Genetics and Genomics Commons^™

The Role Of Cellulose Synthase-Like D Genes In Tip Growth Of Physcomitrella Patens, Erin E. Killeavy, Arielle Chaves, Alison Roberts

Senior Honors Projects

Physcomitrella patens is a non-vascular plant with a relatively small genome and is amongst the few eukaryotic organisms that have a high rate of homologous recombination. This is valuable in biological research because it allows for targeted genetic modification of the organism. In vascular plants like Arabidopsis thaliana, a model organism, Cellulose Synthase-like D (CSLD) genes have been discovered to be important in tip growth. This type of growth is observed in the pollen tubes and root hairs of these plant types. The CSLD genes in Arabidopsis were found to play a crucial role in the growth of …

Hybridization, Population Genetic Structure And Gene Expression In The Genus Boechera, Martin Peter Schilling

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

When we look at life on earth, we can see a lot of different life forms, but we still do not fully understand how these different life forms came to be and at which points in time these life forms began to be different enough from each other so we could call them by different names, or species. Some groups of species on earth, especially plants, seem to reproduce with each other, even though they are already very different from each other so that we call them different species. This process is called hybridization, and it can stir up the …

Network-Driven Plasma Proteomics Expose Molecular Changes In The Alzheimer's Brain, Philipp A. Jaeger, Kurt M. Lucin, Markus Britschgi, Badri Vardarajan, Ruo-Pan Huang, Elizabeth D. Kirby, Rachelle Abbey, Bradley F. Boeve, Adam L. Boxer, Lindsay A. Farrer, Nicole Finch, Neill R. Graff-Radford, Elizabeth Head, Matan Hofree, Ruochun Huang, Hudson Johns, Anna Karydas, David S. Knopman, Andrey Loboda, Eliezer Masliah, Ramya Narasimhan, Ronald C. Petersen, Alexei Podtelezhnikov, Suraj Pradhan, Rosa Rademakers, Chung-Huan Sun, Steven G. Younkin, Bruce L. Miller, Trey Ideker, Tony Wyss-Coray

Pharmacology and Nutritional Sciences Faculty Publications

Background: Biological pathways that significantly contribute to sporadic Alzheimer’s disease are largely unknown and cannot be observed directly. Cognitive symptoms appear only decades after the molecular disease onset, further complicating analyses. As a consequence, molecular research is often restricted to late-stage post-mortem studies of brain tissue. However, the disease process is expected to trigger numerous cellular signaling pathways and modulate the local and systemic environment, and resulting changes in secreted signaling molecules carry information about otherwise inaccessible pathological processes.

Results: To access this information we probed relative levels of close to 600 secreted signaling proteins from patients’ blood samples using …

Global Genetic Connectivity And Diversity In A Shark Of High Conservation Concern, The Oceanic Whitetip, Carcharhinus Longimanus, Cassandra L. Ruck

HCNSO Student Theses and Dissertations

The oceanic whitetip shark, Carcharhinus longimanus, is a circumtropical pelagic shark of high conservation concern (IUCN Red List: “Critically Endangered” in the Western North and Western Central Atlantic and “Vulnerable” globally). I present the first, population genetic assessment of the oceanic whitetip shark on a global scale, based on analysis of two mitochondrial genome regions (entire 1066-1067 bp control region and 784 bp partial ND4 gene), and nine nuclear microsatellite loci. No population structure was detected within the Western Atlantic. However, highly significant population structure was detected between Western Atlantic and Indo-Pacific Ocean sharks across all markers. Additionally, a …

Non-Essentiality Of Alr And Muri Genes In Mycobacteria, Philion L. Hoff, Denise Zinniel, Raúl G. Barletta

UCARE: Research Products

Amino acids are the building blocks of life. If DNA is the blueprint, amino acids are the lumber that proteins are built with. Proteins are built with left-handed, L- forms of amino acids. Bacteria have an essential cell wall component that happens to be an exception: peptidoglycan. Bacteria have enzymes called racemases that convert L- amino acid forms into right-handed, D- forms. Amino acids participate in many reactions with keto acids. Transaminases allow conversion between amino acids by transfer of an amino group.

Previous reports claimed there is no D-ala transaminase activity in mycobacteria and thus alr and murI genes …

Genetic Moderators Of Cognitive Decline In The Health And Retirement Study, Shannon K. Runge

USF Tampa Graduate Theses and Dissertations

The current dissertation used a gene x environment (G x E) approach to examine the independent and interactive effects of specific genetic variants and participation in physical and cognitive/social activities (PA and CSA) on cognitive performance in 4,764 participants of the Health and Retirement Study. Using three-wave data, three sets of multi-level growth models were conducted to examine baseline, longitudinal, and interactive effects of genotype (i.e., ApoE, COMT, and BDNF) and CSA/PA on performance across five cognitive measures: immediate, delayed and total word recall, and serial 7s and backwards counting.

At baseline, the ApoE ε4 allele predicted …

Detecting Gene-Gene Interactions Using A Permutation-Based Random Forest Method, Jing Li, James D. Malley, Angeline S. Andrew, Margaret R. Karagas, Jason H. Moore

Dartmouth Scholarship

Identifying gene-gene interactions is essential to understand disease susceptibility and to detect genetic architectures underlying complex diseases. Here, we aimed at developing a permutation-based methodology relying on a machine learning method, random forest (RF), to detect gene-gene interactions. Our approach called permuted random forest (pRF) which identified the top interacting single nucleotide polymorphism (SNP) pairs by estimating how much the power of a random forest classification model is influenced by removing pairwise interactions.

Nonreplicative Dna Helicases Involved In Maintaining Genome Stability, Salahuddin Syed

USF Tampa Graduate Theses and Dissertations

Double-strand breaks and stalled forks arise when the replication machinery encounters damage from exogenous sources like DNA damaging agents or ionizing radiation, and require specific DNA helicases to resolve these structures. Sgs1 of Saccharomyces cerevisiae is a member of the RecQ family of DNA helicases and has a role in DNA repair and recombination. The RecQ family includes human genes BLM, WRN, RECQL4, RECQL1, and RECQL5. Mutations in BLM, WRN, and RECQL4 result in genetic disorders characterized by developmental abnormalities and a predisposition to cancer. All RecQ helicases have common features including a …

Axonal Transport And Life Cycle Of Mitochondria In Parkinson's Disease Model, Hyun Sung

Open Access Dissertations

In neurons, normal distribution and selective removal of mitochondria are essential for preserving compartmentalized cellular function. Parkin, an E3 ubiquitin ligase associated with familial Parkinson’s disease, has been implicated in mitochondrial dynamics and removal. However, it is not clear how Parkin plays a role in mitochondrial turnover in vivo, and whether the mature neurons possess a compartmentalized Parkin-dependent mitochondrial life cycle. Using the live Drosophila nervous system, here, I investigate the involvement of Parkin in mitochondrial dynamics; organelle distribution, morphology and removal. Parkin deficient animals displayed less number of axonal mitochondria without disturbing organelle motility behaviors, morphology and metabolic state. …

Is A Mitochondrial Plasmid Really A Virus?, Mackenzie Strehle

UCARE: Research Products

In addition to containing a large and complex mitochondrial genome, the mitochondria of several species of plants have been shown to contain an independent, self-replicating DNA molecule in the form of a plasmid. Plants in the Brassica genus contain a linear plasmid that is approximately 11.6 kilobases in length. The plasmid is characterized by the presence of terminal inverted repeats and covalently bonded proteins at its termini (Handa 2008). The plasmid also contains six ORFs that encode DNA and RNA polymerases and a number of unknown proteins (Figure 1). Currently, both the function of this plasmid and the mechanisms by …

Examining Maternal Obesity Effects On Oogenesis, Follicular Development, And Embryonic Myogenesis, Chris Lindeman, Jennifer Wood

UCARE: Research Products

The CDC estimates that more than one-third of U.S. adults (approximately 78.6 million) are obese. Despite national efforts to combat this with diet and exercise, the number of obese adults and children continues to climb. It is critical to emphasize that obesity can lead to lifelong, chronic complications and health risks including hypertension, heart disease, and diabetes.

Diet and obesity also have important impacts on the reproductive health of female including the ability to become pregnant (fertility) and risk for complications during pregnancy. Furthermore, for women who do become pregnant, obesity can affect the development of the embryo and fetus, …

Transgenerational Plasticity Is Sex-Dependent And Persistent In Yellow Monkeyflower (Mimulus Guttatus), Kayla C. Akkerman, Arash Sattarin, John K. Kelly, Alison G. Scoville

Student Published Works

Transgenerational phenotypic plasticity, whereby environmental cues experienced by parents alter the phenotype of their progeny, has now been documented in diverse organisms. Transmission of environmentally determined responses is known to occur through both maternal and paternal gametes, but the underlying mechanisms have rarely been compared. In addition, the persistence of induction over multiple generations appears to vary widely, but has been characterized for relatively few systems. Yellow monkeyflower (Mimulus guttatus) is known to exhibit transgenerational induction of increased glandular trichome production in response to simulated insect damage. Here, we test for differences between maternal and paternal transmission of …

Scalable Parallelization Of A Markov Coalescent Genealogy Sampler, Philip E. Davis

Masters Theses

Coalescent genealogy samplers are effective tools for the study of population genetics. They are used to estimate the historical parameters of a population based upon the sampling of present-day genetic information. A popular approach employs Markov chain Monte Carlo (MCMC) methods. While effective, these methods are very computationally intensive, often taking weeks to run. Although attempts have been made to leverage parallelism in an effort to reduce runtimes, they have not resulted in scalable solutions. Due to the inherently sequential nature of MCMC methods, their performance has suffered diminishing returns when applied to large-scale computing clusters. In the interests of …

Reducing The Potential For Acrylamide Formation In Wheat Products, Amy Hauver, P. Stephen Baenziger, Mary J. Guttieri

UCARE: Research Products

Acrylamide, a chemical formed from free asparagine and reducing sugars during high-temperature cooking via the Maillard reaction (i.e. frying or baking) of high starch foods is deemed ‘probably carcinogenic to humans’ based on its affect in mice. In April of 2002, a group of Swedish researchers reported findings that presented evidence that heat-treated, starch-rich foods contained high levels of acrylamide, later linking the production of acrylamide to the Maillard reaction. A number of other studies have been done to link dietary intake of acrylamide to human cancers and other health effects, although many have had inconclusive results. Nevertheless, the World …

Molecular Analysis Confirming The Introduction Of Nile Crocodiles, Crocodylus Niloticus Laurenti 1768 (Crocodylidae), In Southern Florida, With An Assessment Of Potential For Establishment, Spread, And Impacts., Michael R. Rochford, Kenneth L. Krysko, Frank J. Mazzotti, Matthew W. Shirley, Mark W. Parry, Joseph A. Wasilewski, Jeffrey S. Beauchamp, Christpher R. Gillette, Edward F. Metzger Iii, Michiko A. Squires, Louis A. Somma

Papers in Herpetology

The state of Florida, USA, has more introduced herpetofauna than any other governmental region on Earth. Four species of nonnative crocodilians have been introduced to Florida (all since 1960), one of which is established. Between 2000–2014 we field-collected three nonnative crocodilians in Miami-Dade County, Florida, and one in Hendry County, Florida. We used DNA barcoding and molecular phylogenetics to determine species identification and native range origin. Also, we described diet, movement, and growth for one crocodile. Our molecular analyses illustrated that two of the crocodiles we collected are most closely related to Nile Crocodiles (Crocodylus niloticus) from South Africa, suggesting …

Reinforcement Learning, Error-Related Negativity, And Genetic Risk For Alzheimer's Disease, Christina Marie Figueroa

Dissertations (1934 -)

Reinforcement learning (RL) has been widely used as a model of animal and human learning and decision-making. The neural networks underlying RL involve many of the same structures primarily affected by Alzheimer’s disease (AD) such as the hippocampus. Yet, RL and non-invasive evaluation of its neural underpinnings have been underutilized as a framework for understanding disease pathology and its pre-clinical states. This study aimed to provide a novel approach for assessing subtle changes in asymptomatic apolipoprotein-E (APOE) carriers and non-carriers. Electroencephalography was collected from forty APOE genotyped older adults (Male n = 11; Mage = 79.30; Meducation = 14.88 years) …

Bio-Piracy: Creating Proprietary Rights In Plant Genetic Resources, James O. Odek

Journal of Intellectual Property Law

No abstract provided.

Investigating The Roles And Interactions Of Sad-6 Within The Parameters Of Meiotic Silencing By Unpaired Dna ( Msud )., Zachary J. Smith

Theses and Dissertations

Meiotic silencing by unpaired DNA (MSUD) is a process observed in the model organism Neurospora crassa. During this process unpaired DNA between homologous chromosomes is detected and silenced, resulting in the suppression of unpaired genes. The effects of MSUD can be seen using phenotypic markers such as the Roundspore gene and evidence supports the existence of a physical search for unpaired DNA. However, the mechanism for detecting unpaired DNA remains uncertain. Previously, we have shown evidence that a Rad54-like protein, SAD-6 is required for the efficient completion of MSUD and may be necessary for the detection of unpaired DNA. Currently, …

Evolution Of Kaic-Dependent Timekeepers: A Proto-Circadian Timing Mechanism Confers Adaptive Fitness In The Purple Bacterium Rhodopseudomonas Palustris, Peijun Ma, Tetsuya Mori, Chi Zhao, Teresa Thiel, Carl Johnson

Biology Department Faculty Works

Circadian (daily) rhythms are a fundamental and ubiquitous property of eukaryotic organisms. However, cyanobacteria are the only prokaryotic group for which bona fide circadian properties have been persuasively documented, even though homologs of the cyanobacterial kaiABC central clock genes are distributed widely among Eubacteria and Archaea. We report the purple non-sulfur bacterium Rhodopseudomonas palustris (that harbors homologs of kaiB and kaiC) only poorly sustains rhythmicity in constant conditions–a defining characteristic of circadian rhythms. Moreover, the biochemical characteristics of the Rhodopseudomonas homolog of the KaiC protein in vivo and in vitro are different from those of cyanobacterial KaiC. Nevertheless, R. palustris …

A Mitochondrial Dna-Based Computational Model Of The Spread Of Human Populations, Peter Revesz

School of Computing: Faculty Publications

This paper presents a mitochondrial DNA-based computational model of the spread of human populations. The computation model is based on a new measure of the relatedness of two populations that may be both heterogeneous in terms of their set of mtDNA haplogroups. The measure gives an exponentially increasing weight for the similarity of two haplogroups with the number of levels shared in the mtDNA classification tree. In an experiment, the computational model is applied to the study of the relatedness of seven human populations ranging from the Neolithic through the Bronze Age to the present. The human populations included in …

Genetic Dissection Of Icp-Detected Nutrient Accumulation In The Whole Seed Of Common Bean (Phaseolus Vulgaris L.), Matthew Wohlgemuth Blair, Xingbo Wu, Devendra Bhandari, Carolina Astudillo

Agricultural and Environmental Sciences Faculty Research

Nutrient transport to grain legume seeds is not well studied and can benefit from modern methods of elemental analysis including spectroscopic techniques. Some cations such as potassium (K) and magnesium (Mg) are needed for plant physiological purposes. Meanwhile, some minerals such as copper (Cu), iron (Fe), molybdenum (Mo), and zinc (Zn) are important micronutrients. Phosphorus (P) is rich in legumes, while sulfur (S) concentration is related to essential amino acids. In this research, the goal was to analyze a genetic mapping population of common bean (Phaseolus vulgaris L.) with inductively coupled plasma (ICP) spectrophotometry to determine concentrations of …

The Adp-Ribose Polymerase Tankyrase Regulates Adult Intestinal Stem Cell Proliferation During Homeostasis In Drosophila, Zhenghan Wang, Ai Tian, Hassina Benchabane, Ofelia Tacchelly-Benites, Eungi Yang, Hisashi Nojima, Yashi Ahmed

Dartmouth Scholarship

Wnt/β-catenin signaling controls intestinal stem cell (ISC) proliferation, and is aberrantly activated in colorectal cancer. Inhibitors of the ADP-ribose polymerase Tankyrase (Tnks) have become lead therapeutic candidates for Wnt-driven cancers, following the recent discovery that Tnks targets Axin, a negative regulator of Wnt signaling, for proteolysis. Initial reports indicated that Tnks is important for Wnt pathway activation in cultured human cell lines. However, the requirement for Tnks in physiological settings has been less clear, as subsequent studies in mice, fish and flies suggested that Tnks was either entirely dispensable for Wnt-dependent processes in vivo, or alternatively, had tissue-specific roles. Here, …

Molecular Mechanisms Of Squamous Cell Carcinoma Tumor Stem Cell Creation Via High Nitric Oxide (Hno) Adaptation, Niresh T. Kuganeswaran '16, Krishi Korrapati '17, Thomas Wan '16, Timothy Tamas, James A. Radosevich

Student Publications & Research

Cancer relapse or recurrence is defined as the return of cancer or its signs/symptoms after a period of improvement. Surgery may not remove all cancer cells and leave behind a few which cannot be detected by scans or other tests. It is also possible that some tumor cells are resistant to chemotherapy or radiation. Although many cancer cells are killed by these treatments, there may exist a few which contain a different genetic makeup which allows them to survive. These hypermalignant cancer cells, or cancer stem cells (CSCs), have been associated with causing cancer relapse. It has also been predicted …

Role Of Pseudogenes In Cancer Stem Creation Via High Nitric Oxide (Hno) Adaptation, Krishi Korrapati '17, Niresh T. Kuganeswaran '16, Thomas Wan '16, Timothy Tamas, James A. Radosevich

Student Publications & Research

Gene chip analysis of ten HNO adapted cell lines (Squamous cells: SCC-016, SCC-040, SCC-056, SCC-114, SCC-116; Adenocarcinomas: A549, BT20, Hs578, MCF7, and T47D) was carried out. Known pseudogenes were identified in each line, as well as their coding counterparts.

The adenocarcinoma cell lines had no up regulated pseudogenes, while they had the following down regulated pseudogenes: RP6-159A1.2, RP11-255N24.3, AC004490.1, LDHBP, RP11-572H4.2. The squamous cell carcinomas (SCCs) had the following up regulated pseudogenes: RPL37AP1, AC138972.1, RP11-641D5.1, AC005534.6, AC022431.1, RPL26P12, and they had these down regulated pseudogenes: RP6-159A1.2, RP11-255N24.3, RBMXP1, RP11-20O23.1, RP11-551G24.2. All cell lines adhered to the hypothesis that an increase …

Teaching Internal Medicine Residents About Genetics: One Topic At A Time - Breast Cancer, Maria Henry, Andrew Nance, Charles Macri

GW Research Days 2016 - 2020

Background: Currently, the field of medicine is experiencing rapid changes in genetics and genomics information. While medical school curricula all include some genetics education, the content may vary from one school to another, leaving Internal Medicine (IM) residents with different skills and knowledge. In an IM residency where residents come from different medical schools, presenting an organized genetics curriculum may have value. Patients expect their physicians to be knowledgeable and current about their specific disease, including the genetic components and expect that they can inform them about terminology, inheritance, diagnostic testing, risks and benefits of testing. Physicians will need …

Pi(4)P Promotes Phosphorylation And Conformational Change Of Smoothened Through Interaction With Its C-Terminal Tail, Kai Jiang, Yajuan Liu, Junkai Fan, Jie Zhang, Xiang-An Li, B. Mark Evers, Haining Zhu, Jianhang Jia

Markey Cancer Center Faculty Publications

In Hedgehog (Hh) signaling, binding of Hh to the Patched-Interference Hh (Ptc-Ihog) receptor complex relieves Ptc inhibition on Smoothened (Smo). A longstanding question is how Ptc inhibits Smo and how such inhibition is relieved by Hh stimulation. In this study, we found that Hh elevates production of phosphatidylinositol 4-phosphate (PI(4)P). Increased levels of PI(4)P promote, whereas decreased levels of PI(4)P inhibit, Hh signaling activity. We further found that PI(4)P directly binds Smo through an arginine motif, which then triggers Smo phosphorylation and activation. Moreover, we identified the pleckstrin homology (PH) domain of G protein-coupled receptor kinase 2 (Gprk2) as an …

Genomic Analysis Of Meiothermus Ruber Mrub_1907 And Meiothermus Ruber Mrub_1844 With Potential Ortholog Escherichia Coli B3774 Ilvc And Escherichia Coli B3771 Ilvc Gene Through Bioinformatics, Felipe A. Hernandez, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_1907 and Mrub_1844. We predict that Mrub__1907 encodes the enzyme ketol-acid reductoisomerase (DNA coordinates 1966630..1967649 on the reverse strand), which is the fourth step of the L-isoleucine pathway (from threonine) (KEGG map number 00290). It catalyzes the conversion of (R)-3- Hydroxy-3-methyl-2-oxopentanoate to (R)-2-3 Dihydroxy-3-methylpentanoate. The E. coli K12 MG1655 ortholog is predicted to be b3774, which has the gene …

Comparing Meiothermus Ruber And Myxococcus Xanthus In The Purine Metabolism Pathway, Linnea J. Ritchie, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. I investigated the biological functions of Mrub_1053 Mrub_2281 and Mrub_2299. I predicted that Mrub_1053 and Mrub_2281 (DNA coordinates 1053364..1054359 on the forward strand and 2333172..2334113 on the forward strand respectively) encodes the enzyme phosphoribose-1-pyrophosphate synthetase (PRS) which is the first step of the purine synthesis pathway (KEGG). I also predicted that Mrub_2299 (DNA coordinates: 2352378..2353775 on the forward strand) encodes for Phosphoribosyl pyrophosphate (PRPP) amidotransferase, which is …

E. Coli B3639 And B3634 Are Orthologs Of Mrub_2047 And Mrub_1372, Rong Zheng, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_2047 and Mrub_1372. We predict that Mrub_2047 encodes the enzyme fused 4'-phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN-binding (DNA coordinates 2083590..2084816 on the forward strand), which is the first and the second steps of the CoA biosynthesis pathway (KEGG map number 00770). It catalyzes the conversion of (R)-4’-phosphopantothenate to (R)-4’-phosphopantothenoyl-L-cysteine and the conversion of (R)-4’-phosphopantothenoyl-L-cysteine to 4’-phosphopantetheine. The E. coli K12 MG1655 ortholog …

Dna Sequencing Activity, Sarah O'Leary-Driscoll

Sequencing & Genome Mining

This activity is meant to introduce students to basic DNA sequencing techniques. Using a hands-on approach helps them understand the fundamentals of what is happening in the lab, and the questions that accompany the activity can lead to more in depth discussions about sequencing, and the development of the next generation sequencing techniques.