HUMAN GENOME VARIATIONS AND EVOLUTION WITH A FOCUS ON THE ANALYSIS OF TRANSPOSABLE ELEMENTS

Genome sequence varies in numerous ways among individuals although the gross architecture is fixed for all humans. Retrotransposons create one of the most abundant structural variants in the human genome and are divided in many families, with certain members in some families, e.g., L1, Alu, SVA, and HERV-K, remaining active for transposition. Along with other types of genomic variants, retrotransponson-derived variants contribute to the whole spectrum of genome variants in humans. With the advancement of sequencing techniques, many human genomes are being sequenced at the individual level, fueling the comparative research on these variants among individuals. In this thesis, the evolution and functional impact of structural variations is examined primarily focusing on retrotransposons in the context of human evolution. The thesis comprises of three different studies on the topics that are presented in three data chapters. First, the recent evolution of all human specific AluYb members, representing the second most active subfamily of Alus, was tracked to identify their source/master copy using a novel approach. All human-specific AluYb elements from the reference genome were extracted, aligned with one another to construct clusters of similar copies and each cluster was analyzed to generate the evolutionary relationship between the members of the cluster. The approach resulted in identification of one major driver copy of all human specific Yb8 and the source copy of the Yb9 lineage. Three new subfamilies within the AluYb family – Yb8a1, Yb10 and Yb11 were also identified, with Yb11 being the youngest and most polymorphic. Second, an attempt to construct a relation between transposable elements (TEs) and tandem repeats (TRs) was made at a genome-wide scale for the first time. Upon sequence comparison, positional cross-checking and other relevant analyses, it was observed that over 20% of all TRs are derived from TEs. This result established the first connection between these two types of repetitive elements, and extends our appreciation for the impact of TEs on genomes. Furthermore, only 6% of these TE-derived TRs follow the already postulated initiation and expansion mechanisms, suggesting that the others are likely to follow a yet-unidentified mechanism. Third, by taking a combination of multiple computational approaches involving all types of genetic variations published so far including transposable elements, the first whole genome sequence of the most recent common ancestor of all modern human populations that diverged into different populations around 125,000-100,000 years ago was constructed. The study shows that the current reference genome sequence is 8.89 million base pairs larger than our common ancestor’s genome, contributed by a whole spectrum of genetic mechanisms. The use of this ancestral reference genome to facilitate the analysis of personal genomes was demonstrated using an example genome and more insightful recent evolutionary analyses involving the Neanderthal genome. The three data chapters presented in this thesis conclude that the tandem repeats and transposable elements are not two entirely distinctly isolated elements as over 20% TRs are actually derived from TEs. Certain subfamilies of TEs themselves are still evolving with the generation of newer subfamilies. The evolutionary analyses of all TEs along with other genomic variants helped to construct the genome sequence of the most recent common ancestor to all modern human populations which provides a better alternative to human reference genome and can be a useful resource for the study of personal genomics, population genetics, human and primate evolution.

Myosin Regulatory Light Chain Phosphorylation and Its Effect on the Contractile Economy of Mouse Fast Muscle

Activated by elevations in myoplasmic calcium concentration, myosin light chain kinase (skMLCK) phosphorylates the regulatory light chains (RLCs) of fast muscle myosin. This covalent modification potentiates force production, but requires an investment of ATP. Our objective was to investigate the effect of RLC phosphorylation on the contractile economy (mechanical output:metabolic input) of fast twitch skeletal muscle. Extensor digitorum longus muscles isolated from Wildtype and skMLCK-/- mice mounted in vitro (25°C) were subjected to repetitive low-frequency stimulation (10Hz,15s) known to cause activation of skMLCK, and staircase potentiation of force. With a 3-fold increase in RLC phosphate content, Wildtype generated 44% more force than skMLCK-/- muscles over the stimulation period (P = .002), without an accompanied increase in energy cost (P = .449). Overall, the contractile economy of Wildtype muscles, with an intact RLC phosphorylation mechanism, was 73% greater than skMLCK /- muscles (P = .043), demonstrating an important physiological function of skMLCK during repetitive contractile activity.

Receipt from the St. Catharines and Welland Canal Gas Light Company

Receipt from the St. Catharines and Welland Canal Gas Light Company for gas rent, April 4, 1887.

Receipt from St. Catharines and Welland Canal Gas Light Company

Receipt from St. Catharines and Welland Canal Gas Light Company for gas rent, May 1, 1887.

Receipt from St. Catharines and Welland Canal Gas Light Company

Receipt from St. Catharines and Welland Canal Gas Light Company for gas rent, June 6, 1887.

Receipt from St. Catharines and Welland Canal Gas Light Company for gas rent

Receipt from St. Catharines and Welland Canal Gas Light Company for gas rent, July 4, 1887.

Receipt from St. Catharines and Welland Canal Gas Light Company for gas rent

Receipt from St. Catharines and Welland Canal Gas Light Company for gas rent, Sept. 3, 1887.

Receipt from St. Catharines and Welland Canal Gas Light Company for gas rent

Receipt from St. Catharines and Welland Canal Gas Light Company for gas rent, Dec. 31, 1887.

Evaluación de dos diferentes técnicas de instrumentación Light Speed y Profile en conductos moderadamente curvos (Un estudio comparativo)

Tesis ( Maestría en Ciencias Odontológicas con Especialidad en Endodoncia) U.A.N.L.

The pillar of Light

UANL

The elements of political economy : with some applications to questions of the day

UANL

Elements d'archeologie chretienne

UANL

Elements de droit pénal : pénalité, juridictions, procédure

UANL

Le développement d'une pensée séculière par la diffusion de la religion : une sociologie des humanistes

Ancré dans une perspective historique, ce mémoire cherche à mettre en application une relecture de la théorie wébérienne de la « rationalisation éthique » comme facteur explicatif de la reconfiguration moderne du rapport entretenu entre les individus et la religion. Un retour sur les changements survenus dans la pensée religieuse de la Renaissance — pensée mise en contraste avec la situation religieuse des populations du Moyen-Âge — permet de mettre en évidence le passage d’une religion syncrétique, ritualiste et imprégnée de magie, à un christianisme épuré, intériorisé et rationnel. L’étude de la pensée religieuse de l’humaniste Érasme de Rotterdam, pris comme « figure historique » porteuse de cette transformation, pointe vers la diffusion à la Renaissance d’un christianisme compris comme système philosophique compréhensif dépouillé de son caractère mystique. Cette diffusion d’un « esprit » chrétien, et l’importance accordée à la mise en œuvre d’une conduite de vie méthodique spécifiquement orientée vers le salut, participe au premier chef d’un processus de « quotidianisation » du charisme religieux, prélude essentiel, dans une perspective wébérienne, à la « rationalisation éthique » et à l’autonomisation de la sphère religieuse dans la vie sociale.

Elements of vegetable and animal physiology, in two parts

UANL