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Institute
Die forensische Entomologie nutzt nekrophage Insekten, hauptsächlich Dipteren und ihre juvenilen Stadien, zur Schätzung der minimalen Leichenliegezeit. Dem liegt zugrunde, dass nekrophage Dipteren binnen Minuten nach dem Todeseintritt potentiell in der Lage sind, einen Leichnam zu detektieren und zu besiedeln. Das anschließende Wachstum und die Entwicklung der juvenilen Stadien erfolgt als Funktion von der Art und der Umgebungstemperatur.
Mit Hilfe von Laborstudien konnten bislang für einige forensisch relevante Fliegenarten Entwicklungsdaten erhoben werden, die eine Altersbestimmung der sich an einem Leichnam entwickelnden Larven und Puppen erlauben und so eine Schätzung der minimalen Leichenliegezeit ermöglichen. Als Nährsubstrat für Laborstudien werden tierische Gewebe verwendet. Eine Übertragbarkeit der Daten auf humanes Gewebe wurde aber bislang nicht verifiziert. In der vorliegenden Arbeit wurde das larvale Wachstum und die juvenile Entwicklungsgeschwindigkeit der forensisch relevanten Schmeißfliege Calliphora vicina (Diptera: Calliphoridae) auf humanem Muskelgewebe untersucht und mit dem Wachstum auf Schweineleber, magerem Schweinemuskelfleisch und Schweinehackfleisch verglichen. Die auf humanem Gewebe heranwachsenden Individuen waren mit bis zu 3,5 mm signifikant länger als die Individuen, die sich auf Leber und dem mageren Schweinemuskelfleisch entwickelten. Bei der Verwendung von Hackfleisch vom Schwein zeigte sich kein Unterschied. Darauf basierend wird die Empfehlung ausgesprochen, für zukünftige Entwicklungsstudien Schweinehackfleisch als Ersatz für humanes Gewebe zu verwenden.
Zahlreiche Anleitungen zur Asservierung forensisch-entomologischer Spuren empfehlen das Sammeln getrennt nach Körperregionen eines Leichnams. Dies soll eine mögliche gewebespezifische Entwicklungsrate berücksichtigen. Das für die vorliegende Arbeit durchgeführte systematische Absammeln von Fliegenlarven von 51 Leichnamen getrennt nach Körperregionen zeigte keine artspezifischen Präferenzen für bestimmte Gewebe oder Körperregionen. Das Artenspektrum entsprach größtenteils dem aufgrund von Studien an Schweinekadavern zu erwartendem Artenspektrum für Deutschland und Mitteleuropa. Insgesamt konnten 15 Schmeißfliegenarten nachgewiesen werden, von denen in der Regel mehrere gleichzeitig an einem Leichnam zu finden waren. Dies zeigt, dass ein Faktor wie interspezifische Konkurrenz in Zukunft mehr Beachtung in der Forschung erhalten sollte.
Bislang wurde in der forensischen Entomologie die minimale Leichenliegezeit durch die Untersuchung juveniler Stadien von Fliegen eingegrenzt. Eine eventuell mögliche Ausweitung dieses Zeitfensters könnte durch eine Altersbestimmung der adulten Fliegen oder der leeren Puparien gelingen. Der Nachweis, dass die dafür untersuchten Fliegen bzw. Puparien tatsächlich von dem fraglichen Leichnam stammen, war bislang nicht möglich. Die forensische relevante Schmeißfliege Lucilia sericata wurde in der vorliegenden Arbeit auf humanem Gewebe und Gewebe von elf weiteren Tierarten großgezogen. Durch die Analyse stabiler Kohlen- und Stickstoffisotope konnte ein von diesen elf Tierarten abgrenzbares humanes Isotopenprofil sowohl für die adulten Fliegen von L. sericata, als auch für ihre leeren Puparien detektiert werden. Dieses Profil spiegelte die Nahrungszusammensetzung der Wirte wider.
Die vorliegende Arbeit erhebt Daten zur Entwicklung einer forensisch relevanten Schmeißfliegenart auf humanem Gewebe, belegt das bislang lediglich am tierischen Modell erhobene Schmeißfliegeninventar als für menschliche Leichen relevant und hinterfragt die gewebespezifische Asservierungsempfehlung als ein akademisches Artefakt. Auf dieser Basis konnten Empfehlungen für die Weiterzucht fallrelevanter entomologischer Spuren ausgesprochen werden, die gerichtsverwertbar sind und die Verwendung von tierischem Gewebe oder Tierkadaver in der forensisch-entomologischen Forschung legitimieren. Die Analyse stabiler Isotope legt darüber hinaus einen neuen, innovativen Grundstein für die routinemäßige Spurenzuordnung älterer Entwicklungsstadien und ist damit Vorreiter auf dem Gebiet der forensischen Entomologie.
Im Rahmen dieser Arbeit wurden sRNAs des halophilen Archaeons Haloferax volcanii hinsichtlich ihrer biologischen und ihrer regulatorischen Funktion charakterisiert.
Um einen Überblick über die biologischen Funktionen archaealer sRNAs zu erhalten, wurde eine umfassende phänotypische Charakterisierung von 27 sRNA-Deletionsmutanten im Vergleich zum Wildtyp ausgewertet. Im Zuge dieser phänotypischen Charakterisierungen wurden zehn verschiedene Wachstumsbedingungen, morphologische Unterschiede und Veränderungen in der Zellmotilität untersucht. Hierbei zeigten nahezu alle Deletionsmutanten unter mindestens einer der getesteten Bedingungen phänotypische Unterschiede. Durch den Verlust von sRNAs wurden sowohl sogenannte Gain-of-function als auch Loss-of-function Phänotypen beobachtet. Haloarchaeale sRNAs spielen eine wichtige Rolle beim Wachstum mit verschiedenen Salzkonzentrationen, mit verschiedenen Kohlenstoffquellen und beim Schwärmverhalten, sind jedoch weniger in die Adaptation an diverse Stressbedingungen involviert.
Zur näheren Charakterisierung der regulatorischen Funktion archaealer sRNAs wurden sRNA362, sRNAhtsf468 und sRNA479 mittels molekulargenetischer Methoden wie Northern Blot-Analyse und DNA-Mikroarray sowie bioinformatischer in silico-Analyse untersucht. Das Expressionslevel von sRNA362 konnte bestimmt und potentielle Zielgene für sRNAhtsf468 und sRNA479 identifiziert werden.
Eine vorangegangene Studie zeigte den Einfluss von sRNA30 unter Hitzestress und führte zur Identifikation differentiell produzierter Proteine in Abwesenheit der sRNA. In dieser Arbeit wurde mittels Northern Blot-Analysen die Expression der sRNA30 charakterisiert. Das Wachstum in An- und Abwesenheit von sRNA30 wurde bei 42°C und 51°C phänotypisch charakterisiert und der regulatorische Einfluss der sRNA auf die mRNA differentiell regulierter Proteine durch Northern Blot-Analyse überprüft. Eine Transkriptomanalyse mittels DNA-Mikroarray nach Hitzeschock-Induktion führte zur Identifikation differentiell regulierter Gene involviert in Transportprozesse, Metabolismus, Transkriptionsregulation und die Expression anderer sRNAs. Die differentielle Regulation des Proteoms nach Hitzeschockinduktion in An- und Abwesenheit von sRNA30 konnte bestätigt werden.
Desweiteren wurde in dieser Arbeit sRNA132 und deren phosphatabhängige Regulation der Ziel-mRNA HVO_A0477-80 näher charakterisiert. Eine Induktionskinetik nach Phosphatentzug bestätigte die Bedeutung von sRNA132 für die verstärkte Expression des Operons HVO_A0477-80 unter Phosphatmangel-Bedingungen und verwies auf die Existenz weiterer Regulationsmechanismen. Während vor und nach Phosphatentzug kein Unterschied bezüglich der Zellmorphologie von Wildtyp und Deletionsmutante zu erkennen war, führte das Wachstum mit einem starken Phosphatüberschuss von 5 mM zu einer Zellverlängerung der Deletionsmutante. Die Kompetition der nativen 3‘-UTR des Operons HVO_A0477-80 mit einer Vektor-kodierten artifiziellen 3‘-UTR legt eine Regulation über die Bindung von sRNA132 an die 3‘-UTR nahe. Der Transkriptomvergleich nach Phosphatentzug in An- und Abwesenheit von sRNA132 führte zur Identifikation des Phosphoregulons der sRNA. Zu diesem Phosphoregulon gehören unter anderem zwei Glycerinphosphat-Dehydrogenasen, Transkriptionsregulatoren, eine Polyphosphatkinase und eine Glycerolphosphodiesterase. Zudem waren die Transkriptlevel der beiden ABC-Transporter HVO_A0477-80 und HVO_2375-8 für anorganisches Phosphat und des Transporters HVO_B0292-5 für Glycerinaldehyd-3-Phosphat in Abwesenheit der sRNA verringert. Die beiden ABC-Transportsysteme für anorganisches Phosphat wurden im Rahmen dieser Arbeit deletiert und weiter charakterisiert. Es konnte gezeigt werden, dass das ABC-Transportsystem HVO_2375-8 bei geringen Phosphatkonzentrationen leicht induziert wird und das Transkriptlevel in Anwesenheit von sRNA132 erhöht ist. Wachstumsversuche der jeweiligen Deletionsmutante in direkter Konkurrenz mit dem Wildtyp zeigten, dass keiner der beiden ABC-Transporter den anderen vollständig ersetzen kann und der Wildtyp mit beiden intakten ABC-Transportern unter phosphatlimitierenden Bedingungen einen Wachstumsvorteil besitzt. In silico-Analysen der Promotorbereiche von sRNA und ABC-Transporter legen zudem die Existenz von P-Boxen nahe.
Heat stress transcription factors (Hsfs) have an essential role in heat stress response (HSR) and thermotolerance by controlling the expression of hundreds of genes including heat shock proteins (Hsps) with molecular chaperone functions. Hsf family in plants shows a striking multiplicity, with more than 20 members in many species. In Solanum lycopersicum HsfA1a was reported to act as the master regulator of the onset of HSR and therefore is essential for basal thermotolerance. Evidence for this was provided by the analysis of HsfA1a co-suppression (A1CS) transgenic plants, which exhibited hypersensitivity upon exposure to heat stress (HS) due to the inability of the plants to induce the expression of many HS-genes including HsfA2, HsfB1 and several Hsps. Completion of tomato genome sequencing allowed the completion of the Hsf inventory, which is consisted of 27 members, including another three HsfA1 genes, namely HsfA1b, HsfA1c and HsfA1e.
Consequently, the suppression effect of the short interference RNA in A1CS lin e was re-evaluated for all HsfA1 genes. We found that expression of all HsfA1 proteins was suppressed in A1CS protoplasts. This result suggested that the model of single master regulator needs to be re-examined.
Expression analysis revealed that HsfA1a is constitutively expressed in different tissues and in response to HS, while HsfA1c and HsfA1e are minimally expressed in general, and show an induction during fruit ripening and a weak upregulation in late HSR. Instead HsfA1b shows preferential expression in specific tissues and is strongly and rapidly induced in response to HS. At the protein level HsfA1b and HsfA1e are rapidly degraded while HsfA1a and HsfA1c show a higher stability. In addition, HsfA1a and HsfA1c show a nucleocytosolic distribution, while HsfA1b and HsfA1e a strong nuclear retention.
A major property of a master regulator in HSR is thought to be its ability to cause a strong transactivation of a wide range of genes required for the initial activation of protective mechanisms. GUS reporter assays as well as analysis of transcript levels of several endogenous transcripts in protoplasts transiently expressing HsfA1 proteins revealed that HsfA1a can stimulate the transcription of many genes, while the other Hsfs have weaker activity and only on limited set of target genes. The low activity of HsfA1c and HsfA1e can be attributed to the lower DNA capacity of the two factors as judged by a GUS reporter repressor assay.
HsfA1a has been shown to have synergistic activity with the stress induced HsfA2 and HsfB1. The formation of such complexes is considered as important for stimulation of transcription and long term stress adaptation. All HsfA1 members show synergistic activity with HsfA2, while only HsfA1a act as co-activator of HsfB1 and HsfA7. Interestingly, HsfA1b shows an exceptional synergistic activity with HsfA3, suggesting that different Hsf complexes might regulate different HS-related gene networks. Altogether these results suggest that HsfA1a has unique characteristics within HsfA1 subfamily. This result is interesting considering the very high sequencing similarity among HsfA1s, and particularly among HsfA1a and HsfA1c.
To understand the molecular basis of this discrepancy, a series of domain swapping mutants between HsfA1a and HsfA1c were generated. Oligomerization domain and C-terminal swaps did not affect the basal activity or co-activity of the proteins. Remarkably, an HsfA1a mutant harbouring the N-terminus of HsfA1c shows reduced activity and co-activity, while the reciprocal HsfA1c with the N-terminus of HsfA1a cause a gain of activity and enhanced DNA binding capacity.
Sequence analysis of the DBD of HsfA1 proteins revealed a divergence in the highly conserved C-terminus of the turn of β3-β4 sheet. As the vast majority of HsfA1 proteins, HsfA1a at this position comprises an Arg residue (R107), while HsfA1c a Leu and HsfA1e a Cys. An HsfA1a-R107L mutant has reduced DNA binding capacity and consequently activity. Therefore, the results presented here point to the essential function of this amino acid residue for DNA binding function. Interestingly, the mutation did not affect the activity of the protein on Hsp70-1, suggesting that the functionality of the DBD and consequently the transcription factor on different promoters with variable heat stress element number and architecture is dependent on structural peculiarities of the DBD.
In conclusion, the unique properties including expression pattern, transcriptional activities, stability, DBD-peculiarities are likely responsible for the dominant function of HsfA1a as a master regulator of HSR in tomato. Instead, other HsfA1-members are only participating in HSR or developmental regulations by regulating a specific set of genes. Furthermore, HsfA1b and HsfA1e are likely function as stress primers in specific tissues while HsfA1c as a co-regulator in mild HSR. Thereby, tomato subclass A1 presents another example of function diversity not only within the Hsf family but also within the Hsf-subfamily of closely related members. The diversification based on DBD peculiarities is likely to occur in potato as well. Therefore this might have eliminated the functional redundancy observed in other species such as Arabidopsis thaliana but has probably allowed the more refined regulation of Hsf networks possibly under different stress regimes, tissues and cell types.
Hämophilie A ist eine X-chromosomal rezessiv vererbte Krankheit, die aufgrund von Mutationen innerhalb des Gens von Gerinnungsfaktor VIII (FVIII) zum funktionellen Defekt oder zum Fehlen des körpereigenen FVIII führt. FVIII zirkuliert als Heterodimer und besteht aus einer schweren Kette mit der Domänenstruktur A1-A2-B und einer leichten Kette mit der Domänenstruktur A3-C1-C2. Bei Patienten unter Prophylaxe wird durch regelmäßige Substitution mit rekombinanten oder aus Plasma gewonnenen FVIII-Präparaten die Hämostase wiederhergestellt. Allerdings entwickeln hierbei etwa 30% der Patienten mit einer schweren Hämophilie eine FVIII-spezifische Immunantwort in Form von neutralisierenden Antikörpern (Inhibitoren). Die sogenannte Immuntoleranz-Therapie (engl. immune tolerance induction therapy, ITI) ist bisher die einzige etablierte Therapie, die zu einer dauerhaften Eradikation der FVIII-Inhibitoren und Induktion von Toleranz gegenüber FVIII führen kann. Die Therapie beruht auf einer meist täglichen Gabe hoher FVIII-Dosen, welche sich, je nach Behandlungsdauer, über Wochen bis hin zu Jahren erstrecken kann. Bei etwa 30% der Patienten ist diese Therapie nicht erfolgreich. Für solche Patienten besteht die Gefahr lebensbedrohlicher, unkontrollierbarer Blutungen und erheblicher Gelenkschäden.
Die spezifische Ansteuerung des Membran-gebundenen Immunglobulin G (mIg) des B-Zellrezeptors (BZR) mithilfe von Immuntoxinen ist eine mögliche Option zur selektiven Eliminierung FVIII-spezifischer B-Zellen und somit zur Eradikation von FVIII-Inhibitoren. Solche Immuntoxine bestehen aus einer zellbindenden und einer zytotoxischen Domäne, welche nach Internalisierung zur Apoptose der Zielzelle führen soll. Da FVIII aufgrund der Größe als zellbindende Domäne ungeeignet ist, beschäftigt sich die vorliegende Arbeit mit der Entwicklung und Evaluierung alternativer Immuntoxine zur selektiven Eliminierung FVIII-spezifischer B-Zellen. Die FVIII-spezifische Immunantwort ist zwar polyklonal, jedoch vor allem gegen A2- und die C2-Domäne gerichtet. Aus diesem Grund wurden die humane A2- und C2-Domäne (hA2, hC2) als zellbindende Domäne verwendet und jeweils genetisch an eine verkürzte Version des Exotoxin A (ETA) aus Pseudomonas aeruginosa fusioniert, bei welcher die natürliche zellbindende Domäne entfernt wurde. Die rekombinanten Proteine wurden bakteriell produziert und im Anschluss an die Aufreinigung biochemisch charakterisiert. Während das bakterielle Expressionssystem für hA2-ETA nicht geeignet war, konnte hC2-ETA neben weiteren Kontrollproteinen mit korrekter Konformation der hC2-Domäne hergestellt und aufgereinigt werden.
Die Fähigkeit zur selektiven Eliminierung hC2-spezifischer B-Zellen wurde im weiteren Verlauf sowohl in vitro mithilfe einer hC2-spezifischen Hybridomazelllinie als auch ex vivo und in vivo mithilfe von Splenozyten aus FVIII-immunisierten FVIII-knockout Mäusen untersucht.
Durch Inkubation der hC2-spezifischen Hybridomazelllinie mit hC2-ETA konnten ca. 38 % der Zellen eliminiert werden. Weitere Untersuchungen der Zelllinie ergaben, dass diese keinen vollständigen funktionalen B-Zellrezeptor auf der Oberfläche exprimierte, welcher für die Bindung und die korrekte Internalisierung des Immuntoxins notwendig ist. Aufgrund dessen eignet sich diese Zelllinie nicht als Modell für eine genauere Analyse der in vitro Eliminierungseffizienz von hC2-ETA.
Weitere Analysen mithilfe von Splenozyten aus FVIII-immunisierten FVIII-knockout Mäusen haben jedoch gezeigt, dass durch ex vivo Inkubation der Splenozyten mit hC2-ETA, alle hC2-spezifischen B-Zellen vollständig, selektiv und konzentrations-abhängig eliminiert werden konnten. Auch die mehrfache Applikation von hC2-ETA in FVIII-immunisierten FVIII-knockout Mäusen führte bei der Hälfte der Tiere zur vollständigen Eliminierung aller hC2-spezifischen B-Zellen. Eine Reduktion des hC2-spezifischen Antikörpersignals konnte nach Gabe von hC2-ETA in allen behandelten Tieren beobachtet werden. Die unvollständige Eliminierung in der Hälfte der Tiere ist vermutlich auf die Präsenz hC2-spezifischer Antikörper zurückzuführen, die einen Teil des applizierten Immuntoxins neutralisiert haben, sodass nicht alle hC2-spezifischen Gedächtnis-B-Zellen erreicht und eliminiert werden konnten. Um die Eliminierungseffizienz von hC2-ETA weiter zu erhöhen, müsste das Behandlungsprotokoll geändert werden. Sowohl eine Verlängerung des Behandlungszeitraums als auch eine kombinierte Therapie aus FVIII und hC2-ETA sollte zu einer erhöhten Bioverfügbarkeit des Toxins und dadurch zu einer gesteigerten Eliminierungseffizienz führen.
Die Ausweitung des hier vorgestellten Ansatzes auf weitere FVIII-Domänen ist generell möglich, jedoch muss hierzu ein alternatives Expressionssystem aufgrund des eukaryotischen Ursprungs von FVIII in Betracht gezogen werden. Die hier vorgestellten Ergebnisse zeigen dennoch, dass FVIII-Domänen-Immuntoxine ein wirkungsvolles Mittel sind, um FVIII-spezifische B-Zellen selektiv zu eliminieren. Die Anpassung der Gabe von FVIII-Domänen-Immuntoxinen an die individuelle Immunantwort des Patienten könnte das Auftreten von Nebenwirkungen minimieren. Außerdem könnte eine kombinierte Therapie aus ITI und FVIII-Domänen-Immuntoxinen die Zeit bis zur Induktion von Toleranz verkürzen und die Chancen für den generellen Therapieerfolg erhöhen.
Smut fungi (Ustilaginomycotina) were previously defined as plant parasites that produced blackish or brownish masses of teliospores in or on various organs of plants. Each teliospore germinates to form a single basidium with usually four basidiospores that subsequently grow as a saprobic, yeast-like, haploid stage. The Ustilaginomycotina are a highly diverse group with about 1,700 species in 115 different genera. All of the species were united in a single order, the Ustilaginales, in late 19th century. These teliospore producing fungi are now considered the classic smut fungi. Towards the end of the 20th century, new ideas were brought into this classification system. Most notable was the comparative work regarding the ultrastructure of septal pores and the anatomy of the interaction zones between host and parasite. This work changed the whole concept of smut fungi and their evolutionary relationships. These results were subsequently supported by molecular phylogenetic studies. Both lines of investigation led to the classification of the smut fungi into four different classes, Ustilaginomycetes, Exobasidiomycetes, Malasseziomycetes and Moniliellomycetes (see chapter 1.3).
A reliable taxonomy that reflects phylogenies needed in order to estimate the diversity and the relationships between the diverse groups of smut fungi. In the last 20 years, molecular investigations based mostly on rDNA loci, e.g. ITS (internal transcribed spacer) or LSU (large subunit), have revealed the evolutionary relationships between many taxa of smut fungi. However, there are few phylogenetic studies available for smut fungi (see chapter 1.5.1), and much work is needed to develop backbone phylogenetic trees and to resolve species complexes of many smut fungi.
This thesis reports the results of six different studies that aimed to develop new and improved tools for the phylogenetic analyses of smut fungi, and then apply these methods to selected groups of smut fungi. The first study (Kruse et al. 2017a, Chapter 3) developed a method to improve the amplification of ITS sequences of some smut fungi. Due to its high discrimination value, the ITS gene region is widely used as a barcoding locus for species delimitation of fungi. For this purpose, the general ITS primers ITS1 and ITS4 or more specific modifications, e.g. ITS1F for Ascomycota, ITS4B for Basidiomycota or M-ITS1 for smut fungi, were used. As these primer combinations often yielded unsatisfactory results, due to coamplification of other (contaminant) fungi or the host plant DNA, improvement of the amplification of the ITS region was needed. In order to design new smut specific primers for the ITS region, a representative set of several sequences of the flanking regions of the ITS region (LSU and SSU) of smut fungi, plants and other fungi were downloaded from GenBank. A set of primers was designed on this dataset. These primers were tested on a representative set of about 70 different smut genera under different PCR conditions. Finally, three different primers, one forward primer, smITS-F, and two reverse primers, smITS-R1 and -R2, were selected as the best ones. The following tests with different combinations of these primers, and also under inclusion of the M-ITS1 primer, showed only slight differences in the number of different genera that successfully amplified. But there were some differences regarding the genera that amplified. A broader test on 205 samples in 39 genera showed that the PCR efficiency of the newly designed primers was much better than the primer set ITS4/M-ITS1. With the primers designed in this study almost no non-target ITS was amplified, giving new opportunities especially for amplifying ancient DNA or DNA from older herbarium samples. However, many species groups remain unresolved by only one gene region.
The second study (Kruse et al. 2017c, Chapter 4) found new loci and suitable primers that better resolved multi-locus trees. To date, the most frequently used loci for making multi-locus trees are SSU (small subunit), LSU (large subunit) and ITS (internal transcribed spacer). While the LSU is not always sufficient to distinguish between closely related species, it is highly discriminative above the species level. In an effort to increase the phylogenetic resolution of smut phylogenies, some protein-coding genes were used, including rpb1, rpb2, and atp6 with varying success (see Chapter 2.1.2). As most of these loci are seldom used or sometimes only work on pure cultures because of their low specifity, new protein-coding loci were identified that produced reliable phylogenetic trees. Based on five available genomes, potential gene loci were filtered for possible primers. Initially, 40 different primer combinations for 14 gene loci were tested on a set of twelve different genera of smut fungi. The best candidates were selected and optimized during further tests. Finally, 22 different forward primers and 17 different reverse primers for nine different gene regions were developed, with each differentiating at least one genus of smut fungi (preferably for Ustilaginomycetes). The different primers showed varying discriminative power for different smut genera. They worked best for the Ustilaginaceae, based on the primer designed from Ustilaginomycetes genomes. These new primer sets and loci have the potential to resolve different species groups within the smut fungi and furthermore to produce reliable phylogenetic trees with high resolution. To prove their applicability, three species complexes were investigated in-depth, two from the Ustilaginomycetes and one from the Exobasidiomycetes.
...
Lizards of Paraguay: an integrative approach to solve taxonomic problems in central South America
(2018)
Paraguay is located in the center of South America with drier and warmer climatic conditions in the western part of the country, and more temperate and humid in the eastern region. Biogeographically, Paraguay is a key spot in South America, where several ecoregions converge. In my study, I sampled most of the ecoregions of Paraguay. The main objective of my work is to solve taxonomic problems, identified through genetic barcoding analyses, in the central region of South America. To achieve this objective, I used selected taxa of the Paraguayan Squamata as models taking into consideration the crucial geographic position of the country, plus the scarce available genetic data of Paraguayan reptiles.
The collecting activities were performed in the framework of a barcoding inventory project of the Paraguayan herpetofauna and carried out mostly in rural areas searching for animals in different types of habitats using active search as the sampling technique.
For genetics, the extraction of DNA was performed with DNeasy® Blood & Tissue Kit of Qiagen® for sets of few samples, and the fiber glass plate protocol for sets of 96 samples. I assessed the quality of sequences after amplification in agarose gel electrophoresis. The first marker sequenced was 16S mtDNA, used for barcoding analysis. A DNA barcode is a genetic identifier for a species. Once a taxonomic problem was detected, I generate more gene sequences to target the issue.
All the analyses to test phylogenetic hypotheses (based on single genes or concatenated datasets) were performed under Maximum Likelihood and Bayesian approaches. To root the phylogenetic trees, I chose the available taxon (or taxa) most closely related to the respective studied group as outgroups. For the general tree of Paraguayan Squamata, based on barcodes of 16S, I chose Sphenodon punctatus.
I generated a total of 142 sequences of 64 species of Squamata from Paraguay (Appendix I). The final alignment of 615 bp comprised 249 samples. The best substitution model for the Barcoding dataset based on the gene 16S was GTR+G, according to the BIC.
To complement molecular evidence generated with the ML grouping of 16S barcodes, I took a morphological approach based on voucher specimens collected during fieldwork (usually the same specimens that I used for genetic analysis), supplemented by the revision of museum collections.
Summarizing my results, samples of Colobosaura exhibit large genetic distances, and accordingly I revalidated Colobosaura kraepelini (Appendix II). Tropidurus of the spinulosus group show two clades and among them there is little genetic and morphological variation, I synonymized T. tarara and T. teyumirim with T. lagunablanca, and T. guarani with T. spinulosus (Appendix III). I detected the presence of candidate species of Homonota, and I restricted the name H. horrida for Argentina, and described two new species of Homonota (Appendices IV and V), and a new species of Phyllopezus also in the Family Phyllodactylidae (Appendix VI).
In this work I present the most comprehensive analysis of genetic samples of Squamata from Paraguay. The results obtained here will be useful to help to clarify further taxonomic issues regarding the squamate fauna from the central region of South America. Moreover, the data generated for this study will have a positive impact in a larger geographic context, beyond Paraguayan borders.
Regarding the conservation of the Paraguayan reptiles, and considering the taxonomic changes accomplished here, it is important to note that many species lack legal protection. In Paraguay, the major problem for conservation is habitat loss due to extensive crop farming. Thus, currently, the protected areas are the best strategy for conservation of biodiversity in the country. However, many such areas face legal problems (e.g., lack of official measurements, management plans, forest guards, infrastructure, etc.) so that the maintenance of their biodiversity over time is not guaranteed.
In conclusion, in this study I present contributions on the taxonomy of mostly lizards from Paraguay. Due to lack of samples, I was not able to deal with a deep taxonomic revision of the country's snakes. Based on my results, I can argue that analyses of Xenodontini and Pseudoboini are currently a pressing research issue. This barcoding project may continue since some colleagues in Paraguay are interested in collaboration. Given that the sequenced specimens are yet a small portion of the actual diversity of Paraguay, it will be of utmost importance to continue and expand these studies that will further improve our taxonomic knowledge. Furthermore, it is desirable to have Paraguayan scientists not only involved, but to see them taking the lead of high quality taxonomic research.
Heat stress transcription factors (Hsfs) are required for transcriptional changes during heat stress (HS) thereby playing a crucial role in the heat stress response (HSR). The target genes of Hsfs include heat shock proteins (Hsps), other Hsfs and genes involved in protection of the cell from irreversible damages due to exposure to elevated temperatures. Among 27 Hsfs in Solanum lycopersicum, HsfA1a, HsfA2 and HsfB1 constitute a functional triad which regulates important aspects of the HSR. HsfA1a is constitutively expressed and described as the master regulator of stress response and thermotolerance. Activation of HsfA1a under elevated temperatures leads to the induction of HsfA2 and HsfB1 which further stimulate the transcription of HS-responsive genes by forming highly active complexes with HsfA1a. Despite the well-established role of these three Hsfs in tomato HSR, information about functional relevance of other Hsfs is currently missing.
The heat stress inducible HsfA7 belongs alongside with HsfA2 to a phylogenetically distinct clade. Thereby the two proteins share high homology and a functional redundancy has been assumed. However, HsfA7 function and contribution to stress responses have not been investigated into detail in any plant species.
Tomato HsfA7 protein accumulates already at moderately elevated temperatures (~35°C) while HsfA2 becomes dominant at higher temperatures (>40°C). HsfA7 pre-mRNA undergoes complex and temperature-dependent alternative splicing resulting in several transcripts that encode for three protein isoforms. HsfA7-I contains a functional nuclear export signal (NES) and shows nucleocytoplasmic shuttling while HsfA7-II and HsfA7-III have a truncated NES which leads to the strong nuclear retention of the protein. Differences in the nucleocytoplasmic equilibrium have a major impact on the stability of protein isoforms, as nuclear retention is associated with increased protein turnover. Consequently, HsfA7-I shows a higher stability and can be detected even after 24 hours of stress attenuation, while HsfA7-II is rapidly degraded. The degradation of these factors is mediated by the ubiquitin-proteasome pathway.
HsfA7 can physically interact with HsfA1a and HsfA3 and form co-activator (“superactivator”) complexes with a very high transcriptional activity as shown on different HS-inducible promoters. In order for the complex to be successfully transferred to the nucleus and confer its activity it needs a functional nuclear localization signal (NLS) of HsfA7. In contrast, the activator (AHA) motif of HsfA7 is not essential for its co-activator function. Interestingly, while interaction of HsfA7 with either HsfA3 or HsfA1a stabilizes HsfA7 isoforms, concomitantly this leads to an increased turnover of HsfA1a and HsfA3. In contrast, HsfA2 has a stabilizing effect on the master regulator HsfA1a.
Thus, HsfA7 knockout mutants generated by CRISPR/Cas9 gene editing, show increased HsfA1a levels and a stronger induction of HS-related genes at 35°C compared to wild-type plants and HsfA2 knockout mutants. Consequently, HsfA7 knockout seedlings exhibit increased thermotolerance as shown by the enhanced hypocotyl elongation under a prolonged mild stress treatment at 35°C. In summary, these results highlight the importance of HsfA7 in regulation of cellular responses at elevated temperatures. Under moderately elevated temperatures, the accumulation of HsfA7 and its subsequent interaction with HsfA1a, leads to increased turnover of the latter, thereby ensuring a milder transcriptional activation of temperature-responsive genes like Hsps. In turn, in response to further elevated temperatures, HsfA2 becomes the dominant stress-induced Hsf. HsfA2 forms co-activator complexes with HsfA1a which in contrast to HsfA7, allows the stabilization of the master regulator, leading to the stronger expression of HS-responsive genes required for survival. Thereby, this study uncovers a new regulatory mechanism, where the temperature-dependent competitive interaction of HsfA2 and HsfA7 with HsfA1a control the fate of the master regulator and consequently the activity of temperature-responsive networks.
In the 'Golden Age of Antibiotics', between 1940 and 1970, the global pharmaceutical companies discovered many antibiotics, such as cephalosporins, tetracyclines, aminoglycosides, glycopeptides, etc., as well as antifungal and antiparisitic agents. Due to several reasons, e.g. the steady re-discovery of already known NPs and the associated high costs, many pharmaceutical companies have significantly scaled back or totally abandoned their NP discovery programs since the late 20th century. Instead those companies started to focus on drug discovery based on combinatorial synthesis and thereby on the creation of enormous synthetic libraries containing small molecules. Unfortunately, this synthetic approach dealing with the optimization of existing NP or antibiotic has its limitations. As a result, leading pharmaceutical companies are re-conducting NPs research to discover new antimicrobials for the upcoming antimicrobial resistance threat. The Natural Product Center of Excellence, a collaboration between Sanofi-Aventis and Fraunhofer IME, is advancing in this context the discovery and development of novel antimicrobial agents for the treatment of infectious diseases through the testing of Sanofi's microbial extract library and strain collection. The aim of the present PhD thesis was the discovery and isolation of novel antimicrobial compounds with improved activities and/or novel MOAs as potential lead compound for a further drug discovery.
Bei Autismus-Spektrum-Störungen (ASS) handelt es sich um genetisch komplexe Störungen mit hoher Erblichkeit. Als zugrundeliegender Pathomechanismus von ASS werden unter anderem Veränderungen der neuronalen Entwicklung diskutiert. Der Phänotyp von ASS ist definiert durch Einschränkungen in der sozialen Interaktion und Kommunikation sowie repetitives und stereotypes Verhalten. Genkopiepolymorphismen (englisch „copy number variations“/CNVs), also Deletionen oder Duplikationen einer chromosomalen Region, wurden wiederholt in Probanden mit ASS identifiziert. Hierbei ist in ASS die Region 16p11.2 mit am häufigsten von CNVs betroffen. Einige Gene aus diesem chromosomalen Abschnitt wurden bereits funktionell charakterisiert. Dennoch können die Befunde der bisherigen Einzelgenstudien nicht alle Aspekte erklären, die durch 16p11.2 CNVs hervorgerufen werden. Ziel dieser Studie war es daher, ein weiteres neuronal assoziiertes Kandidatengen dieser Region zu identifizieren und im Anschluss funktionell im Kontext der neuronalen Differenzierung zu charakterisieren.
Das SH-SY5Y Neuroblastom-Zellmodell wurde auf Transkriptom- und morphologischer Ebene auf seine Eignung als Modell für neuronale Differenzierung untersucht und bestätigt. Eine Analyse der Expressionen aller Gene der 16p11.2-Region zeigte, dass das Gen Quinolinat-Phosphoribosyltransferase (QPRT) eine vergleichsweise hohe Expression mit der stärksten und robustesten Regulierung über die Zeit aufwies. Eine de novo Deletion der 16p11.2-Region wurde in einem Patienten im Vergleich zu seinen Eltern validiert. In Patienten-spezifischen lymphoblastoiden Zelllinien derselben Familie konnten wir eine Gendosis-abhängige Expression von QPRT auf RNA-Ebene bestätigen. In SH-SY5Y-Zellen korrelierte die Expression von QPRT signifikant mit der Entwicklung von Neuriten während der Differenzierung. Um QPRT funktionell zu charakterisieren, benutzten wir drei verschiedene Methoden zur Reduktion der QPRT-Gendosis: (i) knock down (KD) durch siRNA, (ii) chemische Inhibition durch Phthalsäure und (iii) knock out (KO) über CRISPR/Cas9-Geneditierung. Eine Reduktion von QPRT durch siRNA führte zu einer schwachen Veränderung der neuronalen Morphologie differenzierter SH-SY5Y-Zellen. Die chemische Inhibition sowie der genetische KO von QPRT waren letal für differenzierende aber nicht für proliferierende Zellen. Eine Metabolitenanalyse zeigte keine Veränderungen des QPRT-assoziierten Tryptophanstoffwechsels. Gene, welche auf Transkriptomebene im Vergleich zwischen KO- und Kontrollzellen differenziell reguliert vorlagen, waren häufig an Prozessen der neuronalen Entwicklung sowie an der Bildung, Stabilität und Funktion synaptischer Strukturen beteiligt. Die Liste differenziell regulierter Gene enthielt außerdem überdurchschnittlich viele ASS-Risikogene und ko-regulierte Gengruppen waren assoziiert mit der Entwicklung des dorsolateralen präfrontalen Cortex, des Hippocampus sowie der Amygdala.
In dieser Studie zeigten wir einen kausalen Zusammenhang zwischen QPRT und der neuronalen Differenzierung in vitro sowie einen Einfluss von QPRT auf die Regulation von ASS-assoziierten Genen und Gen-Netzwerken. Funktionell standen diese Gene im Kontext mit synaptischen Vorgängen, welche durch Veränderungen zu einem Exzitations-Inhibitions-Ungleichgewicht und letztendlich zum Zelltod von Neuronen führen können. Unsere Ergebnisse heben in Summe die wichtige Rolle von QPRT in der Krankheitsentstehung von ASS, insbesondere in Trägern einer 16p11.2 Deletion, hervor.
Microsporidia are a group of parasites that infect a wide range of species, many of which play important roles in agriculture and human disease. At least 14 microsporidian species have been confirmed to cause potentially lifethreatening infectious diseases in both immunocompromised and immunocompetent humans. Approximately 1,400 species of microsporidia have been described. Depending on their host and habitat they are classified into three groups, the aquasporidia, the terresporidia and the marinosporidia.
Microsporidia were originally classified as fungi by Naegeli (1857). However, their lack of typical eukaryotic components – such as mitochondria, Golgi bodies or peroxisomes – suggested to place the microsporidia together with other amitochondriate protists within the Archezoa kingdom. This "microsporidia-early" hypothesis was further supported by molecular phylogenies inferred from individual genes. Despite this evidence, the placement of microsporidia as an early branching eukaryote remained a topic for debate. The phylogeny of microsporidia is prone to suffer from biases in their reconstruction. The high evolutionary rate of microsporidian proteins tends to place these proteins together with other fast evolving lineages, a phenomenon known as long-branch attraction. In 1996, the first molecular phylogenetic studies placed the microsporidia inside the fungi.
Subsequently, several further studies located the microsporidia at different positions inside the fungal clade. Since then, microsporidia have been considered as members of the Ascomycota, Zygomycota, Cryptomycota, or as a sister group to the Ascomycota and Basidiomycota, or even as the sister group of all fungi.
The difficulties in determining the evolutionary origin of microsporidia are not only caused by their lack of several cellular components but also by their reduced genomes and metabolism. Being obligate intracellular parasites, microsporidia successfully reduced their genome sizes, down to the range of bacteria. As the smallest eukaryotic genome described so far, the genome of Encephalitozoon intestinalis is just 2.3 Mbp, about half the size of the one of Escherichia coli. Due to their low number of protein coding genes (less than 4,000), microsporidia are thought to retain only genes essential for their survival and development. Furthermore, several key metabolic pathways are missing in the microsporidia, such as the citric acid cycle, oxidative phosphorylation, or the de novo biosynthesis of nucleotides. As a result they are in an obligatory dependence on many primary metabolites from the hosts. However, the presence of hsp70 protein suggests a more complex genome of the microsporidian ancestor. Consequently, the small microsporidian genomes and the reduced metabolism would be consequences of a secondary loss process that molded the contemporary microsporidia from a functionally more complex ancestral species. However, it remains unclear whether the last common ancestor (LCA) of the microsporidia was already reduced, or whether the genome compaction was lineage-specific and started from a more complex LCA.
We investigated the evolutionary history of the contemporary microsporidia through the reconstruction and analysis of their LCA. As a first step in our analysis, we have developed and implemented a software facilitating an intuitive data analysis of the large presence absence-patterns resulting from the tracing of microsporidian proteins in gene sets of many different species. These so called phylogenetic profiles can now be dynamically visualized and explored with PhyloProfile. The software allows the integration of other additional information layers into the phylogenetic profile, such as the similarity of feature architecture (FAS) between the protein under study and its orthologs. The FAS score can be displayed along the presence-absence pattern, which can help to identify orthologs that have likely diverged in function. PhyloProfile closes the methodological gap that existed between tools to generate large phylogenetic profiles to delineate the evolutionary history and the contemporary distribution of large – and ultimately complete – gene sets, and the more function-oriented analysis of individual protein. In the next step we tackled the problem of how to transfer functional annotation from one protein to another. We have developed HamFAS that integrates a targeted ortholog search based on the HaMStR algorithm with a weighted assessment of feature architecture similarities (FAS) between orthologs. In brief, for a seed protein we identify orthologs in reference species in which proteins have been functionally annotated based on manually curated assignments to KEGG Ortholog (KO) groups. The FAS scores between the orthologs and seed proteins are calculated. Subsequently, we compute pairwise FAS scores for all reference proteins within a KO group. A group's mean FAS score serves then as cutoff that must be exceeded to warrant transfer of its KO identifier to the seed. A benchmark using a manually curated yeast protein set showed that HamFAS yields the best precision (98.5%) when compared with two state-of-the-art annotation tools, KAAS and BlastKOALA. Furthermore, HamFAS achieves a higher sensitivity. On average HamFAS annotates almost 50% more proteins than KAAS or BlastKOALA.
With this extended bioinformatics toolbox at hand, we aimed at reconstructing the evolutionary history of the microsporidia. We generated a robust phylogeny of microsporidia using a phylogenomics approach. As a data basis, we identified a set of microsporidian proteins encoded by 80 core genes with one-to-one orthologs. A maximum likelihood analysis of this data
with 48 fungi and additionally in 13 species from more distantly related such as animals and plants combined in a supermatrix strongly supported the hypothesis that microsporidia form the sister group of the fungi. We confirmed that the data explains this microsporidia-fungi relationship significantly better than any other of the previously proposed phylogenetic hypotheses.
On the basis of this phylogeny, and of the phylogenetic profiles of microsporidian proteins, we then focused on reconstructing the dynamics microsporidian genome evolution. Between 2% of the proteins in the compact microsporidia Encephalitozoon intestinalis and up to 49% of the proteins of Edhazardia aedis are private for individual microsporidian species. A comparison of the sequence characteristics of these proteins to that of proteins with orthologs in other microsporidian species revealed individual differences. Yet, without further evidences it remains unclear whether these private genes are indeed lineage-specific innovations contributing to the adaptation of each microsporidium to its host, or whether these are artifacts introduced in the process of gene annotation. A total of 14,410 microsporidian proteins could then be grouped into 1605 orthologous groups that can be traced back to the last common ancestor of the microsporidia (LCA set). We found that 94% of the microsporidian LCA proteins could be tracked back to the last eukaryotic common ancestor. The high evolutionary age of these proteins, together with the resistance against gene loss in the microsporidia suggests that the corresponding functions are essential for eukaryotic life. Further 3% of the LCA proteins could be dated to the common ancestor microsporidia share with the fungi. Only 3% of the LCA proteins appear as microsporidia specific inventions. These proteins are potentially of importance for the evolutionary of the obligate parasitic lifestyle nowadays shared by all microsporidia.
The functional annotation and metabolic pathway analysis of the microsporidian LCA protein set gave us more insight into the adaptation of the microsporidia to their parasitic lifestyle and the origin of the microsporidian genome reduction. The presence of E1 and E3 components of the pyruvate dehydrogenase complex and the mitochondrial hsp70 protein support an ancestral presence of mitochondria in the ancestral microsporidia. In addition, several ancient proteins that complement gapped metabolic pathways were found in the microsporidian LCA. They suggested a more complex genome and metabolism in the LCA. However, our reconstruction of the metabolic network of the microsporidian LCA still lacks many main pathways. For example, the TCA cycle for effective energy production, and key enzymes that are required for in vivo synthesis of critical metabolites like purines and pyrimidines appear absent. We therefore find that the parasitic lifestyle and the genome reduction already occurred in the microsporidian LCA. This ancestral state was followed by further losses and gains during the evolution of each individual microsporidian lineage.
In conclusion, I described for the first time the in vivo functions of PAK2 during cardiac development and its requirement for heart contractility
AIM1 – Characterization of Pak2a and Pak2b functions during cardiovascular system development: description of the phenotype triggered by the loss of expression of pak2b in the pak2a mutant Firstly, in addition to the confirmation of the published data regarding the pak2a mutant and morphant phenotype, I showed that pak2bbns159 mutant does not exhibit morphological defects, neither in the ISV formation nor in the brain vascular patterning. More importantly, I analyzed in more details the phenotypic consequences of pak2a and pak2b loss of expression in the trunk and brain vasculatures. Indeed, the lack of blood flow in the embryos, was associated with central arteries migration defects and reduced lumen in these central arteries and the ISVs. Moreover, pak2a and pak2b loss of expression resulted in cardiac failure.
AIM2 – Role of Pak2 on cardiac contractility From 40 -46 hpf, I found a weaker heart contractility in the pak2ami149/mi149;pak2bbns159/bns159. Although, the PAK proteins have been shown to impact the actin cytoskeleton organization, the heart morphological defects associated with the altered contractility, were not associated with acto-myosin filament reorganization. However, by analyzing in more details the structure of the sarcomeres, I was able to demonstrate that the proteins constituting the sarcomeres were strongly affected and showed an altered spatial organization. Then, I also described the effects of the loss of expression of both paralogs on the junctional protein localization. I demonstrated the loss of Pak2 function resulted in junction protein rearrangement in the cardiomyocytes in the pak2ami149/mi149;pak2bbns159/bns159 mutants at 40 and 46 hpf.
Thus, I was able for the first time to demonstrate in vivo PAK2 functions during cardiac development and its requirement for proper cardiac contractility activity.
AIM3 – Decipher mechanism of Pak2 signaling cascade involved during cardiac development Both pak2a and pak2b WT mRNAs were able to rescue the pak2ami149/mi149;pak2bbns159/bns159 mutant heart defects and the results indicated that these paralogs share overlapping function during cardiac development. Moreover, although I was not able to examine the control transgenic lines, myocardial and endothelial specific pak2a overexpression did not ameliorate the mutant cardiac deficiency. Thus,the absence of rescue by reactivating pak2a in cardiomyocytes indicates a non-cell autonomous function of Pak2a on cardiomyocytes.
For the first time, this study allowed to follow PAK2 in vivo functions during cardiovascular development. More importantly, its role on heart contractility regulation would enable further investigations to generate new tools for the treatment of cardiomyopathies.
Die Analyse früher Entwicklungsstadien von Säugetierembryonen und daraus gewonnener Stammzelllinien kann entscheidende Erkenntnisse im Bereich der Reproduktionsbiologie und der regenerativen Medizin hervorbringen. Dabei spielt die Maus, als geeignetes Modellsystem für die Übertragbarkeit auf den Menschen eine wichtige Rolle, in erster Linie weil die Blastozysten der Maus verglichen mit menschliche Blastozysten eine morphologische Ähnlichkeit aufweisen. Humane embryonale Stammzelllinien haben großes Potential für die Anwendung in der regenerativen Medizin und vergleichend dazu wurde Gen-Targeting in embryonalen Stammzellen verwendet, um tausende neuer Mausstämme zu generieren. Die Gewinnung embryonaler Stammzellen erfolgt im Blastozystenstadium, diese können dann nach Injektion in eine andere Blastozyste zur Entwicklung aller Gewebearten, einschließlich der Keimbahngewebe, beitragen (Martin, 1981; Evans and Kaufman 1981).
Ursache einer Fehlgeburt können vor allem Defekte in der Entwicklung des Trophoblasten und des primitive Entoderms (PrE) sein, dabei sind ca. 5 % der Paare betroffen die versuchen ein Kind zu bekommen (Stephenson and Kutteh, 2007). Eine Untersuchung dieser Zelllinien im Mausmodell könnte weitere Erkenntnisse für die Gründe einer Fehlentwicklung liefern. Trophoblasten Stammzelllinien können aus den Blastozysten der Maus und dem extraembryonalen Ektoderm von bereits implantieren Embryonen gewonnen werden (Tanaka et al., 1998). Diese Zelllinien geben Aufschluss über die Entwicklung des Trophoblasten, fördern die Entwicklung der Plazenta und sind gleichzeitig ein gutes Modellsystem um die Implantation des Embryos im Uterus näher zu untersuchen. Zellen des primitive Entoderms (PrE) beeinflussen das im Dottersack vorhandene extraembryonale Entoderm, welches dort als “frühe Plazenta” fungiert und für die Versorgung des Embryos mit Nährstoffen zuständig ist (Cross et al., 1994). Des Weiteren besitzt das Entoderm einen induktiven Einfluss auf die Bildung von anterioren Strukturen und die Bildung von Endothelzellen sowie Blutinseln (Byrd et al., 2002).
Extraembryonale Endodermstammzellen (XEN Zellen) können aus Blastozysten gewonnen und in embryonale Stammzellen (ES-Zellen) umgewandelt werden (Fujikura et al., 2002; Kunath et al., 2005). Es war jedoch nicht bekannt, ob XEN-Zellen auch aus Postimplantations-Embryonen gewonnen werden können. XEN-Zellen tragen in vivo zur Entwicklung des Darmendoderms bei (Kwon et al., 2008; Viotti et al., 2014) und könnten als alternative, selbsterneuernde Quelle für extraembryonale Endoderm-abgeleitete Zellen dienen, die zur Herstellung von Geweben für die regenerative Medizin verwendet werden könnten (Niakan et al., 2013).
In der Embryogenese der Maus zeigt sich an Tag E3.0 eine kompakte Morula die sich allmählich in das Trophektoderm (TE) differenziert, welches wiederum den Embryonalknoten (“innere Zellmasse”) umschließt (Johnson and Ziomek, 1981). Ein wichtiger Schritt im Rahmen der Entwicklung findet an Tag E3.5 statt, in diesem Zeitraum gehen aus dem Embryonalknoten der pluripotente Epiblast und das primitive Entoderm hervor. Im späten Blastozystenstadium an Tag E4.5 liegt das PrE als Zellschicht entlang der Oberfläche der Blastocoel-Höhle. Aus dem Epiblast entwickeln sich im weiteren Verlauf der Embryo, das Amnion und das extraembryonale Mesoderm des Dottersacks. Die Zellen des Trophektoderm führen zur Entwicklung der Plazenta. Das PrE differenziert sich im Zuge der Weiterentwicklung in das viszerale Entoderm (VE) und das parietale Entoderm (PE) des Dottersacks (Chazaud et al., 2006; Gardner and Rossant, 1979; Plusa et al., 2008). VE umgibt den Epiblast und extraembryonisches Ektoderm (ExE). PE-Zellen wandern entlang der inneren Oberfläche von TE und sezernieren zusammen mit Trophoblasten-Riesenzellen Basalmembranproteine, um die Reichert-Membran zu bilden (Hogan et al., 1980). Die Reichert-Membran besteht aus Basalmembranproteinen, einschließlich Kollagenen und Lamininen, die zwischen den parietalen Endoderm- und Trophoblastzellen liegen. Diese Membran wirkt als ein Filter, der dem Embryo den Zugang zu Nährstoffen ermöglicht, während er eine Barriere zu den Zellen der Mutter bildet (Gardner, 1983).
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The fungal interaction with plants is a 400 million years old phenomenon, which presumably assisted in the plants’ establishment on land. In a natural ecosystem, all plant-ranging from large trees to sea-grasses-are colonized by fungal endophytes, which can be detected inter- and intracellularly within the tissues of apparently healthy plants, without causing obvious negative effects on their host. These ubiquitous and diverse microorganisms are likely playing important roles in plant fitness and development. However, the knowledge on the ecological functions of fungal root endophytes is scarce. Among possible functions of endophytes, they are implicated in mutualisms with plants, which may increase plant resistance to biotic stressors like herbivores and pathogens, and/or to abiotic factors like soil salinity and drought. Also, endophytes are fascinating microorganisms in regard to their high potential to produce a great spectrum of secondary metabolites with expected ecological functions. However, evidences suggest that the interactions between host plants and endophytes are not static and endophytes express different symbiotic lifestyles ranging from mutualism to parasitism, which makes difficult to predict the ecological roles of these cryptic microorganisms. To reveal the ecological function of fungal root endophytes, this doctoral thesis aims at assessing fungal root endophytes interactions with different plants and their effects on plant fitness, based on their phylogeny, traits, and competition potential in settings encompassing different abiotic contexts. To understand the cryptic implication of nonmycorrhizal endophytes in ecosystem processes, we isolated a diverse spectrum of fungal endophytes from roots of several plant species growing in different natural contexts and tested their effects on different model plants under axenic laboratory conditions. Additionally,we aimed at investigating the effect of abiotic and biotic variables on the outcome of interactions between fungal root endophytes and plants.
In summary, the morphological and physiological traits of 128 fungal endophyte strains within ten fungal orders were studied and artificial experimental systems were used to reproduce their interactions with three plant species under laboratory conditions. Under defined axenic conditions, most endophytes behaved as weak parasites, but their performance varied across plant species and fungal taxa. The variation in the interactions was partly explained by convergent fungal traits that separate groups of endophytes with potentially different niche preferences. According to my findings, I predict that the functional complementarity of strains is essential in structuring natural root endophytic communities. Additionally, the responses of plant-endophyte interactions to different abiotic factors, namely nutrient availability, light intensity, and substrate’s pH, indicate that the outcome of plant-fungus relationships may be robust to changes in the abiotic environment. The assessment of the responses of plant endophyte interactions to biotic context, as combinations of selected dominant root fungal endophytes with different degrees of trait similarity and shared evolutionary history, indicates that frequently coexisting root-colonizing fungi may avoid competition in inter-specific interactions by occupying specific niches, and that their interactions likely define the structure of root-associated fungal communities and influence the microbiome impacts on plant fitness.
In conclusion, my findings suggest that dominant fungal lineages display different ecological preferences and complementary sets of functional traits, with different niche preferences within root tissues to avoid competition. Also, their diverse effects on plant fitness is likely host-isolate dependent and robust to changes in the abiotic environment when these encompass the tolerance range of either symbiont.
The continuous conversion of natural wildlife habitats into agricultural areas, as well as the fragmentation of the last wildlife refuges, is increasing the interface between people and wildlife. When wildlife negatively impacts on people and vice versa, we speak about human-wildlife conflicts (HWCs). This definition includes losses on both sides and takes into consideration the rooting of most of these conflicts between different groups of interest, such as advocates for nature conservation and economic groups. The centres of highest biodiversity are located in developing countries, which are also characterized by poverty. In African and Asian countries, people living in the vicinity of national parks and other conservation areas mostly receive only little support through the government or conservation organisations. Especially for those people who are dependent on agriculture, damage to fields and harvests can have catastrophic consequences. If the species causing damage is protected by national or even international law, the farmer is not allowed to use lethal methods, but has to approach the authority in charge. If this agency, however, cannot offer appropriate support, resentment, anger or even hate develops, and the support for wildlife conservation activities declines. For this reason, HWCs were declared as one of the most important conservation topics today, being particularly relevant for large and threatened species such as the African and Asian elephant, hippopotamus and the greater one-horned rhino, as well as for large predators. Up to today, no general assessment scheme has been recommended for damage caused by protected wildlife species.
In my study, HWCs in Asia and Africa are compared, focussing on all herbivorous species identified which damaged crops. For the French NGO Awely, des animaux et des hommes, I developed a detailed assessment scheme suitable for all terrestrial ecosystems, and any type of HWCs and any species (Chapter 2). This HWC assessment scheme was used in four different study areas located in two African countries (South Luangwa/Zambia (SL), Tarangire/Tanzania (TA)) and two Asian countries (Bardia/Nepal (BA) and Manas/India (MA)). This scheme ran for six consecutive years (2009 to 2014) for Zambia, Nepal and India and two years (2010 to 2011) for Tanzania. To carry out the assessments, I trained local HWC officers (Awely Red Caps) to assess HWCs by field observations (measurement of damage, identification of species through signs of presence, landscape attributes etc.) and interviews with aggrieved parties (socio economic data). Results of this assessment are presented in Chapters 2-4.
To determine whether elephants prefer or avoid specific crop species, two field experiments were carried out, one in SL and one in BA (Chapter 5 and 6). For this, two test plots were set up and damage by elephants (and other herbivores) were quantified.
Within this doctoral thesis, 3306 damage events of 7408 aggrieved parties were analysed. In three out of the four study areas (SL, BA, MA), elephants caused the highest number of damage events compared to all other wildlife species, however, in TA, most fields were damaged by zebra. Furthermore, the greater one-horned rhino, hippopotamus, wild boar, bushpig, deer and antelope, as well as primates, caused damage to fields and harvests. Damage to houses and other property were nearly exclusively caused by elephants.
With this doctoral thesis I was able to show that season, crop availability, type and the phenological stage of the crop played an important role for crop damaging behavior of herbivores (Chapter 2). Elephants especially damaged rice, maize and wheat and preferred all crop types in a mature stage of growth. In contrast, rhinos preferred wheat to rice and similar to antelope and deer, they preferred crops at earlier stages of growth, before ripening. Crop damage by wildlife species varied strongly in size; most damages fell below 40% of the total harvest per farmer, but in several cases (3 to 8% depending on the study area), harvests were completely destroyed. Interestingly, during times of low nutritional availability in the natural habitat (dry season), crop damages in all four study areas were significantly less than during other seasons.
In all four study areas, crop protection strategies, such as active guarding in the fields, chasing wildlife with noise or fire torches or erecting barriers, were used. In some cases protection strategies were combined. Analysis of data revealed that traditional protection strategies did not reduce the costs of damage (Chapter 3). In some cases, costs of damage, on protected fields were even higher than for unprotected fields. Only in MA did strategic and cohesive guarding significantly reduce crop damage by wildlife species.
Besides damage in the fields, elephants also caused damage to properties in the villages. In search for stored staple crops, they damaged houses, grain stores and kitchens. Such damage was analysed in three study areas (SL, BA, MA) (Chapter 4). Although property damage occurred less frequently compared to crop damage in the fields, the mean cost of this damage was found to be double in BA/MA and four times higher in SL, compared to the costs of crop damage in the fields. It is further remarkable that property damage significantly increased towards the dry season, when the harvest was brought into the villages.
The findings of this study underpin the assumption that wildlife herbivores, especially elephants, are lured to fields and crops because the highly nutritional food (crop) being readily available. Traditional crop protection is cost and labour intensive and does not reduce the costs of damage. For this reason, crop types, which are thought to be not consumed by elephants were systematically tested on their attractiveness in field experiments in SL and BA (Chapter 5 and 6). In SL, lemon grass, ginger and garlic were proven to be less attractive to African elephants than maize and in BA, basil, turmeric, chamomile, coriander, mint, citronella and lemon grass were found to be less attractive to Asian elephants than rice.
The results of this doctoral thesis are relevant for the management of wildlife conservation as they can lead to new approaches to the mitigation of HWCs in African and Asian countries. Finally, specific needs for more scientific research in this field have been identified.
In den letzten Jahren findet die Wirkung von Polyphenolen auf den Alterungsprozess oder zur Behandlung von Krankheiten immer mehr Beachtung. Das Ziel dieser Arbeit war die Aufklärung der Wirkmechanismen der Polyphenole Gossypol, Curcumin und Quercetin, um Hinweise für neue oder verbesserte Therapieansätze zu erhalten. Die dazu durchgeführten Untersuchungen lieferten folgende Ergebnisse:
1. Der Ascomycet "P. anserina" eignet sich als Modellorganismus zur Untersuchung der Wirkmechanismen verschiedener Polyphenole, da die bereits aus der Literatur bekannten Effekte auf das Überleben höherer Organismen auch in "P. anserina" beobachtet wurden.
2. Die Mitochondrienfunktion spielt auf unterschiedliche Art eine Rolle in der Kompensation von Dysfunktionen oder Stressbedingungen in der Zelle und wirkt somit positiv auf die Regulation der Lebensspanne von "P. anserina". In der "PaSod3"-Deletionsmutante wurde eine Verschiebung der mitochondrialen Atmung von einer Komplex I-abhängigen hin zu einer vermehrt Komplex II-abhängigen Atmung festgestellt. Die damit verbundene Abnahme des mitochondrialen Membranpotentials dient neben der bereits bekannten hohen Superoxid-Menge als Signal zur Mitophagie-Induktion. Auch die Anpassung der Mitochondrienfunktion durch die erhöhte Bildung von mtRSCs, wie im Falle von Gossypol oder Quercetin, kann zur Kompensation von Dysfunktionen beitragen bzw. sie abschwächen.
3. Es gibt keinen grundlegenden gemeinsamen Wirkmechanimus der drei untersuchten Polyphenole. Zwar spielt Wasserstoffperoxid bei verschiedenen Stoffen eine Rolle, aber nicht bei allen. Zusätzlich wurde gezeigt, dass Wasserstoffperoxid abhängig von der vorherrschenden Konzentration wirkt und daher auch keine Allgemeingültigkeit des Effektes vorherzusagen ist. In niedrigen Konzentrationen sorgt Wasserstoffperoxid z. B. für eine Induktion der Autophagie und damit einhergehende eine Lebensverlängerung. Im Gegensatz dazu wirken hohe Wasserstoffperoxid-Konzentrationen lebensverkürzend und lösen verschiedene Formen von Zelltod aus.
4. Die Curcumin-vermittelte Langlebigkeit wurde das erste Mal in Verbindung mit einer funktionellen Autophagie gebracht. Im Detail führt die Behandlung mit Curcumin durch eine PaSOD1-abhängige leichte Erhöhung der Wasserstoffperoxid-Menge zu einer Induktion von nicht-selektiver Autophagie. Die induzierte Autophagie ist Ursache der Lebensverlängerung durch Curcumin.
5. Gossypol wirkt in Abhängigkeit der mitochondrialen Permeabilitäts-Transitionspore bzw. von ihrem Regulator Cyclophilin D. Hierbei verstärkt die deutlich erhöhte Wasserstoffperoxid-Menge wahrscheinlich die Induktion von programmiertem Zelltod. Gleichzeitig wird eine cytoprotektive Form von Autophagie und ein scheinbar ATG-unabhängiger Abbau von Mitochondrien induziert.
6. Quercetin wirkt in "P. anserina" abhängig vom Methylierungs-Status. Untersuchungen mit Mutanten der "O"-Methyltransferase PaMTH1 ergaben die Notwendigkeit der Anwesenheit von PaMTH1 für den lebensverlängernden Effekt von Quercetin. Analysen mit dem methylierten Derivat Isorhamnetin verdeutlichten diese Abhängigkeit und zeigten zudem, dass Quercetin sowohl in der methylierten als auch unmethylierten Form Effekte hervorruft. Jedoch sind nur die Effekte des unmethylierten Quercetin unabhängig von der Lebensverlängerung und eher schädlich für die Zelle.
The role of the homeobox transcription factor Meis2b in zebrafish heart development and asymmetry
(2018)
Zebrafish heart development: The heart of the zebrafish is the first organ to form and function during embryonic development, and is composed by one atrium and one ventricle. Between 5-17 somites stage, the cardiomyocyte precursors form the bilateral cardiac fields in the anterior lateral plate mesoderm (ALMP); where the endocardial precursors are located anterior to the cardiac fields (Zeng, Wilm et al. 2007). Then, the pools of endocardial andmyocardial precursors fuse at the midline and form the heart disc; where atrial cardiomyocytes are located around, the ventricular cardiomyocytes are located in the centerof the heart disc, and the future endocardium is located in a ventral position relative to the cardiomyocytes (Bakkers 2011). After the heart disc is formed, the cardiomyocyte progenitors start to migrate and rotate asymmetrically to form the heart tube (de Campos-Baptista, Holtzman et al. 2008, Rohr, Otten et al. 2008, Smith, Chocron et al. 2008). This process is followed by a rightward bending of the heart tube, and the arterial and venous poles rotate at different speed and directions (a process known as heart looping) (Smith, Chocron et al. 2008). The heart looping process results in a ventricle located on the right side and a more posterior atrium located on the left side with respect to the midline; at this point the atrium and ventricle are separated by a fine segment called the atrioventricular canal, where the valves will be formed (Staudt and Stainier 2012). The second heart field (SHF) is a pool of cardiac progenitors that are specified later during the formation of the heart disc and until the heart looping stages. The SHF contributes withcells to the distal side of the ventricle, the outflow and inflow tracts, and is important for the specification of the cardiac conduction system (de Pater, Clijsters et al. 2009, Hami, Grimes et al. 2011, Zhou, Cashman et al. 2011, Witzel, Jungblut et al. 2012, Guner-Ataman, Paffett-Lugassy et al. 2013)....
In times of a growing world population and the associated demand for high crop yield, the understanding and improvement of plant reproduction is of central importance. One key step of plant reproduction is the development of the male gametophyte, which is better known as pollen. In addition, the development of pollen was shown to be very sensitive to abiotic stresses, such as heat, which can cause crop damage and yield loss. To obtain new insights in the development and heat stress response of pollen, a combined transcriptome and proteome analysis was performed for three pollen developmental stages of non- and heat-stressed tomato plants.
The analysis of the transcriptomes of non-stressed pollen developmental stages enabled the determination of mRNAs accumulated in certain developmental stages. The functional analysis of these mRNAs led to the identification of protein families and functional processes that are important at different times of pollen development. A subsequent comparison of the transcriptomes of non- and heat-stressed pollen revealed a core set of 49 mRNAs, which are upregulated in all three developmental stages. The encoded proteins include among other things different heat stress transcription factors and heat shock proteins, which are known key players of the plant heat stress response.
Furthermore, 793 potential miRNAs could be identified in the transcriptome of non- and heat-stressed pollen. Interestingly, 38 out of the 793 miRNAs have already been identified in plants. For more than half of these miRNAs potential target mRNAs were identified and the interactions between miRNAs and mRNAs linked to the development and heat stress response of pollen. In total, 207 developmentally relevant interactions could be determined, out of which 34 have an effect on transcriptional-networks. In addition, 24 of the interactions contribute the heat stress response of pollen, whereby this mainly affects post-meiotic pollen.
An initial correlation of the proteome and transcriptome of the developmental stages revealed that transcriptome analyses are not sufficient to draw exact conclusions about the state of the proteome. A closer look on the relationship of the transcriptome and proteome during pollen development revealed two translational modes that are active during the development of pollen. One mode leads to a direct translation of mRNAs, while the second mode leads a delayed translation at a later point in time. Regarding the delayed translation, it could be shown that this is likely due to a short-term storage of mRNAs in so-called EPPs. The comparison of the proteome and transcriptome response to heat stress revealed that the proteome reacts much stronger and that the reaction is mainly independent from the transcriptome. Finally, the comparison of the proteome of non- and heat-stressed pollen provided first indications for changes in the ribosome composition in response to heat stress, as 57 ribosomal proteins are differentially regulated in at least one developmental stage.
The entire chemical modification repertoire of yeast ribosomal RNAs and the enzymes responsible for it have recently been identified. Nonetheless, in most cases the precise roles played by these chemical modifications in ribosome structure, function and regulation remain totally unclear. Previously, we demonstrated that yeast Rrp8 methylates m1A645 of 25S rRNA in yeast. Here, using mung bean nuclease protection assays in combination with quantitative RP-HPLC and primer extension, we report that 25S/28S rRNA of S. pombe, C. albicans and humans also contain a single m1A methylation in the helix 25.1. We characterized nucleomethylin (NML) as a human homolog of yeast Rrp8 and demonstrate that NML catalyzes the m1A1322 methylation of 28S rRNA in humans. Our in vivo structural probing of 25S rRNA, using both DMS and SHAPE, revealed that the loss of the Rrp8-catalyzed m1A modification alters the conformation of domain I of yeast 25S rRNA causing translation initiation defects detectable as halfmers formation, likely because of incompetent loading of 60S on the 43S-preinitiation complex. Quantitative proteomic analysis of the yeast Δrrp8 mutant strain using 2D-DIGE, revealed that loss of m1A645 impacts production of specific set of proteins involved in carbohydrate metabolism, translation and ribosome synthesis. In mouse, NML has been characterized as a metabolic disease-associated gene linked to obesity. Our findings in yeast also point to a role of Rrp8 in primary metabolism. In conclusion, the m1A modification is crucial for maintaining an optimal 60S conformation, which in turn is important for regulating the production of key metabolic enzymes.
Structured illumination microscopy (SIM) is part of the super-resolution methods developed at the beginning of this century. To produce a super-resolution image SIM requires three things: 1) illumination of the sample with a periodic pattern, 2) acquisition of multiple images per plane under different pattern’s phases and orientations and 3) the processing of these images has to be carried with a reconstruction algorithm. The result of the reconstruction is an image with a resolution gain that is proportional to the frequency of the pattern (po). The typical SIM set-up uses an epi-fluorescence configuration, thus the interference angle of the beams that create the pattern is restricted by the angular aperture of the objective. Under this restriction the maximum value of po is given by the cut-off frequency of the objective lens and sets at 2 the maximum resolution gain of SIM under linear illumination.
In the first part of this thesis we present the implementation and characterization of the 2D-SIM set-up designed by Dr. Bo-Jui Chang (B-J. Chang et al., PNAS 2017), this design exploits the concept introduced by light-sheet microscopy, i.e. separation of illumination and detection paths to obtain resolution gains larger than the usual two-fold (Chapter 3). The set-up is named coherent structured illumination light-sheet based fluorescence microscopy (csiLSFM) and it consists of a triangular array of three objectives, such that two are used for illumination and one for detection. With the independent illumination arms is possible to interfere two coherent light-sheets at angles beyond the angular aperture of the detection lens, attaining the maximum interference angle of 180° when the light-sheets counter-propagate. This condition delivers a pattern with a po 1.4 times larger than the cut-off frequency (ωo), hence our set-up provides generic resolution gains of 2.4.
The extraction of the high spatial frequencies that produce the resolution gain in the csiLSFM is a challenge due to a low pattern modulation. The low modulation inherently arises because the frequency associated to the pattern period lies beyond the cut-off frequency of the detection lens. To overcome this challenge we developed a filtering strategy that facilitates the withdrawal of information from a SIM data set, simultaneously the proposed filtering process optimizes the reconstruction algorithm by reducing the periodic artifacts that are recurrent in SIM images. In this same chapter we also performed an spectral analysis of the artifacts and determined that they originate from irregularities in the power spectrum that occur due to the partial or total lack of certain spatial frequencies (fig.4.2 and 4.3), our reconstruction reduces this information drops and diminishes the artifact occurrence. The relevance of our reconstruction pipeline is that it delivers a standardized process to enhance the SIM image in a current context in which the commonly used reconstruction algorithms employ empirical tuning to improve it (fig.4.13). Moreover, the pipeline is applicable to the csiLSFM data and also to images acquired with any other 2D-/3D-SIM set-up (fig.4.10 and 4.11).
The processing of various image data sets acquired with the csiLSFM exposed us to the question of how low the modulation of the illumination pattern can be before no super-resolution frequencies can be extracted. Answering this question is important to guarantee that the SIM data contains enough spatial frequencies to provide significant resolution gains. Thus in chapter 5 we developed a quantitative metric to indirectly determine the pattern modulation from the SIM data and find its critical value to use it as evaluation criterion. We called this metric the quality factor (Q-factor) and it represents the normalized strength (amplitude) of the extracted frequencies respect to the Gaussian noise contained in the images. Through simulations we estimated that Q=0.11 is a critical value and a SIM data set requires this as minimum value is to deliver a significant resolution gain. Q works then as an assessment tool for classifying SIM data as optimal or sub-optimal, i.e. Q≥0.11 or Q<0.11. We demonstrated such application with data acquired in various SIM commercial set-ups to prove its feasibility in the field (fig.5.6-5.11)
As mentioned at the beginning of this abstract SIM requires a specialized set-up and a processing algorithm to produce super-resolution images. This thesis contributes to these two areas in the following aspects: first, in its linear version a structured illumination microscope is highly associated to a 2-fold resolution gain. Here we demonstrated the possibility of extending this gain to 2.4 using our custom set-up the csiLSFM. Second, a reconstructed SIM image is prone to artifacts due to the mathematical process it undergoes, here we analyzed the artifact sources and identified them with drops of spatial information in the reconstructed spectrum, based on these conclusions we designed a processing pipeline to facilitate the extraction of spatial frequencies and directly reduce artifacts. A third and final outcome of this thesis is the development and practical implementation of a quantitative index to evaluate the quality of SIM data in terms of its relevant information content (Q-factor). Accordingly, the overall contributions of this work were done in the areas of SIM set-up, SIM reconstruction procedure and SIM data evaluation.
Die Analyse von DNA-Sequenzen steht spätestens seit der Feststellung ihrer tragenden Rolle in der Vererbung organismischer Eigenschaften im Fokus biologischer Fragestellungen. Seit Kurzem wird mit modernsten Methoden die Untersuchung von kompletten Genomen ermöglicht. Dies eröffnet den Zugang zu genomweiten Informationen gegenüber begrenzt aussagekräftigen markerbasierten Analysen. Eine Genomsequenz ist die ultimative Quelle an organismischer Information. Allerdings sind diese Informationen oft aufgrund technischer und biologischer Gründe komplex und werfen meist mehr Fragen auf, als sie beantworten.
Die Rekonstruktion einer bislang unbekannten Genomsequenz aus kurzen Sequenzen stellt eine technische Herausforderung dar, die mit grundlegenden, aber in der Realität nicht zwingend zutreffenden Annahmen verbunden ist. Außerdem können biologische Faktoren, wie Repeatgehalt oder Heterozygotie, die Fehlerrate einer Assemblierung stark beeinflussen. Die Beurteilung der Qualität einer de novo Assemblierung ist herausfordernd, aber zugleich äußerst notwendig. Anschließend ist eine strukturelle und funktionale Annotation von Genen, kodierenden Bereichen und repeats nötig, um umfangreiche biologische Fragestellungen beantworten zu können. Ein qualitativ hochwertiges und annotiertes assembly ermöglicht genomweite Analysen von Individuen und Populationen. Diese Arbeit beinhaltet die Assemblierung und Annotation des Genoms der Süßwasserschnecke Radix auricularia und eine Studie vergleichender Genomik von fünf Individuen aus verschiedenen molekularen Gruppen (MOTUs).
Mollusken beherbergen nach den Insekten die größte Artenvielfalt innerhalb der Tierstämme und besiedeln verschiedenste, teils extreme, Habitate. Trotz der großen Bedeutung für die Biodiversitätsforschung sind verhältnismäßig wenige genomische Daten öffentlich verfügbar. Zudem sind Arten der Gattung Radix auch aufgrund ihrer großen geografischen Verbreitung in diversen biologischen Disziplinen als Modellorganismen etabliert. Eine annotierte Genomsequenz ermöglicht über bereits untersuchte Felder hinaus die Forschung an grundlegenden biologischen Fragestellungen, wie z.B. die Funktionsweise von Hybridisierung und Artbildung. Durch Assemblierung und scaffolding von sechs whole genome shotgun Bibliotheken verschiedener insert sizes und einem transkriptbasiertem scaffolding konnte trotz des hohen Repeatgehalts ein vergleichsweise kontinuierliches assembly erhalten werden. Die erhebliche Differenz zwischen der Gesamtlänge der Assemblierung und der geschätzten Genomgröße konnte zum Großteil auf kollabierte repeats zurückgeführt werden.
Die strukturelle Annotation basierend auf Transkriptomen, Proteinen einer Datenbank und artspezifisch trainierten Genvorhersagemodellen resultierte in 17.338 proteinkodierenden Genen, die etwa 12,5% der geschätzten Genomgröße abdecken. Der Annotation wird u.a. aufgrund beinhaltender Kernrthologen, konservierter Proteindomänenarrangements und der Übereinstimmung mit de novo sequenzierten Peptiden eine hohe Qualität zugesprochen.
Das mapping der Sequenzen von fünf Radix MOTUs gegen die R. auricularia Assemblierung zeigte stark verringerte coverage außerhalb kodierender Bereiche der nicht-Referenz MOTUs aufgrund hoher Nukleotiddiversität. Für 16.039 Gene konnten Topologien berechnet werden und ein Test auf positive Selektion ausgeführt werden. Insgesamt konnte über alle MOTUs hinweg in 678 verschiedenen Genen positive Selektion detektiert werden, wobei jede MOTU ein nahezu einzigartiges Set positiv selektierter Gene beinhaltet. Von allen 16.039 untersuchten Genen konnten 56,4% funktional annotiert werden. Diese niedrige Rate wird vermutlich durch Mangel an genomischer Information in Mollusken verursacht. Anschließende Analysen auf Anreicherungen von Funktionen sind deshalb nur bedingt repräsentativ.
Neben den biologischen Ergebnissen wurden Methoden und Optimierungen genomischer Analysen von Nichtmodellorganismen entwickelt. Dazu zählen eigens angefertigte Skripte, um beispielsweise Transkriptomalignments zu filtern, Trainings eines Genvorhersagemodells automatisiert und parallelisiert auszuführen und Orthogruppen bestimmter Arten aus einer Orthologievorhersage zu extrahieren. Zusätzlich wurden Abläufe entwickelt, um möglichst viele vorhandene Daten in die Assemblierung und Annotation zu integrieren. Etwa wurde ein zusätzliches scaffolding mit eigens assemblierten Transkripten mehrerer MOTUs sequenziell und phylogenetisch begründet ausgeführt.
Insgesamt wird eine umfassende und qualitativ hochwertige Genomsequenz eines Süßwassermollusken präsentiert, welche eine Grundlage für zukünftige Forschungsprojekte z.B. im Bereich der Biodiversität, Populationsgenomik und molekularen Ökologie bietet. Die Ergebnisse dieser Arbeit stellen einen Wissenszuwachs in der Genomik von Mollusken dar, welche bisher trotz ihrer Artenvielfalt deutlich unterrepräsentiert bezüglich assemblierter und annotierter Genome auffallen.