Nematoda is a very diverse animal phylum. Within Nematoda, species display a multitude of life styles, different reproductive strategies and parasitism has arisen independently several times. Furthermore, morphological conservation and a high rate of homoplasy have impeded the resolution of nematode systematics. To address these issues, single gene (usually the nuclear ribosomal small subunit gene) and mitochondrial gene phylogenies have been used, but the information contained within the sequence of these genes is not enough to resolve the topological relationships between clades that emerged during rapid cladogenesis. Next generation sequencing data have been shown to produce high quality genomic and transcriptomic assemblies at low cost, as a result more and more nematode species are being sequenced. Sequences were gathered or generated for 53 nematode species from ESTs, gene predictions from full genome assemblies and transcripts from RNA-Seq experiments. These sequences were screened for orthologous gene clusters, which were concatenated into a supermatrix with thousands of aminoacid sites. The analysis of the supermatrix with maximum likelihood and Bayesian inference methods sheds light into the early splitting clades of the phylogenetic tree of nematodes and the derived clades III, IV and V. Furthermore, the phylogenetic relationships within the parastitic family Onchocercidae were resolved, unveiling the evolutionary history of these important taxa. Finally, data produced in this work will be useful for subsequent evolutionary studies of the phylum Nematoda.

Nietzsche comme Darwin envisagent la morale de manière évolutive, comme l'héritage temporaire de diverses sédimentations successives. Nietzsche comme Darwin remettent à plat toute une tradition antérieure, philosophique pour l'un, biologique et naturaliste pour l'autre. Tous deux poussent à voir la morale, certes comme un ensemble de règles et d'interdits structurant une société, mais comme un ensemble relatif, déterminé par des contextes, des environnements, des physiologies extra-morales. Le philosophe, comme le scientifique, eux mêmes inscrits dans une histoire et une évolution toujours inachevée à l'heure actuelle, font exploser les normes et les catégories morales anciennes, qu'elles soient métaphysiques, révélées, éternelles, fixes et définitives. Et tous deux, en observant, expliquant et critiquant la morale,provoquent une interrogation sur ses marges et son dépassement, par-delà d'ailleurs la science et la philosophie : qu'est-ce que l'individu pour le troupeau, qu'est-ce que l'homme pour son espèce ? / Nietzsche as Darwin are considering morality in an evolutionary way, as the legacy of various, impermanent and successive layers. Nietzsche as Darwin take a new look at an earlier tradition, one philosophical for the former, one biological and naturalist for the latter. Both evoke morals, indeed as a set of rules and prohibitions structuring a society, but morals as relative, determined by contexts, environments, extra-moral physiologies. The philosopher, like the scientist, whoare themselves enrolled in history and evolution which is yet incomplete, burst standards and old moral categories, whether metaphysical, revealed, eternal, fixed and final. And both, observing, explaining and criticizing the morality, are questionning its margins and its limits, beyond science and philosophy: what does the individual to the herd, what is the man for his species?

The threat superiority effect refers to an ability to quickly and efficiently detect threatening cues in one’s environment. Hence, ensuing and appropriate behavioral defense responses entail greater chances of survival for an organism. Some researchers argue that natural selection has led us to automatically prioritize threats that would have been salient during the period of evolutionary adaptation; as for example snakes. However, others have also argued that activation of our defense response system is more flexible, thus able to also be triggered to dangers of more recent age: such as guns or airplane crashes. The present study has sought to impact this debate, by measuring the electrodermal activity (EDA) – more specifically the skin conductance responses (SCRs) – of subjects who were visually presented with both evolutionary (snakes and spiders) and modern (guns and knives) fear-relevant stimuli. The results demonstrated no significant difference between the two categories within subjects, suggesting that both evolutionary and modern threatening cues activate the defense response system in a similar manner. Although the results are preliminary, and would need further verification in higher powered studies, they can be seen to favor the view that our defense response system is flexibly adaptive in relation to the age of a given threat.

Synaptonemal Komplexe (SC) sind evolutionär konservierte, meiosespezifische, proteinöse Strukturen, die maßgeblich an Synapsis, Rekombination und Segregation der homologen Chromosomen beteiligt sind. Sie zeigen eine dreigliedrige strickleiter-artige Organisation, die sich aus i) zwei Lateralelementen (LE), an die das Chromatin der Homologen angelagert ist, ii) zahlreichen Transversalfilamenten (TF), welche die LE in einer reißverschlussartigen Weise miteinander verknüpfen, und iii) einem zentralen Element (CE) zusammensetzt. Die Hauptproteinkomponenten der Säuger-SC sind das Transversalfilamentprotein SYCP1 und die Lateralelementproteine SYCP2 und SYCP3. Wie sich die SC-Struktur zusammenfügt war bisher nur wenig verstanden; es war nicht bekannt wie die TF innerhalb der LE-Strukturen verankert sind und dabei die homologen Chromosomen verknüpfen. Aufgrund dessen wurde die Interaktion zwischen den Proteinen SYCP1 und SYCP2 untersucht. Mit der Hilfe verschiedenster Interaktionssysteme konnte gezeigt werden, dass der C-Terminus von SYCP1 mit SYCP2 interagieren kann. Aufgrund der Bindungsfähigkeit zu beiden Proteinen, SYCP1 und SYCP3, kann angenommen werden, dass SYCP2 als Linker zwischen diesen Proteinen fungiert und somit möglicherweise das fehlende Bindungsglied zwischen den Lateralelementen und Transversalfilamenten darstellt. Obwohl die SC-Struktur in der Evolution hochkonserviert ist, schien dies nicht für seine Protein-Untereinheiten zuzutreffen. Um die Struktur und Funktion des SC besser verstehen zu können, wurde ein Vergleich zwischen den orthologen SYCP1 Proteinen der evolutionär entfernten Spezies Ratte und Medaka erstellt. Abgesehen von den erheblichen Sequenzunterschieden die sich in 450 Millionen Jahren der Evolution angehäuft haben, traten zwei bisher nicht identifizierte Sequenzmotive hervor, CM1 und CM2, die hochgradig konserviert sind. Anhand dieser Motive konnte in Datenbankanalysen erstmals ein Protein in Hydra vulgaris nachgewiesen werden, bei dem es sich um das orthologe Protein von SYCP1 handeln könnte. Im Vergleich mit dem SYCP1 der Ratte zeigten die Proteine aus Medaka und Hydra, neben den hoch konservierten CM1 und CM2, vergleichbare Domänenorganisationen und im heterologen System zudem sehr ähnliche Polymerisationseigenschaften. Diese Ergebnisse sprechen für eine evolutionäre Konservierung von SYCP1. / Synaptonemal complexes (SCs) are evolutionarily conserved, meiosis-specific proteinaceous structures critically involved in synapsis, recombination and segregation of homologous chromosomes. They show a tripartite ladder-like organization including i) two lateral elements (LEs), to which the chromatin of the homologs is attached, ii) numerous transverse filaments (TFs), that link the two lateral elements in a zipper-like way, and iii) a central element (CE). Major protein components of mammalian SCs are the transverse filaments protein SYCP1, and the lateral element proteins SYCP2 and SYCP3. How SCs become assembled was poorly understood; in particular it was not known how TFs assemble at the plane of LEs to interconnect the homologous chromosomes. Therefore, I have investigated possible interactions between SYCP1 and SYCP2. Using different interaction traps, I was able to show that the C-terminus of SYCP1 interacts with SYCP2. Because of its binding to both, SYCP1 and SYCP3, it can be proposed that SYCP2 acts as a linker between these proteins and therefore would be the missing connecting piece between LEs and TFs. Although the SC-structure is conserved in evolution this appears not to be the case for its protein components. For a better understanding of the conserved SC structure und function, I compared ortholog SYCP1 proteins of evolutionary distant species, namely rat and medaka fish. Despite of the sequence-differences that accumulated during 450 million years of evolution, sequence identity was highest at the level of two previously unidentified motifs (CM1 & CM2). Utilizing these motifs in a database analysis a protein of Hydra vulgaris could be found for the first time. It can be proposed that this protein is the orthologous of SYCP1. Besides the highly conserved motifs the proteins of medaka and hydra show quite similar domain organization and polymerization properties in comparison with rat SYCP1. These results suggest an evolutionary conservation of SYCP1.

Orientador: Cesar Martins / Abstract: One of the biggest challenges in chromosome biology is to understand the occurrence and complex genetics of extra, non-essential karyotype elements, commonly known as supernumerary B chromosomes (Bs). Bs are present in diverse species of eukaryotes and their molecular characterization remains elusive for years. A distinguished feature that makes them different from the normal chromosomes (called A chromosomes) is their way of inheritance in irregular fashion. Over the last decades, their genetic composition, function and evolution have remained an unresolved query, although a few successful attempts have been made to address these phenomena. The non-Mendelian inheritance and unpairing/non-recombining abilities make the B chromosomes immensely interesting for genomics studies, thus arising different questions about their genetic composition, survival, maintenance and role inside the cell. This study aims to uncover these phenomena in different species. Here, we sequenced the genomes of three model organisms including fish species Astyanax mexicanus and Astyanax correntinus, and grasshopper Abracris flavolineata with (B+) and without Bs (B-) to identify the B-localized sequences, called B chromosome blocks (“B-blocks”). We established approaches for this analysis that comprised of steps such as comparative genomics analysis and annotation of B chromosomal genes and DNA repeat types. The next generation sequencing (NGS) analyses identified thousands of genes fragments as well as... (Complete abstract click electronic access below) / Doutor

Thesis presented in fulfilment of the requirements for the degree of Doctor of Philosophy at the University of the Witwatersrand, Johannesburg, 2017. / This thesis investigates in detail the structure of models of turbulent convec tion with phenomenological closures for the eddy-viscosity. It explores the merits of replacing the canonical Mixing Length Theory of stellar convection with more realistic models of fluid turbulence that take into account the full spectrum of eddy sizes. The author provides a detailed exposition of the fun damental assumptions and the modus operandi of various approaches to the treatment of convective energy-transfer in stars. He focuses in particular on spectral descriptions of the convective process. The structure of several clo sure models developed by various authors are investigated, and he identifies and elucidates those aspects of these closures that lead to an improved descrip tion of convective turbulence in the stellar interior. The author also develops an implementation within the public-domain code, called Modules for Experi ments in Stellar Astrophysics, of two of these models and reports and discusses the results of his numerical experiments. / XL2018

In 2008, the topic of “evolution” was introduced into the Life Science syllabus for the first time in South African schools. Evolution is a controversial topic in most countries and the controversy will be experienced in South African schools. This controversy results from the erroneous belief that teachers and most people have that religion and evolutionary theory contradict each other. This research study explored the difficulties faced by teachers with strong religious beliefs when they teach evolution. Eight teachers with strong religious beliefs were identified. Teachers of the Muslim and Christian faith who taught at either religious or secular schools formed part of the research study. The teachers were subjected to an in-depth interview where they were questioned about their religious beliefs and their opinions about creation and evolution. They also described how they taught evolution and explained how they coped with the conflict of faith and science that they experienced when they taught evolution. These teachers also experienced myriad difficulties when they taught evolution. These difficulties were described to me as the researcher. The findings indicated that all of the Muslim teachers and three of the four Christian teachers interviewed are Creationists. This leads to personal conflict that some of the teachers interviewed experience because of their belief that evolution and religious belief contradict each other. Two of the teachers in this study also experience a lack of confidence with the subject knowledge because they lack training in evolutionary theory. Due to this lack of training there are some teachers who harbour misconceptions about evolutionary concepts and who pass these misconceptions to learners. There is also pressure placed on teachers to teach creationism or to teach creationism alongside evolution from some religious leaders, some parents and certain members of the community. A few teachers with strong religious beliefs could teach evolution very superficially or these teachers could even sabotage their teaching of evolution. Teachers also experience difficulties teaching the learners in their class. The findings indicate that learners in religious schools may refuse to learn about evolution and learners in certainschools choosenot to do Life Sciences from Grade 10 to avoid learning about evolution. There are certain strategies that teachers employ to minimise the conflict they experience when teaching evolution. Learners were told they had to study evolution in order to pass the matriculation examination. Teachers also explained to learners that they needed to study evolution so that they could argue for Creationism from a position of knowledge and not ignorance. Certain teachers interviewed taught learners that science needs to be considered separate to religion. The conflict of faith and science that teachers experience when they teach evolution causes difficulties for these teachers.This conflict could arise from personal conflict with their faith or they could experience discord from learners, parents and members from the community in which they teach.

Cells have evolved the ability to change continuously and adapt to their environment. An important way in which this dynamic modulation is achieved is by reversible phosphorylation, mediated by protein kinases and phosphatases. This thesis focuses on the temporal variations in expression of the proteins protein phosphatase 1 (PP1), protein phosphatase 2A (PP2A) and p53 tumour suppressor protein in proliferating and hexamethylene bisacetamide (HMBA) induced differentiating murine erythroleukaemic (MEL) cells. The study included analysis of variations of p53 mRNA in these cells. Protein variations were analysed in cell extracts using western immunoblotting. The p53 variations were evaluated further using enzyme-linked immunosorbent assay (ELISA); p53 mRNA was determined by reverse transcriptase polymerase chain reaction (RT-PCR). Dynamic variations in protein expression and mRNA were detected in both the untreated and HMBA treated MEL cell preparations. For PP1, an immunospecific band of molecular mass 36 kDa, corresponding to the catalytic subunit, was detected, while for PP2A, two immunospecific bands of 32 and 36 kDa were observed. For the PP2A, the 36 kDa band corresponded to the catalytic subunit of this protein and the 32 kDa band was believed to be a proteolytically cleaved form of the catalytic subunit. The mean values of results showed little significant difference between proliferating and differentiating MEL cells, emphasising that single time-point studies give incomplete and probably misleading information. Multiple time analysis for expression clearly showed evidence of oscillatory behaviour and modulation by the differentiating agent. The influence of HMBA on PP1, PP2A and p53 expression was variable for the different experiments and affected both the frequency and phasing of rhythms. The results add support to the view that dynamic oscillatory control processes play an important role in regulating cellular behaviour. Modulation of the dynamics of key proteins in the cell, such as PP1, PP2A and p53, may be an important mechanism of controlling cellular function and reversing neoplastic transformation.

Next generation sequencing can rapidly analyze entire genomes in just hours. However, due to the nature of the sequencing process, errors may arise which limit the accuracy of the reads obtained. Luckily, modern sequencing technologies associate with their reads, a quality score, derived from the sequencing procedures, which represents our confidence in each nucleotide in the sequence. Currently, these quality scores are used as a criteria for the removal or modification of reads in the data set. These methods result in the loss of information contained in those sequences and rely on parameters that are somewhat arbitrary; this may lead to a biased sample and inaccurate analyses. I propose an alternative method for incorporating the error of the sequences without discarding poor quality reads by including the error probabilities of the reads in the likelihood calculations used for sequence analysis. It was found that, despite introducing variability, using the error-informed likelihood method improved analyses compared with those which ignored the error altogether. While this method will likely result in analyses with less definite results compared with those in which the data was treated with a preprocessing technique, these results will utilize all of the provided data and will be more grounded in reality as we take into account the uncertainty that we have in our sequenced samples. / A Thesis submitted to the Department of Scientific Computing in partial fulfillment of the requirements for the degree of Master of Science. / Fall Semester 2015. / November 6, 2015. / error, likelihood, ngs, sequencing / Includes bibliographical references. / Peter Beerli, Professor Directing Thesis; Anke Meyer-Baese, Committee Member; Alan Lemmon, Committee Member.

Thesis advisor: Michelle M. Meyer / Ribosomes play a vital role in all cellular life translating the genetic code into functional proteins. This pivotal function is derived from its structure. The large and small subunits of the ribosome consist of 3 ribosomal RNA strands and over 50 individual ribosomal proteins that come together in a highly coordinated manner. There are striking differences between eukaryotic and prokaryotic ribosomes and many of the most potent antibacterial drugs target bacterial ribosomes (e.g. tetracycline and kanamycin). Bacteria spend a large amount of energy and nutrients on the production and maintenance of these molecular machines: during exponential growth as much as 40% of dry bacterial mass is ribosomes (Harvey 1970). Because of this, bacteria have evolved an elegant negative feedback mechanism for the regulation of their ribosomal proteins, known as autoregulation. When excess ribosomal protein is produced, unneeded for ribosome assembly, the protein binds a structured portion of its own mRNA transcript to prevent further expression of that operon. Autoregulation facilitates a quick response to changing environmental conditions and ensures economical use of nutrients. My thesis has investigated the autoregulatory function of ribosomal protein S15 in diverse bacterial phyla. In many bacterial species, when there is excess S15 the protein interacts with an RNA structure formed in the 5’-UTR of its own mRNA transcript that enables autoregulation of the S15-encoding operon, rpsO. For many ribosomal proteins (ex. L1, L20, S2) there is striking homology and often mimicry between the recognition motifs within the rRNA and the regulatory mRNA structure. However, this is not the case for S15-three different regulatory RNA structures have been previously described in E. coli, G. stearothermophilus, and T. thermophilus (Portier 1990, Scott 2001, Serganov 2003). These RNAs share little to no structural homology to one another, nor the rRNA, and they are narrowly distributed to their respective bacterial phyla, Gammaproteobacteria, Firmicutes, and Thermales. It is unknown which regulatory RNA structures control the expression of S15 outside of these phyla. Additionally, previous work has shown the S15 homolog from G. stearothermophilus is unable to regulate expression using the mRNA from E. coli. These observations formulate the crux of the question this thesis work endeavors to answer: What drove the evolution of such diverse regulatory RNA structures in these different bacteria? In Chapter II, “Discover and Validate Novel Regulatory Structures for Ribosomal Protein S15in Diverse Bacterial Phyla”, I present evidence for the in silico identification of three novel regulatory RNA structures for S15 and present experimental evidence that one of these novel structures is distinct from those previously described. In Chapter III, “Co-evolution of Ribosomal Protein S15 with Diverse Regulatory RNA Structures”, I present evidence that the amino acid differences in S15 homologs contribute to differences in mRNA binding profiles, and likely lead to the development of the structurally diverse array of the regulatory RNAs we observe in diverse bacterial phyla. In Chapter IV, “Synthetic cis-regulatory RNAs for Ribosomal Protein S15”, I investigate the derivation of novel cis-regulatory RNAs for S15 and find novel structures are readily-derived, yet interact with the rRNA-binding face of S15. Together the work presented in this thesis advances our understanding of the co-evolution between ribosomal protein S15 and its regulatory RNAs in diverse bacterial phyla. / Thesis (PhD) — Boston College, 2016. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.