No / Transposable elements (TEs), such as endogenous retroviruses (ERVs), are common in the genomes of vertebrates. ERVs result from retroviral infections of germ-line cells, and once integrated into host DNA they become part of the host's heritable genetic material. ERVs have been ascribed positive effects on host physiology such as the generation of novel, adaptive genetic variation and resistance to infection, as well as negative effects as agents of tumorigenesis and disease. The avian leukosis virus subgroup E family (ALVE) of endogenous viruses of chickens has been used as a model system for studying the effects of ERVs on host physiology, and approximately 30 distinct ALVE proviruses have been described in the Gallus gallus genome. In this report we describe the development of a software tool, which we call Vermillion, and the use of this tool in combination with targeted next-generation sequencing (NGS) to increase the number of known proviruses belonging to the ALVE family of ERVs in the chicken genome by 4-fold, including expanding the number of known ALVE elements on chromosome 1 (Gga1) from the current 9 to a total of 40. Although we focused on the discovery of ALVE elements in chickens, with appropriate selection of target sequences Vermillion can be used to develop profiles of other families of ERVs and TEs in chickens as well as in species other than the chicken. / Financial support was provided by the EW GROUP, as well as grants from the Canada Foundation for Innovation, Canada Research Chairs Program, and the Natural Sciences and Engineering Council of Canada to RGB, and Canada Institutes of Health Research funding to MGIL and CJM.

Since the dawn of the genomics era, the genetics of numerous human disorders has been understood which has led to improvements in targeted therapeutics. However, the focus of most research has been primarily on protein coding genes, which account for only 2% of the entire genome, leaving much of the remaining genome relatively unstudied. In particular, repetitive sequences, called microsatellites (MST), which are tandem repeats of 1 to 6 bases, are known to be mutational hotspots and have been linked to diseases, such as Huntington disease and Fragile X syndrome. This work represents a significant effort towards closing this knowledge gap. Specifically, we developed a next generation sequencing based enrichment method along with the supporting computational pipeline for detecting novel MST sequences in the human genome. Using this global MST enrichment protocol, we have identified 790 novel sequences. Analysis of these novel sequences has identified previously unknown functional elements, demonstrating its potential for aiding in the completion of the euchromatic DNA. We also developed a disease risk diagnostic using a novel target specific enrichment method that produces high resolution MST sequencing data that has the potential to validate, for the first time, the link between MST genotype variation and cancer. Combined with publicly available exome datasets of non-small cell lung cancer and 1000 genomes project, the target specific MST enrichment method uncovered a signature set of 21 MST loci that can differentiate between lung cancer and non-cancer control samples with a sensitivity ratio of 0.93. Finally, to understand the molecular causes of MST instability, we analyzed genomic variants and gene expression data for an autosomal recessive disorder, Fanconi anemia (FA). This first of its kind study quantified the heterogeneity of FA cells and demonstrated the possibility of utilizing the DNA crosslink repair dysfunctional FA cells as a suitable system to further study the causes of MST instability. / Ph. D. / The field of genetics has enjoyed substantial growth since the conclusion of the human genome project, which was declared complete in the year 2003. The human genome project produced the first framework for the human DNA sequence, the human genome. With the availability of this framework, the understanding of the genetic basis for a number of diseases has significantly grown, which has resulted in better methods of clinical diagnosis and treatment. While the current focus on understanding the genomic regions that are responsible for making proteins has inarguably helped, it has also created a gap in knowledge. Protein coding regions of the human genome account only for 2% of the entire human genome and a large part (47%) of the genome is occupied by repetitive DNA. DNA sequences can be complex, with the nucleotides arranged in no particular order, e.g. ATCGTACGA, or DNA sequences can be repetitive, e.g. ATATATATAT. Repetitive sequences, which have repeating units of 1 to 6 bases, are called microsatellites (MST). MSTs have been shown to be unstable and they have been linked to diseases such as Huntington disease and Fragile X syndrome. This work helps to close this knowledge gap by developing molecular methods and computational tools focused on identifying MST variations. Research conducted with this aim has resulted in three major accomplishments. One, we developed novel molecular and computational methods which we used to detect 790 previously unknown sequences in the human genome. This work proved the ability of our method to uncover functional elements in the human genome that can potentially answer numerous biological questions. Two, we developed another novel method for the production of high resolution MST sequence data that not only can improve MST research in general but also shows the potential for the development of new genetic diagnostics and cancer therapeutics. We identified a signature set of 21 MST sequences that can differentiate between lung cancer patient genomes and non-cancer control genomes. These results represent the first potential validation for a proposed link between MST sequence length (genotype) variation and cancer. Three, we attempt to understand a possible molecular cause and consequences of MST instability in a disease called Fanconi anemia. The results from this work not only, for the first time, quantify the effects of this disease on the genome but also establishes Fanconi anemia as a suitable system for studying MST instability in detail.

Thesis advisor: Marc-Jan Gubbels / Thesis advisor: Sarah McMenamin / Toxoplasma gondii, an obligate intracellular parasite, infects nearly one-third of the global population, causing the disease toxoplasmosis. Despite its significant health impact, the molecular mechanisms governing its lytic cycle and stress-induced adaptation remain incompletely understood. The unique asexual cell division mechanism, endodyogeny, used by T. gondii to expand its parasitic biomass in intermediate hosts, including humans, leads to severe pathological consequences through repeated rounds of the lytic cycle, resulting in acute toxoplasmosis. The parasite’s cell cycle is characterized by a prolonged G1 phase, with centrosome duplication marking the onset of the S phase, followed by a transient G2 phase and a near-simultaneous onset of mitosis and cytokinesis. These overlapping division processes, coupled with the challenges of synchronizing T. gondii, obscure the precise molecular mechanisms of its transcriptional programs. To address these challenges, we employed single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq), combined with advanced machine learning tools, to reveal ‘transition points’ in gene expression and chromatin accessibility that correspond to shifts in biological activity during the lytic cycle. RNA velocity and time-course clustering analyses uncovered a significant G1a transcriptional burst and identified specific AP2 family transcription factors (TFs) that peak during the C-to-G1a transition, likely driving this burst to regulate G1 progression. Further, we conducted an in-depth functional characterization of G1-specific TFs, focusing on AP2XII-8, which plays a critical role in activating a ribosome regulon to promote G1 progression. The study identified combinatorial binding motifs and suggested the existence of a large AP2XII-8 protein complex, involving other TFs and epigenetic factors, that reuglates the intricate processes of T. gondii cell cycle replication. Additionally, we examined stress-responsive AP2 TFs associated with enhanced virulence during in vitro evolution, providing insights into adaptive mechanisms that enable T. gondii to thrive under extracellular stress conditions. Collectively, these findings enhance our understanding of T. gondii’s complex regulatory networks, offering potential targets for therapeutic intervention against acute toxoplasmosis. This dissertation provides the time-resolved transcriptional and chromatin accessibility landscapes of T. gondii’s lytic cycle, resolves transcriptional programs to DNA motifs, and identifies key regulatory elements involved in its cell cycle progression and stress response. / Thesis (PhD) — Boston College, 2024. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

No description available.

Wireline telecommunications infrastructure in the customer access network or CAN is undergoing a veritable technological and commercial revolution. The paired-copper CAN is being modernised with optical fibre deployed ever closer to customers, culminating soon with fibre-to-the-home networks or some variant thereof. Although bandwidth ceases to be a scarce commodity, the underlying natural monopoly will most likely be strengthened. National competition policy desires open access to multiple service providers yet commercial pressure calls for closure. This has been the recent experience with the hybrid fibre coaxial networks delivering pay television and Internet access. This research asks the question: What are the factors that prevent open access to the broadband services of next generation wireline infrastructure? How can these obstacles be overcome? A particular focus is given to non-price considerations which come to the fore due to the unique strategic and technological characteristics of optical fibre in the access network. The methodological approach involves data gathering via three case studies - that of the Telstra/Foxtel pay television network, the TransACT broadband network and fibre-to-the-home networks in general. Although the ultimate focus is on the research question above, these cases are discussed in a holistic way with consideration of a number of contextual factors. The research also examines the relationship between the concepts of 'open access' and 'network neutrality', visiting the concept of 'common carriage' in doing so. Several findings are reached that illuminate the field of telecommunications access regulation as applied to infrastructure capable of delivering truly next generation broadband services. Since 1993, our politicians have only paid lip service to the importance of competition and have deferred to the demands of the dominant builder of telecommunications infrastructure. From the viewpoints of end-users and access seekers, the access regime is found to be incapable of dealing with the technical and commercial bottlenecks arising from optical fibre in the CAN. It is concluded that communication between users should be recognised as the prime purpose of telecommunications and that the regulatory regime should not reward discriminatory practices detracting from the development of a networked information economy. It is also concluded that dominant players should never be rewarded with access holidays which could otherwise entrench market dominance through the creation of new bottlenecks. Access regulation is ill-equipped to cope with optical fibre in the CAN until it also recognizes the strategic potential of such infrastructure.

This master thesis focuses on the phylogeny of hybridogenous and polyploid genus Curcuma from family Zingiberaceae using Next-Generation Sequencing data from hundreds to thousands nuclear loci. This approach seems to be better than widely used cpDNA and ITS sequencing especially in the case of hybridogenous and polyploid groups. Data for phylogeny reconstruction were generated using Hybridization-based sequencing (Hyb-Seq) method which combines target enrichment and genome skimming strategies. Data analysis was performed primarily using pipeline HybPhyloMaker especially created for Hyb-Seq data analysis. Twenty-seven species from the genus Curcuma and three outgroup species were sequenced in this work. Phylogenetic trees based on all 1 154 and 811 selected nuclear low- copy genes show high support values of all nodes which is in contrast to plastome and rDNA phylogeny with lower support values in some nodes and incongruences in topology compared to low-copy genes phylogeny. Phylogenetic networks inferred from low-copy genes, lineage movement analysis and monophyly tests agree with published hypotheses of interlineage hybrid origin of three species - C. vamana, C. myanmarensis and C. roscoeana. These analyzes show likely hybrid origin of C. candida too with parents from the group Curcuma I and basal...

Mon projet de doctorat était de créer un pipeline pour taxono-génomique pour la comparaison de plusieurs génomes bactériens. Deuxièmement, je automatisé le processus d'assemblage (NGS) et annotation à l'aide de divers logiciels open source ainsi que la création de scripts de maison pour le laboratoire. Enfin, nous avons intégré le pipeline dans la description de plusieurs espèces bactériennes de laboratoire sur. Cette thèse est divisée principalement en Taxono- génomique et Microbiogenomics. Les avis de la section taxono-génomique, décrit sur les avancées technologiques en génomique et métagénomique pertinentes dans le domaine de la microbiologie médicale et décrit la stratégie taxono-génomique en détail et comment la stratégie polyphasique avec des approches génomiques sont reformatage de la définition de la taxonomie bactérienne. Les articles décrivent les bactéries cliniquement importantes, leur séquençage complet du génome et les études génomiques comparatives, génomiques et taxono-génomique de ces bactéries. Dans cette thèse, j'ai inclus les articles décrivant ces organismes: Megasphaera massiliensis, Corynebacterium ihumii, Collinsella massiliensis, Clostridium dakarense. Bacillus dielmoensis, jeddahense, Occidentia Massiliensis, Necropsobacter rosorum et Pantoea septica. Oceanobacillus / My PhD project was to create a pipeline for taxono-genomics for the comparison of multiple bacterial genomes. Secondly I automated the process of assembly (NGS) and annotation using various open source softwares as well as creating in house scripts for the lab. Finally we incorporated the pipeline in describing several bacterial species from out lab. This thesis is subdivided mainly into Taxono-genomics and Microbiogenomics. The reviews in taxono-genomics section, describes about the technological advances in genomics and metagenomics relevant to the field of medical microbiology and describes the strategy taxono-genomics in detail and how polyphasic strategy along with genomic approaches are reformatting the definition of bacterial taxonomy. The articles describes clinically important bacteria, their whole genome sequencing and the genomic, comparative genomic and taxono-genomic studies of these bacteria.

This masters's thesis contains description of designed and implemented tool for classification of plant microRNA without genome. Properties of mature and star sequences in microRNA duplexes are used. Implemented method is based on clustering of RNA sequences (with CD-HIT) to mainly reduce their count. Selected representants from each clusters are classified using support vector machine. Performance of classification is more than 96% (based on cross-validation method using the training data).

Diese Arbeit beschreibt die Kombination von Phagen-Display-Biopanning und Illumina Next-Generation DNA-Sequencing (NGS) zur Identifizierung peptidbasierter Adhäsionsdomänen für Polypropylen (PP). Eine Biopanning-Runde gefolgt von NGS liefert PP-bindende Peptide, die durch Sanger-Sequenzierung nicht erkennbar sind. NGS bietet den Vorteil eines enorm umfangreichen Datensatzes, welcher tiefgreifende Sequenzanalysen erlaubt. Die selektierten Sequenzen werden als wasserbasierte Primer für PP–Metallhaftung zur Vorbehandlung von PP-Oberflächen eingesetzt und erhöhen die Haftfestigkeit um 100 % gegenüber nicht vorbehandeltem PP. / This thesis describes the combination of phage display biopanning and Illumina Next-Generation DNA-Sequencing (NGS) to identify peptide-based adhesion domains for polypropylene (PP). One round of biopanning followed by NGS yields PP-binding peptides that are undetectable by Sanger sequencing. NGS has the advantage of an extensive data set, which allows in-depth sequence analysis. The selected peptide sequences are then used as water-based primers for PP metal adhesion for the pretreatment of PP surfaces and increase the adhesion by 100% compared to non-pretreated PP.

International Telemetering Conference Proceedings / October 20-23, 2003 / Riviera Hotel and Convention Center, Las Vegas, Nevada / The transmission of high-rate telemetry data for space-based relay systems yields unique system requirements. The NASA Space-based Telemetry and Range-Safety (STARS) study evaluated system design requirements during Phase-1 flight tests. STARS Phase-2 efforts include the development of a high-rate transmitter and antenna system to demonstrate prototype system performance capabilities and new technologies for future operational systems to be incorporated into the NASA Next Generation Launch Technology (NGLT) vehicles. Phase-2 Range User (telemetry) system performance requirements and a prototype implementation approach are presented.