Genetics and Genomics Commons^™

The Role Of The Dosage Compensation Complex As A Pathway For Spiroplasma To Induce Male Lethality In Drosophila Melanogaster, Becky Cheng

CMC Senior Theses

Drosophila melanogaster and many other insects harbor intracellular bacterial symbionts that are transmitted vertically from infected host mothers to their offspring. Many of these bacteria alter host reproductive developmental processes in order to increase their transmission success. For example, Spiroplasma, a spirochete that naturally infects D. melanogaster, selectively kills males during mid-embryogenesis while sparing females. Previous studies suggested that Spiroplasma interacts genetically with the male-specific dosage compensation pathway, which causes ~2-fold up-regulation of most genes located on the male’s single X chromosome so that their expression matches the levels found in females who have two Xs. To further …

The Transcriptome Response Of The White-Rot Fungus Phanerochaete Chrysosporium To Maple And Miscanthus, Mashael Rashed Alaradi

Masters Theses

Lignocellulosic biomass is a valuable feedstock for the production of liquid biofuels. However, liquid biofuel production from lignocellulose is economically challenging due to the difficulties associated with separating the cellulosic sugars from lignin. In addition, the current thermochemical methods to deconstruct lignocellulose typically involve hazardous chemicals that can negatively impact the environment. Recent studies have demonstrated the efficacy of white-rot fungi as alternative pretreatment agents that can lower the costs of lignocellulose deconstruction and reduce negative impacts on the environment. However, understanding of the biochemical mechanisms of lignocellulose breakdown used by these fungi is limited, particularly with respect to the …

Detection Of Antibiotic Resistance Loci In Wastewater And Fresh Water Samples, Mohammed Hamed Almalki

Masters Theses

Proper treatment of municipal wastewater is important not only for prevention of eutrophication but also for public health concerns. One consideration for wastewater treatment is the presence of organisms carrying antibiotic resistance genes. If these organisms survive the wastewater treatment process and are released into the streams, they can pose significant risks to public health. In addition, their presence also raises concerns for lateral gene transfer events at the wastewater plant. The spread of antibiotic loci has a major impact in public health and clinical therapy because resistant organisms render conventional treatments of important illnesses difficult. Beta-lactam drugs are known …

The Role Of Creg1 As A Master Regulator Of Liver Function, Abdulrahman Siran Aldaghmi

Masters Theses

The liver is known as the chemical factory of the body because it performs a wide range of biochemical functions required for life. Since the liver has such an important role in regulation of normal physiological processes, liver diseases cause a high rate of morbidity and mortality. Therefore, understanding the mechanisms of liver development will shed light on the causes of liver disease. In this study, a cell line model that utilizes rat hepatoma cells (Fg14) and hepatoma variant cells (H11) was used to identify master regulators of liver gene expression. Whole genome expression studies identified the gene CREG1 (Cellular …

Analysis Of The Secondary Neurodegenerative Consequences Of Primary Oligodendrocyte Stress Through The Use Of The Novel Obiden Mouse Model, Daniel Zdzislaw Radecki

Wayne State University Dissertations

The work of this project was to develop, test and characterize a potential novel mouse model of the neurodegenerative disease Multiple Sclerosis (MS). Historically, MS has been identified as a primary autoimmune disease of the central nervous system (CNS). However, treatments based on this view have met with limited success, and in most cases, fail to prevent progression of MS from mild to moderate and severe forms. Original observations regarding axonal and neuronal pathology in the white and gray matter of the CNS were rediscovered in the 1990s. These observations indicated that even in the absence of the immune system, …

Sh3 And Multiple Ankyrin Repeat Domain 3 (Shank3) Affects The Expression Of Hyperpolarization-Activated Cyclic Nucleotide-Gated (Hcn) Channels In Mouse Models Of Autism, Nikhil N. Shah

Theses and Dissertations

SH3 and multiple ankyrin repeat domains 3 (SHANK3) is a multidomain scaffold protein that is highly augmented in the postsynaptic density (PSD) of excitatory glutamatergic synapses within the central and peripheral nervous systems. SHANK3 links neurotransmitter receptors, ion channels, and other critical membrane proteins to intracellular cytoskeleton and signal transduction pathways. Mutations in SHANK3 are linked with a number neuropsychiatric disorders including autism spectrum disorders (ASDs). Intellectual disability, impaired memory and learning, and epilepsy are some of the deficits commonly associated with ASDs that result from mutations in SHANK3. Interestingly, these symptoms show some clinical overlap with presentations of human …

Investigation On Genetic Modifiers Of Age At Onset Of Major Depressive Disorder, Huseyin Gedik

Theses and Dissertations

Major Depressive Disorder (MDD) is a complex multifactorial disorder, which would lead to disability. Environmental and genetic factors are involved in MDD etiology. The aim of this project was to identify loci modifying age at onset (AAO) of MDD using survival models after adjusting for Childhood Sexual Abuse (CSA). To achieve this aim, a dataset was made available by the China Oxford and VCU Experimental Research on Genetic Epidemiology (CONVERGE) consortium. The study population had 5,220 controls and 5,282 cases with MDD. We performed two univariate association analyses using Cox Proportional Hazard (Cox PH) models. These two are Full Sample …

Role Of Mitochondrial Beta-Oxidation In Ethanol Response: A Candidate Gene Study Using Caenorhabditis Elegans, Harini Pallikarana Tirumala

Theses and Dissertations

Alcohol use disorder (AUD) is the fourth leading cause of preventable death in the United States, and the fifth leading risk factor for premature death and disability, globally. There are currently very few treatment options for AUD and there is a need for effective preventive and treatment strategies for this condition. AUD risk has a significant hereditary component, with the contribution of genetic factors being estimated to be about 50%. The Davies-Bettinger laboratory uses C. elegans as a model organism to study the contribution of genetic factors in modulating neuronal responses to ethanol. In this project, we examined the role …

Epigenetic Editing To Validate Findings From Methylome-Wide Association Studies Of Neuropsychiatric Disorders, Robin F. Chan

Theses and Dissertations

DNA methylation is necessary for learning, memory consolidation and has been implicated in a number of neuropsychiatric disorders. Obtaining high quality and comprehensive data for the three common forms of methylation in brain is challenging for methylome-wide association studies (MWAS). To address this we optimized a panel of enrichment methods for screening the brain methylome. Results show that these enrichment techniques approach the coverage and fidelity of the current gold standard bisulfite based techniques. Our MBD-based method can also be used with low amounts of genomic material from limited human biomaterials. Psychiatric disorders have high prevalence and are often chronic …

Network Analytics For The Mirna Regulome And Mirna-Disease Interactions, Joseph Jayakar Nalluri

Theses and Dissertations

miRNAs are non-coding RNAs of approx. 22 nucleotides in length that inhibit gene expression at the post-transcriptional level. By virtue of this gene regulation mechanism, miRNAs play a critical role in several biological processes and patho-physiological conditions, including cancers. miRNA behavior is a result of a multi-level complex interaction network involving miRNA-mRNA, TF-miRNA-gene, and miRNA-chemical interactions; hence the precise patterns through which a miRNA regulates a certain disease(s) are still elusive. Herein, I have developed an integrative genomics methods/pipeline to (i) build a miRNA regulomics and data analytics repository, (ii) create/model these interactions into networks and use optimization techniques, motif …

Taf2: A Potential Oncogene For Hepatocellular Carcinoma, Saranya Chidambaranathan Reghupaty

Theses and Dissertations

Astrocyte Elevated Gene 1 (AEG1) is an oncogene for hepatocellular carcinoma (HCC). Its role in HCC pathogenesis has been well studied. A pan cancer analysis of gene expression in multiple databases identified TATA-box binding protein associated factor 2 (TAF2) as the gene that is most frequently co-expressed with AEG1. TAF2 is a protein that is involved in transcription of genes by RNA polymerase II. It is a factor that is dispensable for basal transcription but, required for activated transcription. It has also been shown to be involved in regulating cyclin levels and hence cell cycle progression. Bioinformatic analysis on data …

Deep Sequencing Transcriptome Analysis Of Murine Wound Healing: Effects Of A Multicomponent, Multitarget Natural Product Therapy-Tr14, Georges St. Laurent Iii, Bernd Seilheimer, Michael Tackett, Jianhua Zhou, Dmitry Shtokalo, Ian Toma, +Several Additional Authors

Clinical Research and Leadership Faculty Publications

Wound healing involves an orchestrated response that engages multiple processes, such as hemostasis, cellular migration, extracellular matrix synthesis, and in particular, inflammation. Using a murine model of cutaneous wound repair, the transcriptome was mapped from 12 h to 8 days post-injury, and in response to a multicomponent, multi-target natural product, Tr14. Using single-molecule RNA sequencing (RNA-seq), there were clear temporal changes in known transcripts related to wound healing pathways, and additional novel transcripts of both coding and non-coding genes. Tr14 treatment modulated >100 transcripts related to key wound repair pathways, such as response to wounding, wound contraction, and cytokine response. …

High-Throughput Single-Molecule Mapping Links Subtelomeric Variants And Long-Range Haplotypes With Specific Telomeres, Eleanor Young, Steven Pastor, Ramakrishnan Rajagopalan, Jennifer Mccaffrey, Justin Sibert, Angel C. Y. Mak, Pui-Yan Kwok, Harold Riethman, Ming Xiao

School of Medical Diagnostics & Translational Sciences Publications

Accurate maps and DNA sequences for human subtelomere regions, along with detailed knowledge of subtelomere variation and long-range telomereterminal haplotypes in individuals, are critical for understanding telomere function and its roles in human biology. Here, we use a highly automated whole genome mapping technology in nano-channel arrays to analyze large terminal human chromosome segments extending from chromosome-specific subtelomere sequences through subtelomeric repeat regions to terminal (TTAGGG) n repeat tracts. We establish detailed maps for subtelomere gap regions in the human reference sequence, detect many new large subtelomeric variants and demonstrate the feasibility of long-range haplotyping through segmentally duplicated subtelomere regions. …

Comparing An Atomic Model Or Structure To A Corresponding Cryo-Electron Microscopy Image At The Central Axis Of A Helix, Stephanie Zeil, Julio Kovacs, Willy Wriggers, Jing He

Computer Science Faculty Publications

Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM …

Uncovering Candidate Cold Tolerance Genes In Maize (Zea Mays), Raeann N. Goering

Departmental Honors Projects

With booming populations soon to overwhelm the world's food production capabilities, studying what makes crop organisms, like maize, efficient is crucial to ensure that the demand for food is met. Planting earlier in the spring would lengthen the crop season and produce larger yields provided the crop is tolerant to early spring’s low temperatures. Plants can adjust to abiotic stresses through biochemical changes controlled by transcription of genes. Trained plants can be produced by pre-exposing them to a lesser stress, allowing them to recover, then exposing them to a greater, longer stress. It is hypothesized that trained plants will tolerate …

Improved Performance Of Gene Set Analysis On Genome-Wide Transcriptomics Data When Using Gene Activity State Estimates, Thomas Kamp, Micah Adams, Craig Disselkoen, Nathan L. Tintle

Faculty Work Comprehensive List

Gene set analysis methods continue to be a popular and powerful method of evaluating genome-wide transcriptomics data. These approach require a priori grouping of genes into biologically meaningful sets, and then conducting downstream analyses at the set (instead of gene) level of analysis. Gene set analysis methods have been shown to yield more powerful statistical conclusions than single-gene analyses due to both reduced multiple testing penalties and potentially larger observed effects due to the aggregation of effects across multiple genes in the set. Traditionally, gene set analysis methods have been applied directly to normalized, log-transformed, transcriptomics data. Recently, efforts have …

Protective Effect Of Anti-Phosphatidylserine Antibody In A Guinea Pig Model Of Advanced Hemorrhagic Arenavirus Infection, John M. Thomas, Philip E. Thorpe

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Objective: Host derived markers on virally infected cells or virions may provide targets for the generation of antiviral agents. Recently, we identified phosphatidylserine (PS) as a host marker of virions and virally-infected cells.

Methods and Materials: Under normal physiological conditions, PS is maintained on the inner leaflet of the plasma membrane facing the cytosol. Following viral infection, activation or pre-apoptotic changes cause PS to become externalized. We have previously shown that bavituximab, a chimeric human-mouse antibody that binds PS complexed with β2-glycoprotein I (β2GP1), protected rodents against lethal Pichinde virus and cytomegalovirus infections.

Results: Here, we determined the antiviral activity …

การระบุโปรตีนที่มีปฏิสัมพันธ์กับเอชพีวีไทป์ 16 อี 7 และบทบาทในการเกิดมะเร็งปากมดลูก, นันท์นภัส วงค์มณี

Chulalongkorn University Theses and Dissertations (Chula ETD)

โปรตีน E6 และ E7 ของเชื้อไวรัสเอชพีวีไทป์16 เป็นสาเหตุหลักสาเหตุหนึ่งของการเกิดโรคมะเร็งปากมดลูก ซึ่งโปรตีน E6 และ E7 ของไวรัสจะจับกับโปรตีน p53 และ pRb ของโฮสต์ตามลำดับ นอกจากนี้กระบวนการเปลี่ยนแปลงในระดับเหนือพันธุกรรมยังเป็นอีกหนึ่งสาเหตุของการเกิดมะเร็ง แต่กลไกที่ทำให้เกิดยังไม่เป็นที่เข้าใจมากนัก ซึ่งการศึกษาก่อนหน้านี้พบว่าการแสดงออกของโปรตีน E7 ของเอชพีวีไทป์ 16 ส่งผลต่อการกระตุ้นการเติมหมู่เมทิลที่ตำแหน่งโพรโมเตอร์ของยีน CCNA1 โดยสร้างคอมเพลกซ์กับเอนไซม์ DNMT1 ดังนั้นจึงได้ตั้งสมมติฐานว่าน่าจะมีโปรตีนชนิดที่เป็นทรานสคริปชันแฟกเตอร์เป็นตัวนำพากลุ่มคอมเพลกซ์นี้มายังบริเวณโพรโมเตอร์ของยีน ในงานวิจัยได้นำวิธีการทางโปรติโอมิกส์มาใช้ในการตรวจระบุโปรตีน โดยการใช้โปรตีน E7 เป็นตัวล่อ (bait) จากนั้นนำโปรตีนที่ติดตามมาด้วยกันไปตรวจวิเคราะห์ด้วยวิธีการทางแมสสเปกโตรเมทรี ซึ่งพบทรานสคริปชันแฟกเตอร์ YY1 ในขณะเดียวกันทรานสคริปชันแฟกเตอร์ TFAP2A ถูกพบจากการทำนายด้วยชีวสารสนเทศซึ่งใช้ยีน CCNA1 เป็นต้นแบบของยีนเป้าหมาย เมื่อทดสอบการจับกันระหว่างโปรตีนทั้งสามชนิดพบว่า โปรตีน E7 ของเอชพีวีไทป์ 16 มีอันตรกิริยากับโปรตีน TFAP2A และโปรตีน TFAP2A มีอันตรกิริยากับโปรตีน YY1 นอกจากนั้นยังตรวจพบว่ายีน FOXC1 และ VEGFA มีการลดการแสดงออกเมื่อมียีน E7 ของเชื้อเอชพีวีเข้ามาเกี่ยวข้อง แต่พบการเกิดเมทิลเลชันที่บริเวณโพรโมเตอร์ที่ยีน FOXC1 เพียงยีนเดียว มากไปกว่านั้นเมื่อทำการตรวจยืนยันการจับกันระหว่างโปรตีน E7 ของเอชพีวีไทป์ 16 โปรตีน YY1 และโปรตีน TFAP2 กับดีเอ็นเอบริเวณโพรโมเตอร์ของยีนทั้งสองด้วยวิธี Chromatin immunoprecipitation พบว่ามีเพียงยีน FOXC1 ที่สามารถจับได้กับโปรตีนทั้งสามชนิด ซึ่งอาจกล่าวได้ว่า ยีน FOXC1 ถูกชักนำให้เกิดการเมทิลเลชันแล้วส่งผลให้เกิดการลดการแสดงออกเช่นเดียวกับยีน CCNA1

เซลล์พันธุศาสตร์ของสกุลโหระพา Ocimum L. ในประเทศไทย, ปวีณ์นุช เลขะพันธุ์

Chulalongkorn University Theses and Dissertations (Chula ETD)

สกุลโหระพาจัดอยู่วงศ์ Lamiaceae ประกอบด้วยพืช 65-160 ชนิด ซึ่งมีการกระจายพันธุ์ไปทั่วโลก โดยที่ประเทศไทยพบพืชสกุลโหระพา 5 ชนิด ได้แก่ แมงกะแซง โหระพา แมงลัก กะเพรา และยี่หร่า เนื่องจากการปรับปรุงพันธุ์พืชกลุ่มนี้ และการเกิดลูกผสมโดยธรรมชาติ ส่งผลให้พืชสกุลโหระพามีจำนวนโครโมโซมที่หลากหลาย ดังนั้นการศึกษานี้จึงมีวัตถุประสงค์เพื่อตรวจสอบความหลากหลายของโครโมโซม และอธิบายความสัมพันธ์ทางพันธุกรรมของพืชสกุลโหระพาในประเทศไทย โดยเก็บตัวอย่างพืชสกุลโหระพาจากจังหวัดเชียงใหม่ จังหวัดนครราชสีมา จังหวัดพระนครศรีอยุธยา จังหวัดประจวบคีรีขันธ์ และจังหวัดตรัง นำมาศึกษาโครโมโซมจากการแบ่งนิวเคลียสแบบไมโทซิสและไมโอซิส พบว่าพืชสกุลโหระพาแต่ละชนิดมีจำนวนโครโมโซมแตกต่างกัน กล่าวคือ แมงกะแซง โหระพา แมงลัก กะเพรา และยี่หร่า มีจำนวนโครโมโซม 2n = 26 52 78 36 และ 40 ตามลำดับ ซึ่งความหลากหลายของจำนวนโครโมโซมบ่งบอกถึงที่มาของพืชสกุลโหระพาในประเทศไทย และจากข้อมูลความหลากหลายของขนาดและรูปร่างของโครโมโซม รวมถึงการพบ secondary constriction แสดงให้เห็นความสัมพันธ์ทางพันธุกรรมของพืชสกุลโหระพา โดย แมงกะแซง โหระพา และแมงลัก มีความใกล้ชิดกันทางพันธุกรรม ทั้งนี้แมงลักและโหระพาอาจมี แมงกะแซงเป็นบรรพบุรุษร่วมกัน นอกจากนี้ความแตกต่างทางพันธุกรรมระหว่างกะเพราและยี่หร่าอาจเกิดจากการเกิดวิวัฒนาการในทิศทางที่เป็นอิสระต่อกัน ยิ่งไปกว่านั้นความหลากหลายของโครโมโซมยังแสดงให้เห็นว่าโหระพาและแมงลักอยู่ระหว่างการเปลี่ยนแปลงโครงสร้างของโครโมโซมผ่านการเกิดดีลีชัน อินเวอร์ชัน และทรานสโลเคชัน รวมถึงมีการลดการเกิดรีคอมบิเนชันของโครโมโซม เพื่อลดจำนวนและเพิ่มความเสถียรของโครโมโซม สำหรับกะเพราและยี่หร่า มีความเสถียรของโครโมโซมมากกว่าโหระพาและแมงลัก รวมทั้งมีขนาดของจีโนมเล็กกว่าจีโนมของโหระพาและแมงลัก แสดงว่ากะเพราและยี่หร่ามีวิวัฒนาการสูงกว่าโหระพาและแมงลัก

Pnpase In C. Elegans: Mutagenic Analysis To Complement Knockdown Studies, Danielle K. Seibert

Theses and Dissertations

PNPase is a gene implicated as a potential target for cancer therapy; human mutations also present with deafness, myopathies, and neuropathies. In this study, C. elegans was used to investigate the effect of knocking out PNPase in a whole animal. C. elegans knockdown studies have reported an extended lifespan via an increase in ROS production. Further noted are larger mitochondria and an increase in fzo-1 expression. Knockout animals previously constructed using CRISPR/Cas9 were used for this study. We aimed to confirm these findings validating previous studies. It was discovered that PNPase knockout animals demonstrated a similar lifespan extension that was …

Evolution Of Antagonistic Relationships In Proteins: A Case Study Of Radialis- And Diviricata-Like Genes, Ao Gao

Theses and Dissertations

The antagonistic relationship of proteins describes the opponent interactions that result in one protein suppressing the function of another. Developmental genetic studies of Antirrhinum majus demonstrated that two transcription factors from the MYB gene family, RAD and DIV, interact through antagonism to regulate floral dorsoventral asymmetry. Interestingly, similar antagonistic interactions were found among proteins of FSM1 (RAD-like), MYBI (DIV-like), and DRIF in Solanum lycopersicum, which is involved in fruit development. Here, we report on the homology of these antagonistic MYB proteins based on reconstruction of the phylogeny of I-box-like and R-R-type clades, where RAD- and DIV-like belong, …

Drinking Motives Underlying Internalizing And Externalizing Pathways To Alcohol Misuse In College Students, Jeanne Savage

Theses and Dissertations

Alcohol misuse, including heavy episodic use and negative consequences, is a major public health concern and a particular problem among college students. The etiology of alcohol misuse is not well resolved, with multiple and often contradictory factors implicated in its development. Genetic factors influence alcohol misuse but few specific genes have been identified. A potential reason for these challenges is that alcohol misuse is phenotypically and genetically heterogeneous; that is, there are multiple causal pathways underlying its development. Previous typologies have suggested that distinct internalizing and externalizing pathways are involved, with corresponding differences in profiles of personality, temperament, and comorbid …

The Influence Of Genetic And Environmental Factors On Quit Attempt In Adolescent And Young Adult Twins, Gladys Langi

Theses and Dissertations

The purpose of this study was to examine the genetic and environmental influences on lifetime quit attempt in three US adolescent and young adult twin samples (N total = 6,322). The study utilized a common-contingent-causal (CCC) model to estimate these factors for lifetime quit attempts, after accounting for the factors for lifetime cigarette use and cigarettes per day. The study also examined age and sex differences, as well as the degree of relationship between these smoking phenotypes. The results demonstrated significant genetic influences for lifetime quit attempts in adolescents and young adults. No sex differences were observed for the contributions …

Comparisons Of Isogenic Trisomic And Disomic Cells From People With Mosaicism For Down Syndrome Unmask Cellular Differences Related To Trisomy 21, Kelly A. Rafferty

Theses and Dissertations

It is known that age-related changes impacting multiple organ systems occur earlier in people with Down syndrome (Ds), but the biological basis underlying this trisomy 21-associated propensity for premature aging is poorly understood. Given that the trisomic/normal cells from people with mosaic Ds (mDs) are identical with regards to environmental exposures and genes (except for chromosome 21 copy number), comparisons of these isogenic trisomic/disomic cells allow one to “unmask” the cellular consequences of trisomy 21 by removing extraneous factors. The primary aim of this study was to determine if trisomy 21 results in an increase in the acquisition of age-related …

Antifungal Genome Mining And Genetics In Filamentous Actinomycete Bacteria Isolated From Local Soils, Jacob Alex, Kevin Lou, Bilal Makhdoom

Undergraduate Research Symposium Posters

Actinomycetes are gram positive, filamentous bacteria that produce useful antibiotics, antitumor agents, and agricultural products. A series of enrichments were undertaken to isolate actinomycetes from local soils, varying enrichment media, antibacterials, and soil treatments (including heat and CaCO3). Isolates were characterized by 16S rDNA sequencing, phenotypic and morphological observations, and antibiotic production. The genetic tractability of select isolates was analyzed using a panel of integrating vectors derived from ɸC31, ɸBT1, and OzzyJ phage using intergeneric conjugation. Further, a semi-degenerate multiplex PCR assay to detect ɸBT1 genomic integrants was designed and tested for the first time. Finally, PCR screens were used …

The Localization And Function Of Novel Tetrahymena Thermophila Cytoskeletal Genes Bbc29 And Bbc39, Emily K. Moore, Nicole C. Zanolli

Undergraduate Research Symposium Posters

Ciliary function is known to play an important role in many human conditions, including chronic sinus and pulmonary diseases and problems with infertility. Cilia are cytoskeletal structures that protrude from the cell body to facilitate movement. Ciliary structure is conserved throughout eukaryotes, from unicellular to multicellular organisms, including humans. A clear understanding the proteins that compose cilia and how they interact with one another will increase our knowledge about important cytoskeletal elements. Because cilia are difficult to study in multicellular organisms, the unicellular eukaryote Tetrahymena thermophila serves as a useful model for the study of cytoskeletal genes, due to their …

Contributions Of Gene Copy Number Variation To Genome Evolution And Local Adaptation Of The Cyanobacterium Acaryochloris, Amy L. Gallagher

Graduate Student Theses, Dissertations, & Professional Papers

Acaryochloris is a recently discovered genus of cyanobacteria, unique in its use of an uncommon chlorophyll as its major photosynthetic pigment, and in its peculiar genome dynamics. Members of this genus exhibit increased genic copy number variation (CNV), which is thought to be primarily derived from gene duplications and horizontal gene transfer (HGT). Acaryochloris provides an ideal system to explore mechanisms behind maintenance of gene duplicates and the influence of CNV in local adaptation. Here, I propose a mechanism for retention of gene duplicates of the bacterial recombinase, RecA, in Acaryochloris genomes and provide preliminary evidence that these paralogs are …

The U.S. Culture Collection Network Responding To The Requirements Of The Nagoya Protocol On Access And Benefit Sharing, Kevin Mccluskey, Katharine B. Barker, Hazel A. Barton, Kyria Boundy-Mills, Daniel R. Brown, Jonathan A. Coddington, Kevin Cook, Philippe Desmeth, David Geiser, Jessie A. Glaeser, Stephanie Greene, Seogchan Kang, Michael W. Lomas, Ulrich Melcher, Scott E. Miller, David R. Nobles Jr., Kristina J. Owens, Jerome H. Reichman, Manuela Da Silva, John Wertz, Cale Whitworth, David Smith

Faculty Scholarship

The U.S. Culture Collection Network held a meeting to share information about how culture collections are responding to the requirements of the recently enacted Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity (CBD). The meeting included representatives of many culture collections and other biological collections, the U.S. Department of State, U.S. Department of Agriculture, Secretariat of the CBD, interested scientific societies, and collection groups, including Scientific Collections International and the Global Genome Biodiversity Network. The participants learned about the policies of the United …

Separation Of Blood Mixtures Using Fluorescently Labeled Antibodies, Christopher Ehrhardt, Dani Jabado, Emily Brocato

UROP Posters

Identifying and analyzing biological mixture samples at a crime scene are of paramount concern for forensic scientists, especially if that type of evidence contains only one cell type. The presence of multiple contributors in a biological evidence sample reduces the probative value of DNA evidence and can sometimes lead to its eventual loss of value. As such, this study was performed in an attempt to examine and evaluate flow cytometry analysis as a means to separate blood mixture samples labeled with fluorescent antibodies. Fluorescein Isothiocyanate (FITC) antibodies were specifically targeted and bound to HLA (Human Leukocyte Antigens) markers present on …

Complete Genome Sequences Of 38 Gordonia Sp. Bacteriophages, Welkin H. Pope, Matthew T. Montgomery, Randall J. Dejong

University Faculty Publications and Creative Works

We report here the genome sequences of 38 newly isolated bacteriophages using Gordonia terrae 3612 (ATCC 25594) and Gordonia neofelifaecis NRRL59395 as bacterial hosts. All of the phages are double-stranded DNA (dsDNA) tail phages with siphoviral morphologies, with genome sizes ranging from 17,118 bp to 93,843 bp and spanning considerable nucleotide sequence diversity.