Project Mine: Study Design And Pilot Analyses Of A Large-Scale Whole-Genome Sequencing Study In Amyotrophic Lateral Sclerosis, 2017 University Medical Center Utrecht
Project Mine: Study Design And Pilot Analyses Of A Large-Scale Whole-Genome Sequencing Study In Amyotrophic Lateral Sclerosis, Project Mine Consortium, Wouter Van Rheenen, Kevin P. Kenna, John E. Landers, Jan H. Veldink
University of Massachusetts Medical School Faculty Publications
The most recent genome-wide association study in amyotrophic lateral sclerosis (ALS) demonstrates a disproportionate contribution from low-frequency variants to genetic susceptibility of disease. We have therefore begun Project MinE, an international collaboration that seeks to analyse whole-genome sequence data of at least 15,000 ALS patients and 7,500 controls. Here, we report on the design of Project MinE and pilot analyses of newly whole-genome sequenced 1,264 ALS patients and 611 controls drawn from the Netherlands. As has become characteristic of sequencing studies, we find an abundance of rare genetic variation (minor allele frequency < 0.1%), the vast majority of which is absent in public data sets. Principal component analysis reveals local geographical clustering of these variants within The Netherlands. We use the whole-genome sequence data to explore the implications of poor geographical matching of cases and controls in a sequence-based disease study and to investigate how ancestry-matched, externally sequenced controls can induce false positive associations. Also, we have publicly released genome-wide minor allele counts in cases and controls, as well as results from genic burden tests.
Microarray Analysis Of Aging-Associated Immune System Alterations In The Rostral Ventrolateral Medulla Of F344 Rats, 2017 University of Texas at El Paso
Microarray Analysis Of Aging-Associated Immune System Alterations In The Rostral Ventrolateral Medulla Of F344 Rats, Sivasai Balivada, Chanran K. Ganta, Yongqing Zhang, Hitesh N. Pawar, Richard J. Ortiz, Kevin G. Becker, Arshad M. Khan, Michael J. Kenney
Arshad M. Khan, Ph.D.
Phenomenological And Molecular Basis Of The Cnidarian Immune System, 2017 Florida International University
Phenomenological And Molecular Basis Of The Cnidarian Immune System, Tanya Brown
FIU Electronic Theses and Dissertations
Coral reefs are one of the most diverse ecosystems on the planet due partially to the habitat structure provided by corals. Corals are long lived organisms that can live for hundreds of years and as a result growth of many species is very slow. As a result of this, recovery of corals from disease outbreaks is very slow and difficult and therefore the ecosystem is deteriorating rapidly. Due to this increase in disease and its detrimental effect on coral reefs, it has become imperative to study how corals respond to disease outbreaks. The response of the coral to pathogens is ...
Lichen Conservation In Eastern North America: Population Genomics, Climate Change, And Translocations, 2017 The Graduate Center, City University of New York
Lichen Conservation In Eastern North America: Population Genomics, Climate Change, And Translocations, Jessica Allen
All Dissertations, Theses, and Capstone Projects
Conservation biology is a scientific discipline that draws on methods from diverse fields to address specific conservation concerns and inform conservation actions. This field is overwhelmingly focused on charismatic animals and vascular plants, often ignoring other diverse and ecologically important groups. This trend is slowly changing in some ways; for example, increasing number of fungal species are being added to the IUCN Red-List. However, a strong taxonomic bias still exists. Here I contribute four research chapters to further the conservation of lichens, one group of frequently overlooked organisms. I address specific conservation concerns in eastern North America using modern methods ...
Body Size Regulation Via Bmp Signaling In Caenorhabditis Elegans, 2017 The Graduate Center, City University of New York
Body Size Regulation Via Bmp Signaling In Caenorhabditis Elegans, Uday Madaan
All Dissertations, Theses, and Capstone Projects
The body size of an organism can be a crucial determinant of access to nutrition, reproductive success and overall survival in the wild. However, how body size of an individual is determined is incompletely understood. Body size is a complex trait determined by multiple pathways and genes, making it difficult to understand the role of individual genes and pathways in determining overall size. In Caenorhabditis elegans, a homolog of Bone Morphogenetic Proteins (BMP) is a major regulator of body size; functional loss of DBL-1 leads to a small body size. Due to a drastic change in body size in dbl-1 ...
Partner-Drug Resistance And Population Substructuring Of Artemisinin-Resistant Plasmodium Falciparum In Cambodia, 2017 University of North Carolina
Partner-Drug Resistance And Population Substructuring Of Artemisinin-Resistant Plasmodium Falciparum In Cambodia, Christian M. Parobek, Jonathan B. Parr, Nicholas F. Brazeau, Chanthap Lon, Suwanna Chaorattanakawee, Panita Gosi, Eric J. Barnett, Lauren D. Norris, Steven R. Meshnick, Michele D. Spring, Charlotte A. Lanteri, Jeffrey A. Bailey, David L. Saunders, Jessica T. Lin, Jonathan J. Juliano
Open Access Articles
Plasmodium falciparum in western Cambodia has developed resistance to artemisinin and its partner drugs, causing frequent treatment failure. Understanding this evolution can inform the deployment of new therapies. We investigated the genetic architecture of 78 falciparum isolates using whole-genome sequencing, correlating results to in vivo and ex vivo drug resistance and exploring the relationship between population structure, demographic history, and partner drug resistance. Principle component analysis, network analysis and demographic inference identified a diverse central population with three clusters of clonally expanding parasite populations, each associated with specific K13 artemisinin resistance alleles and partner drug resistance profiles which were consistent ...
Shelterin Components Mediate Genome Reorganization In Response To Replication Stress, 2017 National Institutes of Health
Shelterin Components Mediate Genome Reorganization In Response To Replication Stress, Takeshi Mizuguchi, Nitika Taneja, Emiko Matsuda, Jon-Matthew Belton, Peter Fitzgerald, Job Dekker, Shiv I. Grewal S
Program in Systems Biology Publications and Presentations
The dynamic nature of genome organization impacts critical nuclear functions including the regulation of gene expression, replication, and DNA damage repair. Despite significant progress, the mechanisms responsible for reorganization of the genome in response to cellular stress, such as aberrant DNA replication, are poorly understood. Here, we show that fission yeast cells carrying a mutation in the DNA-binding protein Sap1 show defects in DNA replication progression and genome stability and display extensive changes in genome organization. Chromosomal regions such as subtelomeres that show defects in replication progression associate with the nuclear envelope in sap1 mutant cells. Moreover, high-resolution, genome-wide chromosome ...
Isolation And Comparative Genomic Analysis Of Final Third Of Satis Genome, 2017 Washington University in St. Louis
Isolation And Comparative Genomic Analysis Of Final Third Of Satis Genome, Kelly Hartigan, Nicole Curnutt, Matthew Mcdermut
Undergraduate Research Symposium Posters
A highly novel Streptomyces phage, Satis, was isolated from a direct environmental sample collected from outside Danforth House on the Washington University campus. Satis infects bacterial species Streptomyces lividans producing pinpoint, cloudy plaques less than 1mm in diameter. Electron microscope data shows rare atypical physical features. Rather than the common octahedral capsid shape, Satis has a prolate head with visible cross-linked hexagonal protein structure and average measurements of 285 nm by 47 nm with a long, flexible tail measuring 268 nm. Upon sequencing, it was found that Satis contains the longest phage genome discovered to date through the SEA-PHAGE program ...
Characterization Of Zic2 As An Oncoprotein In Prostate Cancer, 2017 Clark Atlanta University
Characterization Of Zic2 As An Oncoprotein In Prostate Cancer, Keira C. Davis
Electronic Theses & Dissertations Collection for Atlanta University & Clark Atlanta University
The field of prostate cancer research is in need of biological markers that predict which cancers do not need treatment, those that can be treated successfully with a localized treatment and more specific cases in which patients are likely to have an aggressive form of cancer that will require more aggressive surgical and chemotherapeutic treatments. ZIC2 is one of five members of a family of proteins that play critical roles in neural crest and mesoderm growth in normal embryonic brain development and in the adult cerebellum of vertebrates. Found throughout the animal kingdom, ZIC1-5 genes encode five distinct ZIC proteins ...
Using Mathematical Models Of Biological Processes In Genome-Wide Association Studies Of Psychiatric Disorders, 2017 University of Michigan-Ann Arbor
Using Mathematical Models Of Biological Processes In Genome-Wide Association Studies Of Psychiatric Disorders, Amy Cochran
Biology and Medicine Through Mathematics Conference
No abstract provided.
Evolutionary Genetic Aspects Of Host Association In Generalist Ectoparasites, 2017 The University of Western Ontario
Evolutionary Genetic Aspects Of Host Association In Generalist Ectoparasites, Benoit Talbot
Electronic Thesis and Dissertation Repository
Despite the use of the host for dispersal by most parasite species, the extremely loose relationship typical between highly mobile hosts and generalist ectoparasites may lead to very different gene flow patterns between the two, leading in turn to different spatial genetic structure, and potentially different demographic history. I examined how similar gene flow patterns are between Cimex adjunctus, a generalist ectoparasite of bats present throughout North America, and two of its key bat hosts. I first analyzed the continent-scale genetic structure and demographic history of C. adjunctus and compared it to that of two of its hosts, the little ...
Accuracy, Reproducibility And Bias Of Next Generation Sequencing For Quantitative Small Rna Profiling: A Multiple Protocol Study Across Multiple Laboratories, Maria D. Giraldez, Kahraman Tanriverdi, Jane E. Freedman, Muneesh Tewari
University of Massachusetts Medical School Faculty Publications
Small RNA-seq is increasingly being used for profiling of small RNAs. Quantitative characteristics of long RNA-seq have been extensively described, but small RNA-seq involves fundamentally different methods for library preparation, with distinct protocols and technical variations that have not been fully and systematically studied. We report here the results of a study using common references (synthetic RNA pools of defined composition, as well as plasma-derived RNA) to evaluate the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across nine different laboratories. We observed protocol-specific and sequence-specific bias, which was ameliorated using adapters for ligation ...
Guideseq: A Bioconductor Package To Analyze Guide-Seq Datasets For Crispr-Cas Nucleases, 2017 University of Massachusetts Medical School
Guideseq: A Bioconductor Package To Analyze Guide-Seq Datasets For Crispr-Cas Nucleases, Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Herve Pages, Alper Kucukural, Manuel Garber, Scot A. Wolfe
Program in Bioinformatics and Integrative Biology Publications and Presentations
BACKGROUND: Genome editing technologies developed around the CRISPR-Cas9 nuclease system have facilitated the investigation of a broad range of biological questions. These nucleases also hold tremendous promise for treating a variety of genetic disorders. In the context of their therapeutic application, it is important to identify the spectrum of genomic sequences that are cleaved by a candidate nuclease when programmed with a particular guide RNA, as well as the cleavage efficiency of these sites. Powerful new experimental approaches, such as GUIDE-seq, facilitate the sensitive, unbiased genome-wide detection of nuclease cleavage sites within the genome. Flexible bioinformatics analysis tools for processing ...
Three-Dimensional Folding Of Eukaryotic Genomes, 2017 University of Massachusetts Medical School
Three-Dimensional Folding Of Eukaryotic Genomes, Tsung-Han S. Hsieh
GSBS Dissertations and Theses
Chromatin packages eukaryotic genomes via a hierarchical series of folding steps, encrypting multiple layers of epigenetic information, which are capable of regulating nuclear transactions in response to complex signals in environment. Besides the 1-dimensinal chromatin landscape such as nucleosome positioning and histone modifications, little is known about the secondary chromatin structures and their functional consequences related to transcriptional regulation and DNA replication. The family of chromosomal conformation capture (3C) assays has revolutionized our understanding of large-scale chromosome folding with the ability to measure relative interaction probability between genomic loci in vivo. However, the suboptimal resolution of the typical 3C techniques ...
Mrna Decay Pathways Use Translation Fidelity And Competing Decapping Complexes For Substrate Selection, 2017 University of Massachusetts Medical School
Mrna Decay Pathways Use Translation Fidelity And Competing Decapping Complexes For Substrate Selection, Alper Celik
GSBS Dissertations and Theses
mRNA decay is an important step in gene regulation, environmental responsiveness, and mRNA quality control. One such quality control pathway, Nonsense-mediated mRNA Decay (NMD), targets transcripts whose translation terminates prematurely. However, the scope and the defining features of NMD-targeted transcripts remain elusive. To address these issues, we re-evaluated the genome-wide expression of annotated transcripts in yeast cells harboring deletions of the UPF1, UPF2, or UPF3 genes. The vast majority of NMD-regulated transcripts are normal-looking protein-coding mRNAs. Our bioinformatics analyses reveal that this set of NMD-regulated transcripts generally have lower translational efficiency, lower average codon optimality scores, and higher ratios of ...
Hybridization Dynamics Of A Newly Discovered Parrotfish Swarm In The Tropical Eastern Pacific, Robert Barron
Hybrid zones and their dynamics are important in the understanding of the genetic basis of reproductive isolation and speciation. This study seeks to investigate the hybridization dynamics of a Scarus hybrid swarm within the Tropical Eastern Pacific (TEP) that includes four phenotypically distinct species: S. perrico, S. ghobban, S. rubroviolaceus, and S. compressus. Genetic and population structure analyses of four nuclear loci and a mitochondrial locus revealed that one of the four species, S. compressus, was the result of two different hybrid crosses: S. perrico ✕ S. rubroviolaceus and S. perrico ✕ S. ghobban. A NewHybrids model indicated that most of the ...
Study Of Rickettsia Parkeri Colonization And Proliferation In The Tick Host Amblyomma Maculatum (Acari: Ixodidae), 2017 University of Southern Mississippi
Study Of Rickettsia Parkeri Colonization And Proliferation In The Tick Host Amblyomma Maculatum (Acari: Ixodidae), Khemraj B.C.
Amblyomma maculatum (Gulf coast tick) ticks are prevalent across the Atlantic to Gulf Coast region of United States. These ticks are recognized vectors of Rickettsia parkeri, a spotted fever group of Rickettsia (SFGR) known to cause American boutonneuse fever associated with fever and eschar rashes localized to the site of bites. We hypothesized that Rickettsia parkeri colonization and proliferation in the tick vector involve pathogen-symbiont dynamics and tick-pathogen interactions, which influence rickettsial transmission to the victims after tick bites. The rickettsial infection is maintained across the tick life cycle for many generations due to transovarial and transstadial transmission of the ...
Denoising Tandem Mass Spectrometry Data, 2017 East Tennessee State Universtiy
Denoising Tandem Mass Spectrometry Data, Felix Offei
Electronic Theses and Dissertations
Protein identification using tandem mass spectrometry (MS/MS) has proven to be an effective way to identify proteins in a biological sample. An observed spectrum is constructed from the data produced by the tandem mass spectrometer. A protein can be identified if the observed spectrum aligns with the theoretical spectrum. However, data generated by the tandem mass spectrometer are affected by errors thus making protein identification challenging in the field of proteomics. Some of these errors include wrong calibration of the instrument, instrument distortion and noise. In this thesis, we present a pre-processing method, which focuses on the removal of ...
Adolescent Perspectives On Genetic Testing For Adult Onset Conditions, 2017 Sarah Lawrence College
Adolescent Perspectives On Genetic Testing For Adult Onset Conditions, Olivia D’Accordo, Erin Davidson, Christina Miller, Yael Weinstein
Human Genetics Theses and Capstones
The American Society of Human Genetics (ASHG) recommends that testing for adult onset conditions be deferred until adulthood because of the potential for psychological harm combined with lack of medical utility. ASHG’s 2016 DNA Day Essay Contest asked 9- 12th graders to defend or refute this position. 1241 essays were submitted. 572 students defended ASHG’s position statement, while 554 argued against. Essays that addressed Alzheimer’s disease (AD) and BRCA-related Hereditary Breast and Ovarian Cancer syndrome were qualitatively analyzed for themes related to the argued position. 64.4% of students argued for deferred testing of AD, and 46 ...
Statistical Methods For Two Problems In Cancer Research: Analysis Of Rna-Seq Data From Archival Samples And Characterization Of Onset Of Multiple Primary Cancers, 2017 The University of Texas MD ANderson Cancer Center UTHealth Graduate School of Biomedical Sciences
Statistical Methods For Two Problems In Cancer Research: Analysis Of Rna-Seq Data From Archival Samples And Characterization Of Onset Of Multiple Primary Cancers, Jialu Li
UT GSBS Dissertations and Theses (Open Access)
My dissertation is focused on quantitative methodology development and application for two important topics in translational and clinical cancer research.
The first topic was motivated by the challenge of applying transcriptome sequencing (RNA-seq) to formalin-fixation and paraffin-embedding (FFPE) tumor samples for reliable diagnostic development. We designed a biospecimen study to directly compare gene expression results from different protocols to prepare libraries for RNA-seq from human breast cancer tissues, with randomization to fresh-frozen (FF) or FFPE conditions. To comprehensively evaluate the FFPE RNA-seq data quality for expression profiling, we developed multiple computational methods for assessment, such as the uniformity and continuity ...