Deciphering the functionality encoded in the genome constitutes an essential first step to understanding the context through which mutations can cause human disease. In this dissertation, I present multiple studies based on the use or development of comparative genomics techniques to elucidate function (or lack of function) from the genomes of humans and other animal species. Collectively, these studies focus on two biological entities encoded in the human genome: genes related to human disease susceptibility and those that encode microRNAs - small RNAs that have important gene-regulatory roles in normal biological function and in human disease. Extending this work, I investigated the evolution of these biological entities within animals to shed light on how their underlying functions arose and how they can be modeled in non-human species. Additionally, I present a new tool that uses large-scale clinical genomic data to identify human mutations that may affect microRNA regulatory functions, thereby providing a method by which state-of-the-art genomic technologies can be fully utilized in the search for new disease mechanisms and potential drug targets. The scientific contributions made in this dissertation utilize current data sets generated using high-throughput sequencing technologies. For example, recent whole-genome sequencing studies of the most distant animal lineages have effectively restructured the animal tree of life as we understand it. The first two chapters utilize data from this new high-confidence animal phylogeny - in addition to data generated in the course of my work - to demonstrate that (1) certain classes of human disease have uncommonly large proportions of genes that evolved with the earliest animals and/or vertebrates, and (2) that canonical microRNA functionality - absent in at least two of the early branching animal lineages - likely evolved after the first animals. In the third chapter, I expand upon recent research in predicting microRNA target sites, describing a novel tool for predicting clinically significant microRNA target site variants and demonstrating its applicability to the analysis of clinical genomic data. Thus, the studies detailed in this dissertation represent significant advances in our understanding of the functions of disease genes and microRNAs from both an evolutionary and a clinical perspective.

[EN] Our understanding of the biological mechanisms for most common human diseases is far from complete. Even with well established genetic landscapes, our capacity to make accurate phenotypical predictions or determine personalised disease risk using genetics alone is not possible for most diseases due to our lack of understanding of the mechanisms by which genetic alterations cause disease. Several suggestions have been proposed to explain this manifested lack of direct relation between genotype and phenotype, including interactions with other molecules, pleiotropy and environmental perturbations. Due to their essential role in carrying cellular functions, proteins and its interactions seem crucial to translate genomic data to phenotypic states. In this thesis I present three different and independent approaches to integrate human genomic data with prior knowledge in terms of protein-protein interactions (PPIs). The overall objective is, by making use of the interactome structure, to propose functional hypotheses that help to interpret the genetic variability observed in different human phenotypes. First I developed a methodology to extract the network component associated to any gene list ranked by any experimental parameter, as the one coming from case-control genome-wide associations studies. Second I performed a systematic analysis of human variants in the context of the protein interactome. There I study how the interactome structure can help us to explain the amount of apparently deleterious variation observed in actual populations and, therefore, give insight in its role in shaping the patterns of variability. Results are compared against somatic mutation found in Leukemia patients. Finally, I structurally resolved the protein interactome and used it to study how somatic mutations found in primary tumours distribute across the interacting interfaces and identify those with a potential role in driving oncogenesis. Although each chapter covers a different question, all of them demonstrate the potential of the interactome in helping to interpret genomic variation observed under diverse research scenarios. / [ES] Nuestro conocimiento acerca de los mecanismos biológicos causantes de la mayoría de enfermedades humanas comunes es aun pobre. Incluso con mapas genéticos de alta resolución, nuestra capacidad para hacer predicciones fenotípicas certeras o determinar el riesgo de una persona a padecer una enfermedad utilizando solamente marcadores genéticos es muy baja. Entre las principales causas de esta aparente falta de relación directa entre genotipo y fenotipo están las interacciones moleculares, los fenómenos de pleiotropía y la influencia de los factores externos. Debido al papel esencial que ejercen en llevar a cabo las funciones celulares, las proteínas y sus interacciones han adquirido una atención especial en la traducción de los datos genotípicos a estados fenotípicos. En esta tesis se presentan tres estrategias diferentes para la integración de datos genómicos humanos con la red de interacciones proteicas (interactoma). El objetivo común de todas ellas es, haciendo uso de la estructura del interactoma, proponer hipótesis funcionales que ayuden a interpretar los patrones de variabilidad observados en diferentes estados fenotípicos humanos. Primero, se propone una metodología para extraer el componente del interactoma asociado a los genes relevantes en una lista ranqueada por cualquier parámetro experimental, como el estadístico derivado de los estudios de asociación genómicos. Es segundo lugar se describe un análisis sistemático de las variantes genéticas observadas en humanos sanos en el contexto del interactoma. En él se estudia cómo la estructura del interactoma puede ayudar en explicar la aparentemente elevada cantidad de variantes deletéreas observadas en los últimos estudios poblacionales de secuenciación de genomas. Los resultados son comparados con las mutaciones somáticas observadas en pacientes de Leucemia. Finalmente, se presenta un estudio de las mutaciones somáticas observadas en tumores primarios utilizando una versión del interactoma que incluye la estructura tridimensional de las proteínas. Aunque cada estudio presentado en la tesis pretende resolver preguntas diferentes, todos ellos demuestran el potencial del interactoma de proteínas en ayudar a interpretar la variación genómica humana observada en un contexto tanto evolutivo como de enfermedad. / [CAT] El nostre coneixement sobre els mecanismes biològics causants de la majoria de malalties humanes comuns es encara pobre. Tot i que en l'actualitat tenim mapes genètics d'alta resolució, la nostra capacitat per a fer prediccions fenotípiques certeres utilitzant únicament marcadors genètics es encara molt baixa degut a que no entenem les bases moleculars a traves de les quals les alteracions genètiques condicionen un fenotip de malaltia. Entre les principals causes d'aquesta aparent falta de relació directa entre genotip i fenotip estan la complexitat introduïda per les interacciones moleculars, els fenòmens de peleiotropia i la influencia dels factors externs. Degut al paper clau en dur a terme la majoria de funcions cel·lulars, les proteïnes i les seues interaccions han adquirit una especial atenció en la traducció de les dades genotípiques en estats fenotípics. Aquesta tesi presenta tres estartègies diferents per a la integració de dades genòmiques humanes amb la xarxa d'interaccions proteiques (interactoma). L'objectiu comú es, fent ús de l'estructura del interactoma, proposar hipòtesis funcionals que ajuden a interpretar els patrons de variabilitat genètica observats en diferents estats fenotípics. En primer lloc, es proposa una metodologia per a extraure el component de l'interactoma associat als gens rellevants en una llista ranquejada per qualsevol paràmetre experimental, com l'estadístic derivat d'estudis d'assocaició de genoma. En segon lloc, es descriu un anàlisi sistemàtic de les variants genètiques observades en humans sans en el context del interactoma. Ací s'analitza com l'estructura del interactoma pot ajudar a explicar l'aparent elevada quantitat de variants deletèries observades en els últims estudis poblacionals de sequenciació de genomes. Els resultats son comparats amb les mutacions somàtiques observades en pacients de Leucèmia. Finalment, es presenta un estudi de les mutacions somàtiques observades en tumors primaris de més de 20 tipus utilitzant una versió del interactoma més resolutiva, que inclou l'estructura tridimensional de les proteïnes. Encara que cada estudi presentat en la tesi planteja resoldre qüestions diferents, tots ells demostren el potencial del interactoma de proteïnes en ajudar a interpretar la variació genòmica humana observada en un context tant poblacional com de malaltia. / García Alonso, LM. (2015). Functional profiling of human genomic data using the protein interactome [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/55848 / TESIS

<p>    </p> <p>Domestication is the process by which a previously wild population is managed by humans, thereby being subjected to a different set of selective pressures than experienced in its natural setting. Its opposite, feralization, is therefore when a domesticate escapes or is released from a captive setting, reasserting natural selective pressures. The genomics underpinning both domesti- cation and feralization have not been studied in insects; the Western honey bee (<em>Apis mellifera </em>L.) is a good model for this system, as honey bees exist in both a managed and feral state, and have extensive historic and genomic resources to document population changes. My goal in this thesis was to 1) improve upon our understanding of honey bee importation and genetics to the United States to support demographic assertions, and 2) to sequence managed and feral stocks of honey bees to identify the population structure and 3) genetic differences underpinning domestication. Ultimately, I reconstructed 400 years of honey bee importation and management history, creating the most comprehensive understanding to date of importation dates and locations, historical man- agement practices, and genetic bottlenecks. Additionally, I summarized thirty years of honey bee genome sequencing to provide a road map for future studies. Then, I conducted whole genome pooled sequencing on six managed and three feral stocks of honey bees from the United States. The mitochondrial and whole genome ancestry of feral colonies holds relics from their importation history, while managed colonies show evidence of more recent importation events. The managed stocks in my sample set have higher overall genetic diversity, but exhibit little differentiation, but feral stocks exhibit varying levels of differentiation, indicating different levels of ferality likely dictated by the level of reproductive isolation from managed colonies. </p>

Indiana University-Purdue University Indianapolis (IUPUI) / The post genomic era has propelled us to the view that the biological systems are complex network of interacting genes, proteins and small molecules that give rise to biological form and function. The past decade has seen the advent of number of new technologies designed to study the biological systems on a genome wide scale. These new technologies offers an insight in to the activity of thousands of genes and proteins in cell thereby changed the conventional reductionist view of the systems. However the deluge of data surpasses the analytical and critical abilities of the researches and thereby demands the development of new computational methods. The challenge no longer lies in the acquisition of expression profiles, but rather in the interpretation for the results to gain insights into biological mechanisms. In three different case studies, we applied various system biology techniques on publicly available and in-house genomics and proteomics data set to identify sub-network signatures. In First study, we integrated prior knowledge from gene signatures, GSEA and gene/protein network modeling to identify pathways involved in colorectal cancer, while in second, we identified plasma based network signatures for Alzheimer's disease by combining various feature selection and classification approach. In final study, we did an integrated miRNA-mRNA analysis to identify the role of Myeloid Derived Stem Cells (MDSCs) in T-Cell suppression.

No description available.

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.

abstract / Biological Sciences / Doctoral / Doctor of Philosophy

No description available.

<p>A large proportion of the variation in traits between individuals can be attributed to variation in the nucleotide sequence of the genome. The most commonly studied traits in human genetics are related to disease and disease susceptibility. Although scientists have identified genetic causes for over 4,000 monogenic diseases, the underlying mechanisms of many highly prevalent multifactorial inheritance disorders such as diabetes, obesity, and cardiovascular disease remain largely unknown. Identifying genetic mechanisms for complex traits has been challenging because most of the variants are located outside of protein-coding regions, and determining the effects of such non-coding variants remains difficult. In this dissertation, I evaluate the hypothesis that such non-coding variants contribute to human traits and diseases by altering the regulation of genes rather than the sequence of those genes. I will specifically focus on studies to determine the functional impacts of genetic variation associated with two related complex traits: gestational hyperglycemia and fetal adiposity. At the genomic locus associated with maternal hyperglycemia, we found that genetic variation in regulatory elements altered the expression of the HKDC1 gene. Furthermore, we demonstrated that HKDC1 phosphorylates glucose in vitro and in vivo, thus demonstrating that HKDC1 is a fifth human hexokinase gene. At the fetal-adiposity associated locus, we identified variants that likely alter VEPH1 expression in preadipocytes during differentiation. To make such studies of regulatory variation high-throughput and routine, we developed POP-STARR, a novel high throughput reporter assay that can empirically measure the effects of regulatory variants directly from patient DNA. By combining targeted genome capture technologies with STARR-seq, we assayed thousands of haplotypes from 760 individuals in a single experiment. We subsequently used POP-STARR to identify three key features of regulatory variants: that regulatory variants typically have weak effects on gene expression; that the effects of regulatory variants are often coordinated with respect to disease-risk, suggesting a general mechanism by which the weak effects can together have phenotypic impact; and that nucleotide transversions have larger impacts on enhancer activity than transitions. Together, the findings presented here demonstrate successful strategies for determining the regulatory mechanisms underlying genetic associations with human traits and diseases, and value of doing so for driving novel biological discovery.</p> / Dissertation

Thesis advisor: Marc A.T. Muskavitch / The protozoan Plasmodium falciparum, the mosquito-borne pathogen that causes human malaria, remains one of the most difficult infectious parasites to combat and control. Campaigns against malaria eradication have succeeded, in most instances, at the level of vector control, rather than from initiatives that have attempted to decrease malaria burden by targeting parasites. The rapid evolution and spread of insecticide-resistant mosquitoes is threatening our ability to combat vectors and control malaria. Therefore, the development, procurement and distribution of new methods of vector control are paramount. Two aspects of vector biology that can be exploited toward these ends are vector behaviors and vector-specific insecticide targets. In this thesis, I describe three aspects of vector biology with potential for the development of improved means of vector control: photopreference behavior, long non-coding RNA (lncRNA) targets and epigenetic gene ensemble targets. My studies of photopreference have revealed that specific mosquito species within the genus Anopheles, An. gambiae and An. stephensi, exhibit different photopreference behaviors, and that each gender of mosquito in these species exhibits distinct light-dependent resting behaviors. These inter-specific behavioral differences may be affected by differing numbers of long-wavelength sensing Opsin genes in each species, and my findings regarding species-specific photopreferences suggest that some behavioral interventions may need to be tailored for specific vector mosquito species. Based on the advancement of next-generation sequencing technologies and the generation by others of assembled genomes of many anopheline mosquito species, I have identified a comprehensive set of approximately 3,000 lncRNAs and find that RNA secondary structures are notably conserved within the gambiae species complex. As lncRNAs and epigenetic modifiers cooperate to modulate epigenetic regulation, I have also analyzed the conservation of epigenetic gene ensembles across a number of anopheline species, based on identification of homologous epigenetic ensemble genes in An. gambiae compared to Drosophila melanogaster. Further analyses of these ensembles illustrate that these epigenetic genes are highly stable among many anopheline species, in that I detect only eight gene family expansion or contraction events among 169 epigenetic ensemble genes within a set of 12 anopheline species. My hope is that my findings will enable deeper investigations of many behavioral and epigenetic processes in Anopheles gambiae and other anopheline vector mosquitoes and thereby enable the development of new, more effective means of vector and malaria control. / Thesis (PhD) — Boston College, 2015. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.