with an herbivorous field vole (Microtus agrestis) as a heterospecific resource competitor, or with a conspecific resource competitor. Results: We studied behavioural adaptations of vole mothers during pregnancy, parturition, and early lactation, specifically modifications of the burrow architecture and activity at burrow entrances. Further, we measured pre- and postpartum faecal corticosterone metabolites (FCMs) of mothers to test for elevated stress hormone levels. Only in the presence of the nest predator were prepartum FCMs elevated, but we found no loss of vole nestlings and no differences in nestling body weight in the presence of the nest predator or the heterospecific resource competitor. Although the presence of both the shrew and the field vole induced prepartum modifications to the burrow architecture, only nest predators caused an increase in vigilance time at burrow entrances during the sensitive nestling phase. Conclusion: Voles displayed an adequate behavioural response for both resource competitors and nest predators. They modified burrow architecture to improve nest guarding and increased their vigilance at burrow entrances to enhance offspring survival chances. Our study revealed differential behavioural adaptations to resource competitors and nest predators. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 402 KW - behavioural adaptations KW - small mammals KW - interspecific interactions KW - nest predation KW - stress response KW - faecal corticosterone metabolites KW - burrow system KW - shrews KW - voles Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-401184 ER - TY - GEN A1 - Koussoroplis, Apostolos-Manuel A1 - Schwarzenberger, Anke A1 - Wacker, Alexander T1 - Diet quality determines lipase gene expression and lipase/esterase activity in Daphnia pulex N2 - We studied the short- (12 h) and long-term (144 h) response of Daphnia pulex lipases to quality shifts in diets consisting of different mixtures of the green alga Scenedesmus with the cyanobacterium Synechococcus, two species with contrasting lipid compositions. The lipase/esterase activity in both the gut and the body tissues had fast responses to the diet shift and increased with higher dietary contributions of Synechococcus. When screening the Daphnia genome for TAG lipases, we discovered a large gene-family expansion of these enzymes. We used a subset of eight genes for mRNA expression analyses and distinguished between influences of time and diet on the observed gene expression patterns. We identified five diet-responsive lipases of which three showed a sophisticated short- and long-term pattern of expression in response to small changes in food-quality. Furthermore, the gene expression of one of the lipases was strongly correlated to lipase/esterase activity in the gut suggesting its potentially major role in digestion. These findings demonstrate that the lipid-related enzymatic machinery of D. pulex is finely tuned to diet and might constitute an important mechanism of physiological adaptation in nutritionally complex environments. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 336 KW - Cyanobacteria KW - Digestive enzyme activity KW - Nutritional quality KW - Lipases Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-395661 ER - TY - GEN A1 - Weyrich, Alexandra A1 - Jeschek, Marie A1 - Schrapers, Katharina T. A1 - Lenz, Dorina A1 - Chung, Tzu Hung A1 - Ruebensam, Kathrin A1 - Yasar, Sermin A1 - Schneemann, Markus A1 - Ortmann, Sylvia A1 - Jewgenow, Katarina A1 - Fickel, Jörns T1 - Diet changes alter paternally inherited epigenetic pattern in male Wild guinea pigs T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Epigenetic modifications, of which DNA methylation is the most stable, are a mechanism conveying environmental information to subsequent generations via parental germ lines. The paternal contribution to adaptive processes in the offspring might be crucial, but has been widely neglected in comparison to the maternal one. To address the paternal impact on the offspring's adaptability to changes in diet composition, we investigated if low protein diet (LPD) in F0 males caused epigenetic alterations in their subsequently sired sons. We therefore fed F0 male Wild guinea pigs with a diet lowered in protein content (LPD) and investigated DNA methylation in sons sired before and after their father's LPD treatment in both, liver and testis tissues. Our results point to a 'heritable epigenetic response' of the sons to the fathers' dietary change. Because we detected methylation changes also in the testis tissue, they are likely to be transmitted to the F2 generation. Gene-network analyses of differentially methylated genes in liver identified main metabolic pathways indicating a metabolic reprogramming ('metabolic shift'). Epigenetic mechanisms, allowing an immediate and inherited adaptation may thus be important for the survival of species in the context of a persistently changing environment, such as climate change. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1065 KW - DNA methylation KW - exposure KW - wild mammal species KW - inheritance KW - plasticity KW - adaptation Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-460031 SN - 1866-8372 IS - 1065 ER - TY - GEN A1 - Guljamow, Arthur A1 - Barchewitz, Tino A1 - Große, Rebecca A1 - Timm, Stefan A1 - Hagemann, Martin A1 - Dittmann, Elke T1 - Diel Variations of Extracellular Microcystin Influence the Subcellular Dynamics of RubisCO in Microcystis aeruginosa PCC 7806 T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The ubiquitous freshwater cyanobacterium Microcystis is remarkably successful, showing a high tolerance against fluctuations in environmental conditions. It frequently forms dense blooms which can accumulate significant amounts of the hepatotoxin microcystin, which plays an extracellular role as an infochemical but also acts intracellularly by interacting with proteins of the carbon metabolism, notably with the CO2 fixing enzyme RubisCO. Here we demonstrate a direct link between external microcystin and its intracellular targets. Monitoring liquid cultures of Microcystis in a diel experiment revealed fluctuations in the extracellular microcystin content that correlate with an increase in the binding of microcystin to intracellular proteins. Concomitantly, reversible relocation of RubisCO from the cytoplasm to the cell’s periphery was observed. These variations in RubisCO localization were especially pronounced with cultures grown at higher cell densities. We replicated these effects by adding microcystin externally to cultures grown under continuous light. Thus, we propose that microcystin may be part of a fast response to conditions of high light and low carbon that contribute to the metabolic flexibility and the success of Microcystis in the field. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1154 KW - cyanobacterial bloom KW - Microcystis KW - microcystin KW - RubisCO KW - extracellular signaling Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-521287 SN - 1866-8372 IS - 1154 ER - TY - GEN A1 - Dittmann, Thea A1 - Heinken, Thilo A1 - Schmidt, Marcus T1 - Die Wälder von Magdeburgerforth (Fläming, Sachsen-Anhalt) T1 - The forests of Magdeburgerforth (Fläming, NE Germany) BT - eine Wiederholungsuntersuchungnach sechs Jahrzehnten BT - a resurvey study after six decade T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - In einem rund 2.200 ha großen Waldgebiet bei Magdeburgerforth (Fläming, Sachsen-Anhalt) wur-den 1948 bis 1950 von Harro Passarge 120 Vegetationsaufnahmen sowie eine Vegetationskartierung erstellt. Das Gebiet zeichnet sich durch eine große Vielfalt an Waldtypen aus den Verbänden Agrostio-Quercion petraeae, Alnion glutinosae, Alnion incanae, Carpinion betuli, Dicrano-Pinion und Quercion roboris aus. Daher und weil viele der heute in Wäldern wirksamen Prozesse (z. B. Stickstoffeintrag, Klimawandel) vor 60 Jahren noch nicht spürbar waren, bietet sich das Gebiet für eine Wiederholungs-untersuchung besonders an. Da die Aufnahmeflächen von Passarge nicht punktgenau verortet waren, wurden im Jahr 2014 in einem über die Forstabteilungen und die Vegetationskarte definierten Such-raum immer die der Erstaufnahme ähnlichsten Waldbestände erfasst. Insgesamt konnten 97 (81 %) der Aufnahmen wiederholt werden. Vegetationsveränderungen werden mithilfe einer NMDS-Ordination, der Gegenüberstellung von α-Diversität, Zeigerwerten und Waldbindungskategorien für die beiden Aufnahmezeitpunkte sowie über die Identifikation von Gewinner- und Verlierer-Arten analysiert.Auch wenn methodenbedingt bei der Wiederholungsuntersuchung nur die jeweils geringstmögliche Vegetationsveränderung abgebildet wird, konnten Ergebnisse erzielt werden, die mit denen quasi-permanenter Plots übereinstimmen. Die beobachteten allgemeinen Trends (Eutrophierung, Sukzession nach Nutzungswandel, Verlust lichtliebender und magerkeitszeigender Arten, Ausbreitung von stick-stoffliebenden Arten und mesophilen Waldarten, Einwanderung von Neophyten, keine generelle Ab-nahme der Artenzahl) stimmen gut mit den in zahlreichen Studien aus mitteleuropäischen Wäldern festgestellten überein. Durch das von nassen bis trockenen sowie von bodensauer-nährstoffarmen bis zu relativ basenreichen Böden reichende Standortsspektrum innerhalb des Untersuchungsgebietes konnte aber – deutlicher als in den meisten bisherigen Fallstudien – gezeigt werden, dass sich die Resilienz der Wälder gegenüber Vegetationsveränderung je nach Ausgangsgesellschaft stark unterscheidet und jeweils unterschiedliche Treiber wirksam sind. Stellario-Carpinetum und Luzulo-Quercetum erwiesen sich als relativ stabil, und auch in den Feuchtwäldern des Circaeo-Alnetum gab es trotz eines Arten-wechsels wenig Hinweise auf Umweltveränderungen. Dagegen wiesen die Wälder nährstoffarmer Standorte (Sphagno-Alnetum, Betulo-Quercetum, Dicrano-Pinion) viele Verliererarten und eine starke Eutrophierungstendenz auf. Die in besonderem Maße von historischen Waldnutzungsformen abhängi-gen thermophilen Wälder und die Flechten-Kiefernwälder gingen weitgehend verloren. N2 - Between 1948 and 1950 the German phytosociologist Harro Passarge conducted 120 releves in a 2,200 ha large forest area near Magdeburgerforth (Flaming, Saxony-Anhalt, NE Germany). The study area is characterized by a remarkable diversity of forest communities of the alliances Agrostio-Quercion petraeae, Alnion glutinosae, Alnion incanae, Carpinion betuli, Dicrano-Pinion and Quercion roboris. Because of this broad ecological spectrum, and because many processes which impact Central European forests today (nitrogen deposition, climate change) were not noticeable at the date of the first survey, it provides a good opportunity for a resurvey study after 60 years. As the position of Passarge's releves were not marked in a map, in the 2014 resurvey we sampled the most similar forest stands within a search area defined by the forest compartment and the Passarge vegetation map. In this way, 97 (81%) of the releves could be repeated. Vegetation change was analysed by NMDS ordination and the comparison of a diversity, Ellenberg indicator values and linkage to forest habitats of species from both censuses, as well as by the identification of winner and loser species. Although, due to the methodology, only the smallest possible vegetation change was indicated, we nevertheless gained results which conform to those of resurveys based on quasi-permanent plots. The main trends (eutrophication, succession after management change, loss of plant species that are light demanding and linked to oligotrophic sites, spread of nitrophilous and mesophilous forest species, immigration of neophytes, no general decline in species richness) are in agreement with the results of several other resurvey studies in Central and Western European forests. Because of the wide spectrum of habitats within the study area (from wet to dry, as well as from acidic and nutrient-poor to relatively base-rich) we could demonstrate more clearly than in previous studies that the resilience of forests to vegetation change differs strongly according to the initial forest type, and that different drivers of temporal changes are active. Mesophilous forests (Stellario-Carpinetum and Luzulo-Quercetum) turned out to be relatively stable, while Circaeo-Alnetum forests also showed few signs of environmental change despite some species turnover. In contrast, forests of nutrient-poor habitats (Sphagno-Alnetum, Betulo-Quercetum, Dicrano-Pinion) were characterized by many loser species and a strong tendency towards eutrophication. Thermophilous forests and lichen-pine forests, which are especially dependent on historical forest management techniques, largely disappeared. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1053 KW - initial site conditions KW - nitrogen deposition KW - past land use KW - quasi-permanent plots KW - vegetation change KW - winner and loser species Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-460058 SN - 1866-8372 IS - 1053 SP - 11 EP - 42 ER - TY - GEN A1 - Heinken, Thilo T1 - Die natürlichen Kiefernstandorte Deutschlands und ihre Gefährdung T1 - Natural Scots pine forests in Germany : habitats, distribution, and threat N2 - Natürliche Standorte der Waldkiefer gibt es in Deutschland nur kleinflächig. Während Kiefernforste anstelle natürlicher Laubwälder heute oft landschaftsprägend sind, bildet die konkurrenzschwache und lichtbedürftige Kiefer ausschließlich auf extrem trockenen oder nassen, nährstoffarmen Standorten naturnahe Schlusswaldgesellschaften. Regionale Schwerpunkte liegen in subkontinentalen Regionen wie dem nordostdeutschen Tiefland und Bayern, ein „natürliches Kiefernareal" lässt sich aber kaum abgrenzen. An der Trockengrenze des Waldes finden sich auf Kalk- und Dolomitgesteinen artenreiche Karbonat-Trockenkiefernwälder mit Elementen der alpinen Rasen und Kalkmagerrasen in der Bodenvegetation. Diese Wälder besiedeln steile, südexponierte Felsen und morphodynamisch aktive Bereiche wie Rutschhänge und FlussSchotterböden im Umkreis der Alpen, kommen aber auch in den Mittelgebirgen vor. Ihr Gegenstück auf sauren Standorten sind die Sand- und Silikat-Kiefernwälder der Quarzsande und Sandstein-Verwitterungsböden, deren Bodenvegetation durch Zwergsträucher, Moose und Strauchflechten geprägt ist. Hier siedelt die Kiefer in den Tieflagen besonders auf Binnendünen und Sandern, aber auch auf Küstendünen der Ostsee, in den Mittelgebirgen z. B. auf den Sandsteinriffen der Sächsischen Schweiz. Der dritte Wuchsbereich natürlicher Kiefernwälder sind saure, nährstoffarme Moore, die ganz überwiegend von Regenwasser gespeist werden. Auch die Kiefern-Moorwälder sind in Nordostdeutschland und Bayern am häufigsten. Von diesen Standorten ausgehend, wo ihr Platz kaum von anderen Baumarten streitig gemacht wird, tritt die Waldkiefer immer wieder als Pionier auf weniger extremen Standorten auf. In der Naturlandschaft kam dies etwa nach Waldbränden oder Stürmen vor, doch der Mensch förderte die Kiefer durch Auflichtung der Wälder, Waldweide und Streunutzung stark. Auch die damit verbundene Nährstoffverarmung macht eine exakte Abgrenzung natürlicher Kiefernstandorte unmöglich. Die schlechtwüchsigen und forstwirtschaftlich nicht interessanten, ästhetisch aber sehr ansprechenden natürlichen Kiefernbestände sind heute vor allem durch Stickstoff-Immissionen gefährdet. Trotz ihrer oft kargen Erscheinung besitzen sie einen hohen Wert für die Biodiversität und den Artenschutz. Neben bodenbewohnenden Flechten und regionalen Relikt-Endemiten ist vor allem die in den letzten Jahrzehnten zunehmend gefährdete Vielfalt an Mykorrhiza-Pilzen hervorzuheben, die der Kiefer das Leben auf extrem nährstoffarmen Standorten überhaupt ermöglichen. Abschließend werden mögliche Schutz- bzw. Regenerationsmaßnahmen wie das Abplaggen flechtenreicher Kiefernstandorte vorgestellt. N2 - Only small areas of natural Scots pine (Pinus sylvestris) habitat occur in Germany. Today pine plantations instead of natural deciduous forests often dominate the landscape. Yet, due to the competitive weakness and light demands of Scots pine, near-natural Scots pine climax communities are only found on extremely dry or wet, nutrient-poor sites, primarily in subcontinental regions of the north-eastern German lowlands and Bavaria. However, the "natural distribution range" of Scots pine is difficult to define. Species-rich, dry Scots pine forests, with alpine and calcareous grassland species in the ground vegetation, are found at the aridity limit of forests on sites with carbonate rich soils developed from limestone and dolomite parent material. These forests occur on steep south-facing slopes, on morphodynamically active areas such as landslides and coarse river gravel beds in and near the Alps, and also in the low mountain ranges. Scots pine forests are also found on acidic sites, on quartz sands and soils overlying weathered silicate rocks with an understorey dominated by dwarf shrubs, bryophytes and fruticose lichens. These forests are present in the lowlands, particularly on inland dunes and glacifluvial deposits, but also on coastal dunes around the Baltic Sea and in the low mountain ranges, for example on the sandstone cliffs in the Elbe Sandstone Mountains. Acidic, oligo-trophic bogs, mainly supplied by rainwater, comprise the third natural Scots pine forest habitat. These Scots pine bog forests occur most frequently in north-eastern Germany and in Bavaria. Coming from these habitats, where virtually no other tree species grows, Scots pine is found again and again as a pioneer on less extreme sites. In the natural landscape, it occurs mainly after forest fires and storms. Yet humans promote Scots pine by thinning forests, creating woodland pasture and removing litter. The nutrient depletion associated with these practices makes an exact delimitation of natural Scots pine habitats unfeasible. Natural pine forest stands, which, although attractive and appealing, grow poorly and are of little interest for forestry, are endangered mainly by anthropo-genic nitrogen depositions. Despite their meagre appearance, these forests are important for biodiversity and species conservation. In addition to terricolous lichens and regional relic endemic plant species, the diversity of mycorrhiza fungi, which enable Scots pine to exist on these nutrient-poor sites, increasingly is becoming endangered. Finally, possible conservation and regeneration practices, such as manually cutting sods in lichen-rich Scots pine forests, are presented. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 153 KW - Naturschutz KW - Phytodiversität KW - Pinus sylvestris KW - Standort KW - Walddynamik KW - nature conservation KW - phytodiversity KW - Pinus sylvestris KW - site conditions KW - forest dynamics Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-46506 ER - TY - GEN A1 - Durek, Pawel A1 - Schudoma, Christian A1 - Weckwerth, Wolfram A1 - Selbig, Joachim A1 - Walther, Dirk T1 - Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins N2 - Background: Phosphorylation of proteins plays a crucial role in the regulation and activation of metabolic and signaling pathways and constitutes an important target for pharmaceutical intervention. Central to the phosphorylation process is the recognition of specific target sites by protein kinases followed by the covalent attachment of phosphate groups to the amino acids serine, threonine, or tyrosine. The experimental identification as well as computational prediction of phosphorylation sites (P-sites) has proved to be a challenging problem. Computational methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding phosphorylation sites. Results: We characterized the spatial context of phosphorylation sites and assessed its usability for improved phosphorylation site predictions. We identified 750 non-redundant, experimentally verified sites with three-dimensional (3D) structural information available in the protein data bank (PDB) and grouped them according to their respective kinase family. We studied the spatial distribution of amino acids around phosphorserines, phosphothreonines, and phosphotyrosines to extract signature 3D-profiles. Characteristic spatial distributions of amino acid residue types around phosphorylation sites were indeed discernable, especially when kinase-family-specific target sites were analyzed. To test the added value of using spatial information for the computational prediction of phosphorylation sites, Support Vector Machines were applied using both sequence as well as structural information. When compared to sequence-only based prediction methods, a small but consistent performance improvement was obtained when the prediction was informed by 3D-context information. Conclusion: While local one-dimensional amino acid sequence information was observed to harbor most of the discriminatory power, spatial context information was identified as relevant for the recognition of kinases and their cognate target sites and can be used for an improved prediction of phosphorylation sites. A web-based service (Phos3D) implementing the developed structurebased P-site prediction method has been made available at http://phos3d.mpimp-golm.mpg.de. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 141 KW - Support vector machines KW - Microarray data KW - Docking interactions KW - Signal-transduction KW - Sequence alignment Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45129 ER - TY - GEN A1 - Wessig, Pablo A1 - Bader, Denise A1 - Klier, Dennis Tobias A1 - Hettrich, Cornelia A1 - Bier, Frank Fabian T1 - Detecting carbohydrate–lectin interactions using a fluorescent probe based on DBD dyes N2 - Herein we present an efficient synthesis of a biomimetic probe with modular construction that can be specifically bound by the mannose binding FimH protein – a surface adhesion protein of E. coli bacteria. The synthesis combines the new and interesting DBD dye with the carbohydrate ligand mannose via a Click reaction. We demonstrate the binding to E. coli bacteria over a large concentration range and also present some special characteristics of those molecules that are of particular interest for the application as a biosensor. In particular, the mix-and-measure ability and the very good photo-stability should be highlighted here. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 314 KW - conformational-changes KW - green-i KW - protein KW - binding KW - assay Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-394382 SP - 1235 EP - 1238 ER - TY - GEN A1 - Kindermann, Liana A1 - Dobler, Magnus A1 - Niedeggen, Daniela A1 - Chimbioputo Fabiano, Ezequiel A1 - Linstädter, Anja T1 - Dataset on woody aboveground biomass, disturbance losses, and wood density from an African savanna ecosystem T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - This dataset comprises tree inventories and damage assessments performed in Namibia's semi-arid Zambezi Region. Data were sampled in savannas and savanna woodlands along steep gradients of elephant population densities to capture the effects of those (and other) disturbances on individual-level and stand-level aboveground woody biomass (AGB). The dataset contains raw data on dendrometric measures and processed data on specific wood density (SWD), woody aboveground biomass, and biomass losses through disturbance impacts. Allometric proxies (height, canopy diameters, and in adult trees also stem circumferences) were recorded for n = 6,179 tree and shrub individuals. Wood samples were taken for each encountered species to measure specific wood density. These measurements have been used to estimate woody aboveground biomass via established allometric models, advanced through our improved methodologies and workflows that accounted for tree and shrub architecture shaped by disturbance impacts. To this end, we performed a detailed damage assessment on each woody individual in the field. In addition to estimations of standing biomass, our new method also delivered data on biomass losses to different disturbance agents (elephants, fire, and others) on the level of plant individuals and stands. The data presented here have been used within a study published with Ecological Indicators (Kindermann et al., 2022) to evaluate the benefits of our improved methodology in comparison to a standard reference method of aboveground biomass estimations. Additionally, it has been employed in a study on carbon storage and sequestration in vegetation and soils (Sandhage-Hofmann et al., 2021). The raw data of dendrometric measurements can be subjected to other available allometric models for biomass estimation. The processed data can be used to analyze disturbance impacts on woody aboveground biomass, or for regional carbon storage estimates. The data on species-specific wood density can be used for application to other dendrometric datasets to (re-) estimate biomass through allometric models requiring wood density. It can further be used for plant functional trait analyses. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1265 KW - Damage assessment KW - Disturbance impacts KW - Disturbance indicator KW - Elephant disturbance KW - Tree allometry KW - Specific wood density KW - Woody aboveground biomass KW - Wood specific gravity Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-561607 SN - 1866-8372 SP - 1 EP - 16 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - GEN A1 - Sieck, Mungla A1 - Ibisch, Pierre L. A1 - Moloney, Kirk A. A1 - Jeltsch, Florian T1 - Current models broadly neglect specific needs of biodiversity conservation in protected areas under climate change N2 - Background Protected areas are the most common and important instrument for the conservation of biological diversity and are called for under the United Nations' Convention on Biological Diversity. Growing human population densities, intensified land-use, invasive species and increasing habitat fragmentation threaten ecosystems worldwide and protected areas are often the only refuge for endangered species. Climate change is posing an additional threat that may also impact ecosystems currently under protection. Therefore, it is of crucial importance to include the potential impact of climate change when designing future nature conservation strategies and implementing protected area management. This approach would go beyond reactive crisis management and, by necessity, would include anticipatory risk assessments. One avenue for doing so is being provided by simulation models that take advantage of the increase in computing capacity and performance that has occurred over the last two decades. Here we review the literature to determine the state-of-the-art in modeling terrestrial protected areas under climate change, with the aim of evaluating and detecting trends and gaps in the current approaches being employed, as well as to provide a useful overview and guidelines for future research. Results Most studies apply statistical, bioclimatic envelope models and focus primarily on plant species as compared to other taxa. Very few studies utilize a mechanistic, process-based approach and none examine biotic interactions like predation and competition. Important factors like land-use, habitat fragmentation, invasion and dispersal are rarely incorporated, restricting the informative value of the resulting predictions considerably. Conclusion The general impression that emerges is that biodiversity conservation in protected areas could benefit from the application of modern modeling approaches to a greater extent than is currently reflected in the scientific literature. It is particularly true that existing models have been underutilized in testing different management options under climate change. Based on these findings we suggest a strategic framework for more effectively incorporating the impact of climate change in models exploring the effectiveness of protected areas. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 368 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400894 ER - TY - GEN A1 - Omranian, Sara A1 - Nikoloski, Zoran T1 - CUBCO+: prediction of protein complexes based on min-cut network partitioning into biclique spanned subgraphs T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - High-throughput proteomics approaches have resulted in large-scale protein–protein interaction (PPI) networks that have been employed for the prediction of protein complexes. However, PPI networks contain false-positive as well as false-negative PPIs that affect the protein complex prediction algorithms. To address this issue, here we propose an algorithm called CUBCO+ that: (1) employs GO semantic similarity to retain only biologically relevant interactions with a high similarity score, (2) based on link prediction approaches, scores the false-negative edges, and (3) incorporates the resulting scores to predict protein complexes. Through comprehensive analyses with PPIs from Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens, we show that CUBCO+ performs as well as the approaches that predict protein complexes based on recently introduced graph partitions into biclique spanned subgraphs and outperforms the other state-of-the-art approaches. Moreover, we illustrate that in combination with GO semantic similarity, CUBCO+ enables us to predict more accurate protein complexes in 36% of the cases in comparison to CUBCO as its predecessor. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1315 KW - Protein complexes KW - Protein–protein interaction KW - Network clustering KW - Species comparison Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-586863 SN - 1866-8372 IS - 1315 ER - TY - GEN A1 - Beermann, Jan A1 - Westbury, Michael V. A1 - Hofreiter, Michael A1 - Hilgers, Leon A1 - Deister, Fabian A1 - Neumann, Hermann A1 - Raupach, Michael J. T1 - Cryptic species in a well-known habitat BT - applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida) T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1059 KW - multiple sequence alignment KW - Oxidase Subunit-I KW - mitochondrial genome KW - control region KW - Ribosomal-RNA KW - asellota crustacea KW - gammarus crustacea KW - deep-sea KW - DNA KW - evolution Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-460792 SN - 1866-8372 IS - 1059 ER - TY - GEN A1 - Schwarz, Maria A1 - Lossow, Kristina A1 - Kopp, Johannes F. A1 - Schwerdtle, Tanja A1 - Kipp, Anna Patricia T1 - Crosstalk of Nrf2 with the Trace Elements Selenium, Iron, Zinc, and Copper T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Trace elements, like Cu, Zn, Fe, or Se, are important for the proper functioning of antioxidant enzymes. However, in excessive amounts, they can also act as pro-oxidants. Accordingly, trace elements influence redox-modulated signaling pathways, such as the Nrf2 pathway. Vice versa, Nrf2 target genes belong to the group of transport and metal binding proteins. In order to investigate whether Nrf2 directly regulates the systemic trace element status, we used mice to study the effect of a constitutive, whole-body Nrf2 knockout on the systemic status of Cu, Zn, Fe, and Se. As the loss of selenoproteins under Se-deprived conditions has been described to further enhance Nrf2 activity, we additionally analyzed the combination of Nrf2 knockout with feeding diets that provide either suboptimal, adequate, or supplemented amounts of Se. Experiments revealed that the Nrf2 knockout partially affected the trace element concentrations of Cu, Zn, Fe, or Se in the intestine, liver, and/or plasma. However, aside from Fe, the other three trace elements were only marginally modulated in an Nrf2-dependent manner. Selenium deficiency mainly resulted in increased plasma Zn levels. One putative mediator could be the metal regulatory transcription factor 1, which was up-regulated with an increasing Se supply and downregulated in Se-supplemented Nrf2 knockout mice. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1081 KW - Nrf2 KW - selenium KW - iron KW - copper KW - zinc KW - homeostasis Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-472873 SN - 1866-8372 IS - 1081 ER - TY - GEN A1 - Lamanna, Francesco A1 - Kirschbaum, Frank A1 - Waurick, Isabelle A1 - Dieterich, Christoph A1 - Tiedemann, Ralph T1 - Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae) N2 - Background African weakly-electric fishes of the family Mormyridae are able to produce and perceive weak electric signals (typically less than one volt in amplitude) owing to the presence of a specialized, muscle-derived electric organ (EO) in their tail region. Such electric signals, also known as Electric Organ Discharges (EODs), are used for objects/prey localization, for the identification of conspecifics, and in social and reproductive behaviour. This feature might have promoted the adaptive radiation of this family by acting as an effective pre-zygotic isolation mechanism. Despite the physiological and evolutionary importance of this trait, the investigation of the genetic basis of its function and modification has so far remained limited. In this study, we aim at: i) identifying constitutive differences in terms of gene expression between electric organ and skeletal muscle (SM) in two mormyrid species of the genus Campylomormyrus: C. compressirostris and C. tshokwe, and ii) exploring cross-specific patterns of gene expression within the two tissues among C. compressirostris, C. tshokwe, and the outgroup species Gnathonemus petersii. Results Twelve paired-end (100 bp) strand-specific RNA-seq Illumina libraries were sequenced, producing circa 330 M quality-filtered short read pairs. The obtained reads were assembled de novo into four reference transcriptomes. In silico cross-tissue DE-analysis allowed us to identify 271 shared differentially expressed genes between EO and SM in C. compressirostris and C.tshokwe. Many of these genes correspond to myogenic factors, ion channels and pumps, and genes involved in several metabolic pathways. Cross-species analysis has revealed that the electric organ transcriptome is more variable in terms of gene expression levels across species than the skeletal muscle transcriptome. Conclusions The data obtained indicate that: i) the loss of contractile activity and the decoupling of the excitation-contraction processes are reflected by the down-regulation of the corresponding genes in the electric organ’s transcriptome; ii) the metabolic activity of the EO might be specialized towards the production and turn-over of membrane structures; iii) several ion channels are highly expressed in the EO in order to increase excitability; iv) several myogenic factors might be down-regulated by transcription repressors in the EO. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 212 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-86997 ER - TY - GEN A1 - Mazza, Valeria A1 - Czyperreck, Inken A1 - Eccard, Jana A1 - Dammhahn, Melanie T1 - Cross-Context Responses to Novelty in Rural and Urban Small Mammals T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The Anthropocene is the era of urbanization. The accelerating expansion of cities occurs at the expense of natural reservoirs of biodiversity and presents animals with challenges for which their evolutionary past might not have prepared them. Cognitive and behavioral adjustments to novelty could promote animals’ persistence under these altered conditions. We investigated the structure of, and covariance between, different aspects of responses to novelty in rural and urban small mammals of two non-commensal rodent species. We ran replicated experiments testing responses to three novelty types (object, food, or space) of 47 individual common voles (Microtus arvalis) and 41 individual striped field mice (Apodemus agrarius). We found partial support for the hypothesis that responses to novelty are structured, clustering (i) speed of responses, (ii) intensity of responses, and (iii) responses to food into separate dimensions. Rural and urban small mammals did not differ in most responses to novelty, suggesting that urban habitats do not reduce neophobia in these species. Further studies investigating whether comparable response patters are found throughout different stages of colonization, and along synurbanization processes of different duration, will help illuminate the dynamics of animals’ cognitive adjustments to urban life. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1226 KW - animal cognition KW - anthropogenic environment KW - HIREC KW - novelty KW - neophobia KW - neophilia KW - rodents KW - urbanization Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-543863 SN - 1866-8372 ER - TY - GEN A1 - Raatz, Michael A1 - van Velzen, Ellen A1 - Gaedke, Ursula T1 - Co‐adaptation impacts the robustness of predator–prey dynamics against perturbations T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Global change threatens the maintenance of ecosystem functions that are shaped by the persistence and dynamics of populations. It has been shown that the persistence of species increases if they possess larger trait adaptability. Here, we investigate whether trait adaptability also affects the robustness of population dynamics of interacting species and thereby shapes the reliability of ecosystem functions that are driven by these dynamics. We model co‐adaptation in a predator–prey system as changes to predator offense and prey defense due to evolution or phenotypic plasticity. We investigate how trait adaptation affects the robustness of population dynamics against press perturbations to environmental parameters and against pulse perturbations targeting species abundances and their trait values. Robustness of population dynamics is characterized by resilience, elasticity, and resistance. In addition to employing established measures for resilience and elasticity against pulse perturbations (extinction probability and return time), we propose the warping distance as a new measure for resistance against press perturbations, which compares the shapes and amplitudes of pre‐ and post‐perturbation population dynamics. As expected, we find that the robustness of population dynamics depends on the speed of adaptation, but in nontrivial ways. Elasticity increases with speed of adaptation as the system returns more rapidly to the pre‐perturbation state. Resilience, in turn, is enhanced by intermediate speeds of adaptation, as here trait adaptation dampens biomass oscillations. The resistance of population dynamics strongly depends on the target of the press perturbation, preventing a simple relationship with the adaptation speed. In general, we find that low robustness often coincides with high amplitudes of population dynamics. Hence, amplitudes may indicate the robustness against perturbations also in other natural systems with similar dynamics. Our findings show that besides counteracting extinctions, trait adaptation indeed strongly affects the robustness of population dynamics against press and pulse perturbations. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 809 KW - disturbance KW - evolutionary rescue KW - population dynamics KW - stability KW - trait adaptation Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-442489 SN - 1866-8372 IS - 809 ER - TY - GEN A1 - Azuma, Yusuke A1 - Kükenshöner, Tim A1 - Ma, Guangyong A1 - Yasunaga, Jun-ichiro A1 - Imanishi, Miki A1 - Tanaka, Gen A1 - Nakase, Ikuhiko A1 - Maruno, Takahiro A1 - Kobayashi, Yuji A1 - Arndt, Katja Maren A1 - Matsuoka, Masao A1 - Futaki, Shiroh T1 - Controlling leucine-zipper partner recognition in cells through modification of a–g interactions N2 - By focusing on the a–g interactions, successful design and selection were accomplished to obtain a leucine-zipper segment that discriminates the appropriate partner over another that provides very similar patterns of electrostatic interactions. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 276 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-98758 ER - TY - GEN A1 - Herde, Antje A1 - Eccard, Jana T1 - Consistency in boldness, activity and exploration at different stages of life N2 - Background: Animals show consistent individual behavioural patterns over time and over situations. This phenomenon has been referred to as animal personality or behavioural syndromes. Little is known about consistency of animal personalities over entire life times. We investigated the repeatability of behaviour in common voles (Microtus arvalis) at different life stages, with different time intervals, and in different situations. Animals were tested using four behavioural tests in three experimental groups: 1. before and after maturation over three months, 2. twice as adults during one week, and 3. twice as adult animals over three months, which resembles a substantial part of their entire adult life span of several months. Results: Different behaviours were correlated within and between tests and a cluster analysis showed three possible behavioural syndrome-axes, which we name boldness, exploration and activity. Activity and exploration behaviour in all tests was highly repeatable in adult animals tested over one week. In animals tested over maturation, exploration behaviour was consistent whereas activity was not. Voles that were tested as adults with a three-month interval showed the opposite pattern with stable activity but unstable exploration behaviour. Conclusions: The consistency in behaviour over time suggests that common voles do express stable personality over short time. Over longer periods however, behaviour is more flexible and depending on life stage (i.e. tested before/after maturation or as adults) of the tested individual. Level of boldness or activity does not differ between tested groups and maintenance of variation in behavioural traits can therefore not be explained by expected future assets as reported in other studies. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 376 KW - animal personality KW - behavioural type KW - Microtus arvalis KW - common vole KW - plasticity KW - consistency KW - repeatability Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-401395 ER - TY - GEN A1 - Sowemimo, Oluwakemi T. A1 - Knox-Brown, Patrick A1 - Borcherds, Wade A1 - Rindfleisch, Tobias A1 - Thalhammer, Anja A1 - Daughdrill, Gary W. T1 - Conserved glycines control disorder and function in the cold-regulated protein, COR15A T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Cold-regulated (COR) 15A is an intrinsically disordered protein (IDP) from Arabidopsis thaliana important for freezing tolerance. During freezing-induced cellular dehydration, COR15A transitions from a disordered to mostly alpha-helical structure. We tested whether mutations that increase the helicity of COR15A also increase its protective function. Conserved glycine residues were identified and mutated to alanine. Nuclear magnetic resonance (NMR) spectroscopy was used to identify residue-specific changes in helicity for wildtype (WT) COR15A and the mutants. Circular dichroism (CD) spectroscopy was used to monitor the coil-helix transition in response to increasing concentrations of trifluoroethanol (TFE) and ethylene glycol. The impact of the COR15A mutants on the stability of model membranes during a freeze-thaw cycle was investigated by fluorescence spectroscopy. The results of these experiments showed the mutants had a higher content of alpha-helical structure and the increased alpha-helicity improved membrane stabilization during freezing. Comparison of the TFE- and ethylene glycol-induced coil-helix transitions support our conclusion that increasing the transient helicity of COR15A in aqueous solution increases its ability to stabilize membranes during freezing. Altogether, our results suggest the conserved glycine residues are important for maintaining the disordered structure of COR15A but are also compatible with the formation of alpha-helical structure during freezing induced dehydration. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1089 KW - COR15A KW - late embryogenesis abundant KW - intrinsically disordered proteins KW - trifluoroethanol KW - nuclear magnetic resonance Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-472217 SN - 1866-8372 IS - 1089 ER - TY - GEN A1 - Barlow, Axel A1 - Hartmann, Stefanie A1 - Gonzalez, Javier A1 - Hofreiter, Michael A1 - Paijmans, Johanna L. A. T1 - Consensify BT - a method for generating pseudohaploid genome sequences from palaeogenomic datasets with reduced error rates T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1033 KW - palaeogenomics KW - ancient DNA KW - sequencing error KW - error reduction KW - D statistics KW - bioinformatics Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-472521 SN - 1866-8372 IS - 1033 ER - TY - GEN A1 - Weithoff, Guntram A1 - Bell, Elanor Margaret T1 - Complex Trophic Interactions in an Acidophilic Microbial Community T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Extreme habitats often harbor specific communities that differ substantially from non-extreme habitats. In many cases, these communities are characterized by archaea, bacteria and protists, whereas the number of species of metazoa and higher plants is relatively low. In extremely acidic habitats, mostly prokaryotes and protists thrive, and only very few metazoa thrive, for example, rotifers. Since many studies have investigated the physiology and ecology of individual species, there is still a gap in research on direct, trophic interactions among extremophiles. To fill this gap, we experimentally studied the trophic interactions between a predatory protist (Actinophrys sol, Heliozoa) and its prey, the rotifers Elosa woralli and Cephalodella sp., the ciliate Urosomoida sp. and the mixotrophic protist Chlamydomonas acidophila (a green phytoflagellate, Chlorophyta). We found substantial predation pressure on all animal prey. High densities of Chlamydomonas acidophila reduced the predation impact on the rotifers by interfering with the feeding behaviour of A. sol. These trophic relations represent a natural case of intraguild predation, with Chlamydomonas acidophila being the common prey and the rotifers/ciliate and A. sol being the intraguild prey and predator, respectively. We further studied this intraguild predation along a resource gradient using Cephalodella sp. as the intraguild prey. The interactions among the three species led to an increase in relative rotifer abundance with increasing resource (Chlamydomonas) densities. By applying a series of laboratory experiments, we revealed the complexity of trophic interactions within a natural extremophilic community. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1276 KW - acid mine drainage KW - extremophiles KW - food web KW - heliozoa KW - intraguild predation KW - mining lakes KW - Rotifera Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-569945 SN - 1866-8372 SP - 1 EP - 10 ER - TY - GEN A1 - Gräf, Ralph T1 - Comparative biology of centrosomal structures in eukaryotes T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The centrosome is not only the largest and most sophisticated protein complex within a eukaryotic cell, in the light of evolution, it is also one of its most ancient organelles. This special issue of "Cells" features representatives of three main, structurally divergent centrosome types, i.e., centriole-containing centrosomes, yeast spindle pole bodies (SPBs), and amoebozoan nucleus-associated bodies (NABs). Here, I discuss their evolution and their key-functions in microtubule organization, mitosis, and cytokinesis. Furthermore, I provide a brief history of centrosome research and highlight recently emerged topics, such as the role of centrioles in ciliogenesis, the relationship of centrosomes and centriolar satellites, the integration of centrosomal structures into the nuclear envelope and the involvement of centrosomal components in non-centrosomal microtubule organization. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1063 KW - centrosome KW - centriole KW - cilium KW - basal body KW - spindle pole body KW - SPB KW - nucleus-associated body KW - NAB KW - microtubules Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-472294 SN - 1866-8372 IS - 1063 ER - TY - GEN A1 - Schedina, Ina Maria A1 - Hartmann, Stefanie A1 - Groth, Detlef A1 - Schlupp, Ingo A1 - Tiedemann, Ralph T1 - Comparative analysis of the gonadal transcriptomes of the all-female species Poecilia formosa and its maternal ancestor Poecilia mexicana N2 - Background The Amazon molly, Poecilia formosa (Teleostei: Poeciliinae) is an unisexual, all-female species. It evolved through the hybridisation of two closely related sexual species and exhibits clonal reproduction by sperm dependent parthenogenesis (or gynogenesis) where the sperm of a parental species is only used to activate embryogenesis of the apomictic, diploid eggs but does not contribute genetic material to the offspring. Here we provide and describe the first de novo assembled transcriptome of the Amazon molly in comparison with its maternal ancestor, the Atlantic molly Poecilia mexicana. The transcriptome data were produced through sequencing of single end libraries (100 bp) with the Illumina sequencing technique. Results 83,504,382 reads for the Amazon molly and 81,625,840 for the Atlantic molly were assembled into 127,283 and 78,961 contigs for the Amazon molly and the Atlantic molly, respectively. 63% resp. 57% of the contigs could be annotated with gene ontology terms after sequence similarity comparisons. Furthermore, we were able to identify genes normally involved in reproduction and especially in meiosis also in the transcriptome dataset of the apomictic reproducing Amazon molly. Conclusions We assembled and annotated the transcriptome of a non-model organism, the Amazon molly, without a reference genome (de novo). The obtained dataset is a fundamental resource for future research in functional and expression analysis. Also, the presence of 30 meiosis-specific genes within a species where no meiosis is known to take place is remarkable and raises new questions for future research. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 404 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-401420 ER - TY - GEN A1 - Srivastava, Abhishek A1 - Murugaiyan, Jayaseelan A1 - Garcia, Juan A. L. A1 - De Corte, Daniele A1 - Hoetzinger, Matthias A1 - Eravci, Murat A1 - Weise, Christoph A1 - Kumar, Yadhu A1 - Roesler, Uwe A1 - Hahn, Martin W. A1 - Grossart, Hans-Peter T1 - Combined Methylome, Transcriptome and Proteome Analyses Document Rapid Acclimatization of a Bacterium to Environmental Changes T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Polynucleobacter asymbioticus strain QLW-P1DMWA-1T represents a group of highly successful heterotrophic ultramicrobacteria that is frequently very abundant (up to 70% of total bacterioplankton) in freshwater habitats across all seven continents. This strain was originally isolated from a shallow Alpine pond characterized by rapid changes in water temperature and elevated UV radiation due to its location at an altitude of 1300 m. To elucidate the strain’s adjustment to fluctuating environmental conditions, we recorded changes occurring in its transcriptomic and proteomic profiles under contrasting experimental conditions by simulating thermal conditions in winter and summer as well as high UV irradiation. To analyze the potential connection between gene expression and regulation via methyl group modification of the genome, we also analyzed its methylome. The methylation pattern differed between the three treatments, pointing to its potential role in differential gene expression. An adaptive process due to evolutionary pressure in the genus was deduced by calculating the ratios of non-synonymous to synonymous substitution rates for 20 Polynucleobacter spp. genomes obtained from geographically diverse isolates. The results indicate purifying selection. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1011 KW - DNA modification KW - gene expression KW - freshwater heterotrophic bacteria KW - UV radiation KW - purifying selection Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-481993 SN - 1866-8372 IS - 1011 ER - TY - GEN A1 - Wulf, Monika A1 - Heinken, Thilo T1 - Colonization of recent coniferous versus deciduous forest stands by vascular plants at the local scale N2 - Questions: 1. Are there differences among species in their preference for coniferous vs. deciduous forest? 2. Are tree and shrub species better colonizers of recent forest stands than herbaceous species? 3. Do colonization patterns of plant species groups depend on tree species composition? Location: Three deciduous and one coniferous recent forest areas in Brandenburg, NE Germany. Methods: In 34 and 21 transects in coniferous and deciduous stands, respectively, we studied the occurrence and percentage cover of vascular plants in a total of 150 plots in ancient stands, 315 in recent stands and 55 at the ecotone. Habitat preference, diaspore weight, generative dispersal potential and clonal extension were used to explain mechanisms of local migration. Regression analysis was conducted to test whether migration distance was related to species’ life-history traits. Results: 25 species were significantly associated with ancient stands and ten species were significantly more frequent in recent stands. Tree and shrub species were good colonizers of recent coniferous and deciduous stands. In the coniferous stands, all herbaceous species showed a strong dispersal limitation during colonization, whereas in the deciduous stands generalist species may have survived in the grasslands which were present prior to afforestation. Conclusions: The fast colonization of recent stands by trees and shrubs can be explained by their effective dispersal via wind and animals. This, and the comparably efficient migration of herbaceous forest specialists into recent coniferous stands, implies that the conversion of coniferous into deciduous stands adjacent to ancient deciduous forests is promising even without planting of trees. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 149 KW - Clonal growth KW - diaspore weight KW - dispersal potential KW - forest specialist KW - generalist emergent group Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-46080 ER - TY - GEN A1 - Maaß, Stefanie A1 - Hückelheim, Ronja A1 - Rillig, Matthias C. T1 - Collembola laterally move biochar particles T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Biochar is being discussed as a soil amendment to improve soil fertility and mitigate climate change. While biochar interactions with soil microbial biota have been frequently studied, interactions with soil mesofauna are understudied. We here present an experiment in which we tested if the collembolan Folsomia candida I) can transport biochar particles, II) if yes, how far the particles are distributed within 10 days, and III) if it shows a preference among biochars made from different feedstocks, i.e. pine wood, pine bark and spelt husks. In general, biochar particles based on pine bark and pine wood were consistently distributed significantly more than those made of spelt husks, but all types were transported more than 4cm within 10 days. Additionally, we provide evidence that biochar particles can become readily attached to the cuticle of collembolans and hence be transported, potentially even over large distances. Our study shows that the soil mesofauna can indeed act as a vector for the transport of biochar particles and show clear preferences depending on the respective feedstock, which would need to be studied in more detail in the future. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 770 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-438839 SN - 1866-8372 IS - 770 ER - TY - GEN A1 - Banerjee, Pallavi A1 - Lipowsky, Reinhard A1 - Santer, Mark T1 - Coarse-grained molecular model for the Glycosylphosphatidylinositol anchor with and without protein T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Glycosylphosphatidylinositol (GPI) anchors are a unique class of complex glycolipids that anchor a great variety of proteins to the extracellular leaflet of plasma membranes of eukaryotic cells. These anchors can exist either with or without an attached protein called GPI-anchored protein (GPI-AP) both in vitro and in vivo. Although GPIs are known to participate in a broad range of cellular functions, it is to a large extent unknown how these are related to GPI structure and composition. Their conformational flexibility and microheterogeneity make it difficult to study them experimentally. Simplified atomistic models are amenable to all-atom computer simulations in small lipid bilayer patches but not suitable for studying their partitioning and trafficking in complex and heterogeneous membranes. Here, we present a coarse-grained model of the GPI anchor constructed with a modified version of the MARTINI force field that is suited for modeling carbohydrates, proteins, and lipids in an aqueous environment using MARTINI's polarizable water. The nonbonded interactions for sugars were reparametrized by calculating their partitioning free energies between polar and apolar phases. In addition, sugar-sugar interactions were optimized by adjusting the second virial coefficients of osmotic pressures for solutions of glucose, sucrose, and trehalose to match with experimental data. With respect to the conformational dynamics of GPI-anchored green fluorescent protein, the accessible time scales are now at least an order of magnitude larger than for the all-atom system. This is particularly important for fine-tuning the mutual interactions of lipids, carbohydrates, and amino acids when comparing to experimental results. We discuss the prospective use of the coarse-grained GPI model for studying protein-sorting and trafficking in membrane models. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1216 KW - Martini force-field KW - osmotic-pressure KW - potential-functions KW - aqueous-solution KW - dynamics KW - coefficient KW - simulation KW - trypanosoma KW - transition KW - parameters Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523742 SN - 1866-8372 IS - 6 ER - TY - GEN A1 - Bäurle, Isabel A1 - Trindade, Inês T1 - Chromatin regulation of somatic abiotic stress memory T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - In nature, plants are often subjected to periods of recurrent environmental stress that can strongly affect their development and productivity. To cope with these conditions, plants can remember a previous stress, which allows them to respond more efficiently to a subsequent stress, a phenomenon known as priming. This ability can be maintained at the somatic level for a few days or weeks after the stress is perceived, suggesting that plants can store information of a past stress during this recovery phase. While the immediate responses to a single stress event have been extensively studied, knowledge on priming effects and how stress memory is stored is still scarce. At the molecular level, memory of a past condition often involves changes in chromatin structure and organization, which may be maintained independently from transcription. In this review, we will summarize the most recent developments in the field and discuss how different levels of chromatin regulation contribute to priming and plant abiotic stress memory. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1408 KW - abiotic stress KW - chromatin regulation KW - heat stress memory KW - histone modifications, priming KW - transcriptional memory KW - vernalization Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-516668 SN - 1866-8372 IS - 17 ER - TY - GEN A1 - May, Patrick A1 - Christian, Jan-Ole A1 - Kempa, Stefan A1 - Walther, Dirk T1 - ChlamyCyc : an integrative systems biology database and web-portal for Chlamydomonas reinhardtii N2 - Background: The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern highthroughput technologies there is an imperative need to integrate large-scale data sets from highthroughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. Results: In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. Conclusion: ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 127 KW - Biochemical pathway database KW - Gene-expression data KW - Quantitative proteomics KW - Metabolic pathways KW - Genome annotation Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44947 ER - TY - GEN A1 - Mooij, Wolf M. A1 - Trolle, Dennis A1 - Jeppesen, Erik A1 - Arhonditsis, George B. A1 - Belolipetsky, Pavel V. A1 - Chitamwebwa, Deonatus B. R. A1 - Degermendzhy, Andrey G. A1 - DeAngelis, Donald L. A1 - Domis, Lisette Nicole de Senerpont A1 - Downing, Andrea S. A1 - Elliott, J. Alex A1 - Fragoso Jr., Carlos Ruberto A1 - Gaedke, Ursula A1 - Genova, Svetlana N. A1 - Gulati, Ramesh D. A1 - Håkanson, Lars A1 - Hamilton, David P. A1 - Hipsey, Matthew R. A1 - ‘t Hoen, Jochem A1 - Hülsmann, Stephan A1 - Los, F. Hans A1 - Makler-Pick, Vardit A1 - Petzoldt, Thomas A1 - Prokopkin, Igor G. A1 - Rinke, Karsten A1 - Schep, Sebastiaan A. A1 - Tominaga, Koji A1 - Van Dam, Anne A. A1 - Van Nes, Egbert H. A1 - Wells, Scott A. A1 - Janse, Jan H. T1 - Challenges and opportunities for integrating lake ecosystem modelling approaches T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others ('reinventing the wheel'). The other challenge is to avoid focusing on only one type of model, while ignoring new and diverse approaches that have become available ('having tunnel vision'). In this paper, we aim at improving the awareness of existing models and knowledge of concurrent approaches in lake ecosystem modelling, without covering all possible model tools and avenues. First, we present a broad variety of modelling approaches. To illustrate these approaches, we give brief descriptions of rather arbitrarily selected sets of specific models. We deal with static models (steady state and regression models), complex dynamic models (CAEDYM, CE-QUAL-W2, Delft 3D-ECO, LakeMab, LakeWeb, MyLake, PCLake, PROTECH, SALMO), structurally dynamic models and minimal dynamic models. We also discuss a group of approaches that could all be classified as individual based: super-individual models (Piscator, Charisma), physiologically structured models, stage-structured models and traitbased models. We briefly mention genetic algorithms, neural networks, Kalman filters and fuzzy logic. Thereafter, we zoom in, as an in-depth example, on the multi-decadal development and application of the lake ecosystem model PCLake and related models (PCLake Metamodel, Lake Shira Model, IPH-TRIM3D-PCLake). In the discussion, we argue that while the historical development of each approach and model is understandable given its 'leading principle', there are many opportunities for combining approaches. We take the point of view that a single 'right' approach does not exist and should not be strived for. Instead, multiple modelling approaches, applied concurrently to a given problem, can help develop an integrative view on the functioning of lake ecosystems. We end with a set of specific recommendations that may be of help in the further development of lake ecosystem models. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1326 KW - aquatic KW - food web dynamics KW - plankton KW - nutrients KW - spatial KW - lake KW - freshwater KW - marine KW - community KW - population KW - hydrology KW - eutrophication KW - global change KW - climate warming KW - fisheries KW - biodiversity KW - management KW - mitigation KW - adaptive processes KW - non-linear dynamics KW - analysis KW - bifurcation KW - understanding KW - prediction KW - model limitations KW - model integration Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-429839 SN - 1866-8372 IS - 1326 ER - TY - GEN A1 - Schorn, Sina A1 - Salman-Carvalho, Verena A1 - Littmann, Sten A1 - Ionescu, Danny A1 - Grossart, Hans-Peter A1 - Cypionka, Heribert T1 - Cell architecture of the giant sulfur bacterium achromatium oxaliferum BT - Extra-cytoplasmic localization of calcium carbonate bodies T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Achromatium oxaliferum is a large sulfur bacterium easily recognized by large intracellular calcium carbonate bodies. Although these bodies often fill major parts of the cells' volume, their role and specific intracellular location are unclear. In this study, we used various microscopy and staining techniques to identify the cell compartment harboring the calcium carbonate bodies. We observed that Achromatium cells often lost their calcium carbonate bodies, either naturally or induced by treatments with diluted acids, ethanol, sodium bicarbonate and UV radiation which did not visibly affect the overall shape and motility of the cells (except for UV radiation). The water-soluble fluorescent dye fluorescein easily diffused into empty cavities remaining after calcium carbonate loss. Membranes (stained with Nile Red) formed a network stretching throughout the cell and surrounding empty or filled calcium carbonate cavities. The cytoplasm (stained with FITC and SYBR Green for nucleic acids) appeared highly condensed and showed spots of dissolved Ca2+ (stained with Fura-2). From our observations, we conclude that the calcium carbonate bodies are located in the periplasm, in extra-cytoplasmic pockets of the cytoplasmic membrane and are thus kept separate from the cell's cytoplasm. This periplasmic localization of the carbonate bodies might explain their dynamic formation and release upon environmental changes. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1356 KW - sulfur-bacteria KW - calcium carbonate inclusions KW - extra-cytoplasmic pockets KW - calcite Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-549935 SN - 1866-8372 IS - 2 ER - TY - GEN A1 - Scheffler, Christiane A1 - Bogin, Barry A1 - Hermanussen, Michael T1 - Catch-up growth is a better indicator of undernutrition than thresholds for stunting T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Objective: Stunting (height-for-age < −2 SD) is one of the forms of undernutrition and is frequent among children of low- and middle-income countries. But stunting perSe is not a synonym of undernutrition. We investigated association between body height and indicators of energetic undernutrition at three critical thresholds for thinness used in public health: (1) BMI SDS < −2; (2) mid-upper arm circumference divided by height (MUAC (mm) × 10/height (cm) < 1·36) and (3) mean skinfold thickness (SF) < 7 mm and to question the reliability of thresholds as indicators of undernutrition. Design: Cross-sectional study; breakpoint analysis. Setting: Rural and urban regions of Indonesia and Guatemala – different socio-economic status (SES). Participants: 1716 Indonesian children (6·0–13·2 years) and 3838 Guatemalan children (4·0–18·9 years) with up to 50 % stunted children. Results: When separating the regression of BMI, MUAC or SF, on height into distinguishable segments (breakpoint analysis), we failed to detect relevant associations between height, and BMI, MUAC or SF, even in the thinnest and shortest children. For BMI and SF, the breakpoint analysis either failed to reach statistical significance or distinguished at breakpoints above critical thresholds. For MUAC, the breakpoint analysis yielded negative associations between MUAC/h and height in thin individuals. Only in high SES Guatemalan children, SF and height appeared mildly associated with R2 = 0·017. Conclusions: Currently used lower thresholds of height-for-age (stunting) do not show relevant associations with anthropometric indicators of energetic undernutrition. We recommend using the catch-up growth spurt during early re-feeding instead as immediate and sensitive indicator of past undernourishment. We discuss the primacy of education and social-economic-political-emotional circumstances as responsible factors for stunting. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1350 KW - no threshold for stunting KW - catch-up growth KW - social-economic-political-emotional KW - (SEPE) factors Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-550495 SN - 1866-8372 IS - 1 ER - TY - GEN A1 - Bechi, Beatrice A1 - Herter, Susanne A1 - McKenna, Shane A1 - Riley, Christopher A1 - Leimkühler, Silke A1 - Turner, Nicholas J. A1 - Carnell, Andrew J. T1 - Catalytic bio–chemo and bio–bio tandem oxidation reactions for amide and carboxylic acid synthesis N2 - A catalytic toolbox for three different water-based one-pot cascades to convert aryl alcohols to amides and acids and cyclic amines to lactams, involving combination of oxidative enzymes (monoamine oxidase, xanthine dehydrogenase, galactose oxidase and laccase) and chemical oxidants (TBHP or CuI(cat)/H2O2) at mild temperatures, is presented. Mutually compatible conditions were found to afford products in good to excellent yields. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 282 Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-99414 ER - TY - GEN A1 - Stiegler, Jonas A1 - von Hoermann, Christian A1 - Müller, Jörg A1 - Benbow, Mark Eric A1 - Heurich, Marco T1 - Carcass provisioning for scavenger conservation in a temperate forest ecosystem T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Carrion plays an essential role in shaping the structure and functioning of ecosystems and has far‐reaching implications for biodiversity conservation. The change in availability and type of carcasses throughout ecosystems can involve negative effects for scavenging communities. To address this issue, there have been recent conservation management measures of carrion provision in natural systems. However, the optimal conditions under which exposing carcasses to optimize conservation outcomes are still limited. Here, we used camera traps throughout elevational and vegetational gradients to monitor the consumption of 48 deer carcasses over a study period of six years by evaluating 270,279 photographs resulting out of 15,373 trap nights. We detected 17 species visiting carcass deployments, including five endangered species. Our results show that large carcasses, the winter season, and a heterogeneous surrounding habitat enhanced the frequency of carcass visits and the species richness of scavenger assemblages. Contrary to our expectations, carcass species, condition (fresh/frozen), and provision schedule (continuous vs single exposure) did not influence scavenging frequency or diversity. The carcass visitation frequency increased with carcass mass and lower temperatures. The effect of large carcasses was especially pronounced for mesopredators and the Eurasian lynx (Lynx lynx ). Lynx were not too influenced in its carrion acquisition by the season, but exclusively preferred remote habitats containing higher forest cover. Birds of prey, mesopredators, and top predators were also positively influenced by the visiting rate of ravens (Corvus corax ), whereas no biotic or abiotic preferences were found for wild boars (Sus scrofa ). This study provides evidence that any ungulate species of carrion, either in a fresh or in previously frozen condition, attracts a high diversity of scavengers especially during winter, thereby supporting earlier work that carcass provisions may support scavenger communities and endangered species. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 955 KW - anthropogenic food subsidies KW - carrion ecology KW - diversity KW - nature conservation KW - necrobiome KW - vertebrate scavenger KW - wildlife management Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-471099 SN - 1866-8372 IS - 955 ER - TY - GEN A1 - Elsner, Julia A1 - Schibler, Jörg A1 - Hofreiter, Michael A1 - Schlumbaum, Angela T1 - Burial condition is the most important factor for mtDNA PCR amplification success in Palaeolithic equid remains from the Alpine foreland T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Faunal remains from Palaeolithic sites are important genetic sources to study preglacial and postglacial populations and to investigate the effect of climate change and human impact. Post mortem decay, resulting in fragmented and chemically modified DNA, is a key obstacle in ancient DNA analyses. In the absence of reliable methods to determine the presence of endogenous DNA in sub-fossil samples, temporal and spatial surveys of DNA survival on a regional scale may help to estimate the potential of faunal remains from a given time period and region. We therefore investigated PCR amplification success, PCR performance and post mortem damage in c. 47,000 to c. 12,000-year-old horse remains from 14 Palaeolithic sites along the Swiss Jura Mountains in relation to depositional context, tissue type, storage time and age, potentially influencing DNA preservation. The targeted 75 base pair mitochondrial DNA fragment could be amplified solely from equid remains from caves and not from any of the open dry and (temporary) wetland sites. Whether teeth are better than bones cannot be ultimately decided; however, both storage time after excavation and age significantly affect PCR amplification and performance, albeit not in a linear way. This is best explained by the—inevitable—heterogeneity of the data set. The extent of post mortem damage is not related to any of the potential impact factors. The results encourage comprehensive investigations of Palaeolithic cave sites, even from temperate regions. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 727 KW - ancient DNA KW - DNA preservation KW - horse KW - cave KW - Switzerland Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-429763 SN - 1866-8372 IS - 727 SP - 505 EP - 515 ER - TY - GEN A1 - Eccard, Jana A1 - Fey, Karen A1 - Caspers, Barbara A. A1 - Ylönen, Hannu T1 - Breeding state and season affect interspecific interaction types BT - indirect resource competition and direct interference T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Indirect resource competition and interference are widely occurring mechanisms of interspecific interactions. We have studied the seasonal expression of these two interaction types within a two-species, boreal small mammal system. Seasons differ by resource availability, individual breeding state and intraspecific social system. Live-trapping methods were used to monitor space use and reproduction in 14 experimental populations of bank voles Myodes glareolus in large outdoor enclosures with and without a dominant competitor, the field vole Microtus agrestis. We further compared vole behaviour using staged dyadic encounters in neutral arenas in both seasons. Survival of the non-breeding overwintering bank voles was not affected by competition. In the spring, the numbers of male bank voles, but not of females, were reduced significantly in the competition populations. Bank vole home ranges expanded with vole density in the presence of competitors, indicating food limitation. A comparison of behaviour between seasons based on an analysis of similarity revealed an avoidance of costly aggression against opponents, independent of species. Interactions were more aggressive during the summer than during the winter, and heterospecific encounters were more aggressive than conspecific encounters. Based on these results, we suggest that interaction types and their respective mechanisms are not either–or categories and may change over the seasons. During the winter, energy constraints and thermoregulatory needs decrease direct aggression, but food constraints increase indirect resource competition. Direct interference appears in the summer, probably triggered by each individual’s reproductive and hormonal state and the defence of offspring against conspecific and heterospecific intruders. Both interaction forms overlap in the spring, possibly contributing to spring declines in the numbers of subordinate species. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 729 KW - rodents KW - aggression KW - seasonality KW - space use KW - winter biology Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-429398 SN - 1866-8372 IS - 729 SP - 623 EP - 633 ER - TY - GEN A1 - Kehr, Jan-Christoph A1 - Dittmann-Thünemann, Elke T1 - Biosynthesis and function of extracellular glycans in cyanobacteria N2 - The cell surface of cyanobacteria is covered with glycans that confer versatility and adaptability to a multitude of environmental factors. The complex carbohydrates act as barriers against different types of stress and play a role in intra- as well as inter-species interactions. In this review, we summarize the current knowledge of the chemical composition, biosynthesis and biological function of exo- and lipo-polysaccharides from cyanobacteria and give an overview of sugar-binding lectins characterized from cyanobacteria. We discuss similarities with well-studied enterobacterial systems and highlight the unique features of cyanobacteria. We pay special attention to colony formation and EPS biosynthesis in the bloom-forming cyanobacterium, Microcystis aeruginosa. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 346 KW - cyanobacteria KW - exopolysaccharides KW - lipopolysaccharides KW - colony formation Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400121 ER - TY - GEN A1 - Parry, Victor A1 - Schlägel, Ulrike E. A1 - Tiedemann, Ralph A1 - Weithoff, Guntram T1 - Behavioural Responses of Defended and Undefended Prey to Their Predator BT - A Case Study of Rotifera T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Predation is a strong species interaction causing severe harm or death to prey. Thus, prey species have evolved various defence strategies to minimize predation risk, which may be immediate (e.g., a change in behaviour) or transgenerational (morphological defence structures). We studied the behaviour of two strains of a rotiferan prey (Brachionus calyciflorus) that differ in their ability to develop morphological defences in response to their predator Asplanchna brightwellii. Using video analysis, we tested: (a) if two strains differ in their response to predator presence and predator cues when both are undefended; (b) whether defended individuals respond to live predators or their cues; and (c) if the morphological defence (large spines) per se has an effect on the swimming behaviour. We found a clear increase in swimming speed for both undefended strains in predator presence. However, the defended specimens responded neither to the predator presence nor to their cues, showing that they behave indifferently to their predator when they are defended. We did not detect an effect of the spines on the swimming behaviour. Our study demonstrates a complex plastic behaviour of the prey, not only in the presence of their predator, but also with respect to their defence status. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1302 KW - animal behaviour KW - transgenerational response KW - Brachionus calyciflorus KW - Asplanchna brightwellii KW - video analysis Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-577594 SN - 1866-8372 IS - 1302 ER - TY - GEN A1 - Blenau, Wolfgang A1 - Scheiner, Ricarda A1 - Plückhahn, Stephanie A1 - Oney, Bahar A1 - Erber, Joachim T1 - Behavioural pharmacology of octopamine, tyramine and dopamine in honey bees N2 - In the honey bee, responsiveness to sucrose correlates with many behavioural parameters such as age of first foraging, foraging role and learning. Sucrose responsiveness can be measured using the proboscis extension response (PER) by applying sucrose solutions of increasing concentrations to the antenna of a bee. We tested whether the biogenic amines octopamine, tyramine and dopamine, and the dopamine receptor agonist 2-amino-6,7-dihydroxy-1,2,3,4-tetrahydronaphthalene (6,7-ADTN) can modulate sucrose responsiveness. The compounds were either injected into the thorax or fed in sucrose solution to compare different methods of application. Injection and feeding of tyramine or octopamine significantly increased sucrose responsiveness. Dopamine decreased sucrose responsiveness when injected into the thorax. Feeding of dopamine had no effect. Injection of 6,7-ADTN into the thorax and feeding of 6,7-ADTN reduced sucrose responsiveness significantly. These data demonstrate that sucrose responsiveness in honey bees can be modulated by biogenic amines, which has far reaching consequences for other types of behaviour in this insect. (C) 2002 Elsevier Science B.V. All rights reserved. KW - Honey bee KW - insect KW - proboscis extension response KW - sucrose responsiveness KW - biogenic amines Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44308 ER - TY - GEN A1 - Schmidt, Andreas A1 - Rabsch, Wolfgang A1 - Broeker, Nina K. A1 - Barbirz, Stefanie T1 - Bacteriophage tailspike protein based assay to monitor phase variable glucosylations in Salmonella O-antigens N2 - Background Non-typhoid Salmonella Typhimurium (S. Typhimurium) accounts for a high number of registered salmonellosis cases, and O-serotyping is one important tool for monitoring epidemiology and spread of the disease. Moreover, variations in glucosylated O-antigens are related to immunogenicity and spread in the host. However, classical autoagglutination tests combined with the analysis of specific genetic markers cannot always reliably register phase variable glucose modifications expressed on Salmonella O-antigens and additional tools to monitor O-antigen glucosylation phenotypes of S. Typhimurium would be desirable. Results We developed a test for the phase variable O-antigen glucosylation state of S. Typhimurium using the tailspike proteins (TSP) of Salmonella phages 9NA and P22. We used this ELISA like tailspike adsorption (ELITA) assay to analyze a library of 44 Salmonella strains. ELITA was successful in discriminating strains that carried glucose 1-6 linked to the galactose of O-polysaccharide backbone (serotype O1) from non-glucosylated strains. This was shown by O-antigen compositional analyses of the respective strains with mass spectrometry and capillary electrophoresis. The ELITA test worked rapidly in a microtiter plate format and was highly O-antigen specific. Moreover, TSP as probes could also detect glucosylated strains in flow cytometry and distinguish multiphasic cultures differing in their glucosylation state. Conclusions Tailspike proteins contain large binding sites with precisely defined specificities and are therefore promising tools to be included in serotyping procedures as rapid serotyping agents in addition to antibodies. In this study, 9NA and P22TSP as probes could specifically distinguish glucosylation phenotypes of Salmonella on microtiter plate assays and in flow cytometry. This opens the possibility for flow sorting of cell populations for subsequent genetic analyses or for monitoring phase variations during large scale O-antigen preparations necessary for vaccine production. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 313 KW - Bacteriophage KW - Flow cytometry KW - O-antigen KW - O-serotyping KW - Phase variation KW - Salmonella Typhimurium KW - Tailspike protein Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-103769 ER - TY - GEN A1 - Kunstmann, Ruth Sonja A1 - Scheidt, Tom A1 - Buchwald, Saskia A1 - Helm, Alexandra A1 - Mulard, Laurence A. A1 - Fruth, Angelika A1 - Barbirz, Stefanie T1 - Bacteriophage Sf6 Tailspike Protein for Detection of Shigella flexneri Pathogens T2 - Viruses N2 - Bacteriophage research is gaining more importance due to increasing antibiotic resistance. However, for treatment with bacteriophages, diagnostics have to be improved. Bacteriophages carry adhesion proteins, which bind to the bacterial cell surface, for example tailspike proteins (TSP) for specific recognition of bacterial O-antigen polysaccharide. TSP are highly stable proteins and thus might be suitable components for the integration into diagnostic tools. We used the TSP of bacteriophage Sf6 to establish two applications for detecting Shigella flexneri (S. flexneri), a highly contagious pathogen causing dysentery. We found that Sf6TSP not only bound O-antigen of S. flexneri serotype Y, but also the glucosylated O-antigen of serotype 2a. Moreover, mass spectrometry glycan analyses showed that Sf6TSP tolerated various O-acetyl modifications on these O-antigens. We established a microtiter plate-based ELISA like tailspike adsorption assay (ELITA) using a Strep-tag®II modified Sf6TSP. As sensitive screening alternative we produced a fluorescently labeled Sf6TSP via coupling to an environment sensitive dye. Binding of this probe to the S. flexneri O-antigen Y elicited a fluorescence intensity increase of 80% with an emission maximum in the visible light range. The Sf6TSP probes thus offer a promising route to a highly specific and sensitive bacteriophage TSP-based Shigella detection system. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 472 KW - Shigella flexneri KW - bacteriophage KW - tailspike proteins KW - O-antigen KW - serotyping KW - microtiter plate assay KW - fluorescence sensor Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-417831 ER - TY - GEN A1 - Nakamura, Moritaka A1 - Claes, Andrea R. A1 - Grebe, Tobias A1 - Hermkes, Rebecca A1 - Viotti, Corrado A1 - Ikeda, Yoshihisa A1 - Grebe, Markus T1 - Auxin and ROP GTPase signaling of polar nuclear migration in root epidermal hair cells T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Polar nuclear migration is crucial during the development of diverse eukaryotes. In plants, root hair growth requires polar nuclear migration into the outgrowing hair. However, knowledge about the dynamics and the regulatory mechanisms underlying nuclear movements in root epidermal cells remains limited. Here, we show that both auxin and Rho-of-Plant (ROP) signaling modulate polar nuclear position at the inner epidermal plasma membrane domain oriented to the cortical cells during cell elongation as well as subsequent polar nuclear movement to the outer domain into the emerging hair bulge in Arabidopsis (Arabidopsis thaliana). Auxin signaling via the nuclear AUXIN RESPONSE FACTOR7 (ARF7)/ARF19 and INDOLE ACETIC ACID7 pathway ensures correct nuclear placement toward the inner membrane domain. Moreover, precise inner nuclear placement relies on SPIKE1 Rho-GEF, SUPERCENTIPEDE1 Rho-GDI, and ACTIN7 (ACT7) function and to a lesser extent on VTI11 vacuolar SNARE activity. Strikingly, the directionality and/or velocity of outer polar nuclear migration into the hair outgrowth along actin strands also are ACT7 dependent, auxin sensitive, and regulated by ROP signaling. Thus, our findings provide a founding framework revealing auxin and ROP signaling of inner polar nuclear position with some contribution by vacuolar morphology and of actin-dependent outer polar nuclear migration in root epidermal hair cells. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 992 KW - Arabidopsis-thaliana KW - planar polarity KW - tip growth KW - morphogenesis KW - gene KW - proteins KW - dynamics KW - transformation KW - activation KW - initiation Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-441278 SN - 1866-8372 IS - 992 SP - 378 EP - 391 ER - TY - GEN A1 - Ziege, Madlen A1 - Mahlow, Kristin A1 - Hennige-Sulz, Carmen A1 - Kronmarck, Claudia A1 - Tiedemann, Ralph A1 - Streit, Bruno A1 - Plath, Martin T1 - Audience effects in the Atlantic molly (Poecilia mexicana) : prudent male mate choice in response to perceived sperm competition risk? N2 - Background: Multidirectional interactions in social networks can have a profound effect on mate choice behavior; e.g., Poecilia mexicana males show weaker expression of mating preferences when being observed by a rival. This may be an adaptation to reduce sperm competition risk, which arises because commonly preferred female phenotypes will receive attention also from surrounding males, and/or because other males can copy the focal male's mate choice. Do P. mexicana males indeed respond to perceived sperm competition risk? We gave males a choice between two females and repeated the tests under one of the following conditions: (1) an empty transparent cylinder was presented (control); (2) another ("audience") male inside the cylinder observed the focal male throughout the 2nd part, or (3) the audience male was presented only before the tests, but could not eavesdrop during the actual choice tests (non-specific sperm competition risk treatments); (4) the focal male could see a rival male interact sexually with the previously preferred, or (5) with the non-preferred female before the 2nd part of the tests (specific sperm competition risk treatments). Results: The strength of individual male preferences declined slightly also during the control treatment (1). However, this decrease was more than two-fold stronger in audience treatment (2), i.e., with non-specific sperm competition risk including the possibility for visual eavesdropping by the audience male. No audience effect was found in treatments (3) and (5), but a weak effect was also observed when the focal male had seen the previously preferred female sexually interact with a rival male (treatment 4; specific sperm competition risk). Conclusion: When comparing the two 'non-specific sperm competition risk' treatments, a very strong effect was found only when the audience male could actually observe the focal male during mate choice [treatment (2)]. This suggests that focal males indeed attempt to conceal their mating preferences so as to prevent surrounding males from copying their mate choice. When there is no potential for eavesdropping [treatment (3)], non-specific specific sperm competition risk seems to play a minor or no role. Our results also show that P. mexicana males tend to share their mating effort more equally among females when the resource value of their previously preferred mate decreases after mating with a rival male (perceived specific sperm competition risk), but this effect is comparatively weak. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 143 KW - Siamese fighting fish KW - Guppies poecilia-reticulata KW - Betta-splendens KW - Public information KW - Mating preferences Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45171 ER - TY - GEN A1 - Pawlak, Julia A1 - Noetzel, Dominique Christian A1 - Drago, Claudia A1 - Weithoff, Guntram T1 - Assessing the toxicity of polystyrene beads and silica particles on the microconsumer Brachionus calyciflorus at different timescales T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Environmental pollution by microplastics has become a severe problem in terrestrial and aquatic ecosystems and, according to actual prognoses, problems will further increase in the future. Therefore, assessing and quantifying the risk for the biota is crucial. Standardized short-term toxicological procedures as well as methods quantifying potential toxic effects over the whole life span of an animal are required. We studied the effect of the microplastic polystyrene on the survival and reproduction of a common freshwater invertebrate, the rotifer Brachionus calyciflorus, at different timescales. We used pristine polystyrene spheres of 1, 3, and 6 µm diameter and fed them to the animals together with food algae in different ratios ranging from 0 to 50% nonfood particles. As a particle control, we used silica to distinguish between a pure particle effect and a plastic effect. After 24 h, no toxic effect was found, neither with polystyrene nor with silica. After 96 h, a toxic effect was detectable for both particle types. The size of the particles played a negligible role. Studying the long-term effect by using life table experiments, we found a reduced reproduction when the animals were fed with 3 µm spheres together with similar-sized food algae. We conclude that the fitness reduction is mainly driven by the dilution of food by the nonfood particles rather than by a direct toxic effect. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1277 KW - microplastics KW - rotifer KW - freshwater KW - natural particle KW - toxicity KW - environmental pollution Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-569967 SN - 1866-8372 IS - 1277 SP - 1 EP - 11 ER - TY - GEN A1 - Roggenbuck, Dirk A1 - Borghi, Maria Orietta A1 - Somma, Valentina A1 - Büttner, Thomas A1 - Schierack, Peter A1 - Hanack, Katja A1 - Grossi, Claudia A1 - Bodio, Caterina A1 - Macor, Paolo A1 - von Landenberg, Philipp A1 - Boccellato, Francesco A1 - Mahler, Michael A1 - Meroni, Pier Luigi T1 - Antiphospholipid antibodies detected by line immunoassay differentiate among patients with antiphospholipid syndrome, with infections and asymptomatic carriers T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Background Antiphospholipid antibodies (aPL) can be detected in asymptomatic carriers and infectious patients. The aim was to investigate whether a novel line immunoassay (LIA) differentiates between antiphospholipid syndrome (APS) and asymptomatic aPL+ carriers or patients with infectious diseases (infectious diseases controls (IDC)). Methods Sixty-one patients with APS (56 primary, 22/56 with obstetric events only, and 5 secondary), 146 controls including 24 aPL+ asymptomatic carriers and 73 IDC were tested on a novel hydrophobic solid phase coated with cardiolipin (CL), phosphatic acid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylserine, beta2-glycoprotein I (β2GPI), prothrombin, and annexin V. Samples were also tested by anti-CL and anti-β2GPI ELISAs and for lupus anticoagulant activity. Human monoclonal antibodies (humoAbs) against human β2GPI or PL alone were tested on the same LIA substrates in the absence or presence of human serum, purified human β2GPI or after CL-micelle absorption. Results Comparison of LIA with the aPL-classification assays revealed good agreement for IgG/IgM aß2GPI and aCL. Anti-CL and anti-ß2GPI IgG/IgM reactivity assessed by LIA was significantly higher in patients with APS versus healthy controls and IDCs, as detected by ELISA. IgG binding to CL and ß2GPI in the LIA was significantly lower in aPL+ carriers and Venereal Disease Research Laboratory test (VDRL) + samples than in patients with APS. HumoAb against domain 1 recognized β2GPI bound to the LIA-matrix and in anionic phospholipid (PL) complexes. Absorption with CL micelles abolished the reactivity of a PL-specific humoAb but did not affect the binding of anti-β2GPI humoAbs. Conclusions The LIA and ELISA have good agreement in detecting aPL in APS, but the LIA differentiates patients with APS from infectious patients and asymptomatic carriers, likely through the exposure of domain 1. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 436 KW - Antiphospholipid syndrome KW - Antiphospholipid antibody KW - Phospholipid binding proteins KW - Beta2 - glycoprotein I KW - Line immunoassay Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407211 SN - 1866-8372 IS - 436 ER - TY - GEN A1 - Ilicic, Doris A1 - Woodhouse, Jason A1 - Karsten, Ulf A1 - Zimmermann, Jonas A1 - Wichard, Thomas A1 - Quartino, Maria Liliana A1 - Campana, Gabriela Laura A1 - Livenets, Alexandra A1 - Van den Wyngaert, Silke A1 - Grossart, Hans-Peter T1 - Antarctic Glacial Meltwater Impacts the Diversity of Fungal Parasites Associated With Benthic Diatoms in Shallow Coastal Zones T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Aquatic ecosystems are frequently overlooked as fungal habitats, although there is increasing evidence that their diversity and ecological importance are greater than previously considered. Aquatic fungi are critical and abundant components of nutrient cycling and food web dynamics, e.g., exerting top-down control on phytoplankton communities and forming symbioses with many marine microorganisms. However, their relevance for microphytobenthic communities is almost unexplored. In the light of global warming, polar regions face extreme changes in abiotic factors with a severe impact on biodiversity and ecosystem functioning. Therefore, this study aimed to describe, for the first time, fungal diversity in Antarctic benthic habitats along the salinity gradient and to determine the co-occurrence of fungal parasites with their algal hosts, which were dominated by benthic diatoms. Our results reveal that Ascomycota and Chytridiomycota are the most abundant fungal taxa in these habitats. We show that also in Antarctic waters, salinity has a major impact on shaping not just fungal but rather the whole eukaryotic community composition, with a diversity of aquatic fungi increasing as salinity decreases. Moreover, we determined correlations between putative fungal parasites and potential benthic diatom hosts, highlighting the need for further systematic analysis of fungal diversity along with studies on taxonomy and ecological roles of Chytridiomycota. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1290 KW - Antarctica KW - aquatic fungi KW - Chytridiomycota KW - phytoplankton host KW - salinity gradient KW - Illumina amplicon sequencing KW - Carlini Station Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-572895 SN - 1866-8372 IS - 1290 ER - TY - GEN A1 - Hartmann, Stefanie A1 - Preick, Michaela A1 - Abelt, Silke A1 - Scheffel, André A1 - Hofreiter, Michael T1 - Annotated genome sequences of the carnivorous plant Roridula gorgonias and a non-carnivorous relative, Clethra arborea T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Objective Plant carnivory is distributed across the tree of life and has evolved at least six times independently, but sequenced and annotated nuclear genomes of carnivorous plants are currently lacking. We have sequenced and structurally annotated the nuclear genome of the carnivorous Roridula gorgonias and that of a non-carnivorous relative, Madeira’s lily-of-the-valley-tree, Clethra arborea, both within the Ericales. This data adds an important resource to study the evolutionary genetics of plant carnivory across angiosperm lineages and also for functional and systematic aspects of plants within the Ericales. Results Our assemblies have total lengths of 284 Mbp (R. gorgonias) and 511 Mbp (C. arborea) and show high BUSCO scores of 84.2% and 89.5%, respectively. We used their predicted genes together with publicly available data from other Ericales’ genomes and transcriptomes to assemble a phylogenomic data set for the inference of a species tree. However, groups of orthologs showed a marked absence of species represented by a transcriptome. We discuss possible reasons and caution against combining predicted genes from genome- and transriptome-based assemblies. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1141 KW - Carnivorous plant KW - Roridula gorgonias KW - Clethra arborea KW - Genome assembly KW - Transcriptome assembly KW - Phylogenomics KW - Orthologous Matrix (OMA) Project Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-503752 SN - 1866-8372 ER - TY - GEN A1 - Paijmans, Johanna L. A. A1 - Barlow, Axel A1 - Henneberger, Kirstin A1 - Fickel, Jörns A1 - Hofreiter, Michael A1 - Foerste, Daniel W. G. T1 - Ancestral mitogenome capture of the Southeast Asian banded linsang T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 972 KW - Shotgun sequencing KW - Mitochondria KW - Phylogenetics KW - Phylogenetic analysis KW - Paleogenetics KW - Sequence alignment KW - Genomics KW - Museum collections Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-474441 SN - 1866-8372 IS - 972 ER - TY - GEN A1 - Blenau, Wolfgang A1 - Mustard, Julie A. A1 - Hamilton, Ingrid S. A1 - Ward, Vernon K. A1 - Ebert, Paul R. A1 - Mercer, Alison R. T1 - Analysis of two D1-like dopamine receptors from the honey bee Apis mellifera reveals agonist-independent activity N2 - Dopamine is found in many invertebrate organisms, including insects, however, the mechanisms through which this amine operates remain unclear. We have expressed two dopamine receptors cloned from honey bee (AmDOP1 and AmDOP2) in insect cells (Spodoptera frugiperda), and compared their pharmacology directly using production of cAMP as a functional assay. In each assay, AmDOP1 receptors required lower concentrations of dopamine and 6,7-ADTN for maximal activation than AmDOP2 receptors. Conversely, butaclamol and cis(Z)-flupentixol were more potent at blocking the cAMP response mediated through AmDOP2 than AmDOP1 receptors. Expression of AmDOP1, but not AmDOP2, receptors significantly increased levels of cAMP even in the absence of ligand. This constitutive activity was blocked by cis(Z)-flupentixol. This work provides the first evidence of a constitutively activated dopamine receptor in invertebrates and suggests that although AmDOP1 and AmDOP2 share much less homology than their vertebrate counterparts, they display a number of functional parallels with the mammalian D1-like dopamine receptors. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 109 KW - G protein-coupled receptor KW - Biogenic amine KW - Invertebrate KW - cAMP KW - Baculovirus Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44378 ER - TY - GEN A1 - He, Hai A1 - Höper, Rune A1 - Dodenhöft, Moritz A1 - Marlière, Philippe A1 - Bar-Even, Arren T1 - An optimized methanol assimilation pathway relying on promiscuous formaldehyde-condensing aldolases in E. coli T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Engineering biotechnological microorganisms to use methanol as a feedstock for bioproduction is a major goal for the synthetic metabolism community. Here, we aim to redesign the natural serine cycle for implementation in E. coli. We propose the homoserine cycle, relying on two promiscuous formaldehyde aldolase reactions, as a superior pathway design. The homoserine cycle is expected to outperform the serine cycle and its variants with respect to biomass yield, thermodynamic favorability, and integration with host endogenous metabolism. Even as compared to the RuMP cycle, the most efficient naturally occurring methanol assimilation route, the homoserine cycle is expected to support higher yields of a wide array of products. We test the in vivo feasibility of the homoserine cycle by constructing several E. coli gene deletion strains whose growth is coupled to the activity of different pathway segments. Using this approach, we demonstrate that all required promiscuous enzymes are active enough to enable growth of the auxotrophic strains. Our findings thus identify a novel metabolic solution that opens the way to an optimized methylotrophic platform. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 997 KW - Pathway design KW - Promiscuous enzymes KW - Formaldehyde assimilation KW - Serine cycle KW - Growth selection Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-476452 SN - 1866-8372 IS - 997 SP - 1 EP - 13 ER - TY - GEN A1 - Blenau, Wolfgang A1 - Baumann, Arnd T1 - Aminergic signal transduction in invertebrates : focus on tyramine and octopamine receptors N2 - Electro-chemical signal transduction is the basis of communication between n eurons and their target cells. An important group of neuroactive substances that are released by action potentials from neurons are the biogenic amines. These a re small organic molecules that bind to specific receptors located in the target cell membrane. Once activated these receptors cause changes in the intracellula r concentration of second messengers, i.e. cyclic nucleotides, phosphoinositides , or Ca2+, leading to slow but long-lasting cellular responses. Biochemical, pha rmacological, physiological, and molecular biological approaches have unequivoca lly shown that biogenic amines are important regulators of cellular function in both vertebrates and invertebrates. In this review, we will concentrate on the p roperties of two biogenic amines and their receptors that were originally identi fied in invertebrates: tyramine and octopamine.  T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 107 Y1 - 2003 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44271 ER - TY - GEN A1 - Scheiner, Ricarda A1 - Baumann, Arnd A1 - Blenau, Wolfgang T1 - Aminergic control and modulation of honeybee behaviour N2 - Biogenic amines are important messenger substances in the central nervous system and in peripheral organs of vertebrates and of invertebrates. The honeybee, Apis mellifera, is excellently suited to uncover the functions of biogenic amines in behaviour, because it has an extensive behavioural repertoire, with a number of biogenic amine receptors characterised in this insect. In the honeybee, the biogenic amines dopamine, octopamine, serotonin and tyramine modulate neuronal functions in various ways. Dopamine and serotonin are present in high concentrations in the bee brain, whereas octopamine and tyramine are less abundant. Octopamine is a key molecule for the control of honeybee behaviour. It generally has an arousing effect and leads to higher sensitivity for sensory inputs, better learning performance and increased foraging behaviour. Tyramine has been suggested to act antagonistically to octopamine, but only few experimental data are available for this amine. Dopamine and serotonin often have antagonistic or inhibitory effects as compared to octopamine. Biogenic amines bind to membrane receptors that primarily belong to the large gene-family of GTP-binding (G) protein coupled receptors. Receptor activation leads to transient changes in concentrations of intracellular second messengers such as cAMP, IP3 and/or Ca2+. Although several biogenic amine receptors from the honeybee have been cloned and characterised more recently, many genes still remain to be identified. The availability of the completely sequenced genome of Apis mellifera will contribute substantially to closing this gap. In this review, we will discuss the present knowledge on how biogenic amines and their receptor-mediated cellular responses modulate different behaviours of honeybees including learning processes and division of labour. KW - Serotonin KW - dopamine KW - octopamine KW - tyramine KW - honeybee Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-46106 ER - TY - GEN A1 - Schlenstedt, Jana A1 - Balfanz, Sabine A1 - Baumann, Arnd A1 - Blenau, Wolfgang T1 - Am5-HT7 : molecular and pharmacological characterization of the first serotonin receptor of the honeybee (Apis mellifera) N2 - The biogenic amine serotonin (5-HT) plays a key role in the regulation and modulation of many physiological and behavioural processes in both vertebrates and invertebrates. These functions are mediated through the binding of serotonin to its receptors, of which 13 subtypes have been characterized in vertebrates. We have isolated a cDNA from the honeybee Apis mellifera (Am5-ht7) sharing high similarity to members of the 5-HT7 receptor family. Expression of the Am5-HT7 receptor in HEK293 cells results in an increase in basal cAMP levels, suggesting that Am5-HT7 is expressed as a constitutively active receptor. Serotonin application to Am5-ht7-transfected cells elevates cyclic adenosine 3',5'-monophosphate (cAMP) levels in a dose-dependent manner (EC50 = 1.1-1.8 nM). The Am5-HT7 receptor is also activated by 5-carboxamidotryptamine, whereas methiothepin acts as an inverse agonist. Receptor expression has been investigated by RT-PCR, in situ hybridization, and western blotting experiments. Receptor mRNA is expressed in the perikarya of various brain neuropils, including intrinsic mushroom body neurons, and in peripheral organs. This study marks the first comprehensive characterization of a serotonin receptor in the honeybee and should facilitate further analysis of the role(s) of the receptor in mediating the various central and peripheral effects of 5-HT. KW - Behaviour KW - biogenic amine KW - cellular signalling KW - constitutive activity KW - cyclic AMP Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44423 ER - TY - GEN A1 - Zhu, Fangjun A1 - Schlupp, Ingo A1 - Tiedemann, Ralph T1 - Allele-specific expression at the androgen receptor alpha gene in a hybrid unisexual fish, the Amazon molly (Poecilia formosa) N2 - The all-female Amazon molly (Poecilia formosa) is the result of a hybridization of the Atlantic molly (P. mexicana) and the sailfin molly (P. latipinna) approximately 120,000 years ago. As a gynogenetic species, P. formosa needs to copulate with heterospecific males including males from one of its bisexual ancestral species. However, the sperm only triggers embryogenesis of the diploid eggs. The genetic information of the sperm donor typically will not contribute to the next generation of P. formosa. Hence, P. formosa possesses generally one allele from each of its ancestral species at any genetic locus. This raises the question whether both ancestral alleles are equally expressed in P. formosa. Allele-specific expression (ASE) has been previously assessed in various organisms, e.g., human and fish, and ASE was found to be important in the context of phenotypic variability and disease. In this study, we utilized Real-Time PCR techniques to estimate ASE of the androgen receptor alpha (arα) gene in several distinct tissues of Amazon mollies. We found an allelic bias favoring the maternal ancestor (P. mexicana) allele in ovarian tissue. This allelic bias was not observed in the gill or the brain tissue. Sequencing of the promoter regions of both alleles revealed an association between an Indel in a known CpG island and differential expression. Future studies may reveal whether our observed cis-regulatory divergence is caused by an ovary-specific trans-regulatory element, preferentially activating the allele of the maternal ancestor. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 395 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-403875 ER - TY - GEN A1 - Reeg, Jette A1 - Strigl, Lea A1 - Jeltsch, Florian T1 - Agricultural buffer zone thresholds to safeguard functional bee diversity: Insights from a community modeling approach T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Wild bee species are important pollinators in agricultural landscapes. However, population decline was reported over the last decades and is still ongoing. While agricultural intensification is a major driver of the rapid loss of pollinating species, transition zones between arable fields and forest or grassland patches, i.e., agricultural buffer zones, are frequently mentioned as suitable mitigation measures to support wild bee populations and other pollinator species. Despite the reported general positive effect, it remains unclear which amount of buffer zones is needed to ensure a sustainable and permanent impact for enhancing bee diversity and abundance. To address this question at a pollinator community level, we implemented a process-based, spatially explicit simulation model of functional bee diversity dynamics in an agricultural landscape. More specifically, we introduced a variable amount of agricultural buffer zones (ABZs) at the transition of arable to grassland, or arable to forest patches to analyze the impact on bee functional diversity and functional richness. We focused our study on solitary bees in a typical agricultural area in the Northeast of Germany. Our results showed positive effects with at least 25% of virtually implemented agricultural buffer zones. However, higher amounts of ABZs of at least 75% should be considered to ensure a sufficient increase in Shannon diversity and decrease in quasi-extinction risks. These high amounts of ABZs represent effective conservation measures to safeguard the stability of pollination services provided by solitary bee species. As the model structure can be easily adapted to other mobile species in agricultural landscapes, our community approach offers the chance to compare the effectiveness of conservation measures also for other pollinator communities in future. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1281 KW - agricultural landscape KW - buffer zones KW - community model KW - functional traits KW - solitary bees KW - spatially explicit Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-570800 SN - 1866-8372 IS - 1281 ER - TY - GEN A1 - Romero-Mujalli, Daniel A1 - Rochow, Markus A1 - Kahl, Sandra M. A1 - Paraskevopoulou, Sofia A1 - Folkertsma, Remco A1 - Jeltsch, Florian A1 - Tiedemann, Ralph T1 - Adaptive and nonadaptive plasticity in changing environments: Implications for sexual species with different life history strategies T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Populations adapt to novel environmental conditions by genetic changes or phenotypic plasticity. Plastic responses are generally faster and can buffer fitness losses under variable conditions. Plasticity is typically modeled as random noise and linear reaction norms that assume simple one-to- one genotype–phenotype maps and no limits to the phenotypic response. Most studies on plasticity have focused on its effect on population viability. However, it is not clear, whether the advantage of plasticity depends solely on environmental fluctuations or also on the genetic and demographic properties (life histories) of populations. Here we present an individual-based model and study the relative importance of adaptive and nonadaptive plasticity for populations of sexual species with different life histories experiencing directional stochastic climate change. Environmental fluctuations were simulated using differentially autocorrelated climatic stochasticity or noise color, and scenarios of directiona climate change. Nonadaptive plasticity was simulated as a random environmental effect on trait development, while adaptive plasticity as a linear, saturating, or sinusoidal reaction norm. The last two imposed limits to the plastic response and emphasized flexible interactions of the genotype with the environment. Interestingly, this assumption led to (a) smaller phenotypic than genotypic variance in the population (many-to- one genotype–phenotype map) and the coexistence of polymorphisms, and (b) the maintenance of higher genetic variation—compared to linear reaction norms and genetic determinism—even when the population was exposed to a constant environment for several generations. Limits to plasticity led to genetic accommodation, when costs were negligible, and to the appearance of cryptic variation when limits were exceeded. We found that adaptive plasticity promoted population persistence under red environmental noise and was particularly important for life histories with low fecundity. Populations produing more offspring could cope with environmental fluctuations solely by genetic changes or random plasticity, unless environmental change was too fast. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1170 KW - developmental canalization KW - environmental change KW - genetic accommodation KW - Individual-based models KW - limits KW - many-to-one genotype–phenotype map KW - noise color KW - phenotypic plasticity KW - reaction norms KW - stochastic fluctuations Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523201 SN - 1866-8372 IS - 1170 ER - TY - GEN A1 - Hoffmann, Stefan A. A1 - Wohltat, Christian A1 - Müller, Kristian M. A1 - Arndt, Katja Maren T1 - A user-friendly, low-cost turbidostat with versatile growth rate estimation based on an extended Kalman filter N2 - For various experimental applications, microbial cultures at defined, constant densities are highly advantageous over simple batch cultures. Due to high costs, however, devices for continuous culture at freely defined densities still experience limited use. We have developed a small-scale turbidostat for research purposes, which is manufactured from inexpensive components and 3D printed parts. A high degree of spatial system integration and a graphical user interface provide user-friendly operability. The used optical density feedback control allows for constant continuous culture at a wide range of densities and offers to vary culture volume and dilution rates without additional parametrization. Further, a recursive algorithm for on-line growth rate estimation has been implemented. The employed Kalman filtering approach based on a very general state model retains the flexibility of the used control type and can be easily adapted to other bioreactor designs. Within several minutes it can converge to robust, accurate growth rate estimates. This is particularly useful for directed evolution experiments or studies on metabolic challenges, as it allows direct monitoring of the population fitness. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 390 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-403406 ER - TY - GEN A1 - Cao, Xianyong A1 - Tian, Fang A1 - Andreev, Andrei A1 - Anderson, Patricia M. A1 - Lozhkin, Anatoly V. A1 - Bezrukova, Elena A1 - Ni, Jian A1 - Rudaya, Natalia A1 - Stobbe, Astrid A1 - Wieczorek, Mareike A1 - Herzschuh, Ulrike T1 - A taxonomically harmonized and temporally standardized fossil pollen dataset from Siberia covering the last 40 kyr T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Pollen records from Siberia are mostly absent in global or Northern Hemisphere synthesis works. Here we present a taxonomically harmonized and temporally standardized pollen dataset that was synthesized using 173 palynological records from Siberia and adjacent areas (northeastern Asia, 42-75 degrees N, 50-180 degrees E). Pollen data were taxonomically harmonized, i.e. the original 437 taxa were assigned to 106 combined pollen taxa. Age-depth models for all records were revised by applying a constant Bayesian age-depth modelling routine. The pollen dataset is available as count data and percentage data in a table format (taxa vs. samples), with age information for each sample. The dataset has relatively few sites covering the last glacial period between 40 and 11.5 ka (calibrated thousands of years before 1950 CE) particularly from the central and western part of the study area. In the Holocene period, the dataset has many sites from most of the area, with the exception of the central part of Siberia. Of the 173 pollen records, 81 % of pollen counts were downloaded from open databases (GPD, EPD, PANGAEA) and 10 % were contributions by the original data gatherers, while a few were digitized from publications. Most of the pollen records originate from peatlands (48 %) and lake sediments (33 %). Most of the records (83 %) have >= 3 dates, allowing the establishment of reliable chronologies. The dataset can be used for various purposes, including pollen data mapping (example maps for Larix at selected time slices are shown) as well as quantitative climate and vegetation reconstructions. The datasets for pollen counts and pollen percentages are available at https://doi.org/10.1594/PANGAEA.898616 (Cao et al., 2019a), also including the site information, data source, original publication, dating data, and the plant functional type for each pollen taxa. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1427 KW - Late Quaternary vegetation KW - Holocene environmental history KW - eastern continental Asia KW - plant macrofossil data KW - late pleistocene KW - paleoenvironmental records KW - Verkhoyansk mountains KW - climate dynamics KW - glacial maximum KW - Northern Asia Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-512438 SN - 1866-8372 IS - 1 ER - TY - GEN A1 - Rojas-Jimenez, Keilor A1 - Rieck, Angelika A1 - Wurzbacher, Christian A1 - Jürgens, Klaus A1 - Labrenz, Matthias A1 - Grossart, Hans-Peter T1 - A Salinity Threshold Separating Fungal Communities in the Baltic Sea T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Salinity is a significant factor for structuring microbial communities, but little is known for aquatic fungi, particularly in the pelagic zone of brackish ecosystems. In this study, we explored the diversity and composition of fungal communities following a progressive salinity decline (from 34 to 3 PSU) along three transects of ca. 2000 km in the Baltic Sea, the world’s largest estuary. Based on 18S rRNA gene sequence analysis, we detected clear changes in fungal community composition along the salinity gradient and found significant differences in composition of fungal communities established above and below a critical value of 8 PSU. At salinities below this threshold, fungal communities resembled those from freshwater environments, with a greater abundance of Chytridiomycota, particularly of the orders Rhizophydiales, Lobulomycetales, and Gromochytriales. At salinities above 8 PSU, communities were more similar to those from marine environments and, depending on the season, were dominated by a strain of the LKM11 group (Cryptomycota) or by members of Ascomycota and Basidiomycota. Our results highlight salinity as an important environmental driver also for pelagic fungi, and thus should be taken into account to better understand fungal diversity and ecological function in the aquatic realm. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 739 KW - fungal diversity KW - baltic sea KW - salinity gradient KW - brackish waters KW - chytridiomycota KW - cryptomycota Y1 - 1019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-434937 SN - 1866-8372 IS - 739 ER - TY - GEN A1 - Blenau, Wolfgang A1 - Hauser, Frank A1 - Cazzamali, Giuseppe A1 - Williamson, Michael A1 - Grimmelikhuijzen, Cornelis J. P. T1 - A review of neurohormone GPCRs present in the fruitfly Drosophila melanogaster and the honey bee Apis mellifera N2 - G protein-coupled receptor (GPCR) genes are large gene families in every animal, sometimes making up to 1-2% of the animal's genome. Of all insect GPCRs, the neurohormone (neuropeptide, protein hormone, biogenic amine) GPCRs are especially important, because they, together with their ligands, occupy a high hierarchic position in the physiology of insects and steer crucial processes such as development, reproduction, and behavior. In this paper, we give a review of our current knowledge on Drosophila melanogaster GPCRs and use this information to annotate the neurohormone GPCR genes present in the recently sequenced genome from the honey bee Apis mellifera. We found 35 neuropeptide receptor genes in the honey bee (44 in Drosophila) and two genes, coding for leucine-rich repeats-containing protein hormone GPCRs (4 in Drosophila). In addition, the honey bee has 19 biogenic amine receptor genes (21 in Drosophila). The larger numbers of neurohormone receptors in Drosophila are probably due to gene duplications that occurred during recent evolution of the fly. Our analyses also yielded the likely ligands for 40 of the 56 honey bee neurohormone GPCRs identified in this study. In addition, we made some interesting observations on neurohormone GPCR evolution and the evolution and co-evolution of their ligands. For neuropeptide and protein hormone GPCRs, there appears to be a general co-evolution between receptors and their ligands. This is in contrast to biogenic amine GPCRs, where evolutionarily unrelated GPCRs often bind to the same biogenic amine, suggesting frequent ligand exchanges ("ligand hops") during GPCR evolution. (c) 2006 Elsevier Ltd. All rights reserved. KW - GPCR KW - neuropeptide KW - neurohormone KW - hormone KW - biogenic amine Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44326 ER - TY - GEN A1 - Spikes, Montrai A1 - Rodríguez-Silva, Rodet A1 - Bennett, Kerri-Ann A1 - Bräger, Stefan A1 - Josaphat, James A1 - Torres-Pineda, Patricia A1 - Ernst, Anja A1 - Havenstein, Katja A1 - Schlupp, Ingo A1 - Tiedemann, Ralph T1 - A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Objective The Caribbean is an important global biodiversity hotspot. Adaptive radiations there lead to many speciation events within a limited period and hence are particularly prominent biodiversity generators. A prime example are freshwater fish of the genus Limia, endemic to the Greater Antilles. Within Hispaniola, nine species have been described from a single isolated site, Lake Miragoâne, pointing towards extraordinary sympatric speciation. This study examines the evolutionary history of the Limia species in Lake Miragoâne, relative to their congeners throughout the Caribbean. Results For 12 Limia species, we obtained almost complete sequences of the mitochondrial cytochrome b gene, a well-established marker for lower-level taxonomic relationships. We included sequences of six further Limia species from GenBank (total N  = 18 species). Our phylogenies are in concordance with other published phylogenies of Limia. There is strong support that the species found in Lake Miragoâne in Haiti are monophyletic, confirming a recent local radiation. Within Lake Miragoâne, speciation is likely extremely recent, leading to incomplete lineage sorting in the mtDNA. Future studies using multiple unlinked genetic markers are needed to disentangle the relationships within the Lake Miragoâne clade. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1238 KW - Cytochrome b KW - Island biogeography KW - Fresh water fish KW - Phylogeny Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-548882 SN - 1866-8372 SP - 1 EP - 8 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - GEN A1 - Göthel, Markus A1 - Listek, Martin A1 - Messerschmidt, Katrin A1 - Schlör, Anja A1 - Hönow, Anja A1 - Hanack, Katja T1 - A New Workflow to Generate Monoclonal Antibodies against Microorganisms T2 - Mathematisch-Naturwissenschaftliche Reihe N2 - Monoclonal antibodies are used worldwide as highly potent and efficient detection reagents for research and diagnostic applications. Nevertheless, the specific targeting of complex antigens such as whole microorganisms remains a challenge. To provide a comprehensive workflow, we combined bioinformatic analyses with novel immunization and selection tools to design monoclonal antibodies for the detection of whole microorganisms. In our initial study, we used the human pathogenic strain E. coli O157:H7 as a model target and identified 53 potential protein candidates by using reverse vaccinology methodology. Five different peptide epitopes were selected for immunization using epitope-engineered viral proteins. The identification of antibody-producing hybridomas was performed by using a novel screening technology based on transgenic fusion cell lines. Using an artificial cell surface receptor expressed by all hybridomas, the desired antigen-specific cells can be sorted fast and efficiently out of the fusion cell pool. Selected antibody candidates were characterized and showed strong binding to the target strain E. coli O157:H7 with minor or no cross-reactivity to other relevant microorganisms such as Legionella pneumophila and Bacillus ssp. This approach could be useful as a highly efficient workflow for the generation of antibodies against microorganisms. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1174 KW - monoclonal antibody KW - antibody producing cell selection KW - hybridoma KW - epitope prediction Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523341 SN - 1866-8372 IS - 20 ER - TY - GEN A1 - Obbard, Darren J. A1 - Shi, Mang A1 - Roberts, Katherine E. A1 - Longdon, Ben A1 - Dennis, Alice B. T1 - A new lineage of segmented RNA viruses infecting animals T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1411 KW - metagenome KW - RNA virus KW - dark virus KW - arthropod KW - RNA interference Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-516040 SN - 1866-8372 IS - 1 ER - TY - GEN A1 - Schittko, Conrad A1 - Bernard-Verdier, Maud A1 - Heger, Tina A1 - Buchholz, Sascha A1 - Kowarik, Ingo A1 - von der Lippe, Moritz A1 - Seitz, Birgit A1 - Joshi, Jasmin Radha A1 - Jeschke, Jonathan M. T1 - A multidimensional framework for measuring biotic novelty: How novel is a community? T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Anthropogenic changes in climate, land use, and disturbance regimes, as well as introductions of non-native species can lead to the transformation of many ecosystems. The resulting novel ecosystems are usually characterized by species assemblages that have not occurred previously in a given area. Quantifying the ecological novelty of communities (i.e., biotic novelty) would enhance the understanding of environmental change. However, quantification remains challenging since current novelty metrics, such as the number and/or proportion of non-native species in a community, fall short of considering both functional and evolutionary aspects of biotic novelty. Here, we propose the Biotic Novelty Index (BNI), an intuitive and flexible multidimensional measure that combines (a) functional differences between native and non-native introduced species with (b) temporal dynamics of species introductions. We show that the BNI is an additive partition of Rao's quadratic entropy, capturing the novel interaction component of the community's functional diversity. Simulations show that the index varies predictably with the relative amount of functional novelty added by recently arrived species, and they illustrate the need to provide an additional standardized version of the index. We present a detailed R code and two applications of the BNI by (a) measuring changes of biotic novelty of dry grassland plant communities along an urbanization gradient in a metropolitan region and (b) determining the biotic novelty of plant species assemblages at a national scale. The results illustrate the applicability of the index across scales and its flexibility in the use of data of different quality. Both case studies revealed strong connections between biotic novelty and increasing urbanization, a measure of abiotic novelty. We conclude that the BNI framework may help building a basis for better understanding the ecological and evolutionary consequences of global change. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1209 KW - alien species KW - biological invasions KW - coexistence KW - ecological novelty KW - functional diversity KW - novel ecosystems KW - novel species KW - standard metrics Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-525657 SN - 1866-8372 IS - 8 ER - TY - GEN A1 - Krupinski, Pawel A1 - Bozorg, Behruz A1 - Larsson, André A1 - Pietra, Stefano A1 - Grebe, Markus A1 - Jönsson, Henrik T1 - A model analysis of mechanisms for radial microtubular patterns at root hair initiation sites T2 - Frontiers in plant science N2 - Plant cells have two main modes of growth generating anisotropic structures. Diffuse growth where whole cell walls extend in specific directions, guided by anisotropically positioned cellulose fibers, and tip growth, with inhomogeneous addition of new cell wall material at the tip of the structure. Cells are known to regulate these processes via molecular signals and the cytoskeleton. Mechanical stress has been proposed to provide an input to the positioning of the cellulose fibers via cortical microtubules in diffuse growth. In particular, a stress feedback model predicts a circumferential pattern of fibers surrounding apical tissues and growing primordia, guided by the anisotropic curvature in such tissues. In contrast, during the initiation of tip growing root hairs, a star-like radial pattern has recently been observed. Here, we use detailed finite element models to analyze how a change in mechanical properties at the root hair initiation site can lead to star-like stress patterns in order to understand whether a stress-based feedback model can also explain the microtubule patterns seen during root hair initiation. We show that two independent mechanisms, individually or combined, can be sufficient to generate radial patterns. In the first, new material is added locally at the position of the root hair. In the second, increased tension in the initiation area provides a mechanism. Finally, we describe how a molecular model of Rho-of-plant (ROP) GTPases activation driven by auxin can position a patch of activated ROP protein basally along a 2D root epidermal cell plasma membrane, paving the way for models where mechanical and molecular mechanisms cooperate in the initial placement and outgrowth of root hairs. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 435 KW - plant cell wall KW - finite element modeling KW - computational morphodynamics KW - root hair initiation KW - microtubules KW - cellulose fibers KW - composite material Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407181 ER - TY - GEN A1 - Cox, Tom A1 - Maris, Tom A1 - Soetart, Karline A1 - Conley, Daniel A1 - van Damme, Stefan A1 - Meire, Patrick A1 - Middelburg, Jack J. A1 - Vos, Matthijs A1 - Struyf, Eric T1 - A macro-tidal freshwater ecosystem recovering from hypereutrophication : the Schelde lease study N2 - We report a 40 year record of eutrophication and hypoxia on an estuarine ecosystem and its recovery from hypereutrophication. After decades of high inorganic nutrient concentrations and recurring anoxia and hypoxia, we observe a paradoxical increase in chlorophyll-a concentrations with decreasing nutrient inputs. We hypothesise that algal growth was inhibited due to hypereutrophication, either by elevated ammonium concentrations, severe hypoxia or the production of harmful substances in such a reduced environment. We study the dynamics of a simple but realistic mathematical model, incorporating the assumption of algal growth inhibition. It shows a high algal biomass, net oxygen production equilibrium with low ammonia inputs, and a low algal biomass, net oxygen consumption equilibrium with high ammonia inputs. At intermediate ammonia inputs it displays two alternative stable states. Although not intentional, the numerical output of this model corresponds to observations, giving extra support for assumption of algal growth inhibition. Due to potential algal growth inhibition, the recovery of hypereutrophied systems towards a classical eutrophied state, will need reduction of waste loads below certain thresholds and will be accompanied by large fluctuations in oxygen concentrations. We conclude that also flow-through systems, heavily influenced by external forcings which partly mask internal system dynamics, can display multiple stable states. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 144 KW - Estuary SW Netherlands KW - southern North-Sea KW - Past 50 years KW - Westerschelde estuary KW - Marine ecosystems Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45180 ER - TY - GEN A1 - Jantzen, Friederike A1 - Wozniak, Natalia Joanna A1 - Kappel, Christian A1 - Sicard, Adrien A1 - Lenhard, Michael T1 - A high‑throughput amplicon‑based method for estimating outcrossing rates T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Background: The outcrossing rate is a key determinant of the population-genetic structure of species and their long-term evolutionary trajectories. However, determining the outcrossing rate using current methods based on PCRgenotyping individual offspring of focal plants for multiple polymorphic markers is laborious and time-consuming. Results: We have developed an amplicon-based, high-throughput enabled method for estimating the outcrossing rate and have applied this to an example of scented versus non-scented Capsella (Shepherd’s Purse) genotypes. Our results show that the method is able to robustly capture differences in outcrossing rates. They also highlight potential biases in the estimates resulting from differential haplotype sharing of the focal plants with the pollen-donor population at individual amplicons. Conclusions: This novel method for estimating outcrossing rates will allow determining this key population-genetic parameter with high-throughput across many genotypes in a population, enabling studies into the genetic determinants of successful pollinator attraction and outcrossing. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 745 KW - Outcrossing KW - Mixed mating KW - Outcrossing rate KW - Capsella KW - Amplicon sequencing Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-435657 SN - 1866-8372 IS - 745 ER - TY - GEN A1 - Dortay, Hakan A1 - Müller-Röber, Bernd T1 - A highly efficient pipeline for protein expression in Leishmania tarentolae using infrared fluorescence protein as marker N2 - Background: Leishmania tarentolae, a unicellular eukaryotic protozoan, has been established as a novel host for recombinant protein production in recent years. Current protocols for protein expression in Leishmania are, however, time consuming and require extensive lab work in order to identify well-expressing cell lines. Here we established an alternative protein expression work-flow that employs recently engineered infrared fluorescence protein (IFP) as a suitable and easy-to-handle reporter protein for recombinant protein expression in Leishmania. As model proteins we tested three proteins from the plant Arabidopsis thaliana, including a NAC and a type-B ARR transcription factor. Results: IFP and IFP fusion proteins were expressed in Leishmania and rapidly detected in cells by deconvolution microscopy and in culture by infrared imaging of 96-well microtiter plates using small cell culture volumes (2 mu L - 100 mu L). Motility, shape and growth of Leishmania cells were not impaired by intracellular accumulation of IFP. In-cell detection of IFP and IFP fusion proteins was straightforward already at the beginning of the expression pipeline and thus allowed early pre-selection of well-expressing Leishmania clones. Furthermore, IFP fusion proteins retained infrared fluorescence after electrophoresis in denaturing SDS-polyacrylamide gels, allowing direct in-gel detection without the need to disassemble cast protein gels. Thus, parameters for scaling up protein production and streamlining purification routes can be easily optimized when employing IFP as reporter. Conclusions: Using IFP as biosensor we devised a protocol for rapid and convenient protein expression in Leishmania tarentolae. Our expression pipeline is superior to previously established methods in that it significantly reduces the hands-on-time and work load required for identifying well-expressing clones, refining protein production parameters and establishing purification protocols. The facile in-cell and in-gel detection tools built on IFP make Leishmania amenable for high-throughput expression of proteins from plant and animal sources. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 366 KW - System KW - Donovani Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400876 ER - TY - GEN A1 - Dortay, Hakan A1 - Müller-Röber, Bernd T1 - A highly efficient pipeline for protein expression in Leishmania tarentolae sing infrared fluorescence protein as marker N2 - Background: Leishmania tarentolae, a unicellular eukaryotic protozoan, has been established as a novel host for recombinant protein production in recent years. Current protocols for protein expression in Leishmania are, however, time consuming and require extensive lab work in order to identify well-expressing cell lines. Here we established an alternative protein expression work-flow that employs recently engineered infrared fluorescence protein (IFP) as a suitable and easy-to-handle reporter protein for recombinant protein expression in Leishmania. As model proteins we tested three proteins from the plant Arabidopsis thaliana, including a NAC and a type-B ARR transcription factor. Results: IFP and IFP fusion proteins were expressed in Leishmania and rapidly detected in cells by deconvolution microscopy and in culture by infrared imaging of 96-well microtiter plates using small cell culture volumes (2 μL - 100 μL). Motility, shape and growth of Leishmania cells were not impaired by intracellular accumulation of IFP. In-cell detection of IFP and IFP fusion proteins was straightforward already at the beginning of the expression pipeline and thus allowed early pre-selection of well-expressing Leishmania clones. Furthermore, IFP fusion proteins retained infrared fluorescence after electrophoresis in denaturing SDS-polyacrylamide gels, allowing direct in-gel detection without the need to disassemble cast protein gels. Thus, parameters for scaling up protein production and streamlining purification routes can be easily optimized when employing IFP as reporter. Conclusions: Using IFP as biosensor we devised a protocol for rapid and convenient protein expression in Leishmania tarentolae. Our expression pipeline is superior to previously established methods in that it significantly reduces the hands-on-time and work load required for identifying well-expressing clones, refining protein production parameters and establishing purification protocols. The facile in-cell and in-gel detection tools built on IFP make Leishmania amenable for high-throughput expression of proteins from plant and animal sources. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 122 KW - System KW - Donovani Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44773 ER - TY - GEN A1 - Zhang, Youjun A1 - Chen, Moxian A1 - Siemiatkowska, Beata A1 - Toleco, Mitchell Rey A1 - Jing, Yue A1 - Strotmann, Vivien A1 - Zhang, Jianghua A1 - Stahl, Yvonne A1 - Fernie, Alisdair R. T1 - A highly efficient agrobacterium-mediated method for transient gene expression and functional studies in multiple plant species T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used in species such as Nicotiana benthamiana for the rapid detection of gene expression and protein interaction analysis, but this technique does not work efficiently in other plant species, including Arabidopsis thaliana. As an efficient high-throughput transient expression system is currently lacking in the model plant species A. thaliana, we developed a method that is characterized by high efficiency, reproducibility, and suitability for transient expression of a variety of functional proteins in A. thaliana and 7 other plant species, including Brassica oleracea, Capsella rubella, Thellungiella salsuginea, Thellungiella halophila, Solanum tuberosum, Capsicum annuum, and N. benthamiana. Efficiency of this method was independently verified in three independent research facilities, pointing to the robustness of this technique. Furthermore, in addition to demonstrating the utility of this technique in a range of species, we also present a case study employing this method to assess protein-protein interactions in the sucrose biosynthesis pathway in Arabidopsis. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1189 KW - transient expression KW - agro-infiltration KW - subcellular localization KW - protein-protein interaction Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-524254 SN - 1866-8372 IS - 5 ER - TY - GEN A1 - Liaimer, Anton A1 - Jensen, John B. A1 - Dittmann-Thünemann, Elke T1 - A genetic and chemical perspective on symbiotic recruitment of cyanobacteria of the genus Nostoc into the host plant Blasia pusilla L. T2 - Frontiers in microbiology N2 - Liverwort Blasia pusilla L. recruits soil nitrogen-fixing cyanobacteria of genus Nostoc as symbiotic partners. In this work we compared Nostoc community composition inside the plants and in the soil around them from two distant locations in Northern Norway. STRR fingerprinting and 16S rDNA phylogeny reconstruction showed a remarkable local diversity among isolates assigned to several Nostoc clades. An extensive web of negative allelopathic interactions was recorded at an agricultural site, but not at the undisturbed natural site. The cell extracts of the cyanobacteria did not show antimicrobial activities, but four isolates were shown to be cytotoxic to human cells. The secondary metabolite profiles of the isolates were mapped by MALDI-TOF MS, and the most prominent ions were further analyzed by Q-TOF for MS/MS aided identification. Symbiotic isolates produced a great variety of small peptide-like substances, most of which lack any record in the databases. Among identified compounds we found microcystin and nodularin variants toxic to eukaryotic cells. Microcystin producing chemotypes were dominating as symbiotic recruits but not in the free-living community. In addition, we were able to identify several novel aeruginosins and banyaside-like compounds, as well as nostocyclopeptides and nosperin. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 434 KW - cyanobacteria KW - secondary metabolites KW - symbiosis KW - Blasia KW - Nostoc KW - allelopathy Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407179 ER - TY - GEN A1 - Wolff, Martin A1 - Gast, Klaus A1 - Evers, Andreas A1 - Kurz, Michael A1 - Pfeiffer-Marek, Stefania A1 - Schüler, Anja A1 - Seckler, Robert A1 - Thalhammer, Anja T1 - A Conserved Hydrophobic Moiety and Helix-Helix Interactions Drive the Self-Assembly of the Incretin Analog Exendin-4 T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Exendin-4 is a pharmaceutical peptide used in the control of insulin secretion. Structural information on exendin-4 and related peptides especially on the level of quaternary structure is scarce. We present the first published association equilibria of exendin-4 directly measured by static and dynamic light scattering. We show that exendin-4 oligomerization is pH dependent and that these oligomers are of low compactness. We relate our experimental results to a structural hypothesis to describe molecular details of exendin-4 oligomers. Discussion of the validity of this hypothesis is based on NMR, circular dichroism and fluorescence spectroscopy, and light scattering data on exendin-4 and a set of exendin-4 derived peptides. The essential forces driving oligomerization of exendin-4 are helix–helix interactions and interactions of a conserved hydrophobic moiety. Our structural hypothesis suggests that key interactions of exendin-4 monomers in the experimentally supported trimer take place between a defined helical segment and a hydrophobic triangle constituted by the Phe22 residues of the three monomeric subunits. Our data rationalize that Val19 might function as an anchor in the N-terminus of the interacting helix-region and that Trp25 is partially shielded in the oligomer by C-terminal amino acids of the same monomer. Our structural hypothesis suggests that the Trp25 residues do not interact with each other, but with C-terminal Pro residues of their own monomers. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1161 KW - biophysics KW - diabetes KW - peptides KW - oligomerization KW - conformational change KW - molecular modeling KW - static and dynamic light scattering KW - spectroscopy Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-522081 SN - 1866-8372 IS - 9 ER - TY - GEN A1 - Zór, K. A1 - Heiskanen, A. A1 - Caviglia, Claudia A1 - Vergani, M. A1 - Landini, E. A1 - Shah, F. A1 - Carminati, Marco A1 - Martínez-Serrano, A. A1 - Ramos Moreno, T. A1 - Kokaia, M. A1 - Benayahu, Dafna A1 - Keresztes, Zs. A1 - Papkovsky, D. A1 - Wollenberger, Ursula A1 - Svendsen, W. E. A1 - Dimaki, M. A1 - Ferrari, G. A1 - Raiteri, R. A1 - Sampietro, M. A1 - Dufva, M. A1 - Emnéus, J. T1 - A compact multifunctional microfluidic platform for exploring cellular dynamics in real-time using electrochemical detection N2 - Downscaling of microfluidic cell culture and detection devices for electrochemical monitoring has mostly focused on miniaturization of the microfluidic chips which are often designed for specific applications and therefore lack functional flexibility. We present a compact microfluidic cell culture and electrochemical analysis platform with in-built fluid handling and detection, enabling complete cell based assays comprising on-line electrode cleaning, sterilization, surface functionalization, cell seeding, cultivation and electrochemical real-time monitoring of cellular dynamics. To demonstrate the versatility and multifunctionality of the platform, we explored amperometric monitoring of intracellular redox activity in yeast (Saccharomyces cerevisiae) and detection of exocytotically released dopamine from rat pheochromocytoma cells (PC12). Electrochemical impedance spectroscopy was used in both applications for monitoring cell sedimentation and adhesion as well as proliferation in the case of PC12 cells. The influence of flow rate on the signal amplitude in the detection of redox metabolism as well as the effect of mechanical stimulation on dopamine release were demonstrated using the programmable fluid handling capability. The here presented platform is aimed at applications utilizing cell based assays, ranging from e.g. monitoring of drug effects in pharmacological studies, characterization of neural stem cell differentiation, and screening of genetically modified microorganisms to environmental monitoring. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 289 Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-99492 ER -