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Genetics and Genomics

Genomics

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Articles 1 - 30 of 205

Full-Text Articles in Life Sciences

From Mendelian Inheritance To Molecular Genomics: A Brief Appreciation Of Genetics, Tim Nguyen Jan 2020

From Mendelian Inheritance To Molecular Genomics: A Brief Appreciation Of Genetics, Tim Nguyen

Synthesis: A Digital Journal of Student Science Communication

Biology is one of many sciences advancing society and the human conquest for knowledge. Its transition from speculation to lifestyle has been a turbulent ride for centuries, but nevertheless, implications for health improvement has only allowed the field to be advocated by more and more people beyond the professions. Revolutionary findings in genetics increased rapidly for either the advancement of knowledge or its promise for medicine, and while its celebration is heard in academia and achievements like Nobel Prizes, many of the details and reasons for these celebrations are not fully understood. In this mini retrospect, I reflect on a ...


Promises And Challenges Of Eco-Physiological Genomics In The Field: Tests Of Drought Responses In Switchgrass. Plant Physiology, John T. Lovell, Eugene V. Shakirov, Scott Schwartz, David B. Lowry, Michael J. Aspinwall, Samuel H. Taylor, Jason Bonnette, Juan Diego Palacio-Mejia, Christine V. Hawkes, Philip A. Fay, Thomas E. Juenger Oct 2019

Promises And Challenges Of Eco-Physiological Genomics In The Field: Tests Of Drought Responses In Switchgrass. Plant Physiology, John T. Lovell, Eugene V. Shakirov, Scott Schwartz, David B. Lowry, Michael J. Aspinwall, Samuel H. Taylor, Jason Bonnette, Juan Diego Palacio-Mejia, Christine V. Hawkes, Philip A. Fay, Thomas E. Juenger

Yevgeniy (Eugene) Shakirov

Identifying the physiological and genetic basis of stress tolerance in plants has proven to be critical to understanding adaptation in both agricultural and natural systems. However, many discoveries were initially made in the controlled conditions of greenhouses or laboratories, not in the field. To test the comparability of drought responses across field and greenhouse environments, we undertook three independent experiments using the switchgrass reference genotype Alamo AP13. We analyzed physiological and gene expression variation across four locations, two sampling times, and three years. Relatively similar physiological responses and expression coefficients of variation across experiments masked highly dissimilar gene expression responses ...


Integrating Human Omics Data To Prioritize Candidate Genes., Yong Chen, Xuebing Wu, Rui Jiang Sep 2019

Integrating Human Omics Data To Prioritize Candidate Genes., Yong Chen, Xuebing Wu, Rui Jiang

Yong Chen

BACKGROUND: The identification of genes involved in human complex diseases remains a great challenge in computational systems biology. Although methods have been developed to use disease phenotypic similarities with a protein-protein interaction network for the prioritization of candidate genes, other valuable omics data sources have been largely overlooked in these methods.

METHODS: With this understanding, we proposed a method called BRIDGE to prioritize candidate genes by integrating disease phenotypic similarities with such omics data as protein-protein interactions, gene sequence similarities, gene expression patterns, gene ontology annotations, and gene pathway memberships. BRIDGE utilizes a multiple regression model with lasso penalty to ...


Tracing Evolutionary Footprints To Identify Novel Gene Functional Linkages., Yong Chen, Li Yang, Yunfeng Ding, Shuyan Zhang, Tong He, Fenglou Mao, Congyan Zhang, Huina Zhang, Chaoxing Huo, Pingsheng Liu Sep 2019

Tracing Evolutionary Footprints To Identify Novel Gene Functional Linkages., Yong Chen, Li Yang, Yunfeng Ding, Shuyan Zhang, Tong He, Fenglou Mao, Congyan Zhang, Huina Zhang, Chaoxing Huo, Pingsheng Liu

Yong Chen

Systematic determination of gene function is an essential step in fully understanding the precise contribution of each gene for the proper execution of molecular functions in the cell. Gene functional linkage is defined as to describe the relationship of a group of genes with similar functions. With thousands of genomes sequenced, there arises a great opportunity to utilize gene evolutionary information to identify gene functional linkages. To this end, we established a computational method (called TRACE) to trace gene footprints through a gene functional network constructed from 341 prokaryotic genomes. TRACE performance was validated and successfully tested to predict enzyme ...


Integrated Omics Study Delineates The Dynamics Of Lipid Droplets In Rhodococcus Opacus Pd630., Yong Chen, Yunfeng Ding, Li Yang, Jinhai Yu, Guiming Liu, Xumin Wang, Shuyan Zhang, Dan Yu, Lai Song, Hangxiao Zhang, Congyan Zhang, Linhe Huo, Chaoxing Huo, Yang Wang, Yalan Du, Huina Zhang, Peng Zhang, Huimin Na, Shimeng Xu, Yaxin Zhu, Zhensheng Xie, Tong He, Yue Zhang, Guoliang Wang, Zhonghua Fan, Fuquan Yang, Honglei Liu, Xiaowo Wang, Xuegong Zhang, Michael Q Zhang, Yanda Li, Alexander Steinbüchel, Toyoshi Fujimoto, Simon Cichello, Jun Yu, Pingsheng Liu Sep 2019

Integrated Omics Study Delineates The Dynamics Of Lipid Droplets In Rhodococcus Opacus Pd630., Yong Chen, Yunfeng Ding, Li Yang, Jinhai Yu, Guiming Liu, Xumin Wang, Shuyan Zhang, Dan Yu, Lai Song, Hangxiao Zhang, Congyan Zhang, Linhe Huo, Chaoxing Huo, Yang Wang, Yalan Du, Huina Zhang, Peng Zhang, Huimin Na, Shimeng Xu, Yaxin Zhu, Zhensheng Xie, Tong He, Yue Zhang, Guoliang Wang, Zhonghua Fan, Fuquan Yang, Honglei Liu, Xiaowo Wang, Xuegong Zhang, Michael Q Zhang, Yanda Li, Alexander Steinbüchel, Toyoshi Fujimoto, Simon Cichello, Jun Yu, Pingsheng Liu

Yong Chen

Rhodococcus opacus strain PD630 (R. opacus PD630), is an oleaginous bacterium, and also is one of few prokaryotic organisms that contain lipid droplets (LDs). LD is an important organelle for lipid storage but also intercellular communication regarding energy metabolism, and yet is a poorly understood cellular organelle. To understand the dynamics of LD using a simple model organism, we conducted a series of comprehensive omics studies of R. opacus PD630 including complete genome, transcriptome and proteome analysis. The genome of R. opacus PD630 encodes 8947 genes that are significantly enriched in the lipid transport, synthesis and metabolic, indicating a super ...


Rare Degs1 Variant Significantly Alters De Novo Ceramide Synthesis Pathway, Nicholas B. Blackburn, Joanne E. Curran, Laura F. Michael, Peter J. Meikle, Juan M. Peralta, Marian Mosio, Scott Mcahern, Hai H. Bui, Melissa A. Bellinger, Corey Giles, Satish Kumar, Ana C. Leandro, Marcio Alameida, Jacquelyn M. Weir, Michael C. Mahaney, Thomas D. Dyer, Laura Almasy, John L. Vandeberg, Sarah Williams-Blangero, David C. Glahn, Ravindranath Duggirala, Mark Kowola, John Blangero Sep 2019

Rare Degs1 Variant Significantly Alters De Novo Ceramide Synthesis Pathway, Nicholas B. Blackburn, Joanne E. Curran, Laura F. Michael, Peter J. Meikle, Juan M. Peralta, Marian Mosio, Scott Mcahern, Hai H. Bui, Melissa A. Bellinger, Corey Giles, Satish Kumar, Ana C. Leandro, Marcio Alameida, Jacquelyn M. Weir, Michael C. Mahaney, Thomas D. Dyer, Laura Almasy, John L. Vandeberg, Sarah Williams-Blangero, David C. Glahn, Ravindranath Duggirala, Mark Kowola, John Blangero

School of Medicine Publications and Presentations

The de novo ceramide synthesis pathway is essential to human biology and health but genetic influences remain unexplored. The core function of this pathway is the generation of biologically active ceramide from its precursor, dihydroceramide. Dihydroceramides have diverse, often protective, biological roles; conversely, increased ceramide levels are biomarkers of complex disease. To explore the genetics of the ceramide synthesis pathway, we searched for deleterious nonsynonymous variants in the genomes of 1,020 Mexican Americans from extended pedigrees. We identified a Hispanic ancestry−specific rare functional variant, L175Q, in DEGS1, a key enzyme in the pathway that converts dihydroceramide to ceramide ...


A Unified Encyclopedia Of Human Functional Dna Elements Through Fully Automated Annotation Of 164 Human Cell Types, Maxwell W. Libbrecht, Oscar L. Rodriguez, Zhiping Weng, Jeffrey A. Bilmes, Michael M. Hoffman, William Stafford Noble Aug 2019

A Unified Encyclopedia Of Human Functional Dna Elements Through Fully Automated Annotation Of 164 Human Cell Types, Maxwell W. Libbrecht, Oscar L. Rodriguez, Zhiping Weng, Jeffrey A. Bilmes, Michael M. Hoffman, William Stafford Noble

Open Access Articles

Semi-automated genome annotation methods such as Segway take as input a set of genome-wide measurements such as of histone modification or DNA accessibility and output an annotation of genomic activity in the target cell type. Here we present annotations of 164 human cell types using 1615 data sets. To produce these annotations, we automated the label interpretation step to produce a fully automated annotation strategy. Using these annotations, we developed a measure of the importance of each genomic position called the "conservation-associated activity score." We further combined all annotations into a single, cell type-agnostic encyclopedia that catalogs all human regulatory ...


Distinct Features Of Nucleolus-Associated Domains In Mouse Embryonic Stem Cells, Aizhan Bizhanova, Aimin Yan, Jun Yu, Lihua Julie Zhu, Paul D. Kaufman Aug 2019

Distinct Features Of Nucleolus-Associated Domains In Mouse Embryonic Stem Cells, Aizhan Bizhanova, Aimin Yan, Jun Yu, Lihua Julie Zhu, Paul D. Kaufman

University of Massachusetts Medical School Faculty Publications

Background Heterochromatin in eukaryotic interphase cells frequently localizes to the nucleolar periphery (nucleolus-associated domains, NADs) and the nuclear lamina (lamina-associated domains, LADs). Gene expression in somatic cell NADs is generally low, but NADs have not been characterized in mammalian stem cells.

Results Here, we generated the first genome-wide map of NADs in mouse embryonic stem cells (mESCs) via deep sequencing of chromatin associated with biochemically-purified nucleoli. As we had observed in mouse embryonic fibroblasts (MEFs), the large Type I subset of NADs overlaps with constitutive LADs and is enriched for features of constitutive heterochromatin, including late replication timing and low ...


Gain-Of-Function Mutations In The Unc-2/Cav2alpha Channel Lead To Excitation-Dominant Synaptic Transmission In C. Elegans, Yung-Chi Huang, Jennifer K. Pirri, Diego Rayes, Shangbang Gao, Ben Mulcahy, Jeff Grant, Yasunori Saheki, Michael M. Francis, Mei Zhen, Mark J. Alkema Aug 2019

Gain-Of-Function Mutations In The Unc-2/Cav2alpha Channel Lead To Excitation-Dominant Synaptic Transmission In C. Elegans, Yung-Chi Huang, Jennifer K. Pirri, Diego Rayes, Shangbang Gao, Ben Mulcahy, Jeff Grant, Yasunori Saheki, Michael M. Francis, Mei Zhen, Mark J. Alkema

Neurobiology Publications and Presentations

Mutations in pre-synaptic voltage gated calcium channels can lead to familial hemiplegic migraine type 1 (FHM1). While mammalian studies indicate that the migraine brain is hyperexcitable due to enhanced excitation or reduced inhibition, the molecular and cellular mechanisms underlying this excitatory/inhibitory (E/I) imbalance are poorly understood. We identified a gain-of-function (gf) mutation in the Caenorhabditis elegans CaV2 channel alpha1 subunit, UNC-2, which leads to increased calcium currents. unc-2(zf35gf) mutants exhibit hyperactivity and seizure-like motor behaviors. Expression of the unc-2 gene with FHM1 substitutions R192Q and S218L leads to hyperactivity similar to that of unc-2(zf35gf) mutants. unc-2 ...


A Method For Improving The Accuracy And Efficiency Of Bacteriophage Genome Annotation, Alicia Salisbury, Philippos K. Tsourkas Jul 2019

A Method For Improving The Accuracy And Efficiency Of Bacteriophage Genome Annotation, Alicia Salisbury, Philippos K. Tsourkas

Life Sciences Faculty Publications

Bacteriophages are the most numerous entities on Earth. The number of sequenced phage genomes is approximately 8000 and increasing rapidly. Sequencing of a genome is followed by annotation, where genes, start codons, and functions are putatively identified. The mainstays of phage genome annotation are auto-annotation programs such as Glimmer and GeneMark. Due to the relatively small size of phage genomes, many groups choose to manually curate auto-annotation results to increase accuracy. An additional benefit of manual curation of auto-annotated phage genomes is that the process is amenable to be performed by students, and has been shown to improve student recruitment ...


A Chromosome Folding Intermediate At The Condensin-To-Cohesin Transition During Telophase, Kristin Abramo, Anne-Laure Valton, Sergey V. Venev, Hakan Ozadam, A. Nicole Fox, Job Dekker Jun 2019

A Chromosome Folding Intermediate At The Condensin-To-Cohesin Transition During Telophase, Kristin Abramo, Anne-Laure Valton, Sergey V. Venev, Hakan Ozadam, A. Nicole Fox, Job Dekker

University of Massachusetts Medical School Faculty Publications

Chromosome folding is extensively modulated as cells progress through the cell cycle. During mitosis, condensin complexes fold chromosomes in helically arranged nested loop arrays. In interphase, the cohesin complex generates loops that can be stalled at CTCF sites leading to positioned loops and topologically associating domains (TADs), while a separate process of compartmentalization drives the spatial segregation of active and inactive chromatin domains. We used synchronized cell cultures to determine how the mitotic chromosome conformation is transformed into the interphase state. Using Hi-C, chromatin binding assays, and immunofluorescence we show that by telophase condensin-mediated loops are lost and a transient ...


Genome Of The Tropical Plant Marchantia Inflexa: Implications For Sex Chromosome Evolution And Dehydration Tolerance, Rose A. Marks, Jeramiah J. Smith, Quentin Cronk, Christopher J. Grassa, D. Nicholas Mcletchie Jun 2019

Genome Of The Tropical Plant Marchantia Inflexa: Implications For Sex Chromosome Evolution And Dehydration Tolerance, Rose A. Marks, Jeramiah J. Smith, Quentin Cronk, Christopher J. Grassa, D. Nicholas Mcletchie

Biology Faculty Publications

We present a draft genome assembly for the tropical liverwort, Marchantia inflexa, which adds to a growing body of genomic resources for bryophytes and provides an important perspective on the evolution and diversification of land plants. We specifically address questions related to sex chromosome evolution, sexual dimorphisms, and the genomic underpinnings of dehydration tolerance. This assembly leveraged the recently published genome of related liverwort, M. polymorpha, to improve scaffolding and annotation, aid in the identification of sex-linked sequences, and quantify patterns of sequence differentiation within Marchantia. We find that genes on sex chromosomes are under greater diversifying selection than autosomal ...


Differential Effects Of Influenza Virus Na, Ha Head, And Ha Stalk Antibodies On Peripheral Blood Leukocyte Gene Expression During Human Infection., Kathie-Anne Walters, Ruoqing Zhu, Michael Welge, Kelsey Scherler, Jae-Keun Park, Zainab Rahil, Hao Wang, Loretta Auvil, Colleen Bushell, Min Young Lee, David Baxter, Tyler Bristol, Luz Angela Rosas, Adriana Cervantes-Medina, Lindsay Czajkowski, Alison Han, Matthew J Memoli, Jeffery K Taubenberger, John C Kash May 2019

Differential Effects Of Influenza Virus Na, Ha Head, And Ha Stalk Antibodies On Peripheral Blood Leukocyte Gene Expression During Human Infection., Kathie-Anne Walters, Ruoqing Zhu, Michael Welge, Kelsey Scherler, Jae-Keun Park, Zainab Rahil, Hao Wang, Loretta Auvil, Colleen Bushell, Min Young Lee, David Baxter, Tyler Bristol, Luz Angela Rosas, Adriana Cervantes-Medina, Lindsay Czajkowski, Alison Han, Matthew J Memoli, Jeffery K Taubenberger, John C Kash

Articles, Abstracts, and Reports

In this study, we examined the relationships between anti-influenza virus serum antibody titers, clinical disease, and peripheral blood leukocyte (PBL) global gene expression during presymptomatic, acute, and convalescent illness in 83 participants infected with 2009 pandemic H1N1 virus in a human influenza challenge model. Using traditional statistical and logistic regression modeling approaches, profiles of differentially expressed genes that correlated with active viral shedding, predicted length of viral shedding, and predicted illness severity were identified. These analyses further demonstrated that challenge participants fell into three peripheral blood leukocyte gene expression phenotypes that significantly correlated with different clinical outcomes and prechallenge serum ...


The Relationship Between Uncertainty Tolerance And Oncologists’ Perceptions Of Large-Panel Genomic Tumor Testing, Eric Anderson, Alexandra Hinton, Christine Lary, Kimberly Murray, Leo Waterson, Paul Han, Maine Cancer Genomics Initiative May 2019

The Relationship Between Uncertainty Tolerance And Oncologists’ Perceptions Of Large-Panel Genomic Tumor Testing, Eric Anderson, Alexandra Hinton, Christine Lary, Kimberly Murray, Leo Waterson, Paul Han, Maine Cancer Genomics Initiative

Maine Medical Center

Introduction:

Large-panel genomic tumor testing (GTT) is a new technology that promises to make cancer treatment more precise, but that currently poses many uncertainties regarding its clinical value and appropriate use. Uncertainty Tolerance (UT), a psychological construct that describes trait-level differences in individuals’ responses to uncertainty, may influence oncologists’ perceptions and attitudes regarding GTT.


Community Oncology Clinicians’ Knowledge, Beliefs, And Attitudes Regarding Genomic Tumor Testing, Eric Anderson, Alexandra Hinton, Kimberly Murray, Hayley Mandeville, Caitlin Gutheil, Leo Waterston, Lee Lucas, Christine Duarte, Christian Thomas, Susan Miesfeldt, Petra Helbig, Andrey Antov, Jens Rueter, Paul Han May 2019

Community Oncology Clinicians’ Knowledge, Beliefs, And Attitudes Regarding Genomic Tumor Testing, Eric Anderson, Alexandra Hinton, Kimberly Murray, Hayley Mandeville, Caitlin Gutheil, Leo Waterston, Lee Lucas, Christine Duarte, Christian Thomas, Susan Miesfeldt, Petra Helbig, Andrey Antov, Jens Rueter, Paul Han

Maine Medical Center

Introduction: Genomic tumor testing (GTT) is a new technology that promises to make cancer treatment more precise. However, little is known about clinicians’ knowledge, beliefs, and attitudes regarding GTT, particularly in community oncology settings.


Genomics Based Approaches To Fungal Evolution, Aaron J. Robinson, Donald O. Natvig Mar 2019

Genomics Based Approaches To Fungal Evolution, Aaron J. Robinson, Donald O. Natvig

Biology ETDs

Advances in DNA sequencing and data analysis make it possible to address questions in population genetics and evolution at the genomic level. Fungi are excellent subjects for such studies, because they are found in diverse environments, have short generation times, can be maintained in culture and have relatively small genomes. My research employed genetic approaches using a variety of sequencing technologies and methods of analysis to explore questions in fungal evolution.

In one study, I explored the genetics behind differences in thermotolerance between isolates of Neurospora discreta from Alaska and New Mexico. Isolates from the two states exhibited differences in ...


Shared Heritability And Functional Enrichment Across Six Solid Cancers, Xia Jiang, Hilary K. Finucane, Fredrick R. Schumacher, Stephanie L. Schmit, Jonathan P. Tyrer, Younghun Han, Kyriaki Michailidou, Corina Lesseur, Karoline B. Kuchenbaecker, Joe Dennis, David V. Conti, Graham Casey, Mia M. Gaudet, Jeroen R. Huyghe, Demetrius Albanes, Melinda C. Aldrich, Angeline S. Andrew, Irene L. Andrulis, Hoda Anton-Culver, Antonis C. Antoniou, Natalia N. Antonenkova, Susanne M. Arnold, Kristan J. Aronson, Banu K. Arun, Elisa V. Bandera, Rosa B. Barkardottir, Daniel R. Barnes, Jyotsna Batra, Matthias W. Beckmann, Javier Benitez Jan 2019

Shared Heritability And Functional Enrichment Across Six Solid Cancers, Xia Jiang, Hilary K. Finucane, Fredrick R. Schumacher, Stephanie L. Schmit, Jonathan P. Tyrer, Younghun Han, Kyriaki Michailidou, Corina Lesseur, Karoline B. Kuchenbaecker, Joe Dennis, David V. Conti, Graham Casey, Mia M. Gaudet, Jeroen R. Huyghe, Demetrius Albanes, Melinda C. Aldrich, Angeline S. Andrew, Irene L. Andrulis, Hoda Anton-Culver, Antonis C. Antoniou, Natalia N. Antonenkova, Susanne M. Arnold, Kristan J. Aronson, Banu K. Arun, Elisa V. Bandera, Rosa B. Barkardottir, Daniel R. Barnes, Jyotsna Batra, Matthias W. Beckmann, Javier Benitez

Markey Cancer Center Faculty Publications

Quantifying the genetic correlation between cancers can provide important insights into the mechanisms driving cancer etiology. Using genome-wide association study summary statistics across six cancer types based on a total of 296,215 cases and 301,319 controls of European ancestry, here we estimate the pair-wise genetic correlations between breast, colorectal, head/neck, lung, ovary and prostate cancer, and between cancers and 38 other diseases. We observed statistically significant genetic correlations between lung and head/neck cancer (rg = 0.57, p = 4.6 × 10−8), breast and ovarian cancer (rg = 0.24, p = 7 × 10−5), breast and ...


Intraspecific Variation In Dehydration Tolerance: Insights From The Tropical Plant Marchantia Inflexa, Rose A. Marks Jan 2019

Intraspecific Variation In Dehydration Tolerance: Insights From The Tropical Plant Marchantia Inflexa, Rose A. Marks

Theses and Dissertations--Biology

Plants are threatened by global change, increasing variability in weather patterns, and associated abiotic stress. Consequently, there is an urgent need to enhance our ability to predict plant community dynamics, shifts in species distributions, and physiological responses to environmental challenges. By building a fundamental understanding of plant stress tolerance, it may be possibly to protect the ecological services, economic industries, and communities that depend on plants. Dehydration tolerance (DhT) is an important mechanism of water stress tolerance with promising translational applications. Here, I take advantage natural variation in DhT to gain a deeper insight into this complex trait. In addition ...


Uncovering Evolutionary Changes In The Mitochondrial Genomes Of Lichenized Fungi Within The Order Arthoniales, Dustin Bailey Jan 2019

Uncovering Evolutionary Changes In The Mitochondrial Genomes Of Lichenized Fungi Within The Order Arthoniales, Dustin Bailey

Undergraduate Honors Theses

Lichens are symbiotic organisms that are understudied despite their usefulness to a wide range of disciplines. Studying the genetics of lichen, will contribute to a better understanding of the genetic mechanisms behind symbiosis and fill in grey areas of taxonomic classification of lichens. The lichen order of Arthoniales is even less studied compared to its sister order Lecanorales. This study expands the genomic resources for the former order of lichen and reveals some novel genetic trends found among species within Arthoniales. Some genetic trends have yet to be identified in other lichen species such as the trans-splicing of nad4 among ...


Evidence-Based Practice Self-Study Education Program For Staff Nurses On Genomics, Nancy L. Norman-Marzella Jan 2019

Evidence-Based Practice Self-Study Education Program For Staff Nurses On Genomics, Nancy L. Norman-Marzella

Walden Dissertations and Doctoral Studies

Nurses routinely obtain genomic data when collecting family health histories. However, they report low confidence in their knowledge and understanding of genomics and the genetically engineered medications prescribed for their patients. The purpose of this project was the development and implementation of an evidence-based online education program about genetics and genomics to increase the nurses' understanding and ability to provide competent care for their patients receiving treatments based on the science of genomics. Knowles's principles of adult learning theory guided the development and delivery of the online education project to 12 medical-surgical registered nurses employed in a hospital in ...


Genome-Wide Systems Genetics Of Alcohol Consumption And Dependence, Kristin Mignogna Jan 2019

Genome-Wide Systems Genetics Of Alcohol Consumption And Dependence, Kristin Mignogna

Theses and Dissertations

Widely effective treatment for alcohol use disorder is not yet available, because the exact biological mechanisms that underlie this disorder are not completely understood. One way to gain a better understanding of these mechanisms is to examine the genetic frameworks that contribute to the risk for developing this disorder. This dissertation examines genetic association data in combination with gene expression networks in the brain to identify functional groups of genes associated with alcohol consumption and dependence.

The first study took advantage of the behavioral complexity of human samples, and experimental capabilities provided by mouse models, by co-analyzing gene expression networks ...


Population Structure And Connectivity Of A Groundwater Crustacean Across Northwestern Montana Aquifers, Megan N. Ritter Jan 2019

Population Structure And Connectivity Of A Groundwater Crustacean Across Northwestern Montana Aquifers, Megan N. Ritter

Master’s Theses

Floodplain aquifer systems are diverse and heterogenous ecosystems that serve many ecological functions, including habitat provision to a range of groundwater species. The Flathead River system of northwestern Montana is home to many floodplain aquifers of great ecological importance to the region. The basic biology, population structure, and dispersal patterns of obligate groundwater organisms that reside within the aquifers of the Flathead are still largely unknown. In this study, we investigate the population structure of one such taxon, an undescribed species of the amphipod genus Stygobromus. For our low-coverage RADseq dataset, we tested the suitability of three different analysis pipelines ...


Saccharomyces Genome Database & Uniprot Bioinformatics Analysis, Ray A. Enke Dec 2018

Saccharomyces Genome Database & Uniprot Bioinformatics Analysis, Ray A. Enke

Ray Enke Ph.D.

This in class activity introduces basic bioinformatics analysis using the Saccharomyces Genome Database (SGD) and the UniProt Database. The yeast URA3 gene is studied in this activity, however, any other yeast gene can be substituted. This activity is designed for novice instructors and students for implementation into core biology lecture or lab courses.


The Trim-Nhl Protein Nhl-2 Is A Co-Factor In The Nuclear And Somatic Rnai Pathways In C. Elegans, Gregory M. Davis, Shikui Tu, Jacqueline A. Wilce, Julie M. Claycomb, Zhiping Weng, Peter R. Boag Dec 2018

The Trim-Nhl Protein Nhl-2 Is A Co-Factor In The Nuclear And Somatic Rnai Pathways In C. Elegans, Gregory M. Davis, Shikui Tu, Jacqueline A. Wilce, Julie M. Claycomb, Zhiping Weng, Peter R. Boag

Program in Bioinformatics and Integrative Biology Publications and Presentations

Proper regulation of germline gene expression is essential for fertility and maintaining species integrity. In the C. elegans germline, a diverse repertoire of regulatory pathways promote the expression of endogenous germline genes and limit the expression of deleterious transcripts to maintain genome homeostasis. Here we show that the conserved TRIM-NHL protein, NHL-2, plays an essential role in the C. elegans germline, modulating germline chromatin and meiotic chromosome organization. We uncover a role for NHL-2 as a co-factor in both positively (CSR-1) and negatively (HRDE-1) acting germline 22G-small RNA pathways and the somatic nuclear RNAi pathway. Furthermore, we demonstrate that NHL-2 ...


Two Contrasting Classes Of Nucleolus-Associated Domains In Mouse Fibroblast Heterochromatin, Anastassiia Vertii, Jianhong Ou, Jun Yu, Aimin Yan, Hervé Pagès, Haibo Liu, Lihua Julie Zhu, Paul D. Kaufman Dec 2018

Two Contrasting Classes Of Nucleolus-Associated Domains In Mouse Fibroblast Heterochromatin, Anastassiia Vertii, Jianhong Ou, Jun Yu, Aimin Yan, Hervé Pagès, Haibo Liu, Lihua Julie Zhu, Paul D. Kaufman

University of Massachusetts Medical School Faculty Publications

In interphase eukaryotic cells, almost all heterochromatin is located adjacent to the nucleolus or to the nuclear lamina, thus defining Nucleolus Associated Domains (NADs) and Lamina Associated Domains (LADs), respectively. Here, we determined the first genome-scale map of murine NADs in mouse embryonic fibroblasts (MEFs) via deep sequencing of chromatin associated with purified nucleoli. We developed a Bioconductor package called NADfinder and demonstrated that it identifies NADs more accurately than other peak-calling tools, due to its critical feature of chromosome-level local baseline correction. We detected two distinct classes of NADs. Type I NADs associate frequently with both the nucleolar periphery ...


Improved Reference Genome For The Domestic Horse Increases Assembly Contiguity And Composition, Theodore S. Kalbfleisch, Edward S. Rice, Michael S. Depriest Jr., Brian P. Walenz, Matthew S. Hestand, Joris R. Vermeesch, Brendan L. O'Connell, Ian T. Fiddes, Alisa O. Vershinina, Nedda F. Saremi, Jessica L. Petersen, Carrie J. Finno, Rebecca R. Bellone, Molly E Mccue, Samantha A. Brooks, Ernest Bailey, Ludovic Orlando, Richard E. Green, Donald C. Miller, Douglas F. Antczak, James N. Macleod Nov 2018

Improved Reference Genome For The Domestic Horse Increases Assembly Contiguity And Composition, Theodore S. Kalbfleisch, Edward S. Rice, Michael S. Depriest Jr., Brian P. Walenz, Matthew S. Hestand, Joris R. Vermeesch, Brendan L. O'Connell, Ian T. Fiddes, Alisa O. Vershinina, Nedda F. Saremi, Jessica L. Petersen, Carrie J. Finno, Rebecca R. Bellone, Molly E Mccue, Samantha A. Brooks, Ernest Bailey, Ludovic Orlando, Richard E. Green, Donald C. Miller, Douglas F. Antczak, James N. Macleod

Gluck Equine Research Center Faculty Publications

Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. Here, we present EquCab3. The count of ...


Speciation And Hybridization In Jamaican-Endemic Streamertail Hummingbirds (Trochilus Polytmus And T. Scitulus), Caroline D. Judy Nov 2018

Speciation And Hybridization In Jamaican-Endemic Streamertail Hummingbirds (Trochilus Polytmus And T. Scitulus), Caroline D. Judy

LSU Doctoral Dissertations

Streamertails hummingbirds (Trochilus polytmus and T. scitulus) are recently diverged sister taxa that appear to have speciated in situ on the island of Jamaica. They are distinguished by male bill color, a secondary sexual trait that is coral red in T. polytmus and jet black in T. scitulus. They hybridize in a narrow zone where their ranges meet in eastern Jamaica. In Chapter 2, I performed a formal population survey of T. scitulus to determine the size of the population, which was unknown. I determined that the total population contains well over 100,000 individuals despite its limited geographic range ...


Differential Analysis Of Chromatin Accessibility And Histone Modifications For Predicting Mouse Developmental Enhancers, Shaliu Fu, Qin Wang, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Kaili Fan, Cuihua Gu, Cizhong Jiang, Ruixin Zhu, Anshul Kundaje, Aiping Lu, Zhiping Weng Aug 2018

Differential Analysis Of Chromatin Accessibility And Histone Modifications For Predicting Mouse Developmental Enhancers, Shaliu Fu, Qin Wang, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Kaili Fan, Cuihua Gu, Cizhong Jiang, Ruixin Zhu, Anshul Kundaje, Aiping Lu, Zhiping Weng

Program in Bioinformatics and Integrative Biology Publications and Presentations

Enhancers are distal cis-regulatory elements that modulate gene expression. They are depleted of nucleosomes and enriched in specific histone modifications; thus, calling DNase-seq and histone mark ChIP-seq peaks can predict enhancers. We evaluated nine peak-calling algorithms for predicting enhancers validated by transgenic mouse assays. DNase and H3K27ac peaks were consistently more predictive than H3K4me1/2/3 and H3K9ac peaks. DFilter and Hotspot2 were the best DNase peak callers, while HOMER, MUSIC, MACS2, DFilter and F-seq were the best H3K27ac peak callers. We observed that the differential DNase or H3K27ac signals between two distant tissues increased the area under the precision-recall ...


The Search For A Hero Gene: Fact Or Fiction?, Olivia Efthimiou Jul 2018

The Search For A Hero Gene: Fact Or Fiction?, Olivia Efthimiou

Heroism Science

The radical entry of heroism research into scientific inquiry presents interesting challenges and possibilities for the study of heroism and the human condition more broadly. This ‘final frontier’ of the enduring phenomenon of heroism stands to offer remarkable, unprecedented, and controversial advances in our understanding of heroic and human behaviour. Is a genetic basis for heroism a real possibility? If so, what would its impacts be? Advances in genomics and increased interest in the fields of epigenetics and neuroplasticity might hold the key to its discovery. This article considers some of the leading emerging research in global health genomics and ...


Analytical “Bake-Off” Of Whole Genome Sequencing Quality For The Genome Russia Project Using A Small Cohort For Autoimmune Hepatitis, Daria V. Zhernakova, Sergei Kliver, Nikolay Cherkasov, Gaik Tamazian, Mikhail Rotkevich, Ksenia Krasheninnikova, Igor Evsyukov, Sviatoslav Sidorov, Pavel Dobrynin, Andrey A. Yurchenko, Valentin Shimansky, Irina V. Shcherbakova, Andrey S. Glotov, David L. Valle, Minzhong Tang, Emilia Shin, Kathleen B. Schwarz, Stephen James O'Brien Jul 2018

Analytical “Bake-Off” Of Whole Genome Sequencing Quality For The Genome Russia Project Using A Small Cohort For Autoimmune Hepatitis, Daria V. Zhernakova, Sergei Kliver, Nikolay Cherkasov, Gaik Tamazian, Mikhail Rotkevich, Ksenia Krasheninnikova, Igor Evsyukov, Sviatoslav Sidorov, Pavel Dobrynin, Andrey A. Yurchenko, Valentin Shimansky, Irina V. Shcherbakova, Andrey S. Glotov, David L. Valle, Minzhong Tang, Emilia Shin, Kathleen B. Schwarz, Stephen James O'Brien

Biology Faculty Articles

A comparative analysis of whole genome sequencing (WGS) and genotype calling was initiated for ten human genome samples sequenced by St. Petersburg State University Peterhof Sequencing Center and by three commercial sequencing centers outside of Russia. The sequence quality, efficiency of DNA variant and genotype calling were compared with each other and with DNA microarrays for each of ten study subjects. We assessed calling of SNPs, indels, copy number variation, and the speed of WGS throughput promised. Twenty separate QC analyses showed high similarities among the sequence quality and called genotypes. The ten genomes tested by the centers included eight ...