TY - THES A1 - Makower, Katharina T1 - The roles of secondary metabolites in microcystis inter-strain interactions T1 - Die Rolle von Sekundärmetaboliten in den Wechselbeziehungen zwischen Microcystis-Stämmen N2 - Among the bloom-forming and potentially harmful cyanobacteria, the genus Microcystis represents a most diverse taxon, on the genomic as well as on morphological and secondary metabolite levels. Microcystis communities are composed of a variety of diversified strains. The focus of this study lies on potential interactions between Microcystis representatives and the roles of secondary metabolites in these interaction processes. The role of secondary metabolites functioning as signaling molecules in the investigated interactions is demonstrated exemplary for the prevalent hepatotoxin microcystin. The extracellular and intracellular roles of microcystin are tested in microarray-based transcriptomic approaches. While an extracellular effect of microcystin on Microcystis transcription is confirmed and connected to a specific gene cluster of another secondary metabolite in this study, the intracellularly occurring microcystin is related with several pathways of the primary metabolism. A clear correlation of a microcystin knockout and the SigE-mediated regulation of carbon metabolism is found. According to the acquired transcriptional data, a model is proposed that postulates the regulating effect of microcystin on transcriptional regulators such as the alternative sigma factor SigE, which in return captures an essential role in sugar catabolism and redox-state regulation. For the purpose of simulating community conditions as found in the field, Microcystis colonies are isolated from the eutrophic lakes near Potsdam, Germany and established as stably growing under laboratory conditions. In co-habitation simulations, the recently isolated field strain FS2 is shown to specifically induce nearly immediate aggregation reactions in the axenic lab strain Microcystis aeruginosa PCC 7806. In transcriptional studies via microarrays, the induced expression program in PCC 7806 after aggregation induction is shown to involve the reorganization of cell envelope structures, a highly altered nutrient uptake balance and the reorientation of the aggregating cells to a heterotrophic carbon utilization, e.g. via glycolysis. These transcriptional changes are discussed as mechanisms of niche adaptation and acclimation in order to prevent competition for resources. N2 - Die Gattung Microcystis stellt unter den blüten-bildenden Cyanobakterien ein Taxon besonderer Diversität dar. Dies gilt sowohl für die Genomstruktur als auch für morphologische Charakteristika und Sekundärmetabolite. Microcystis-Communities weisen eine Zusammensetzung aus einer Vielzahl von diversifizierten Stämmen auf. Das Hauptaugenmerk dieser Arbeit lag darauf, potentielle Wechselwirkungen zwischen Microcystis-Vertretern zu charakterisieren und die Rolle von Sekundärmetaboliten in Interaktions-Prozessen zu untersuchen. Die Rolle von Sekundärmetaboliten als Signalstoffe in Microcystis-Interaktionen wurde exemplarisch für das Hepatotoxin Microcystin demonstriert. Sowohl die extrazelluläre als auch die intrazellulare Funktion von Microcystin wurde anhand von Microarray-basierten Transkriptomstudien getestet. Dabei konnte eine extrazelluläre Wirkung von Microcystin bestätigt werden und mit der Transkription eines spezifischen anderen Sekundärmetaboliten in Verbindung gebracht werden. Intrazellulär vorkommendes Microcystin wurde hingegen mit verschiedenen Stoffwechselwegen des Primärstoffwechsels verknüpft. Es konnte ein deutlicher Zusammenhang zwischen einem Microcystin-Knockout und der SigE-vermittelten Regulation des Kohlenstoffmetabolismus festgestellt werden. Anhand der erworbenen Transkriptionsdaten wurde ein Modell vorgeschlagen, das eine regulierende Wirkung von Microcystin auf Transkriptionsfaktoren wie den alternativen Sigmafaktor SigE postuliert, welcher seinerseits eine zentrale Rolle in Zuckerabbauprozessen und zellulärer Redoxregulation einnimmt. Mit dem Ziel, Community-ähnliche Bedingungen zu simulieren, wurden Microcystis-Freiland-Kolonien aus eutrophen Gewässern in der Umgebung von Potsdam isoliert und ein stabiles Wachstum unter Laborbedingungen etabliert. Es konnte gezeigt werden, dass der frisch isolierte Freilandstamm FS2 spezifisch eine starke Zellaggregation in Microcystis aeruginosa PCC 7806 (einem axenischen Labortstamm) auslösen konnte. In Transkriptionsstudien mit Hilfe von Microarrays wurden Expressionsprogramme gefunden, die sowohl einen Umbau von Zellhüllstrukturen, als auch einen stark veränderten transmembranen Nährstofftransport beinhalteten. Darüber hinaus konnte in den aggregierenden PCC 7806-Zellen eine Verlagerung zu heterotrophen Kohlenstoffabbauprozessen wie der Glykolyse gefunden werden. Die transkriptionellen Veränderungen wurden als Akklimationsmechanismen zur Positionierung in ökologische Nischen diskutiert, um Konkurrenzen um Ressourcen zu vermeiden. KW - microcystis KW - microcystin KW - secondary metabolites KW - transcriptomics KW - interactions KW - Sekundärmetabolite KW - Transkriptomik KW - Wechselwirkungen Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-93916 ER - TY - THES A1 - Lopes Fernando, Raquel Sofia T1 - The impact of aging on proteolytic systems, transcriptome and metabolome of slow and fast muscle fiber types N2 - Aging is a complex process characterized by several factors, including loss of genetic and epigenetic information, accumulation of chronic oxidative stress, protein damage and aggregates and it is becoming an emergent drug target. Therefore, it is the utmost importance to study aging and agerelated diseases, to provide treatments to develop a healthy aging process. Skeletal muscle is one of the earliest tissues affected by age-related changes with progressive loss of muscle mass and function from 30 years old, effect known as sarcopenia. Several studies have shown the accumulation of protein aggregates in different animal models, as well as in humans, suggesting impaired proteostasis, a hallmark of aging, especially regarding degradation systems. Thus, different publications have explored the role of the main proteolytic systems in skeletal muscle from rodents and humans, like ubiquitin proteasomal system (UPS) and autophagy lysosomal system (ALS), however with contradictory results. Yet, most of the published studies are performed in muscles that comprise more than one fiber type, that means, muscles composed by slow and fast fibers. These fiber types, exhibit different metabolism and contraction speed; the slow fibers or type I display an oxidative metabolism, while fast fibers function towards a glycolytic metabolism ranging from fast oxidative to fast glycolytic fibers. To this extent, the aim of this thesis sought to understand on how aging impacts both fiber types not only regarding proteostasis but also at a metabolome and transcriptome network levels. Therefore, the first part of this thesis, presents the differences between slow oxidative (from Soleus muscle) and fast glycolytic fibers (Extensor digitorum longus, EDL) in terms of degradation systems and how they cope with oxidative stress during aging, while the second part explores the differences between young and old EDL muscle transcriptome and metabolome, unraveling molecular features. More specifically, the results from the present work show that slow oxidative muscle performs better at maintaining the function of UPS and ALS during aging than EDL muscle, which is clearly affected, accounting for the decline in the catalytic activity rates and accumulation of autophagy-related proteins. Strinkingly, transcriptome and metabolome analyses reveal that fast glycolytic muscle evidences significant downregulation of mitochondrial related processes and damaged mitochondria morphology during aging, despite of having a lower oxidative metabolism compared to oxidative fibers. Moreover, predictive analyses reveal a negative association between aged EDL gene signature and lifespan extending interventions such as caloric restriction (CR). Although, CR intervention does not alter the levels of mitochondrial markers in aged EDL muscle, it can reverse the higher mRNA levels of muscle damage markers. Together, the results from this thesis give new insights about how different metabolic muscle fibers cope with age-related changes and why fast glycolytic fibers are more susceptible to aging than slow oxidative fibers. N2 - Altern ist ein komplexer Prozess, der durch mehrere Faktoren gekennzeichnet ist, darunter der Verlust genetischer und epigenetischer Informationen, oxidativer Stress, sowie die Anhäufung von Proteinschäden und Aggregaten. Daher ist es von größter Bedeutung, das Altern und altersbedingte Krankheiten zu erforschen, um Arzneimittel und andere Behandlungen für einen gesunden Alterungsprozess zu entwickeln. Die Skelettmuskulatur ist eines der ersten Gewebe, das von altersbedingten Veränderungen betroffen ist. Ab einem Alter von 30 Jahren kommt es zu einem fortschreitenden Verlust der Muskelmasse und -funktion, der auch als Sarkopenie bezeichnet wird. Mehrere Studien haben die Anhäufung von Proteinaggregaten beim Altern in verschiedenen Tiermodellen und auch beim Menschen gezeigt, was auf eine gestörte Proteostase, insbesondere hinsichtlich der Abbauprozesse schließen lässt. Demnach wurde weiterführend die Rolle der wichtigsten proteolytischen Systeme, das Ubiquitin Proteasom System (UPS) und AutophagieLysosomale System (ALS), im alternden Skelettmuskel von Nagetieren und Menschen untersucht. Die Ergebnisse waren widersprüchlich, jedoch wurden die meisten der veröffentlichten Studien an Muskeln durchgeführt, die aus mehr als einem Muskelfasertyp bestehen, d.h. Muskeln, die aus langsamen und schnellen Muskelfasern zusammengesetzt sind. Diese Muskelfasertypen unterscheiden sich hinsichtlich des Stoffwechsels und der Kontraktionsgeschwindigkeit. Die langsamen Fasern oder der Typ I haben einen oxidativen Stoffwechsel, während die schnellen Fasern einen glykolytischen Stoffwechsel aufweisen und aus schnellen oxidativen bis zu schnellen glykolytischen Fasern bestehen können. Insofern war es das Ziel dieser Arbeit zu verstehen, wie sich das Altern auf beide Fasertypen auswirkt, und zwar nicht nur im Hinblick auf die Proteostase, sondern auch auf das Metabolom und Transkriptom. Im ersten Teil dieser Arbeit werden die Unterschiede zwischen langsamen oxidativen (Soleus-Muskel) und schnellen glykolytischen Fasern (Extensor digitorum longus-Muskel; EDL) in Bezug auf die Proteinabbausysteme und die Art und Weise, wie sie mit oxidativem Stress während des Alterns umgehen, dargestellt. Im zweiten Teil werden die Unterschiede zwischen dem Transkriptom und dem Metabolom des jungen und alten EDL-Muskels untersucht, um die molekularen Merkmale zu entschlüsseln. Im Einzelnen zeigen die Ergebnisse der vorliegenden Arbeit, dass der langsam oxidierende Muskel im Vergleich zum EDL-Muskel besser in der Lage ist, die Funktion von UPS und ALS während des Alterns aufrechtzuerhalten. Die Funktionalität des UPS und ALS ist im alternden EDL-Muskels vermindert, was durch den Rückgang der katalytischen Aktivitätsraten und die Anhäufung von mit Autophagie-assoziierten Proteinen gezeigt wurde. Transkriptom- und Metabolomanalysen zeigen, dass schnelle glykolytische Muskeln eine signifikante Herabregulierung mitochondrialer Prozesse und eine geschädigte Mitochondrienmorphologie während des Alterns aufweisen, obwohl sie im Vergleich zu oxidativen Fasern durch einen geringeren oxidativen Stoffwechsel charakterisiert sind. Darüber hinaus ergeben prädiktive Analysen einen negativen Zusammenhang zwischen der Gensignatur des gealterten EDL-Muskels und lebensverlängernden Maßnahmen wie der kalorischenRestriktion. Obwohl die kalorischen Restriktion Intervention die Werte der mitochondrialen Marker im gealterten EDL-Muskel nicht verändert, kann sie die höheren mRNA-Werte der Muskelschädigungsmarker umkehren. Zusammenfassend liefern die Ergebnisse dieser Arbeit neue Erkenntnisse darüber, wie verschiedene metabolische Muskelfasern mit altersbedingten. Veränderungen umgehen und warum schnelle glykolytische Fasern anfälliger für die Alterung als langsame oxidative Fasern sind. KW - skeletal muscle aging KW - proteostasis KW - slow and fast fiber types KW - transcriptomics KW - metabolomics KW - sarcopenia KW - Skelettmuskelalterung KW - Proteostase KW - langsame und schnelle Fasertypen KW - Transkriptom KW - Metabolom KW - ubiquitin proteasomal system KW - autophagy lysosomal system KW - Ubiquitin Proteasom System KW - Autophagie Lysosomale System Y1 - 2023 U6 - https://doi.org/10.25932/publishup-60579 ER - TY - GEN A1 - Witzel, Katja A1 - Neugart, Susanne A1 - Ruppel, Silke A1 - Schreiner, Monika A1 - Wiesner, Melanie A1 - Baldermann, Susanne T1 - Recent progress in the use of ‘omics technologies in brassicaceous vegetables T2 - Frontiers in plant science N2 - Continuing advances in 'omics methodologies and instrumentation is enhancing the understanding of how plants cope with the dynamic nature of their growing environment. 'Omics platforms have been only recently extended to cover horticultural crop species. Many of the most widely cultivated vegetable crops belong to the genus Brassica: these include plants grown for their root (turnip, rutabaga/swede), their swollen stem base (kohlrabi), their leaves (cabbage, kale, pak choi) and their inflorescence (cauliflower, broccoli). Characterization at the genome, transcript, protein and metabolite levels has illustrated the complexity of the cellular response to a whole series of environmental stresses, including nutrient deficiency, pathogen attack, heavy metal toxicity, cold acclimation, and excessive and sub optimal irradiation. This review covers recent applications of omics technologies to the brassicaceous vegetables, and discusses future scenarios in achieving improvements in crop end-use quality. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 429 KW - genomics KW - transcriptomics KW - metabolomics KW - proteomics KW - crop KW - microbiomics Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-406479 ER - TY - JOUR A1 - Witzel, Katja A1 - Neugart, Susanne A1 - Ruppel, Silke A1 - Schreiner, Monika A1 - Wiesner, Melanie A1 - Baldermann, Susanne T1 - Recent progress in the use of 'omics technologies in brassicaceous vegetables JF - Frontiers in plant science N2 - Continuing advances in 'omics methodologies and instrumentation is enhancing the understanding of how plants cope with the dynamic nature of their growing environment. 'Omics platforms have been only recently extended to cover horticultural crop species. Many of the most widely cultivated vegetable crops belong to the genus Brassica: these include plants grown for their root (turnip, rutabaga/swede), their swollen stem base (kohlrabi), their leaves (cabbage, kale, pak choi) and their inflorescence (cauliflower, broccoli). Characterization at the genome, transcript, protein and metabolite levels has illustrated the complexity of the cellular response to a whole series of environmental stresses, including nutrient deficiency, pathogen attack, heavy metal toxicity, cold acclimation, and excessive and sub optimal irradiation. This review covers recent applications of omics technologies to the brassicaceous vegetables, and discusses future scenarios in achieving improvements in crop end-use quality. KW - genomics KW - transcriptomics KW - metabolomics KW - proteomics KW - crop KW - microbiomics Y1 - 2015 U6 - https://doi.org/10.3389/fpls.2015.00244 SN - 1664-462X VL - 6 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Omolaoye, Temidayo S. A1 - Omolaoye, Victor Adelakun A1 - Kandasamy, Richard K. A1 - Hachim, Mahmood Yaseen A1 - Du Plessis, Stefan S. T1 - Omics and male infertility BT - highlighting the application of transcriptomic data JF - Life : open access journal N2 - Male infertility is a multifaceted disorder affecting approximately 50% of male partners in infertile couples. Over the years, male infertility has been diagnosed mainly through semen analysis, hormone evaluations, medical records and physical examinations, which of course are fundamental, but yet inefficient, because 30% of male infertility cases remain idiopathic. This dilemmatic status of the unknown needs to be addressed with more sophisticated and result-driven technologies and/or techniques. Genetic alterations have been linked with male infertility, thereby unveiling the practicality of investigating this disorder from the "omics" perspective. Omics aims at analyzing the structure and functions of a whole constituent of a given biological function at different levels, including the molecular gene level (genomics), transcript level (transcriptomics), protein level (proteomics) and metabolites level (metabolomics). In the current study, an overview of the four branches of omics and their roles in male infertility are briefly discussed; the potential usefulness of assessing transcriptomic data to understand this pathology is also elucidated. After assessing the publicly obtainable transcriptomic data for datasets on male infertility, a total of 1385 datasets were retrieved, of which 10 datasets met the inclusion criteria and were used for further analysis. These datasets were classified into groups according to the disease or cause of male infertility. The groups include non-obstructive azoospermia (NOA), obstructive azoospermia (OA), non-obstructive and obstructive azoospermia (NOA and OA), spermatogenic dysfunction, sperm dysfunction, and Y chromosome microdeletion. Findings revealed that 8 genes (LDHC, PDHA2, TNP1, TNP2, ODF1, ODF2, SPINK2, PCDHB3) were commonly differentially expressed between all disease groups. Likewise, 56 genes were common between NOA versus NOA and OA (ADAD1, BANF2, BCL2L14, C12orf50, C20orf173, C22orf23, C6orf99, C9orf131, C9orf24, CABS1, CAPZA3, CCDC187, CCDC54, CDKN3, CEP170, CFAP206, CRISP2, CT83, CXorf65, FAM209A, FAM71F1, FAM81B, GALNTL5, GTSF1, H1FNT, HEMGN, HMGB4, KIF2B, LDHC, LOC441601, LYZL2, ODF1, ODF2, PCDHB3, PDHA2, PGK2, PIH1D2, PLCZ1, PROCA1, RIMBP3, ROPN1L, SHCBP1L, SMCP, SPATA16, SPATA19, SPINK2, TEX33, TKTL2, TMCO2, TMCO5A, TNP1, TNP2, TSPAN16, TSSK1B, TTLL2, UBQLN3). These genes, particularly the above-mentioned 8 genes, are involved in diverse biological processes such as germ cell development, spermatid development, spermatid differentiation, regulation of proteolysis, spermatogenesis and metabolic processes. Owing to the stage-specific expression of these genes, any mal-expression can ultimately lead to male infertility. Therefore, currently available data on all branches of omics relating to male fertility can be used to identify biomarkers for diagnosing male infertility, which can potentially help in unravelling some idiopathic cases. KW - male infertility KW - omics KW - genomics KW - transcriptomics KW - proteomics KW - metabolomics Y1 - 2022 U6 - https://doi.org/10.3390/life12020280 SN - 2075-1729 VL - 12 IS - 2 PB - MDPI CY - Basel ER - TY - JOUR A1 - Wagner, Nicole D. A1 - Hillebrand, Helmut A1 - Wacker, Alexander A1 - Frost, Paul C. T1 - Nutritional indicators and their uses in ecology JF - Ecology letters N2 - The nutrition of animal consumers is an important regulator of ecological processes due to its effects on their physiology, life-history and behaviour. Understanding the ecological effects of poor nutrition depends on correctly diagnosing the nature and strength of nutritional limitation. Despite the need to assess nutritional limitation, current approaches to delineating nutritional constraints can be non-specific and imprecise. Here, we consider the need and potential to develop new complementary approaches to the study of nutritional constraints on animal consumers by studying and using a suite of established and emerging biochemical and molecular responses. These nutritional indicators include gene expression, transcript regulators, protein profiling and activity, and gross biochemical and elemental composition. The potential applications of nutritional indicators to ecological studies are highlighted to demonstrate the value that this approach would have to future studies in community and ecosystem ecology. KW - Ecological stoichiometry KW - lipid profiling KW - metabolism KW - nutrient-stress KW - nutrition KW - proteomics KW - transcriptomics Y1 - 2013 U6 - https://doi.org/10.1111/ele.12067 SN - 1461-023X VL - 16 IS - 4 SP - 535 EP - 544 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Bizic, Mina A1 - Ionescu, Danny A1 - Karnatak, Rajat A1 - Musseau, Camille L. A1 - Onandia, Gabriela A1 - Berger, Stella A. A1 - Nejstgaard, Jens C. A1 - Lischeid, Gunnar A1 - Gessner, Mark O. A1 - Wollrab, Sabine A1 - Grossart, Hans-Peter T1 - Land-use type temporarily affects active pond community structure but not gene expression patterns JF - Molecular ecology N2 - Changes in land use and agricultural intensification threaten biodiversity and ecosystem functioning of small water bodies. We studied 67 kettle holes (KH) in an agricultural landscape in northeastern Germany using landscape-scale metatranscriptomics to understand the responses of active bacterial, archaeal and eukaryotic communities to land-use type. These KH are proxies of the millions of small standing water bodies of glacial origin spread across the northern hemisphere. Like other landscapes in Europe, the study area has been used for intensive agriculture since the 1950s. In contrast to a parallel environmental DNA study that suggests the homogenization of biodiversity across KH, conceivably resulting from long-lasting intensive agriculture, land-use type affected the structure of the active KH communities during spring crop fertilization, but not a month later. This effect was more pronounced for eukaryotes than for bacteria. In contrast, gene expression patterns did not differ between months or across land-use types, suggesting a high degree of functional redundancy across the KH communities. Variability in gene expression was best explained by active bacterial and eukaryotic community structures, suggesting that these changes in functioning are primarily driven by interactions between organisms. Our results indicate that influences of the surrounding landscape result in temporary changes in the activity of different community members. Thus, even in KH where biodiversity has been homogenized, communities continue to respond to land management. This potential needs to be considered when developing sustainable management options for restoration purposes and for successful mitigation of further biodiversity loss in agricultural landscapes. KW - agriculture KW - eRNA KW - land use KW - metacommunity KW - transcriptomics Y1 - 2022 U6 - https://doi.org/10.1111/mec.16348 SN - 0962-1083 SN - 1365-294X VL - 31 IS - 6 SP - 1716 EP - 1734 PB - Wiley CY - Hoboken ER - TY - THES A1 - Mutwil, Marek T1 - Integrative transcriptomic approaches to analyzing plant co-expression networks T1 - Integrative Ansätze zur Analyse von Koexpressionsnetzwerken in Pflanzen N2 - It is well documented that transcriptionally coordinated genes tend to be functionally related, and that such relationships may be conserved across different species, and even kingdoms. (Ihmels et al., 2004). Such relationships was initially utilized to reveal functional gene modules in yeast and mammals (Ihmels et al., 2004), and to explore orthologous gene functions between different species and kingdoms (Stuart et al., 2003; Bergmann et al., 2004). Model organisms, such as Arabidopsis, are readily used in basic research due to resource availability and relative speed of data acquisition. A major goal is to transfer the acquired knowledge from these model organisms to species that are of greater importance to our society. However, due to large gene families in plants, the identification of functional equivalents of well characterized Arabidopsis genes in other plants is a non-trivial task, which often returns erroneous or inconclusive results. In this thesis, concepts of utilizing co-expression networks to help infer (i) gene function, (ii) organization of biological processes and (iii) knowledge transfer between species are introduced. An often overlooked fact by bioinformaticians is that a bioinformatic method is as useful as its accessibility. Therefore, majority of the work presented in this thesis was directed on developing freely available, user-friendly web-tools accessible for any biologist. N2 - Es ist bereits ausgiebig gezeigt worden, dass Gene, deren Expression auf Transkriptionsebene koordiniert ist, häufig auch funktional in verwandten Stoffwechselwegen vorkommen, und dass sich dies wahrscheinlich auch Spezies- und sogar Reichübergreifend sagen lässt (Ihmels et al., 2004). Anfänglich wurden solche Beziehungen verwendet, um sogenannte Genfunktionsmodule in Hefe und Säugern aufzudecken (Ihmels et al., 2004), um dann orthologe Genfunktionen zwischen verschiedene Spezies und Reichen zu entdecken (Stuart et al., 2003; Bergmann et al., 2004). Modellorganismen wie Arabidopsis werden bevorzugt in der Forschung verwendet, weil man durch die schnelle Generationszeit in kurzer Zeit viele Daten erheben kann und aufgrund dessen die Ressourcen- und Informationsvielfalt um ein Vielfaches größer ist. Ein Hauptziel ist der Wissenstransfer von Modellorganismen auf Spezies, die gesellschaftlich von höherer Bedeutung sind wie z.B. Getreidearten oder andere Feldfrüchte. Pflanzen besitzen oft große Genfamilien und die eindeutige Identifizierung von gut charakterisierten Arabidopsisorthologen in besagten Nutzpflanzen ist kein triviales Vorhaben. In der vorliegenden Arbeit werden Konzepte zur Nutzung von Co-expressionsnetzwerken beschrieben, die helfen sollen (i) Genfunktionen zu identifizieren, (ii) die Organisation von biologischen Prozessen aufzuklären und (iii) das erworbene Wissen auf andere Spezies übertragbar zu machen. Ein häufig von Bioinformatikern übersehender Umstand ist, dass bioinformatische Methoden nur so sinnvoll sind wie ihre Zugänglichkeit. Deshalb basiert der Großteil dieser Arbeit auf freiverfügbaren und vor allem für Biologen nutzerfreundlichen Webtools. KW - Koexpression KW - vergleichend KW - Transkriptom KW - co-expression KW - comparative KW - transcriptomics Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-50752 ER - TY - THES A1 - Reinert, Armin T1 - Identifizierung und funktionelle Charakterisierung von für die arbuskuläre Mykorrhizasymbiose spezifischen Genen in Medicago truncatula T1 - Identification and functional characterization of genes specific for the arbuscular mycorrhizal symbiosis in Medicago truncatula N2 - Die Mykorrhiza (griechisch: mýkēs für „Pilz”; rhiza für „Wurzel”) stellt eine Symbiose zwischen Pilzen und einem Großteil der Landpflanzen dar. Der Pilz verbessert durch die Symbiose die Versorgung der Pflanze mit Nährstoffen, während die Pflanze den Pilz mit Kohlenhydraten versorgt. Die arbuskuläre Mykorrhiza (AM) stellt dabei einen beson-dere Form der Mykorrhiza dar. Der AM-Pilz bildet dabei während der Symbiose die namensgebenden Arbuskeln innerhalb der Wurzelzellen als Ort des primären Nährstoff- austausches aus. Die AM-Symbiose (AMS) ist der Forschungsschwerpunkt dieser Arbeit. Als Modellorganismen wurden Medicago truncatula und Glomus intraradices verwendet. Es wurden Transkriptionsanalysen durchgeführt um u.a. AMS regulierte Transkriptions- faktoren (TFs) zu identifizieren. Die Aktivität der Promotoren von drei der so identifizier-ten AMS-regulierten TFs (MtOFTN, MtNTS, MtDES) wurde mit Hilfe eine Reportergens visualisiert. Der Bereich der größten Promotoraktivität waren in einem Fall nur die ar- buskelhaltigen Zellen (MtOFTN). Im zweiten Fall war der Promotor auch aktiv in nicht arbuskelhaltigen Zellen, jedoch am stärksten aktiv in den arbuskelhaltigen Zellen (MtNTS). Ein weiterer Promotor war in arbuskelhaltigen Zellen und den diesen benach-barten Zellen gleich aktiv (MtDES). Zusätzlich wurden weitere Gene als AMS-reguliert identifiziert und es wurde für drei dieser Gene (MtPPK, MtAmT, MtMDRL) ebenfalls eine Promotor::Reporter-Aktivitäts- studie durchgeführt. Die Promotoren der Kinase (MtPPK) und des Ammoniumtrans-porters (MtAmt) waren dabei ausschließlich in arbuskelhaltigen Zellen aktiv, während die Aktivität des ABC-Transporters (MtMDRL) keinem bestimmten Zelltyp zuzuordnen war. Für zwei weitere identifizierte Gene, ein Kupfertransporter (MtCoT) und ein Zucker- bzw. Inositoltransporter (MtSuT), wurden RNA-Interferenz (RNAi)-Untersuchungen durchgeführt. Dabei stellte sich in beiden Fällen heraus, dass, sobald ein RNAi-Effekt in den transformierten Wurzeln vorlag, diese in einem deutlich geringerem Ausmaß wie in der Wurzelkontrolle von G. intraradices kolonisiert worden sind. Im Falle von MtCoT könnte das aus dem selben Grund geschehen, wie im Falle von MtPt4. Welche Rolle MtSuT genau in der Ausbildung der AMS spielt und welche Rolle Inositol in der Aus- bildung der AMS spielt müsste durch weitere Untersuchungen am Protein untersucht werden. Weitere Untersuchen an den in dieser Arbeit als spezifisch für arbuskelhaltige Zellen gezeigten Genen MtAmT, MtPPK und MtOFTN könnten ebenfalls aufschlussreich für das weitere Verständnis der AMS sein. Dies trifft auch auf die TFs MtNTS und MtDES zu, die zwar nicht ausschließlich arbuskelspezifisch transkribiert werden, aber auch eine Rolle in der Regulation der AMS innerhalb von M. truncatula Wurzeln zu spielen scheinen. N2 - The mycorrhiza (Greek: mýkēs for "mushroom"; rhiza for "root") is a symbiosis between fungi and the vast majority of land plants. The fungus improves the nutrient supply of the plant, while the plant provides the fungus with carbohydrates. The arbuscular my-corrhiza (AM) represents a special type of mycorrhiza. The AM forms during the sym-biosis eponymous arbuscules within the root cells as the supposed site of the major nu-trient exchange. The AM symbiosis (AMS) is the research focus of this work. Medicago truncatula and Glomus intraradices were used as model organisms. During the project several transcription analysis were performed to identify AMS re-gulated transcription factors (TFs). The activity of the promoters of three of the identified AMS regulated TFs (MtOFTN, MtNTS, MtDES) were visualised using a reporter gene. Cells with promoter activity were in one case the arbuscle containing cells (MtOFTN). In the another case, the promoter was also weakly active in non arbuscle containing cells, however the major site of activity were the arbuscle containing cells (MtNTS). Another promoter was active in arbuscle containing and adjacent cells (MtDES). In addition, other genes were identified as AMS regulated and for three of these genes (MtPPK, MtAmT, MtMDRL) a promoter::reporter activity study was conducted, too. The promoters of the kinase (MtPPK) and the ammonium transporter (MtAmT) were active exclusively in arbuscle containing cells, whereas the activity of the ABC-transporter (MtMDRL) could not be assigned to a specific cell type. For two other identified genes (a copper transporter (MtCoT) and a sugar/ inositol transporter (MtSuT)) RNA-interference (RNAi) studies were carried out. The studies revealed in both cases that, once an RNAi effect was present in the transformed roots, the roots were colonised by G. intraradices in a much lesser extent as in the vector-control. In the case of MtCoT it maybe has the same basic principle as in the case of the phosphate transporter MtPt4. Which role MtSuT and inositol plays during the fo-rmation of the AMS has to be reviewed. Further examinations on the genes MtAmT, MtPPK and MtOFTN could also be reveal-ing for the understanding of the AMS, as their promotors, as shown in this thesis, are exclusively active in arbuscle containing cells The same can be said for the TFs MtNFTS and MtDES. They are not exclusively transcripted in arbuscle containing cells, but nevertheless seem to play a role in the formation of the AMS within M. truncatula roots. KW - Mykorrhiza KW - Medicago truncatula KW - Transkriptom KW - RNAi KW - Promotor KW - Mycorrhiza KW - Medicago truncatula KW - transcriptomics KW - RNAi KW - Promotor Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-63805 ER - TY - JOUR A1 - Aga-Barfknecht, Heja A1 - Hallahan, Nicole A1 - Gottmann, Pascal A1 - Jähnert, Markus A1 - Osburg, Sophie A1 - Schulze, Gunnar A1 - Kamitz, Anne A1 - Arends, Danny A1 - Brockmann, Gudrun A1 - Schallschmidt, Tanja A1 - Lebek, Sandra A1 - Chadt, Alexandra A1 - Al-Hasani, Hadi A1 - Joost, Hans-Georg A1 - Schürmann, Annette A1 - Vogel, Heike T1 - Identification of novel potential type 2 diabetes genes mediating beta-cell loss and hyperglycemia using positional cloning JF - Frontiers in genetics N2 - Type 2 diabetes (T2D) is a complex metabolic disease regulated by an interaction of genetic predisposition and environmental factors. To understand the genetic contribution in the development of diabetes, mice varying in their disease susceptibility were crossed with the obese and diabetes-prone New Zealand obese (NZO) mouse. Subsequent whole-genome sequence scans revealed one major quantitative trait loci (QTL),Nidd/DBAon chromosome 4, linked to elevated blood glucose and reduced plasma insulin and low levels of pancreatic insulin. Phenotypical characterization of congenic mice carrying 13.6 Mbp of the critical fragment of DBA mice displayed severe hyperglycemia and impaired glucose clearance at week 10, decreased glucose response in week 13, and loss of beta-cells and pancreatic insulin in week 16. To identify the responsible gene variant(s), further congenic mice were generated and phenotyped, which resulted in a fragment of 3.3 Mbp that was sufficient to induce hyperglycemia. By combining transcriptome analysis and haplotype mapping, the number of putative responsible variant(s) was narrowed from initial 284 to 18 genes, including gene models and non-coding RNAs. Consideration of haplotype blocks reduced the number of candidate genes to four (Kti12,Osbpl9,Ttc39a, andCalr4) as potential T2D candidates as they display a differential expression in pancreatic islets and/or sequence variation. In conclusion, the integration of comparative analysis of multiple inbred populations such as haplotype mapping, transcriptomics, and sequence data substantially improved the mapping resolution of the diabetes QTLNidd/DBA. Future studies are necessary to understand the exact role of the different candidates in beta-cell function and their contribution in maintaining glycemic control. KW - type 2 diabetes KW - beta-cell loss KW - insulin KW - positional cloning KW - transcriptomics KW - haplotype Y1 - 2020 U6 - https://doi.org/10.3389/fgene.2020.567191 SN - 1664-8021 VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Cahsan, Binia De A1 - Westbury, Michael V. A1 - Paraskevopoulou, Sofia A1 - Drews, Hauke A1 - Ott, Moritz A1 - Gollmann, Günter A1 - Tiedemann, Ralph T1 - Genomic consequences of human-mediated translocations in margin populations of an endangered amphibian JF - Evolutionary Applications N2 - Due to their isolated and often fragmented nature, range margin populations are especially vulnerable to rapid environmental change. To maintain genetic diversity and adaptive potential, gene flow from disjunct populations might therefore be crucial to their survival. Translocations are often proposed as a mitigation strategy to increase genetic diversity in threatened populations. However, this also includes the risk of losing locally adapted alleles through genetic swamping. Human-mediated translocations of southern lineage specimens into northern German populations of the endangered European fire-bellied toad (Bombina bombina) provide an unexpected experimental set-up to test the genetic consequences of an intraspecific introgression from central population individuals into populations at the species range margin. Here, we utilize complete mitochondrial genomes and transcriptome nuclear data to reveal the full genetic extent of this translocation and the consequences it may have for these populations. We uncover signs of introgression in four out of the five northern populations investigated, including a number of introgressed alleles ubiquitous in all recipient populations, suggesting a possible adaptive advantage. Introgressed alleles dominate at the MTCH2 locus, associated with obesity/fat tissue in humans, and the DSP locus, essential for the proper development of epidermal skin in amphibians. Furthermore, we found loci where local alleles were retained in the introgressed populations, suggesting their relevance for local adaptation. Finally, comparisons of genetic diversity between introgressed and nonintrogressed northern German populations revealed an increase in genetic diversity in all German individuals belonging to introgressed populations, supporting the idea of a beneficial transfer of genetic variation from Austria into North Germany. KW - adaptive introgression KW - admixture KW - Bombina bombina KW - genetic rescue KW - mitogenomes KW - transcriptomics Y1 - 2020 SN - 1752-4563 VL - 14 IS - 6 PB - John Wiley & Sons, Inc. CY - New Jersey ER - TY - GEN A1 - Cahsan, Binia De A1 - Westbury, Michael V. A1 - Paraskevopoulou, Sofia A1 - Drews, Hauke A1 - Ott, Moritz A1 - Gollmann, Günter A1 - Tiedemann, Ralph T1 - Genomic consequences of human-mediated translocations in margin populations of an endangered amphibian T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Due to their isolated and often fragmented nature, range margin populations are especially vulnerable to rapid environmental change. To maintain genetic diversity and adaptive potential, gene flow from disjunct populations might therefore be crucial to their survival. Translocations are often proposed as a mitigation strategy to increase genetic diversity in threatened populations. However, this also includes the risk of losing locally adapted alleles through genetic swamping. Human-mediated translocations of southern lineage specimens into northern German populations of the endangered European fire-bellied toad (Bombina bombina) provide an unexpected experimental set-up to test the genetic consequences of an intraspecific introgression from central population individuals into populations at the species range margin. Here, we utilize complete mitochondrial genomes and transcriptome nuclear data to reveal the full genetic extent of this translocation and the consequences it may have for these populations. We uncover signs of introgression in four out of the five northern populations investigated, including a number of introgressed alleles ubiquitous in all recipient populations, suggesting a possible adaptive advantage. Introgressed alleles dominate at the MTCH2 locus, associated with obesity/fat tissue in humans, and the DSP locus, essential for the proper development of epidermal skin in amphibians. Furthermore, we found loci where local alleles were retained in the introgressed populations, suggesting their relevance for local adaptation. Finally, comparisons of genetic diversity between introgressed and nonintrogressed northern German populations revealed an increase in genetic diversity in all German individuals belonging to introgressed populations, supporting the idea of a beneficial transfer of genetic variation from Austria into North Germany. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1168 KW - adaptive introgression KW - admixture KW - Bombina bombina KW - genetic rescue KW - mitogenomes KW - transcriptomics Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523140 SN - 1866-8372 IS - 6 ER - TY - THES A1 - Cheng, Feng T1 - Evolution and ontogeny of electric organ discharge in African weakly electric fish genus Campylomormyrus: a genomic and transcriptomic perspective N2 - The African weakly electric fishes (Mormyridae) exhibit a remarkable adaptive radiation possibly due to their species-specific electric organ discharges (EODs). It is produced by a muscle-derived electric organ that is located in the caudal peduncle. Divergence in EODs acts as a pre-zygotic isolation mechanism to drive species radiations. However, the mechanism behind the EOD diversification are only partially understood. The aim of this study is to explore the genetic basis of EOD diversification from the gene expression level across Campylomormyrus species/hybrids and ontogeny. I firstly produced a high quality genome of the species C. compressirostris as a valuable resource to understand the electric fish evolution. The next study compared the gene expression pattern between electric organs and skeletal muscles in Campylomormyrus species/hybrids with different types of EOD duration. I identified several candidate genes with an electric organ-specific expression, e.g. KCNA7a, KLF5, KCNJ2, SCN4aa, NDRG3, MEF2. The overall genes expression pattern exhibited a significant association with EOD duration in all analyzed species/hybrids. The expression of several candidate genes, e.g. KCNJ2, KLF5, KCNK6 and KCNQ5, possibly contribute to the regulation of EOD duration in Campylomormyrus due to their increasing or decreasing expression. Several potassium channel genes showed differential expression during ontogeny in species and hybrid with EOD alteration, e.g. KCNJ2. I next explored allele specific expression of intragenus hybrids by crossing the duration EOD species C. compressirostris with the medium duration EOD species C. tshokwe and the elongated duration EOD species C. rhynchophorus. The hybrids exhibited global expression dominance of the C. compressirostris allele in the adult skeletal muscle and electric organ, as well as in the juvenile electric organ. Only the gene KCNJ2 showed dominant expression of the allele from C. rhynchophorus, and this was increasingly dominant during ontogeny. It hence supported our hypothesis that KCNJ2 is a key gene of regulating EOD duration. Our results help us to understand, from a genetic perspective, how gene expression effect the EOD diversification in the African weakly electric fish. N2 - Die Mormyridae, eine Familie afrikanischer schwach elektrischer Süßwasserfische, zeigen eine außergewöhnliche adaptive Radiation. Eine Erklärung für die Diversifizierung dieser Gruppe stellen die artspezifischen elektrischen Organentladungen (EODs) dar. Diese werden von einem elektrischen Organ muskulären Ursprungs im Ansatz der Schwanzflosse erzeugt. Die verschiedenen EODs könnten als präzygotischer Isolationsmechanismus für die Radiation verantwortlich sein. Dennoch ist der Mechanismus hinter der EOD-Diversifizierung bisher nicht vollständig geklärt. Ziel dieser Studie ist es, die genetische Grundlage der EOD-Diversifizierung auf der Ebene der Genexpression bei verschiedenen Campylomormyrus-Arten bzw. -Hybriden und während der Ontogenese zu ermitteln. Zunächst wurde erstmals das Genom der Art C. compressirostris in hoher Qualität sequenziert. Dies bildet eine bedeutende Grundlage für das Verständnis der Evolution der elektrischen Fische. In der zweiten Studie wurden Genexpressionsmuster von elektrischen Organen und Skelettmuskeln bei Campylomormyrus-Arten bzw. -Hybriden mit unterschiedlicher EOD-Dauer verglichen. Dabei konnten mehrere Kandidatengene identifiziert werden, die potentiell Elektroorgan-spezifisch exprimiert sind, i.a. KCNA7a, KLF5, KCNJ2, SCN4aa, NDRG3, MEF2. Bei allen untersuchten Arten/Hybriden wies das Genexpressionsmuster einen signifikanten Zusammenhang mit der EOD-Dauer auf. Die Expression mehrerer Kandidatengene, wie beispielsweise KCNJ2, KLF5, KCNK6 und KCNQ5, trägt möglicherweise zur Regulierung der EOD-Dauer bei Campylomormyrus bei. Bei Arten und Hybriden mit EOD-Unterschieden zeigten Kaliumkanal-Gene wie KCNJ2 eine unterschiedliche Expression während der Ontogenese. Zudem wurde die Allel-spezifische Expression bei Intragenus-Hybriden unter Verwendung der Arten C. compressirostris, C. tshokwe und C. rhynchophorus, die jeweils eine kurze, intermediäre bzw. lange EOD-Dauer aufweisen, untersucht. Die Hybriden wiesen eine generell dominante Expression der Allele von C. compressirostris in der adulten Skelettmuskulatur und im elektrischen Organ sowie im juvenilen elektrischen Organ auf. Einzig im Gen KCNJ2 dominierte das Allel von C. rhynchophorus, mit zunehmender Dominanz mit fortschreitender Ontogenese. Dies stützt unsere Hypothese einer Beteiligung des KCNJ2-Gens an der Regulation der EOD-Dauer. Unsere Ergebnisse stellen einen wesentlichen Beitrag zum Verständnis des Einflusses der Genexpression auf die EOD-Diversifizierung bei afrikanischen schwach elektrischen Fischen dar. KW - tropical freshwater fish KW - weakly electric fish KW - genomics KW - transcriptomics KW - Genomik KW - Transkriptomik KW - tropische Süßwasserfische KW - schwach elektrischer Fisch Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-630172 ER - TY - JOUR A1 - Aga-Barfknecht, Heja A1 - Soultoukis, George A. A1 - Stadion, Mandy A1 - Garcia-Carrizo, Francisco A1 - Jähnert, Markus A1 - Gottmann, Pascal A1 - Vogel, Heike A1 - Schulz, Tim Julius A1 - Schürmann, Annette T1 - Distinct adipogenic and fibrogenic differentiation capacities of mesenchymal stromal cells from pancreas and white adipose tissue JF - International journal of molecular sciences N2 - Pancreatic steatosis associates with beta-cell failure and may participate in the development of type-2-diabetes. Our previous studies have shown that diabetes-susceptible mice accumulate more adipocytes in the pancreas than diabetes-resistant mice. In addition, we have demonstrated that the co-culture of pancreatic islets and adipocytes affect insulin secretion. The aim of this current study was to elucidate if and to what extent pancreas-resident mesenchymal stromal cells (MSCs) with adipogenic progenitor potential differ from the corresponding stromal-type cells of the inguinal white adipose tissue (iWAT). miRNA (miRNome) and mRNA expression (transcriptome) analyses of MSCs isolated by flow cytometry of both tissues revealed 121 differentially expressed miRNAs and 1227 differentially expressed genes (DEGs). Target prediction analysis estimated 510 DEGs to be regulated by 58 differentially expressed miRNAs. Pathway analyses of DEGs and miRNA target genes showed unique transcriptional and miRNA signatures in pancreas (pMSCs) and iWAT MSCs (iwatMSCs), for instance fibrogenic and adipogenic differentiation, respectively. Accordingly, iwatMSCs revealed a higher adipogenic lineage commitment, whereas pMSCs showed an elevated fibrogenesis. As a low degree of adipogenesis was also observed in pMSCs of diabetes-susceptible mice, we conclude that the development of pancreatic steatosis has to be induced by other factors not related to cell-autonomous transcriptomic changes and miRNA-based signals. KW - MSCs KW - fatty pancreas KW - WAT KW - lineage commitment KW - transcriptomics KW - miRNAs Y1 - 2022 U6 - https://doi.org/10.3390/ijms23042108 SN - 1422-0067 VL - 23 IS - 4 PB - Molecular Diversity Preservation International CY - Basel ER - TY - THES A1 - Leer, Marina T1 - Computational analysis of the effects of ageing and diet on stem cell function and ectopic fat accumulation in the musculoskeletal system N2 - The musculoskeletal system provides support and enables movement to the body, and its deterioration is a crucial aspect of age-related functional decline. Mesenchymal stromal cells (MSCs) play an important role in musculoskeletal homeostasis due to their broad differentiation potentials and their ability to support osteogenic and myogenic tissue maintenance and regeneration. In the bone, MSCs differentiate either into osteochondrogenic progenitors to form osteocytes and chondrocytes, or increasingly with age into adipogenic progenitors which give rise to bone-resident adipocytes. In skeletal muscle, during healthy regeneration MSCs provide regulatory signals that activate local, tissue-specific stem cells, known as satellite cells, which regenerate contractile myofibres. This process involves a significant cross-talk to immune cells stemming from both lymphoid and myeloid lineages. During ageing, muscle-resident MSCs undergo increased adipogenic lineage commitment, causing niche changes that contribute to fatty infiltration in muscles. These shifts in cell populations in bone lead to the loss of osteogenic cells and subsequently osteoporosis, or in muscle to impaired regeneration and to the development of sarcopenia. However, the signals that drive transition of MSCs into their respective cellular fates remain elusive. This thesis aims to elucidate the transcriptional shifts modulating cell states and cell types in musculoskeletal MSC fate determination. Single-cell RNA-sequencing (scRNA-seq) was used to characterise cell type-specific transcript regulation. State-of-the-art bioinformatics tools were combined with different analytical platforms that include both droplet-based scRNA-seq for large heterogeneous populations, and microfluidics-based scRNA-seq to assess small, rare subpopulations. For each platform, distinct computational pipelines were established including filtering steps to exclude low-quality cells, and data visualisation was performed by dimensionality reduction. Downstream analysis included clustering, cell type annotation, and differential gene expression to investigate transcriptional states in defined cell types during ageing and injury in the muscle and bone. Finally, a novel tool to assess publication activities in defined areas of research for the identified marker genes was developed. The results in the bone indicate that ageing MSCs increasingly commit towards an adipogenic fate at the expense of osteogenic specialisation. The data also suggests that significant cell population shifts of MSC-type fibro-adipogenic progenitors during muscle ageing underlie the pathologies observed in homeostatic and post-injury regenerative conditions. High-throughput visualisation of publication activity for candidate genes enabled more effective biological evaluation of scRNA-seq data. These results expose critical age-related changes in the stem cell niches of skeletal muscle and bone, highlight their respective sensitivity to nutrition and pathology, and elucidate novel factors that modulate stem cell-based regeneration. Targeting these processes might improve musculoskeletal health in the context of ageing and prevent the negative effects of pathological lineage determination. N2 - Der Stütz- und Bewegungsapparat durchläuft eine altersbedingte gesundheitliche Verschlechterung, welche mit voranschreitendem Funktionsverlust einhergeht. Mesenchymale Stromazellen (MSCs) spielen aufgrund ihres breiten Differenzierungspotenzials und ihrer Fähigkeit, myogene bzw. osteogene Regenerationsprozesse zu unterstützen, eine wichtige Rolle in der muskuloskelettalen Homöostase. Im Knochen differenzieren MSCs entweder zu osteochondrogenen Vorläufern, um Knochen- bzw. Knorpelzellen zu bilden. Oder mit zunehmendem Alter werden vermehrt adipogene Vorläufer gebildet, aus denen Knochen-Fettzellen entstehen. Im Skelettmuskel sezernieren MSCs während der Muskelregeneration beispielsweise regulatorische Signale, die lokale, gewebespezifische Stammzellen, sogenannte Satellitenzellen, aktivieren, und diese daraufhin die kontraktilen Muskelfasern regenerieren. Dieser Prozess umfasst bedeutsame Wechselwirkung von Stammzellen mit Immunzellen sowohl der lymphoiden als auch aus myeloischen Abstammungslinien. Während des Alterns erhalten muskelresidente MSCs jedoch ein erhöhtes adipogenenes Potential, welches Nischenveränderung verursacht und damit zu einer Fettinfiltration in den Muskeln beitragen kann. Die Verschiebungen der Zellpopulationen verursachen einerseits den Verlust von osteogenen Vorläufern und fördern degenerative Prozesse im Knochengewebe, die Osteoporose zur Folge haben, oder beeinträchtigen die Regeneration im Muskel sowie dessen Funktionalität, und können damit zur altersbedingten Sarkopenie beitragen. MSCs durchlaufen einen Entscheidungsprozess um final zu differenzieren, der jedoch bislang nur unzureichend charakterisiert ist. Um diesen Aspekt zu beleuchten, untersucht diese Dissertation die diesem Prozess zugrundeliegende Veränderung der Transkriptionsprofile, welche die Zellzustände und Zelltypen bei der Differenzierung von muskuloskelettalen MSCs steuern. Einzelzell-RNA-Sequenzierung (scRNA-Seq) wurde verwendet, um die zelltyp-spezifische Transkriptionsregulation zu charakterisieren. Moderne bioinformatische Analyse-Tools und -Plattformen wurden kombiniert, die sowohl droplet-basierte (für große heterogene Populationen) als auch mikrofluidik-basierte scRNA-seq (für kleine, seltene Subpopulationen), umfassten. Es wurden plattform-spezifische Datenverarbeitungs-Pipelines generiert, einschließlich des Herausfilterns von Zellen geringer Qualität und Datenvisualisierung mit verschiedenen Dimensionsreduktions-Methoden. Die anschließende Analyse umfasste Clustering von Subpopulationen, Zelltyp-Annotation und differenzielle Genexpression, um die Transkriptionszustände in den definierten Zelltypen während des Alterns und bei Regeneration im Muskel und Knochen zu untersuchen. Abschließend wurde eine Software zur Bewertung der Publikationsaktivitäten in definierten Forschungsgebieten für die identifizierten Markergene entwickelt. Die Ergebnisse deuten im Knochen darauf hin, dass alternde MSCs auf Kosten der osteogenen Spezialisierung zunehmend adipogener werden. Weiterhin deuten unsere Daten darauf hin, dass im alternden Muskel eine signifikante Zellpopulationsanreicherung von MSCs zu fibro-adipogenen Vorläuferzellen stattfindet, welche den Pathologien in den Prozessen der Homöostase und Muskelregeneration nach Verletzung unterliegen. Die Visualisierung der Publikationsaktivität für Kandidatengene ermöglicht eine effektivere biologische Bewertung von scRNA-seq-Daten. Diese Ergebnisse offenbaren kritische altersbedingte Veränderungen innerhalb der Stammzellnischen von Skelettmuskeln und Knochen, und identifizieren neue Faktoren, die an stammzell-basierten Regeneration beteiligt sind. Diese Prozesse gezielt zu beeinflussen, könnte die muskuloskelettale Gesundheit im Alter verbessern und negative Effekte einer pathologischen Differenzierung verhindern. KW - single-cell RNA-sequencing KW - single-cell analysis KW - transcriptomics KW - mesenchymal stromal cells KW - musculoskeletal system KW - stem cell differentiation KW - mesenchymale stromale Zellen KW - Muskel-Skelett-System / Bewegungsapparat KW - Einzelzell-Sequenzierung KW - Einzelzell-Analyse KW - Stammzelldifferenzierung KW - Transkriptomik Y1 - 2023 ER - TY - THES A1 - Lamanna, Francesco T1 - Adaptive radiation and speciation in African weakly-electric fish T1 - Adaptive Radiation und Artbildung von elektrischen Fischen Afrikas BT - a phylogenetic and transcriptomic perspective BT - eine phylogenetische und transkriptomische Perspektive N2 - The rise of evolutionary novelties is one of the major drivers of evolutionary diversification. African weakly-electric fishes (Teleostei, Mormyridae) have undergone an outstanding adaptive radiation, putatively owing to their ability to communicate through species-specific Electric Organ Discharges (EODs) produced by a novel, muscle-derived electric organ. Indeed, such EODs might have acted as effective pre-zygotic isolation mechanisms, hence favoring ecological speciation in this group of fishes. Despite the evolutionary importance of this organ, genetic investigations regarding its origin and function have remained limited. The ultimate aim of this study is to better understand the genetic basis of EOD production by exploring the transcriptomic profiles of the electric organ and of its ancestral counterpart, the skeletal muscle, in the genus Campylomormyrus. After having established a set of reference transcriptomes using “Next-Generation Sequencing” (NGS) technologies, I performed in silico analyses of differential expression, in order to identify sets of genes that might be responsible for the functional differences observed between these two kinds of tissues. The results of such analyses 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; ii) the metabolic activity of the electric organ might be specialized towards the production and turnover of membrane structures; iii) several ion channels are highly expressed in the electric organ in order to increase excitability, and iv) several myogenic factors might be down-regulated by transcription repressors in the EO. A secondary task of this study is to improve the genus level phylogeny of Campylomormyrus by applying new methods of inference based on the multispecies coalescent model, in order to reduce the conflict among gene trees and to reconstruct a phylogenetic tree as closest as possible to the actual species-tree. By using 1 mitochondrial and 4 nuclear markers, I was able to resolve the phylogenetic relationships among most of the currently described Campylomormyrus species. Additionally, I applied several coalescent-based species delimitation methods, in order to test the hypothesis that putatively cryptic species, which are distinguishable only from their EOD, belong to independently evolving lineages. The results of this analysis were additionally validated by investigating patterns of diversification at 16 microsatellite loci. The results suggest the presence of a new, yet undescribed species of Campylomormyrus. N2 - Das übergreifende Ziel dieser Arbeit ist das bessere Verständnis der Bedeutung der schwachen Elektrizität für die adaptive radiation der Mormyriden Afrikas. Das gewählte Modell-Taxon, die Mormyriden-Gattung Campylomormyrus, zeigt eine große Vielfalt an elektrischen Entladungsformen. Diese Entladungsformen sind artspezifisch. Die genetische Basis dieses Merkmales ist allerdings noch unbekannt. In dieser Arbeit habe ich transkriptomische Untersuchungen vom elektrischen Organ und Skelettmuskel durchgeführt. Die Ergebnisse dieser Analysen zeigen, dass die phenotypischen Unterschiede zwischen dem elektrischen Organ und dem Skelettmusckel in den jeweiligen transkriptomen gespiegelt sind. Ich habe auch einen phylogenetischen Stammbaum für die Gattung Campylomormyrus hergestellt, durch die Anwendung von „Multispecies Coalescent Models“-basierten Methoden. Außerdem, durch die Anwendung von Mikrosatellitdaten, die als unabhängiger Beweis dienten, konnte ich zeigen, dass die identifizierten phylogenetischen Gruppen reproduktiv isolierte biologische Arten sind. Auf diese Weise konnte ich ein neuen, noch unbeschriebenen Art nachweisen. KW - evolution KW - transcriptomics KW - phylogeny KW - Evolution KW - Transkriptomik KW - Phylogenese Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-80097 ER -