Genetics and Genomics Commons^™

A Systematic Approach To Rna-Associated Motif Discovery, Tian Gao, Jiang Shu, Juan Cui

School of Computing: Faculty Publications

Background: Sequencing-based large screening of RNA-protein and RNA-RNA interactions has enabled the mechanistic study of post-transcriptional RNA processing and sorting, including exosome-mediated RNA secretion. The downstream analysis of RNA binding sites has encouraged the investigation of novel sequence motifs, which resulted in exceptional new challenges for identifying motifs from very short sequences (e.g., small non-coding RNAs or truncated messenger RNAs), where conventional methods tend to be ineffective. To address these challenges, we propose a novel motif-finding method and validate it on a wide range of RNA applications.

Results: We first perform motif analysis on microRNAs and longer RNA fragments from …

Metatranscriptome Of Human Faecal Microbial Communities In A Cohort Of Adult Men, Galeb S. Abu-Ali, Raaj S. Mehta, Jason Lloyd-Price, Himel Mallick, Tobyn Branck, Kerry L. Ivey, David A. Drew, Casey Dulong, Eric Rimm, Jacques Izard, Andrew T. Chan, Curtis Huttenhower

Department of Food Science and Technology: Faculty Publications

The gut microbiome is intimately related to human health, but it is not yet known which functional activities are driven by specific microorganisms' ecological configurations or transcription. We report a large-scale investigation of 372 human fecal metatranscriptomes and 929 metagenomes from a subset of 308 men in the Health Professionals Follow-Up Study. We identified a metatranscriptomic 'core' universally transcribed over time and across participants, often by different microorganisms. In contrast to the housekeeping functions enriched in this core, a 'variable' metatranscriptome included specialized pathways that were differentially expressed both across participants and among microorganisms. Finally, longitudinal metagenomic profiles allowed ecological …

Brain Is A Potential Sanctuary For Subtype C Hiv-1 Irrespective Of Art Treatment Outcome, For Yue Tso, Guobin Kang, Eun Hee Kwon, Peter Julius, Qingsheng Li, John T. West, Charles Wood

Nebraska Center for Virology: Faculty Publications

Subtype C HIV-1 is responsible for the largest proportion of people living with HIV-1 infection. However, there is limited information about the roles of the brain and its cell types as a potential sanctuary for this subtype and how the sanctuary may be affected by the administration of anti-retroviral therapy (ART). To address this issue, we collected postmortem brain tissues from ART treated HIV-1 infected Zambian individuals who experienced complete viral suppression and those who did not. Tissues from various brain compartments were collected from each individual as frozen and formalin-fixed paraffin embedded brain specimens, for detection and quantification of …

Brain Is A Potential Sanctuary For Subtype C Hiv-1 Irrespective Of Art Treatment Outcome, For Yue Tso, Guobin Kang, Peter Julius, Qingsheng Li, John T. West, Charles Wood

Nebraska Center for Virology: Faculty Publications

Subtype C HIV-1 is responsible for the largest proportion of people living with HIV-1 infection. However, there is limited information about the roles of the brain and its cell types as a potential sanctuary for this subtype and how the sanctuary may be affected by the administration of anti-retroviral therapy (ART). To address this issue, we collected postmortem brain tissues from ART treated HIV-1 infected Zambian individuals who experienced complete viral suppression and those who did not. Tissues from various brain compartments were collected from each individual as frozen and formalin-fixed paraffin embedded brain specimens, for detection and quantification of …

Contribution Of The Gp120 V3 Loop To Envelope Glycoprotein Trimer Stability In Primate Immunodeficiency Viruses, Dane Bowder, Haley Hollingsead, Kate Durst, Duoyi Hu, Wenzhong Wei, Joshua Wiggins, Halima Medjahed, Andrés Finzi, Joseph Sodroski, Shi-Hua Xiang

Nebraska Center for Virology: Faculty Publications

The V3 loop of the human immunodeficiency virus type 1 (HIV-1) gp120 exterior envelope glycoprotein (Env) becomes exposed after CD4 binding and contacts the coreceptor to mediate viral entry. Prior to CD4 engagement, a hydrophobic patch located at the tip of the V3 loop stabilizes the non-covalent association of gp120 with the Env trimer of HIV-1 subtype B strains. Here, we show that this conserved hydrophobic patch (amino acid residues 307, 309 and 317) contributes to gp120-trimer association in HIV-1 subtype C, HIV-2 and SIV. Changes that reduced the hydrophobicity of these V3 residues resulted in increased gp120 shedding and …

Ultrastructure Of Meelsvirus: A Nuclear Virus Of Arrow Worms (Phylum Chaetognatha) Producing Giant "Tailed" Virions, George L. Shinn, Brianna L. Bullard

Nebraska Center for Virology: Faculty Publications

Most known giant viruses, i.e., viruses producing giant virions, parasitize amoebae and other unicellular eukaryotes. Although they vary in the level of dependence on host nuclear functions, their virions self-assemble in the host cell's cytoplasm. Here we report the discovery of a new prototype of giant virus infecting epidermal cells of the marine arrow worm Adhesisagitta hispida. Its 1.25 μm-long virions self-assemble and accumulate in the host cell's nucleus. Conventional transmission electron microscopy reveals that the virions have a unique bipartite structure. An ovoid nucleocapsid, situated in a broad "head" end of the virion is surrounded by a thin …

Alcohol Intoxication Moderates The Association Between A Polygenic Risk Score And Unprovoked Intimate Partner Aggression, Christa C. Christ, Laura E. Watkins, David Dilillo, Scott F. Stoltenberg

Department of Psychology: Faculty Publications

Despite evidence that genetic variation contributes to aggression, few studies have examined how genetic variation contributes to IPA specifically. In the current study, 69 couples from a Midwestern university completed self-report measures of IPA, childhood trauma exposure, and hazardous alcohol use, and were randomly assigned to consume either a placebo or alcohol beverage before participating in an analogue aggression task against their partner. Genetic risk (i.e., association with lower transcriptional efficiency) for aggression was measured with a polygenic risk score (PRS) created from four polymorphisms (HTR1B rs13212041, HTR2B rs6437000, 5-HTTLPR, and MAOA uVNTR). Among individuals with a low PRS, …

Bacterial Inoculants, Endophytic Bacteria And Their Influence On Nicotiana Physiology, Development And Microbiome, Andrea Marisa Sanchez Barrios

Theses and Dissertations--Plant and Soil Sciences

Soil and root microbial communities have been studied for decades, and the incorporation of high-throughput techniques and analysis has allowed the identification of endophytic/non-culturable organisms. This has helped characterize and establish the core microbiome of many model plant species which include underground and aboveground organs. Unfortunately, the information obtained from some of these model plants is not always transferable to other agronomic species. In this project, we decided to study the microbiome of the Nicotiana genus because of its importance in plant physiological and plant-microbe interactions studies. The data obtained was used as baseline information that allowed us to better …

Chemical Topping Burley Tobacco, Mitchell D. Richmond

Theses and Dissertations--Plant and Soil Sciences

The act of topping tobacco (Nicotiana tabacum L.) involves the removal of the terminal bud or inflorescence of the tobacco plant. This practice ordinarily is accomplished by manually removing the top of each tobacco plant in an entire field which is labor intensive and costly. Chemical topping utilizes sucker control products to inhibit the terminal bud and axillary bud growth without manually removing the top of the tobacco plant. There were several research objectives in order to determine the utility of a chemical topping system: 1) determine if burley tobacco could be chemically topped with currently registered suckercide products …

Tetratricopeptide 39c (Ttc39c) Is Upregulated During Skeletal Muscle Atrophy And Is Necessary For Muscle Cell Differentiation, Caleb Hayes

UNF Graduate Theses and Dissertations

Ttc39c has been identified as a novel gene in skeletal muscle that is upregulated in response to neurogenic atrophy in mice. Quantitative PCR and Western blot analysis confirmed that Ttc39c is expressed in both proliferating and differentiated muscle cells. Furthermore, comparison of Ttc39c expression in undifferentiated and differentiated C₂C₁₂ cells demonstrated that Ttc39c levels peak in early differentiation, but decreases as cells become fully differentiated myotubes. The transcriptional regulation of Ttc39c was examined by cloning promoter fragments of the gene and fusing it with the SEAP reporter gene. The Ttc39c reporter gene constructs were transfected into muscle …

Development Of Biclustering Techniques For Gene Expression Data Modeling And Mining, Juan Xie

Electronic Theses and Dissertations

The next-generation sequencing technologies can generate large-scale biological data with higher resolution, better accuracy, and lower technical variation than the arraybased counterparts. RNA sequencing (RNA-Seq) can generate genome-scale gene expression data in biological samples at a given moment, facilitating a better understanding of cell functions at genetic and cellular levels. The abundance of gene expression datasets provides an opportunity to identify genes with similar expression patterns across multiple conditions, i.e., co-expression gene modules (CEMs). Genomescale identification of CEMs can be modeled and solved by biclustering, a twodimensional data mining technique that allows clustering of rows and columns in a gene …

The Transcriptional Response Of Trametes Versicolor To Growth On Maple Chips And Miscanthus Straw, Maha Alanazi

Masters Theses

This thesis research explored the transcriptional response of Trametes versicolor, a white-rot fungus, in response to fundamentally different types of lignocellulosic biomass (miscanthus and maple) and rich medium (malt extract agar). After five weeks of growth by the fungus on the biomass, the fungal RNA was extracted from three biological replicates per biomass type and mRNA was sequenced (approximately 30 million reads per sample). The reads were processed using ArrayStar to covert to RPKM and annotated using JGI's T. versicolor GO annotation file along with NCBI's BLAST. Comparisons were made between average gene expression of the fungus grown on …

College Student Alcohol Use And Engagement In Prevention Programming, Alexis H. Branch, Shimona Kumar, Christina Mcgrath

UROP Posters

Social problems and adverse consequences have been associated with risky alcohol use (Paschall et al, 2015). Personalized Normative Feedback (PNF) has been utilized to address these problems (White and Hingson, 2014) by comparing students’ alcohol use to campus or national norms (Butler et al, 2009). The current investigation sought to understand differences in alcohol use behaviors in freshmen who did and did not report completion of a personalized feedback intervention (PFI) in a diverse sample of college students from the Spit for Science (S4S) project. S4S is a campus-wide, longitudinal study on the genetic and environmental factors that contribute to …

Genome-Wide Association Study For The Relationship Between Temperature And Feed Intake In Beef Cattle, Robel Araya Ghebrewold

Department of Animal Science: Dissertations, Theses, and Student Research

Environmental conditions, such as changes in ambient temperature, can cause changes in animal behavior and performance. In general, it is believed that as ambient temperature increases, dry matter intake (DMI) of beef cattle decreases. However, our hypothesis was that the degree to which animals adjust their daily DMI due to changes in ambient temperature is partially controlled by genetic effects. Consequently, the objective of this study was to estimate the genetic component of the regression of DMI on ambient temperature using an admixed beef cattle population consisting of various crosses of Angus, Simmental, and Piedmontese (n = 239). Ambient …

Analyzing Metabolomics Data For Association With Genotypes Using Two-Component Gaussian Mixture Distributions, Jason Westra, Nicholas Hartman, Bethany Lake, Gregory Shearer, Nathan L. Tintle

Faculty Work Comprehensive List

Standard approaches to evaluate the impact of single nucleotide polymorphisms (SNP) on quantitative phenotypes use linear models. However, these normal-based approaches may not optimally model phenotypes which are better represented by Gaussian mixture distributions (e.g., some metabolomics data). We develop a likelihood ratio test on the mixing proportions of two-component Gaussian mixture distributions and consider more restrictive models to increase power in light of a priori biological knowledge. Data were simulated to validate the improved power of the likelihood ratio test and the restricted likelihood ratio test over a linear model and a log transformed linear model. Then, using real …

การระบุยีนที่สามารถจับกับโปรตีนอี 7 เอชพีวีไทป์ 16 ที่เกี่ยวข้องกับการเกิดโพรโมเตอร์เมทิลเลชันในเซลล์ไลน์ C33a, จุฑามาศ สุขพัฒน์ธี

Chulalongkorn University Theses and Dissertations (Chula ETD)

โปรตีนอี 7 ที่สร้างจากไวรัสเอชพีวี ไทป์ 16 เป็นสาเหตุหลักที่ทำให้เกิดมะเร็งปากมดลูก จากการศึกษาก่อนหน้านี้พบว่าโปรตีนอี 7 สามารถจับกับโปรตีน DNA methyltransferase 1 (Dnmt1) แล้วจับที่โพรโมเตอร์ของยีน CCNA1 และชักนำให้เกิดเมทิลเลชันและลดการแสดงออกของยีน การศึกษานี้จึงมุ่งเน้นเพื่อหายีนอื่นๆ และกลไกของโปรตีนอี 7 ที่สามารถจับที่บริเวณโพรโมเตอร์ของยีนแล้วชักนำให้เกิดเมทิลเลชันได้ โดยมีสมมติฐานว่า เมื่อโปรตีน E7 จับกับทรานสคริปชันแฟคเตอร์แล้ว จะสามารถจับกับโพรโมเตอร์ของยีนแล้วเหนี่ยวนำให้เกิดเมทิลเลชันได้ โดยในการศึกษานี้ได้ทำการค้นหายีนที่สามารถจับกับโปรตีน อี 7 ของ HPV ไทป์ 16 ด้วย 2 วิธีการ คือ การทำ Chromatin immunoprecipitation Sequencing ด้วยการถ่ายโอนพลาสมิดลูกผสมที่บรรจุยีน E7 เข้าในเซลล์สายพันธุ์มะเร็งปากมดลูก C33A จากนั้นทำการตกตะกอนดีเอ็นเอที่สามารถจับกับโปรตีน E7 แล้วนำมาหาลำดับเบส เพื่อสืบหายีนเป้าหมายของ E7 ซึ่งค้นพบทั้งหมด 3 ยีน ได้แก่ FAM189A1, ASAH2B, และ RAPGEF4 และวิธีการทางชีวสารสนเทศ (Bioinformatics) โดยการใช้ลำดับเบสบริเวณโพรโมเตอร์ของยีน CCNA1 ที่เป็น cis-element ของ AP2 ซึ่งเป็นทรานสคริปชันแฟคเตอร์ที่สามารถจับกับโปรตีน E7 ไปค้นหาในฐานข้อมูลจีโนมมนุษย์เพื่อค้นหาโพรโมเตอร์ของยีนอื่นๆ ที่มี cis-element ตรงกัน จากนั้นคัดเลือกยีนที่มีลำดับเบสบริเวณโพรโมเตอร์ตรงกับลำดับเบสบริเวณโพรโมเตอร์ของยีน CCNA1 ที่ AP2 สามารถจับได้ แล้วนำมาคัดเลือกเฉพาะยีนที่สามารถจับกับทรานสคริปชันแฟคเตอร์ YY1 ซึ่งมีรายงานว่าสามารถจับกับโปรตีน E7 ได้เช่นกัน พบทั้งหมด 9 ยีน ได้แก่ NOP56, MAG, FUS, EIF2S2, RPL7, RPL10, NINJ1, LGALS1 และ CLDN5 แล้วจึงทำการคัดเลือกยีน FAM189A1 และยีน NOP56 เพื่อทำการตรวจสอบการเปลี่ยนแปลงของระดับการแสดงออกของยีน …

การจำแนกลักษณะทางโมเลกุลของเชื้อ Escherichia Coli ที่สร้างเอนไซม์ Extended-Spectrum Beta-Lactamases ที่แยกได้จากสุกรและประชากรในอำเภอเมือง จังหวัดลำพูน, จักรพงษ์ สีนามะ

Chulalongkorn University Theses and Dissertations (Chula ETD)

ปัจจุบันพบเชื้อ Escherichia coli ที่สร้างเอนไซม์ extended-spectrum beta-lactamase (ESBL) แพร่กระจายในชุมชนอย่างกว้างขวาง เชื้อแบคทีเรียดังกล่าวสามารถพบได้ว่าเป็นเชื้อประจำถิ่นในลำไส้ของคน และสัตว์ รวมไปถึงสามารถพบได้ในสิ่งแวดล้อมทั่วไป ซึ่งอาจกลายเป็นแหล่งเก็บกักเชื้อแบคทีเรียดื้อสารต้านจุลชีพ ที่สามารถแพร่กระจายในชุมชนต่างๆ ทั่วโลก การศึกษาครั้งนี้ทำการจำแนกลักษณะทางโมเลกุลของเชื้อ E. coli ที่สร้างเอนไซม์ ESBL ซึ่งแยกได้จากสุกรในฟาร์มปศุสัตว์และประชากรในชุมชน ในพื้นที่อำเภอเมือง จังหวัดลำพูน เพื่อศึกษารูปแบบของยีนที่ควบคุมการสร้างเอนไซม์ ESBL และศึกษาหาความสัมพันธ์ของเชื้อในกลุ่มตัวอย่างทั้งสอง เชื้อ E. coli ที่สร้างเอนไซม์ ESBL จำนวนทั้งสิ้น 212 สายพันธุ์ แยกได้จากอุจจาระของสุกรและประชากรที่มีสุขภาพดี และทำการจำแนกยีนที่ควบคุมการสร้างเอนไซม์ ESBL ได้แก่ ยีน blaCTX-M ยีน blaTEM และยีน blaSHV ด้วยเทคนิค multiplex-PCR และเทคนิค whole genome sequencing และศึกษาความสัมพันธ์ของเชื้อ E. coli ที่สร้างเอนไซม์ ESBL ที่แยกได้จากทั้งสองกลุ่มตัวอย่างด้วยเทคนิค multilocus sequence typing ผลการศึกษาพบว่าเชื้อ E. coli ที่สร้างเอนไซม์ ESBL ส่วนใหญ่เป็นเชื้อดื้อยาหลายขนาน และมักดื้อยากลุ่ม fluoroquinolones ยากลุ่ม aminoglycosides และยา trimethoprim/sulfamethoxazole ในขณะที่เชื้อทุกสายพันธุ์ดื้อต่อยา ampicillin ยา ceftriaxone และยา cefotaxime ยีนที่ควบคุมการสร้างเอนไซม์ ESBL ที่พบมากที่สุดได้แก่ ยีน blaCTX-M ซึ่งพบได้ 95.75% รองลงมาคือยีน blaTEM และยีน blaSHV พบได้ 62.73% และ 2.40% ตามลำดับ โดย subgroup ของยีนที่ควบคุมการสร้างเอนไซม์ ESBL ที่พบมากที่สุด ได้แก่ ยีน blaCTX-M-55 …

Quantitative And Molecular Analysis Of Habituation At The Maize R1 Locus, Robert C. Lindsay

Theses and Dissertations

Epigenetics is the study of heritable changes in phenotypes that are not the result of changes in DNA sequence. Examples of epigenetic affecters include methylation changes, chromatin modifications, transcription factors, and RNA-based changes. The molecular mechanisms behind epigenetic changes are not fully understood. Canalization is the buffering of gene expression against environmental changes over time, while habituation is semi-stable expression change over time due to selection. This work characterized the molecular changes associated with the kernel color changes of the R-sc:86-17pale allele at the maize red color1 (r1) locus to determine if the changes are epigenetic in nature. …

Alternative Splicing Of Cytoplasmic Polyadenylation Element Binding Protein 2 Is Modulated Via Serine Arginine Splicing Factor 3 In Cancer Metastasis, James T. Deligio, James Thomas Deligio

Theses and Dissertations

Our laboratory delineated a role for alternative pre-mRNA splicing (AS) in triple negative breast cancer (TNBC). We found the translational regulator cytosolic polyadenylation element binding protein 2 (CPEB2) which has two isoforms, CPEB2A and CPEB2B, is alternatively spliced during acquisition of anoikis resistance (AnR) and metastasis. The splicing event which determines the CPEB2 isoform is via inclusion/ exclusion of exon four in the mature mRNA transcript. The loss of CPEB2A with a concomitant increase in CPEB2B is required for TNBC cells to metastasize in vivo. We examined RNAseq profiles of TNBC cells which had CPEB2 isoforms specifically downregulated to …

Snd1-Targeted Gene Therapy For Hepatocellular Carcinoma, Bryan D. Mckiver

Theses and Dissertations

Staphylococcal nuclease and tudor-domain containing 1 (SND1) is an oncogene for a wide variety of cancers, including hepatocellular carcinoma (HCC). SND1 is a multifunctional protein regulating gene expression of proto-oncogenes and tumor suppressor genes, making SND1 a prime target for developing cancer therapeutics. This notion is especially attributed to HCC as most patients are diagnosed in advanced stages and the therapeutic options available for these patients are severely limited. In this study, we evaluated the therapeutic potential of a replication-defective adenovirus vector delivering SND1 shRNA (Ad.SND1sh) to human HCC cell lines, HepG3, HuH-7, and Hep3B. Adenovirus infection in HCC cells …

Processing Of 3′-Blocked Dna Double-Strand Breaks By Tyrosyl-Dna Phosphodiesterase 1, Artemis And Polynucleotide Kinase/ Phosphatase, Ajinkya S. Kawale

Theses and Dissertations

DNA double-strand breaks (DSBs) containing unligatable termini are potent cytotoxic lesions leading to growth arrest or cell death. The Artemis nuclease and tyrosyl-DNA phosphodiesterase (TDP1) are each capable of resolving protruding 3′-phosphoglycolate (PG) termini of DNA double-strand breaks (DSBs). Consequently, a knockout of Artemis and a knockout/knockdown of TDP1 rendered cells sensitive to the radiomimetic agent neocarzinostatin (NCS), which induces 3′-PG-terminated DSBs. Unexpectedly, however, a knockdown or knockout of TDP1 in Artemis-null cells did not confer any greater sensitivity than either deficiency alone, indicating a strict epistasis between TDP1 and Artemis. Moreover, a deficiency in Artemis, but not TDP1, resulted …

Natural And Anthropogenic Drivers Of Tree Evolutionary Dynamics, Brandon M. Lind

Theses and Dissertations

Species of trees inhabit diverse and heterogeneous environments, and often play important ecological roles in such communities. As a result of their vast ecological breadth, trees have become adapted to various environmental pressures. In this dissertation I examine various environmental factors that drive evolutionary dynamics in threePinusspecies in California and Nevada, USA. In chapter two, I assess the role of management influence of thinning, fire, and their interaction on fine-scale gene flow within fire-suppressed populations of Pinus lambertiana, a historically dominant and ecologically important member of mixed-conifer forests of the Sierra Nevada, California. Here, I find evidence …

The Effects Of Increased Camp Levels On Neuronal Differentiation In Murine Embryonic Stem Cells, And The Creation Of A Crispr-Induced C.1252c>T Point Mutation In The Adcy5 Gene, Elizabeth Zepeda

Cal Poly Humboldt theses and projects

ADCY5-related dyskinesia is a rare movement disorder with early onset in childhood and adolescence. Previous studies linked this disease to various point mutations in the ADCY5 gene. Recent studies show that two of the point mutations cause an increase in cyclic adenosine monophosphate (cAMP) levels. However, it remains unknown how increased levels of cAMP result in the phenotypes associated with this disease. My study examines the effects of increased cAMP levels on neuronal differentiation of mouse embryonic stem cells (mESCs). My experiments demonstrated successful differentiation of mESCs into the dopaminergic neuronal lineage, indicated by the presence of Tuj 1 (a …

The Genome Of Austrofundulus Limnaeus Offers Insights Into Extreme Vertebrate Stress Tolerance And Embryonic Development, Josiah Tad Wagner, Param Priya Singh, Amie L. Romney, Claire L. Riggs, Patrick Minx, Steven Cody Woll, Jake Roush, Wesley C. Warren, Anne Brunet, Jason E. Podrabsky

Center for Life in Extreme Environments Publications

Background: The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in northern Venezuela, South America, and is an emerging extremophile model for vertebrate diapause, stress tolerance, and evolution. Embryos of A. limnaeus regularly experience extended periods of desiccation and anoxia as a part of their natural history and have unique metabolic and developmental adaptations. Currently, there are limited genomic resources available for gene expression and evolutionary studies that can take advantage of A. limnaeus as a unique model system.

Results: We describe the first draft genome sequence of A. limnaeus. The genome was assembled de novo using a merged assembly strategy …

Draft Genome Sequence Of Streptomyces Sp. Strain Jv178, A Producer Of Clifednamide-Type Polycyclic Tetramate Macrolactams, Yunci Qi, John M. D’Alessandro, Joshua A.V Blodgett

Biology Faculty Research

Here, we report the draft genome sequence of Streptomyces sp. JV178, a strain originating from Connecticut (USA) garden soil. This strain produces the polycyclic tetramate macrolactam compounds clifednamides A and B. The draft genome contains 10.65 Mb, 9,045 predicted protein coding sequences, and several natural product biosynthetic loci.

Estimating The Heritability Of Thermal Tolerance In Acropora Cervicornis And The Physiological Basis Of Adaptation That Correlates To Survival At Elevated Temperatures, Kelsey L. Yetsko

UNF Graduate Theses and Dissertations

Human activities have substantially increased the atmospheric concentrations of greenhouse gases, resulting in warmer ocean temperatures that are having a negative impact on reef corals, which are highly susceptible to changes in temperature. Understanding the degree to which species vary in their tolerance to elevated temperatures and whether this variation is heritable is important in determining their ability to adapt to climate change. In order to address this, Acropora cervicornis fragments from 20 genetically distinct colonies were kept at either ambient or elevated temperatures, and mortality was monitored for 26 days. Heritability of thermal tolerance was estimated using a clonal …

Molecular And Evolutionary Analysis Of Cyanobacterial Taxonomic Methods, Chelsea Denise Villanueva

UNF Graduate Theses and Dissertations

Cyanobacteria are a group of photo-oxygenic bacteria found in nearly every ecosystem, but much cyanobacterial diversity, in various habitats, has yet to be explored. Cyanobacteria are often conspicuous components of photosynthetic flora, providing significant carbon and nitrogen inputs to surrounding systems. As possible primary colonizers of stone substrates not native to this region, cyanobacteria isolated from headstones may provide biogeographically informative data. An exploratory study of lichen-dominated microbial consortia, growing on headstones, was conducted to isolate and identify novel microaerophytic cyanobacteria, and resulted in the establishment of four novel cyanobacterial taxa. Phylogenetic analyses of photobionts in one tripartite lichen revealed …

Implementation And Performance Comparison Of Some Heuristic Algorithms For Block Sorting, Sandhya Turlapaty

UNF Graduate Theses and Dissertations

An implementation framework has been developed in this thesis for a well-known APX-hard combinatorial optimization problem known as Block Sorting. The motivation for the study of this problem comes from applications such as computational biology and optical character recognition. While existing Block Sorting research has been theoretically focused on the development and analysis of several approximation algorithms for Block Sorting, little or no work has been carried out thus far on the implementation of the proposed approximation algorithms. The conceptualization of an implementation framework and illustrating its use by experimenting with the existing approximation algorithms will provide means for discovering …

Conservation And Variation Of Dna Methylation In Lactuca Sativa And Lactuca Serriola, Trudi A. Baker

Graduate Doctoral Dissertations

Molecular techniques for guiding plant breeding have successfully used wild progenitors of domestic crops as sources of genetic variants conveying desirable traits. However, epigenetic variation, in particular DNA methylation, is a significant source of phenotypic variation and epigenetic effects of plant domestication are poorly understood. Described herein are the first single-base pair resolution methylomes of the highly valued crop iceberg lettuce (Lactuca sativa cv. Salinas) and its close relative, and ubiquitous weed, L. serriola. This work suggests several roles for acquisition and inheritance of methylation in the evolution of Lactuca spp. in response to stress. The Lactuca spp. have conserved …

Improvements To Bayesian Gene Activity State Estimation From Genome-Wide Transcriptomics Data, Craig Disselkoen, Nathan Hekman, Brian Gilbert, Sydney Benson, Matthew Anderson, Matthew Dejongh, Aaron Best, Nathan L. Tintle

Faculty Work Comprehensive List

An important question in many biological applications, is to estimate or classify gene activity states (active or inactive) based on genome-wide transcriptomics data. Recently, we proposed a Bayesian method, titled MultiMM, which showed superior results compared to existing methods. In short, MultiMM performed better than existing methods on both simulated and real gene expression data, confirming well-known biological results and yielding better agreement with fluxomics data. Despite these promising results, MultiMM has numerous limitations. First, MultiMM leverages co-regulatory models to improve activity state estimates, but information about co-regulation is incorporated in a manner that assumes that networks are known with …