Genetics and Genomics Commons^™

De Novo Sequencing And Analysis Of Salvia Hispanica Tissue-Specific Transcriptome And Identification Of Genes Involved In Terpenoid Biosynthesis, James Wimberley, Joseph Cahill, Hagop S. Atamian

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Salvia hispanica (commonly known as chia) is gaining popularity worldwide as a healthy food supplement due to its low saturated fatty acid and high polyunsaturated fatty acid content, in addition to being rich in protein, fiber, and antioxidants. Chia leaves contain plethora of secondary metabolites with medicinal properties. In this study, we sequenced chia leaf and root transcriptomes using the Illumina platform. The short reads were assembled into contigs using the Trinity software and annotated against the Uniprot database. The reads were de novo assembled into 103,367 contigs, which represented 92.8% transcriptome completeness and a diverse set of Gene Ontology …

Author Correction: New Paradigms For Understanding And Step Changes In Treating Active And Chronic, Persistent Apicomplexan Infections., Martin Mcphillie, Ying Zhou, Kamal El Bissati, Jitender Dubey, Hernan Lorenzi, Michael Capper, Amanda K Lukens, Mark Hickman, Stephen Muench, Shiv Kumar Verma, Christopher R Weber, Kelsey Wheeler, James Gordon, Justin Sanders, Hong Moulton, Kai Wang, Taek-Kyun Kim, Yuqing He, Tatiana Santos, Stuart Woods, Patty Lee, David Donkin, Eric Kim, Laura Fraczek, Joseph Lykins, Farida Esaa, Fatima Alibana-Clouser, Sarah Dovgin, Louis Weiss, Gael Brasseur, Dyann Wirth, Michael Kent, Leroy Hood, Brigitte Meunieur, Craig W Roberts, S Samar Hasnain, Svetlana V Antonyuk, Colin Fishwick, Rima Mcleod

Articles, Abstracts, and Reports

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Liver Ubd Is Upregulated In The Lew.1wr1 Rat, Helen Gibson, Amelia Clopp, Genoah Collins

Research Horizons Day Posters

No abstract provided.

Care: Collecting And Assessing Cancer Family History To Identify At Risk Individuals Educational Intervention For Community Health Workers, Laura Moreno

USF Tampa Graduate Theses and Dissertations

Background: Collection of family health history (FHH) can identify individuals at increased risk and guide disease-specific recommendations for management, early detection, and prevention. Yet, collection of FHH is often low or infrequent despite national initiatives. In the Hispanic/Latino population, community outreach and education professionals (CORE-Ps) have effectively increased cancer prevention and control behaviors; but, limited research has been conducted to assess genetic and family health history knowledge among CORE-Ps. We sought to evaluate an educational program designed to improve cancer FHH and cancer genetics knowledge, self-efficacy and attitudes. Methods: The ARBOLES Program educates bilingual (Spanish-English) CORE-P to increase knowledge about …

The Sineb1 Element In The Long Non-Coding Rna Malat1 Is Necessary For Tdp-43 Proteostasis, Tuan M Nguyen, Elena B Kabotyanski, Lucas C Reineke, Jiaofang Shao, Feng Xiong, Joo-Hyung Lee, Julien Dubrulle, Hannah Johnson, Fabio Stossi, Phoebe S Tsoi, Kyoung-Jae Choi, Alexander G Ellis, Na Zhao, Jin Cao, Oluwatoyosi Adewunmi, Josephine C Ferreon, Allan Chris M Ferreon, Joel R Neilson, Michael A Mancini, Xi Chen, Jongchan Kim, Li Ma, Wenbo Li, Jeffrey M Rosen

Faculty, Staff and Students Publications

Transposable elements (TEs) comprise a large proportion of long non-coding RNAs (lncRNAs). Here, we employed CRISPR to delete a short interspersed nuclear element (SINE) in Malat1, a cancer-associated lncRNA, to investigate its significance in cellular physiology. We show that Malat1 with a SINE deletion forms diffuse nuclear speckles and is frequently translocated to the cytoplasm. SINE-deleted cells exhibit an activated unfolded protein response and PKR and markedly increased DNA damage and apoptosis caused by dysregulation of TDP-43 localization and formation of cytotoxic inclusions. TDP-43 binds stronger to Malat1 without the SINE and is likely 'hijacked' by cytoplasmic Malat1 to the …

Using Active Learning To Build A Foundation For Bioinformatics Training., Stacey E. Wahl Ph.D., Amy L. Olex Ms

Transforming Libraries for Graduate Students

As Health Sciences Libraries evolve, the support they offer graduate students has evolved to incorporate many aspects of the research life cycle. At Tompkins-McCaw Library for the Health Sciences, we have partnered with the Wright Center for Clinical and Translational Research to offer training workshops for graduate students who are interested in using bioinformatics to plan, analyze, or execute scientific experiments. We offer two series: 1) an 8-week, 1-hour per week seminar series providing a general overview of available techniques and 2) a week-long intensive, two hours per session, series on utilizing free databases from the National Center for Biotechnology …

Cellulolytic Enzymes From The Maize Seed Production System—Characterization, Inhibition, And Novel Activities, Hong Fang

Student Theses and Dissertations

Enzymatic saccharification of ligno-cellulosic material is a key process in advanced biofuel production. Different enzymes are required in the enzymatic saccharification. To meet the large demand of these enzymes for industrial purposes, a transgenic maize seed expression system had been utilized in our laboratory to acquire adequate and cost-effective pure enzymes including β-1,4-endoglucanase, cellobiohydrolase I, cellobiohydrolase II and expansin. In this dissertation, the possibility of utilizing maize-produced recombinant cellulases in promoting the saccharification of ligno-cellulosic material was investigated. From the purification and basic characterization of these target enzymes to the identification of different inhibitors, this project has partially addressed the …

Journey Mapping The Minority Student’S Path Toward Genetic Counseling: A Holistic Picture, Tatiana E. Alvarado-Wing

USF Tampa Graduate Theses and Dissertations

Reasons for limited ethnic and racial diversity among genetic counselors in the United States may be elucidated through better understanding the experiences of minority students who are attending genetic counseling graduate programs as well as recent graduates. Semi-structured interviews were conducted with minority participants using Journey Mapping to elicit touchpoints that positively or negatively impact success at varying points on the path to becoming a genetic counselor. Touchpoints with negative impacts include; late awareness of the profession, observing the lack of diversity in the field, the financial burden of the application process, and microaggressions from peers, program leadership, and clinical …

Terms Of Service: The Use And Protection Of Genomic Information By Companies, Databases, And Law Enforcement, Sophia Kallas

Honors Program: Senior Projects (Public)

Private genomic companies have become a popular trend in the last two decades by providing customers with information regarding their ancestry and health risks. However, the profiles received from these companies can also be uploaded to public databases for various purposes, including locating other family members. Both testing companies and public databases have private interests, and both are at risk of law enforcement intervention for the purpose of forensic familial searching. There is little federal legislation protecting the privacy of an individual’s genetic profile. Consequently, it has been up to federal agencies, state laws, and judicial precedents to prevent the …

Evaluating Effects Of Cancer Genetic Counseling On Several Brief Patient Impact Measures, Alyson Kneusel

USF Tampa Graduate Theses and Dissertations

Many outcomes for assessing cancer genetic counseling (GC) utility have been proposed, with few studies evaluating multiple, theory-based, brief patient-reported experience and outcome measures simultaneously as part of a single study. We conducted a pilot study in which patients seen for pre-test cancer GC took a survey before and after their GC session to evaluate the session’s impact on multiple patient impact measures and assess the relationship between these measures. Measures based on the self-determination theory (SDT) assessed three basic needs including: 1) perceived autonomy support, 2) relatedness to the provider, and 3) competence to make a decision. SDT posits …

Functions Of Cdk/Cyclin Complexes In Endoreplication Regulation By The Cdk Inhibitor Siamese, Kai Wang

LSU Doctoral Dissertations

Arabidopsis trichome (leaf hair) is a specialized single cell extended from epidermal cell on the leaves, which is a typical endoreplication and is also known as endoreduplication. Several D-type cyclins were tested to check the cell division in trichome, and the trichome expressing either CYCB1;2 or CDKB2;2 cannot trigger cell division, even if simultaneous expression of CYCB1;2 and CDKB2;2 failed to produce mitosis in trichome. Only CYCD3;1 specifically promotes multicellular trichome. cdkb1;1cdbk1;2 double mutants and sim cdkb1;1cdkb1;2 triple mutants exhibit the phenotype similar to the wild type and very limited cell division respectively. Overexpression of a CDKB1;1 dominant-negative construct that …

Molecular Differentiation Of Astragalus Species And Varieties From The Western United States: The Chloroplast Dna Bridge Between Evolution And Molecular Systematics, Marwa Neyaz, Daniel Cook, Rebecca Creamer

Poisonous Plant Research (PPR)

Locoweeds are the most widespread poisonous plant problem in the world and have been reported in the Western United States since the 1800s, causing tremendous losses in livestock. Consumption of locoweeds by grazing animals stimulates the neurological disease, locoism, characterized by weight loss, ataxia, and lack of muscular coordination. The name locoweed is used for Astragalus and Oxytropis species known to contain swainsonine, the toxic principle produced by the plant endophytic fungus Undifilum. Astragalus includes 2,500-3,000 species and many varieties that have almost identical morphological characteristics that overlap among species, leading to improper identification. Therefore, the aim of this study …

Dibutyltin Alters Immune Cell Production Of The Pro-Inflammatory Cytokines Interleukin (Il) 1Β And Il-6: Role Of Mitogen-Activated Protein Kinases And Changes In Mrna, Linda B Sushak, Sahra Gabure, Jaquel Maise, Jessica Arnett, Margaret Whalen

Chemistry Faculty Research

Dibutyltin (DBT) is used to stabilize plastics and as a deworming agent in some poultry. It is found in human blood (levels as high as 0.3 μM). Interleukin (IL) 1β (IL-1β) and IL-6 are pro-inflammatory cytokines produced by lymphocytes, monocytes, and other cells. Elevated levels of IL-1β and IL-6 have been associated with pathologies including rheumatoid arthritis and cancers. DBT was shown to decrease IL-1β and IL-6 secretion from immune cells at higher concentrations while causing increases at lower concentrations. However, it was not clear if these changes were due to DBT's alteration of the secretory process or due its …

Natural Variation And Evolutionary Responses To Climate Change Stressors In Marine Invertebrates, Joanna Sarah Griffiths

LSU Doctoral Dissertations

Our rapidly changing climate is putting many species at risk of extinction and there is an urgent need to understand how species will respond to these changes. In this dissertation, I evaluate how three species of marine invertebrates (corals, oysters, and copepods) respond to stressful conditions in their current environments and how plasticity and evolutionary adaptation could alter their response to future climate change stressors. I first employed a space for time study to elucidate population differences in the response of cold-water corals, Balanophyllia elegans, to future ocean acidification. I found evidence that upwelling history (natural low pH exposure) influences …

Multiplexed Capture Of Spatial Configuration And Temporal Dynamics Of Locus-Specific 3d Chromatin By Biotinylated Dcas9., Xin Liu, Yong Chen, Yuannyu Zhang, Yuxuan Liu, Nan Liu, Giovanni A Botten, Hui Cao, Stuart H Orkin, Michael Q Zhang, Jian Xu

College of Science & Mathematics Departmental Research

The spatiotemporal control of 3D genome is fundamental for gene regulation, yet it remains challenging to profile high-resolution chromatin structure at cis-regulatory elements (CREs). Using C-terminally biotinylated dCas9, endogenous biotin ligases, and pooled sgRNAs, we describe the dCas9-based CAPTURE method for multiplexed analysis of locus-specific chromatin interactions. The redesigned system allows for quantitative analysis of the spatial configuration of a few to hundreds of enhancers or promoters in a single experiment, enabling comparisons across CREs within and between gene clusters. Multiplexed analyses of the spatiotemporal configuration of erythroid super-enhancers and promoter-centric interactions reveal organizational principles of genome structure and function.

Genetic Parameters Of Growth And Adaptive Traits In Aspen (Populus Tremuloides): Implications For Tree Breeding In A Warming World, Chen Ding, Andreas Hamann, Rong-Cai Yang, Jean S. Brouard

Aspen Bibliography

Aspen (Populus tremuloides Michx) is a widespread commercial forest tree of high economic importance in western Canada and has been subject to tree improvement efforts over the past two decades. Such improvement programs rely on accurate estimates of the genetic gain in growth traits and correlated response in adaptive traits that are important for forest health. Here, we estimated genetic parameters in 10 progeny trials containing >30,000 trees with pedigree structures based on a partial factorial mating design that includes 60 half-sibs, 100 full-sib families and 1,400 clonally replicated genotypes. Estimated narrow-sense and broad-sense heritabilities were low for height …

Expression Level Of Sh2 And Bt2 Genes In Some Advanced Corn Lines Under Tropical Environment, Fatemeh Abna, Farhat A. Avin, Noorma Wati Haron

Agricultural and Environmental Sciences Faculty Research

The rate-limiting step in starch synthesis entails the synthesis of ADP-Glc from Glc-1-P and ATP by AGPase. AGPase is a heterotetramer composed of two large subunits encoded by Sh2 and two small subunits encoded by Bt2. We examined the transcript level of each gene that encodes AGPase through quantitative real-time PCR (qRT_PCR) within endosperm and leaf tissues from 6 newer composite corn lines. The Sh2 and Bt2 genes presented upregulated expression levels in leaf and endosperm tissue. The highest expression level of these two genes in leaf tissues was observed in UM 1 with 6.96 fold and in UM 11 …

A Positive Feedback Loop Of Hippo- And C-Jun-Amino-Terminal Kinase Signaling Pathways Regulates Amyloid-Beta-Mediated Neurodegeneration, Madison Irwin, Meghana Tare, Aditi Singh, Oorvashi Roy Puli, Neha Gogia, Matthew Riccetti, Prajakta Deshpande, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

Alzheimer's disease (AD, OMIM: 104300) is an age-related disorder that affects millions of people. One of the underlying causes of AD is generation of hydrophobic amyloid-beta 42 (Aβ42) peptides that accumulate to form amyloid plaques. These plaques induce oxidative stress and aberrant signaling, which result in the death of neurons and other pathologies linked to neurodegeneration. We have developed a Drosophila eye model of AD by targeted misexpression of human Aβ42 in the differentiating retinal neurons, where an accumulation of Aβ42 triggers a characteristic neurodegenerative phenotype. In a forward deficiency screen to look for genetic modifiers, we identified a molecularly …

Memote For Standardized Genome-Scale Metabolic Model Testing., Christian Lieven, Moritz E Beber, Brett G Olivier, Frank T Bergmann, Meric Ataman, Parizad Babaei, Jennifer A Bartell, Lars M Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E Ebert, Janaka N Edirisinghe, José P Faria, Adam M Feist, Georgios Fengos, Ronan M T Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout Van Helvoirt, Christopher S Henry, Henning Hermjakob, Markus J Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary King, Steffen Klamt, Edda Klipp, Jasper J Koehorst, Matthias König, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L Medlock, Jonathan M Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Mark Poolman, Nathan D Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J Sánchez, Peter J Schaap, Rahuman S Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A H Wodke, Joana C Xavier, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang

Articles, Abstracts, and Reports

No abstract provided.

Gene Expression Analysis Of Effectors Involved In Early Interaction Of Banana And Fusarium Oxysporum F. Sp. Cubense, Nee Kiew Poon

Student Works (2020-2029)

Banana is a popular but disease-laden fruit crop. It is very susceptible to various phytopathogens such as viruses, bacteria, fungi and nematodes. A particularly infectious and economically important fungal disease in banana is Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc). The disease has been plaguing the banana industry since late 19th century. Despite the early discovery of this phytopathogen of banana, little is known on its the mechanism of pathogenicity. In other plants, fungal effectors have been found to function in manipulating plant mechanisms during infection and many have been identified and characterized. In this study, the …

Evidence For Gene-Smoking Interactions For Hearing Loss And Deafness In Japanese American Families, Jia Y Wan, Christina Cataby, Andrew Liem, Emily Jeffrey, Trina M Norden-Krichmar, Deborah Goodman, Stephanie A Santorico, Karen L Edwards

Faculty, Staff and Student Publications

BACKGROUND: This study investigated the relationship between smoking and hearing loss and deafness (HLD) and whether the relationship is modified by genetic variation. Data for these analyses was from the subset of Japanese American families collected as part of the American Diabetes Association Genetics of Non-insulin Dependent Diabetes Mellitus study. Logistic regression with generalized estimating equations assessed the relationship between HLD and smoking. Nonparametric linkage analysis identified genetic regions harboring HLD susceptibility genes and ordered subset analysis was used to identify regions showing evidence for gene-smoking interactions. Genetic variants within these candidate regions were then each tested for interaction with …

Probing The Function Of Long Noncoding Rnas In The Nucleus, Sajal Medha K. Akkipeddi , '20, A. J. Velleca, Dawn M. Carone

Biology Faculty Works

The nucleus is a highly organized and dynamic environment where regulation and coordination of processes such as gene expression and DNA replication are paramount. In recent years, noncoding RNAs have emerged as key participants in the regulation of nuclear processes. There are a multitude of functional roles for long noncoding RNA (lncRNA), mediated through their ability to act as molecular scaffolds bridging interactions with proteins, chromatin, and other RNA molecules within the nuclear environment. In this review, we discuss the diversity of techniques that have been developed to probe the function of nuclear lncRNAs, along with the ways in which …

Imaging Local Genetic Influences On Cortical Folding, Aaron F. Alexander-Bloch, Armin Raznahan, Simon N. Vandeker, Jakob Seidlitz, Zhixin Lu, Samuel R. Matthias, Emma Knowles, Josephine Mollon, Amanda Rodrigue, Joanne E. Curran, Harald H. H. Goring, Peter T. Fox, John Blangero

School of Medicine Publications

Recent progress in deciphering mechanisms of human brain cortical folding leave unexplained whether spatially patterned genetic influences contribute to this folding. High-resolution in vivo brain MRI can be used to estimate genetic correlations (covariability due to shared genetic factors) in interregional cortical thickness, and biomechanical studies predict an influence of cortical thickness on folding patterns. However, progress has been hampered because shared genetic influences related to folding patterns likely operate at a scale that is much more local (cm) than that addressed in prior imaging studies. Here, we develop methodological approaches to examine local genetic influences on cortical thickness and …

Geographic Life History Differences Predict Genomic Divergence Better Than Mitochondrial Barcodes Or Phenotype, Daniel P. Duran, Robert A. Laroche, Harlan M. Gough, Rodger A. Gwiazdowski, Charles B. Knisley, David P. Herrmann, Stephen J. Roman, Scott P. Egan

School of Earth & Environment Departmental Research

Species diversity can be inferred using multiple data types, however, results based on genetic data can be at odds with patterns of phenotypic variation. Tiger beetles of the Cicindelidia politula (LeConte, 1875) species complex have been taxonomically problematic due to extreme phenotypic variation within and between populations. To better understand the biology and taxonomy of this group, we used mtDNA genealogies and multilocus nuclear analyses of 34,921 SNPs to elucidate its evolutionary history and evaluate the validity of phenotypically circumscribed species and subspecies. Genetic analyses recovered two divergent species that are also ecologically distinct, based on adult life history. These …

Mitochondrial Dna Diversity And Evolutionary History Of Native Human Populations Of Northwest Patagonia (Argentina), María Bárbara Postillone, Virginia Agustina Cobos, Celmira Urrutia, Cristina Beatriz Dejean, Paula N. Gonzalez, Sergio Ivan Perez, Valeria Bernal

Human Biology Open Access Pre-Prints

The genetic composition of Amerindian descendants from Patagonia has long been a focus of interest, although the information available is still scarce for many geographic areas. Here, we report the first analysis of the variation in the mtDNA control region for an area of northwestern Patagonia, the North of Neuquén, with the aim of studying the processes and historical events that modeled the evolutionary history of these human groups. We analyzed 113 individuals from two localities of northern Neuquén, along with 6 from southern Neuquén and 223 mtDNA sequences previously published from neighboring areas from Argentina and Chile. We estimated …

Editorial: Deep Learning For Toxicity And Disease Prediction, Ping Gong, Chaoyang Zhang, Minjun Chen

Faculty Publications

No abstract provided.

Urine As A High-Quality Source Of Host Genomic Dna From Wild Populations, Andrew T. Ozga, Timothy H. Webster, Ian C. Gilby, Melissa A. Wilson, Rebecca Nockerts, Michael L. Wilson, Anne Pusey, Yingying Li, Beatrice H. Hahn, Anne C. Stone

Biology Faculty Articles

The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, in the case of many species, it is impossible legally, ethically, or logistically to obtain tissues samples of high-quality necessary for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (feces, urine, dentin, and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that …

The Bacillus Subtilis K-State Promotes Stationary-Phase Mutagenesis Via Oxidative Damage, Holly A. Martin, Amanda A. Kidman, Jillian Socea, Carmen Vallin, Mario Pedraza-Reyes, Eduardo A. Robleto

Life Sciences Faculty Research

Bacterial cells develop mutations in the absence of cellular division through a process known as stationary-phase or stress-induced mutagenesis. This phenomenon has been studied in a few bacterial models, including Escherichia coli and Bacillus subtilis; however, the underlying mechanisms between these systems differ. For instance, RecA is not required for stationary-phase mutagenesis in B. subtilis like it is in E. coli. In B. subtilis, RecA is essential to the process of genetic transformation in the subpopulation of cells that become naturally competent in conditions of stress. Interestingly, the transcriptional regulator ComK, which controls the development of competence, does influence the …

Characterization Of A Species E Adenovirus Vector As A Zika Virus Vaccine, Brianna L. Bullard, Brigette N. Corder, David N. Gordon, Theodore C. Pierson, Eric A. Weaver

Nebraska Center for Virology: Faculty Publications

The development of a safe and efficacious Zika virus (ZIKV) vaccine remains a global health priority. In our previous work, we developed an Adenovirus vectored ZIKV vaccine using a low-seroprevalent human Adenovirus type 4 (Ad4-prM-E) and compared it to an Ad5 vector (Ad5-prM-E). We found that vaccination with Ad4-prM-E leads to the development of a strong anti-ZIKV T-cell response without eliciting significant anti-ZIKV antibodies, while vaccination with Ad5-prM-E leads to the development of both anti-ZIKV antibody and T-cell responses in C57BL/6 mice. However, both vectors conferred protection against ZIKV infection in a lethal challenge model. Here we continued to characterize …

Iread: A Tool For Intron Retention Detection From Rna-Seq Data., Hong-Dong Li, Cory C Funk, Nathan D Price

Articles, Abstracts, and Reports

BACKGROUND: Intron retention (IR) has been traditionally overlooked as 'noise' and received negligible attention in the field of gene expression analysis. In recent years, IR has become an emerging field for interrogating transcriptomes because it has been recognized to carry out important biological functions such as gene expression regulation and it has been found to be associated with complex diseases such as cancers. However, methods for detecting IR today are limited. Thus, there is a need to develop novel methods to improve IR detection.

RESULTS: Here we present iREAD (intron REtention Analysis and Detector), a tool to detect IR events …