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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 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.

The rostral ventrolateral medulla (RVLM) is an area of the brain stem that contains diverse neural substrates that are involved in systems critical for physiological function. There is evidence that aging affects some neural substrates within the RVLM, although age-related changes in RVLM molecular mechanisms are not well established. The goal of the present study was to characterize the transcriptomic profile of the aging RVLM and to test the hypothesis that aging is associated with altered gene expression in the RVLM, with an emphasis on immune system associated gene transcripts. RVLM tissue punches from young, middle-aged, and aged F344 rats ...


Phenomenological And Molecular Basis Of The Cnidarian Immune System, Tanya Brown 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, Jessica Allen 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, Uday Madaan 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, 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 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, Takeshi Mizuguchi, Nitika Taneja, Emiko Matsuda, Jon-Matthew Belton, Peter FitzGerald, Job Dekker, Shiv I. Grewal S 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, Kelly Hartigan, Nicole Curnutt, Matthew McDermut 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, Keira C. Davis 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, Amy Cochran 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, Benoit Talbot 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 2017 University of Michigan

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, Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Herve Pages, Alper Kucukural, Manuel Garber, Scot A. Wolfe 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, Tsung-Han S. Hsieh 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, Alper Celik 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 2017 Bowdoin College

Hybridization Dynamics Of A Newly Discovered Parrotfish Swarm In The Tropical Eastern Pacific, Robert Barron

Honors Projects

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. perricoS. rubroviolaceus and S. perricoS. ghobban. A NewHybrids model indicated that most of the ...


Study Of Rickettsia Parkeri Colonization And Proliferation In The Tick Host Amblyomma Maculatum (Acari: Ixodidae), Khemraj B.C. 2017 University of Southern Mississippi

Study Of Rickettsia Parkeri Colonization And Proliferation In The Tick Host Amblyomma Maculatum (Acari: Ixodidae), Khemraj B.C.

Dissertations

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, Felix Offei 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 ...


Genome Sequence Of A Novel Positive-Sense, Single-Stranded Rna Virus Isolated From Western Corn Rootworm, Diabrotica Virgifera Virgifera Leconte, Sijun Liu, Yuting Chen, Thomas W. Sappington, Bryony C. Bonning 2017 Iowa State University

Genome Sequence Of A Novel Positive-Sense, Single-Stranded Rna Virus Isolated From Western Corn Rootworm, Diabrotica Virgifera Virgifera Leconte, Sijun Liu, Yuting Chen, Thomas W. Sappington, Bryony C. Bonning

Entomology Publications

The genome sequence of a novel small RNA virus was assembled from the transcriptome of the western corn rootworm, Diabrotica virgifera virgifera. The assembled genome has 13,182 nucleotides with a 3′ polyadenylated tail. Two open reading frames are predicted to encode polyproteins of 2,838 and 1,073 amino acids.


Genome Sequence Of Diabrotica Virgifera Virgifera Virus 2, A Novel Small Rna Virus Of The Western Corn Rootworm, Diabrotica Virgifera Virgifera Leconte, Sijun Liu, Yuting Chen, Thomas W. Sappington, Bryony C. Bonning 2017 Iowa State University

Genome Sequence Of Diabrotica Virgifera Virgifera Virus 2, A Novel Small Rna Virus Of The Western Corn Rootworm, Diabrotica Virgifera Virgifera Leconte, Sijun Liu, Yuting Chen, Thomas W. Sappington, Bryony C. Bonning

Entomology Publications

The genome of a novel small RNA virus, tentatively named Diabrotica virgifera virgifera virus 2 (DvvV2), was identified in the western corn rootworm, Diabrotica virgifera virgifera LeConte, through transcriptome sequencing and confirmed by reverse transcription-PCR. Here, we report the near-complete nucleotide sequence and the genome organization of DvvV2.


Systematics, Diversification, And Functional Diversity Of Russulaceae (Russulales), Brian Patrick Looney 2017 University of Tennessee, Knoxville

Systematics, Diversification, And Functional Diversity Of Russulaceae (Russulales), Brian Patrick Looney

Doctoral Dissertations

The family Russulaceae is an iconic family of mushroom-forming Basidiomycetes both because of their importance as edible mushrooms in many parts of the world and their species richness in both temperate and tropical forested biomes. While much mycological research has been focused on this group, recent systematic and ecological research has failed to develop a comprehensive or cohesive organization by which to understand the evolutionary relationships, patterns of diversification, or functional importance of the group. Recently, interest in ectomycorrhizal fungi (EmF), of which Russulaceae is a key lineage, has greatly increased due to the recognition of the importance of EmF ...


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