TY - GEN A1 - Zancolli, Giulia A1 - Baker, Timothy G. A1 - Barlow, Axel A1 - Bradley, Rebecca K. A1 - Calvete, Juan J. A1 - Carter, Kimberley C. A1 - de Jager, Kaylah A1 - Owens, John Benjamin A1 - Price, Jenny Forrester A1 - Sanz, Libia A1 - Scholes-Higham, Amy A1 - Shier, Liam A1 - Wood, Liam A1 - Wüster, Catharine E. A1 - Wüster, Wolfgang T1 - Is hybridization a source of adaptive venom variation in rattlesnakes? BT - a test, using a crotalus scutulatus × viridis hybrid zone in southwestern New Mexico T2 - Toxins N2 - Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter-and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A2 such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 443 KW - adaptation KW - Crotalus KW - evolution KW - hybridization KW - introgression KW - Mojave toxin KW - molecular evolution KW - venom Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407595 ER - TY - JOUR A1 - Zancolli, Giulia A1 - Baker, Timothy G. A1 - Barlow, Axel A1 - Bradley, Rebecca K. A1 - Calvete, Juan J. A1 - Carter, Kimberley C. A1 - de Jager, Kaylah A1 - Owens, John Benjamin A1 - Price, Jenny Forrester A1 - Sanz, Libia A1 - Scholes-Higham, Amy A1 - Shier, Liam A1 - Wood, Liam A1 - Wüster, Catharine E. A1 - Wüster, Wolfgang T1 - Is Hybridization a Source of Adaptive Venom Variation in Rattlesnakes? A Test, Using a Crotalus scutulatus x viridis Hybrid Zone in Southwestern New Mexico JF - Toxins N2 - Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter-and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A2 such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species. KW - adaptation KW - Crotalus KW - evolution KW - hybridization KW - introgression KW - Mojave toxin KW - molecular evolution KW - venom Y1 - 2016 U6 - https://doi.org/10.3390/toxins8060188 SN - 2072-6651 VL - 8 PB - MDPI CY - Basel ER - TY - JOUR A1 - Westbury, Michael V. A1 - Hartmann, Stefanie A1 - Barlow, Axel A1 - Wiesel, Ingrid A1 - Leo, Viyanna A1 - Welch, Rebecca A1 - Parker, Daniel M. A1 - Sicks, Florian A1 - Ludwig, Arne A1 - Dalen, Love A1 - Hofreiter, Michael T1 - Extended and continuous decline in effective population size results in low genomic diversity in the world's rarest hyena species, the brown hyena JF - Molecular biology and evolution N2 - Hyenas (family Hyaenidae), as the sister group to cats (family Felidae), represent a deeply diverging branch within the cat-like carnivores (Feliformia). With an estimated population size of <10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) represents the rarest of the four extant hyena species and has been listed as Near Threatened by the IUCN. Here, we report a high-coverage genome from a captive bred brown hyena and both mitochondrial and low-coverage nuclear genomes of 14 wild-caught brown hyena individuals from across southern Africa. We find that brown hyena harbor extremely low genetic diversity on both the mitochondrial and nuclear level, most likely resulting from a continuous and ongoing decline in effective population size that started similar to 1 Ma and dramatically accelerated towards the end of the Pleistocene. Despite the strikingly low genetic diversity, we find no evidence of inbreeding within the captive bred individual and reveal phylogeographic structure, suggesting the existence of several potential subpopulations within the species. KW - evolution KW - hyena KW - genomics KW - population genomics KW - diversity Y1 - 2018 U6 - https://doi.org/10.1093/molbev/msy037 SN - 0737-4038 SN - 1537-1719 VL - 35 IS - 5 SP - 1225 EP - 1237 PB - Oxford Univ. Press CY - Oxford ER - TY - THES A1 - Romero Mujalli, Daniel T1 - Ecological modeling of adaptive evolutionary responses to rapid climate change T1 - Ökologische Modellierung anpassungsfähiger evolutionärer Reaktionen auf schnellen Klimawandel N2 - A contemporary challenge in Ecology and Evolutionary Biology is to anticipate the fate of populations of organisms in the context of a changing world. Climate change and landscape changes due to anthropic activities have been of major concern in the contemporary history. Organisms facing these threats are expected to respond by local adaptation (i.e., genetic changes or phenotypic plasticity) or by shifting their distributional range (migration). However, there are limits to their responses. For example, isolated populations will have more difficulties in developing adaptive innovations by means of genetic changes than interconnected metapopulations. Similarly, the topography of the environment can limit dispersal opportunities for crawling organisms as compared to those that rely on wind. Thus, populations of species with different life history strategy may differ in their ability to cope with changing environmental conditions. However, depending on the taxon, empirical studies investigating organisms’ responses to environmental change may become too complex, long and expensive; plus, complications arising from dealing with endangered species. In consequence, eco-evolutionary modeling offers an opportunity to overcome these limitations and complement empirical studies, understand the action and limitations of underlying mechanisms, and project into possible future scenarios. In this work I take a modeling approach and investigate the effect and relative importance of evolutionary mechanisms (including phenotypic plasticity) on the ability for local adaptation of populations with different life strategy experiencing climate change scenarios. For this, I performed a review on the state of the art of eco-evolutionary Individual-Based Models (IBMs) and identify gaps for future research. Then, I used the results from the review to develop an eco-evolutionary individual-based modeling tool to study the role of genetic and plastic mechanisms in promoting local adaption of populations of organisms with different life strategies experiencing scenarios of climate change and environmental stochasticity. The environment was simulated through a climate variable (e.g., temperature) defining a phenotypic optimum moving at a given rate of change. The rate of change was changed to simulate different scenarios of climate change (no change, slow, medium, rapid climate change). Several scenarios of stochastic noise color resembling different climatic conditions were explored. Results show that populations of sexual species will rely mainly on standing genetic variation and phenotypic plasticity for local adaptation. Population of species with relatively slow growth rate (e.g., large mammals) – especially those of small size – are the most vulnerable, particularly if their plasticity is limited (i.e., specialist species). In addition, whenever organisms from these populations are capable of adaptive plasticity, they can buffer fitness losses in reddish climatic conditions. Likewise, whenever they can adjust their plastic response (e.g., bed-hedging strategy) they will cope with bluish environmental conditions as well. In contrast, life strategies of high fecundity can rely on non-adaptive plasticity for their local adaptation to novel environmental conditions, unless the rate of change is too rapid. A recommended management measure is to guarantee interconnection of isolated populations into metapopulations, such that the supply of useful genetic variation can be increased, and, at the same time, provide them with movement opportunities to follow their preferred niche, when local adaptation becomes problematic. This is particularly important for bluish and reddish climatic conditions, when the rate of change is slow, or for any climatic condition when the level of stress (rate of change) is relatively high. N2 - Eine aktuelle Herausforderung in der Ökologie und Evolutionsbiologie besteht darin, das Schicksal von Populationen verschiedener Lebewesen im Kontext einer sich verändernden Welt zu antizipieren. Der Klimawandel und die durch anthropologische Aktivitäten verursachten Landschaftsveränderungen sind im Laufe der Geschichte von großer Bedeutung geworden. Von den Organismen, die sich diesen Veränderungen stellen, wird erwartet, dass sie durch lokale Anpassung (d.h. genetische Veränderungen oder phänotypische Plastizität) oder durch Verschiebung ihres Verbreitungsgebietes (Migration) darauf reagieren. Allerdings sind diese Reaktionen begrenzt. So werden beispielsweise isolierte Populationen mehr Schwierigkeiten bei der Entwicklung adaptiver Neuheiten mittels genetischer Variation haben als vernetzte Metapopulationen. Ebenso kann die Topographie der Umgebung die Ausbreitungsmöglichkeiten für zum Beispiel kriechende Organismen im Vergleich zu denen, die auf Wind angewiesen sind, einschränken. So können Populationen von Arten mit unterschiedlichen Lebensstrategien verschiedene Fähigkeiten haben, mit den sich ändernden Umweltbedingungen umzugehen. Empirische Studien, die die Reaktionen von Organismen auf Umweltveränderungen untersuchen, können jedoch, je nach Taxon, zu komplex, langwierig und teuer werden. Ebenso sollten Komplikationen im Umgang mit gefährdeten Arten nicht außer Acht gelassen werden. Die ökoevolutionäre Modellierung bietet jedoch die Möglichkeit, diese Einschränkungen zu überwinden und empirische Studien zu ergänzen, die Wirkung und Grenzen der zugrunde liegenden Mechanismen zu verstehen und mögliche Zukunftsszenarien zu erstellen. In dieser Arbeit untersuche ich mittels einer Modellierungsmethode die Wirkung und relative Bedeutung evolutionärer Mechanismen (einschließlich phänotypischer Plastizität) auf die Fähigkeit zur lokalen Anpassung von Populationen mit unterschiedlichen Lebensstrategien, die Szenarien des Klimawandels durchleben. Dazu habe ich in einem Review den Stand der Technik ökoevolutionärer individuenbasierender Modelle (Individual-Based Models; IBMs) zusammengefasst und Ansätze für eine zukünftige Forschung identifiziert. Die Erkenntnisse des Reviews nutzte ich, um ein ökoevolutionäres, individuelles Modellierungsprogramm zu entwickeln. Dieses analysiert die Rolle genetischer und plastischer Mechanismen zur Förderung der lokalen Anpassung organismischer Populationen mit unterschiedlichen Lebensstrategien, welche Szenarien des Klimawandels und der ökologischen Stochastik erfahren. Die Umweltbedingungen wurden durch eine klimatische Variable (z.B. Temperatur) simuliert, die ein phänotypisches Optimum definiert, das sich mit einer bestimmten Änderungsrate bewegt. Verschiedene Änderungsraten wurden angewandt, um unterschiedliche Szenarien des Klimawandels darzustellen (keine Veränderung, langsamer, mittlerer, schneller Klimawandel). Es wurden mehrere Szenarien stochastischen Farbrauschens untersucht, die verschiedene klimatische Bedingungen widerspiegeln. Die Ergebnisse zeigen, dass Populationen sexueller Arten hauptsächlich auf genetische Variation und phänotypische Plastizität hinsichtlich lokalen Anpassung angewiesen sind. Populationen von Arten mit relativ langsamer Wachstumsrate (z.B. große Säugetiere), und insbesondere die mit kleiner Populationsgröße, sind am anfälligsten, vor allem wenn ihre Plastizität begrenzt ist (d.h. spezialisierte Arten). Wenn Individuen dieser Populationen zu adaptiver Plastizität fähig sind, können sie Fitnessverluste unter „rötlichen“ Klimabedingungen ausgleichen. Zugleich können diese Populationen durch Anpassung der Plastizität auch unter bläulichen Umweltbedingungen zurecht kommen (z.B. Bed-Hedging-Strategie). Im Gegensatz dazu können sich Lebensstrategen mit hoher Reproduktionszahl auf nicht-adaptive Plastizität zur lokalen Anpassung an neue Umweltbedingungen verlassen, es sei denn, die Änderungsrate ist zu schnell. Eine empfohlene Handlungsmaßnahme ist es, die Eingliederung von isolierten Populationen in Metapopulationen zu gewährleisten, so dass die genetische Variation erhöht werden kann. Wenn eine lokale Anpassung problematisch wird, sollte ihnen gleichzeitig Migrationsfreiraum gegeben werden, um ihrer bevorzugten Nische zu folgen. Dies ist besonders wichtig für „bläuliche“ und „rötliche“ Klimabedingungen, bei denen die Änderungsrate langsam ist, oder für jede klimatische Bedingung, wenn die Belastung (Änderungsrate) relativ hoch ist. KW - climate change KW - local adaptation KW - plasticity KW - evolution KW - individual-based model KW - Klimawandel KW - lokale Anpassung KW - Plastizität KW - Evolution KW - Individuen-basierende Modelle Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-430627 ER - TY - THES A1 - Riaño-Pachón, Diego Mauricio T1 - Identification of transcription factor genes in plants T1 - Identifizierung von Transkriptionsfaktorgenen in Pflanzen N2 - In order to function properly, organisms have a complex control mechanism, in which a given gene is expressed at a particular time and place. One way to achieve this control is to regulate the initiation of transcription. This step requires the assembly of several components, i.e., a basal/general machinery common to all expressed genes, and a specific/regulatory machinery, which differs among genes and is the responsible for proper gene expression in response to environmental or developmental signals. This specific machinery is composed of transcription factors (TFs), which can be grouped into evolutionarily related gene families that possess characteristic protein domains. In this work we have exploited the presence of protein domains to create rules that serve for the identification and classification of TFs. We have modelled such rules as a bipartite graph, where families and protein domains are represented as nodes. Connections between nodes represent that a protein domain should (required rule) or should not (forbidden rule) be present in a protein to be assigned into a TF family. Following this approach we have identified putative complete sets of TFs in plant species, whose genome is completely sequenced: Cyanidioschyzon merolae (red algae), Chlamydomonas reinhardtii (green alga), Ostreococcus tauri (green alga), Physcomitrella patens (moss), Arabidopsis thaliana (thale cress), Populus trichocarpa (black cottonwood) and Oryza sativa (rice). The identification of the complete sets of TFs in the above-mentioned species, as well as additional information and reference literature are available at http://plntfdb.bio.uni-potsdam.de/. The availability of such sets allowed us performing detailed evolutionary studies at different levels, from a single family to all TF families in different organisms in a comparative genomics context. Notably, we uncovered preferential expansions in different lineages, paving the way to discover the specific biological roles of these proteins under different conditions. For the basic leucine zipper (bZIP) family of TFs we were able to infer that in the most recent common ancestor (MRCA) of all green plants there were at least four bZIP genes functionally involved in oxidative stress and unfolded protein responses that are bZIP-mediated processes in all eukaryotes, but also in light-dependent regulations. The four founder genes amplified and diverged significantly, generating traits that benefited the colonization of new environments. Currently, following the approach described above, up to 57 TF and 11 TR families can be identified, which are among the most numerous transcription regulatory families in plants. Three families of putative TFs predate the split between rhodophyta (red algae) and chlorophyta (green algae), i.e., G2-like, PLATZ, and RWPRK, and may have been of particular importance for the evolution of eukaryotic photosynthetic organisms. Nine additional families, i.e., ABI3/VP1, AP2-EREBP, ARR-B, C2C2-CO-like, C2C2-Dof, PBF-2-like/Whirly, Pseudo ARR-B, SBP, and WRKY, predate the split between green algae and streptophytes. The identification of putative complete list of TFs has also allowed the delineation of lineage-specific regulatory families. The families SBP, bHLH, SNF2, MADS, WRKY, HMG, AP2-EREBP and FHA significantly differ in size between algae and land plants. The SBP family of TFs is significantly larger in C. reinhardtii, compared to land plants, and appears to have been lost in the prasinophyte O. tauri. The families bHLH, SNF2, MADS, WRKY, HMG, AP2-EREBP and FHA preferentially expanded with the colonisation of land, and might have played an important role in this great moment in evolution. Later, after the split of bryophytes and tracheophytes, the families MADS, AP2-EREBP, NAC, AUX/IAA, PHD and HRT have significantly larger numbers in the lineage leading to seed plants. We identified 23 families that are restricted to land plants and that might have played an important role in the colonization of this new habitat. Based on the list of TFs in different species we have started to develop high-throughput experimental platforms (in rice and C. reinhardtii) to monitor gene expression changes of TF genes under different genetic, developmental or environmental conditions. In this work we present the monitoring of Arabidopsis thaliana TFs during the onset of senescence, a process that leads to cell and tissue disintegration in order to redistribute nutrients (e.g. nitrogen) from leaves to reproductive organs. We show that the expression of 185 TF genes changes when leaves develop from half to fully expanded leaves and finally enter partial senescence. 76% of these TFs are down-regulated during senescence, the remaining are up-regulated. The identification of TFs in plants in a comparative genomics setup has proven fruitful for the understanding of evolutionary processes and contributes to the elucidation of complex developmental programs. N2 - Organismen weisen einen komplexen Steuerungsmechanismus auf, bei dem die Aktivität eines Gens räumlich und zeitlich reguliert wird. Eine Möglichkeit der Kontrolle der Genaktivität ist Regulation der Initiation der Transkription. Eine Voraussetzung für die Transkriptionsinitiation ist die Zusammenlagerung verschiedener Komponenten: eine allgemeine Maschinerie, die für alle exprimierten Gene gleich ist und eine spezifische Maschinerie, die sich von Gen zu Gen unterscheidet und die für die korrekte Genexpression in Abhängigkeit der Entwicklung und von Umweltsignalen verantwortlich ist. Diese spezifische Maschinerie besteht aus Transkriptionsfaktoren (TFs), welche in evolutionär verwandte Genefamilien eingeteilt werden können, die charakteristische Proteindomänen aufweisen. In dieser Arbeit habe ich die Proteindomänen genutzt, um Regeln aufzustellen, die die Identifizierung und Klassifizierung von TFs erlauben. Solche Regeln wurden als Graphen modelliert, in denen die Familien und Proteindomänen als Knoten repräsentiert wurden. Verbindungen zwischen den Knoten bedeuten, dass eine Proteindomäne in einem Protein entweder vorhanden sein sollte oder nicht vorhanden sein darf, damit das Protein einer TF-Familie zugeordnet wird. Mit Hilfe dieses Ansatzes wurden vermutlich vollständige Datensätze von TFs in Pflanzenspezies generiert, deren Genom komplett sequenziert wurde: C. merolae, C. reinhardtii, O. tauri, P. patens, A. thaliana, P. trichocarpa and O. sativa. Diese kompletten TF-Sätze sowie weitergehende Informationen und Literaturhinweise wurden unter der Internetadresse http://plntfdb.bio.uni-potsdam.de/ öffentlich zugänglich gemacht. Die Datensätze erlaubten es, detailliertere evolutionäre Studien mit unterschiedlichen Schwerpunkten durchzuführen. Diese reichten von der Analyse einzelner Familien bis hin zum genomweiten Vergleich aller TF-Familien in verschiedenen Organismen. Als Resultat besonders erwähnenswert ist, dass bevorzugt einige bestimmte TF-Familien in verschiedenen Spezies expandierten. Diese Studien ebnen den Weg, um die spezifische biologische Rolle dieser Proteine unter verschiedenen Bedingungen zu ergründen. Für die wichtige TF-Familie bZIP konnte gezeigt werden, dass der letzte gemeinsame Vorfahr aller Grünpflanzen mindestens vier bZIP Gene hatte, die funktionell in die Antwort auf oxidativen Stress eingebunden waren. Aus den vier Gründergene entstand durch Genverdopplung und –differenzierung eine große Familie, die Eigenschaften hervorbrachte, die die Besiedelung neuer Lebensräume ermöglichten. Mit Hilfe des oben beschriebenen Ansatzes können derzeit aus der Vielzahl der Transkriptionsregulatorfamilien in Pflanzen bis zu 57 TF und 11 TR Familien identifiziert werden. Drei Familien mutmaßlicher TFs markieren die Trennung zwischen Rhodophyta (Rotalgen) und Chlorophyta (Grünalgen): G2-like, PLATZ und RWPRK. Diese könnten eine besondere Rolle bei der Evolution eukaryotischer photosynthetisch aktiver Organismen gespielt haben. Neun zusätzliche Familien (ABI3/VP1, AP2-EREBP, ARR-B, C2C2-CO-like, C2C2-Dof, PBF-2-like/Whirly, Pseudo ARR-B, SBP und WRKY) kennzeichnen die Trennung zwischen Grünalgen und Streptophyten. Die Identifizierung putativer kompletter Listen an TFs erlaubte auch die Identifizierung abtammungsspezifischer regulatorischer Familien. Die Familien SBP, bHLH, SNF2, MADS, WRKY, HMG, AP2-EREBP und FHA unterscheiden sich signifikant in ihrer Größe zwischen Algen und Landpflanzen. Die SBP Familie ist in C. reinhardtii signifikant größer als in Landpflanzen. In der Parasinophyte O. tauri scheint diese Familie verloren gegangen zu sein. Die Familien bHLH, SNF2, MADS, WRKY, HMG, AP2-EREBP und FHA expandierten präferenziell mit der Kolonialisation an Land. Sie könnten eine wichte Rolle während dieses einschneidenden Ereignisses der Evolution gespielt haben. Später, nach der Trennung von Bryophyten und Tracheophyten sind die Familien MADS, AP2-EREBP, NAC, AUX/IAA, PHD und HRT stärker in den Linien, die zu Samenpflanzen führten, gewachsen. 23 TF-Familien wurden identifiziert, die es nur in Landpflanzen gibt. Sie könnten eine besondere Rolle bei der Besiedelung des neuen Lebensraum gespielt haben. Aufbauend auf die Transkriptionsfaktordatensätze, die in dieser Arbeit erstellt wurden, wurde mittlerweile damit begonnen, experimentelle Hochdurchsatz-Plattformen zu entwickeln (für Reis und für C. reinhardtii), um Änderungen in der Genaktivität der TF-Gene unter verschiedenen genetischen, Entwicklungs- oder Umweltbedingungen zu untersuchen. In dieser Arbeit wird die Analyse von TFs aus A. thaliana im Verlauf der Seneszenz vorgestellt. Seneszenz ist ein Prozess, der zur Zell- und Gewebeauflösung führt, um Nährstoffe aus den Blättern für den Transport in reproduktive Organe freizusetzen. Es wird gezeigt, dass sich die Expression von 187 TF Gene verändert, wenn sich die Blätter voll entfalten und schließlich teilweise in den Prozess der Seneszenz eintreten. 76% der TFs waren runterreguliert, die übrigen waren hochreguliert. KW - Transkriptionfaktorgenen KW - Regulation KW - Evolution KW - Datenbank KW - Pflanzen KW - transcription factor genes KW - regulation KW - evolution KW - plants KW - database Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-27009 ER - TY - JOUR A1 - Qiu, Liang A1 - Zhang, Haoran A1 - Bick, Thomas A1 - Martin, Johannes A1 - Wendler, Petra A1 - Böker, Alexander A1 - Glebe, Ulrich A1 - Xing, Chengfen T1 - Construction of highly ordered glyco-inside nano-assemblies through RAFT dispersion polymerization of galactose-decorated monomer JF - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition N2 - Glyco-assemblies derived from amphiphilic sugar-decorated block copolymers (ASBCs) have emerged prominently due to their wide application, for example, in biomedicine and as drug carriers. However, to efficiently construct these glyco-assemblies is still a challenge. Herein, we report an efficient technology for the synthesis of glyco-inside nano-assemblies by utilizing RAFT polymerization of a galactose-decorated methacrylate for polymerization-induced self-assembly (PISA). Using this approach, a series of highly ordered glyco-inside nano-assemblies containing intermediate morphologies were fabricated by adjusting the length of the hydrophobic glycoblock and the polymerization solids content. A specific morphology of complex vesicles was captured during the PISA process and the formation mechanism is explained by the morphology of its precursor and intermediate. Thus, this method establishes a powerful route to fabricate glyco-assemblies with tunable morphologies and variable sizes, which is significant to enable the large-scale fabrication and wide application of glyco-assemblies. KW - galactose-decorated monomer KW - glyco-inside nano-assemblies KW - morphology KW - evolution KW - PISA KW - RAFT dispersion polymerization Y1 - 2021 U6 - https://doi.org/10.1002/anie.202015692 SN - 1433-7851 SN - 1521-3773 VL - 60 IS - 20 SP - 11098 EP - 11103 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Nguyen, Hung M. A1 - Schippers, Jos H. M. A1 - Goni-Ramos, Oscar A1 - Christoph, Mathias P. A1 - Dortay, Hakan A1 - van der Hoorn, Renier A. L. A1 - Müller-Röber, Bernd T1 - An upstream regulator of the 26S proteasome modulates organ size in Arabidopsis thaliana JF - The plant journal N2 - In both animal and plant kingdoms, body size is a fundamental but still poorly understood attribute of biological systems. Here we report that the Arabidopsis NAC transcription factor Regulator of Proteasomal Gene Expression' (RPX) controls leaf size by positively modulating proteasome activity. We further show that the cis-element recognized by RPX is evolutionarily conserved between higher plant species. Upon over-expression of RPX, plants exhibit reduced growth, which may be reversed by a low concentration of the pharmacological proteasome inhibitor MG132. These data suggest that the rate of protein turnover during growth is a critical parameter for determining final organ size. KW - Arabidopsis thaliana KW - organ size KW - evolution KW - leaf development KW - proteasome KW - gene regulatory network Y1 - 2013 U6 - https://doi.org/10.1111/tpj.12097 SN - 0960-7412 VL - 74 IS - 1 SP - 25 EP - 36 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Malchow, Anne-Kathleen A1 - Bocedi, Greta A1 - Palmer, Stephen C. F. A1 - Travis, Justin M. J. A1 - Zurell, Damaris T1 - RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and speciesu0027 responses to environmental changes JF - Ecography N2 - Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models. KW - connectivity KW - conservation KW - dispersal KW - evolution KW - population dynamics KW - range dynamics Y1 - 2021 SN - 1600-0587 VL - 44 IS - 10 PB - John Wiley & Sons, Inc. CY - New Jersey ER - TY - GEN A1 - Malchow, Anne-Kathleen A1 - Bocedi, Greta A1 - Palmer, Stephen C. F. A1 - Travis, Justin M. J. A1 - Zurell, Damaris T1 - RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and speciesu0027 responses to environmental changes T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1178 KW - connectivity KW - conservation KW - dispersal KW - evolution KW - population dynamics KW - range dynamics Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523979 SN - 1866-8372 IS - 10 ER - TY - JOUR A1 - Malchow, Anne-Kathleen A1 - Bocedi, Greta A1 - Palmer, Stephen C. F. A1 - Travis, Justin M. J. A1 - Zurell, Damaris T1 - RangeShiftR BT - an R package for individual-based simulation of spatial changes JF - Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos N2 - Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models. KW - connectivity KW - conservation KW - dispersal KW - evolution KW - population dynamics KW - range dynamics Y1 - 2021 U6 - https://doi.org/10.1111/ecog.05689 SN - 1600-0587 VL - 44 IS - 10 SP - 1443 EP - 1452 PB - Wiley-Blackwell CY - Oxford [u.a.] ER -