Genetics and Genomics Commons^™

A Common Genetic Mechanism Underlies Morphological Diversity In Fruits And Other Plant Organs, Shan Wu, Biyao Zhang, Neda Keyhaninejad, Gustavo R. Rodríguez, Hyun Jung Kim, Manohar Chakrabarti, Eudald Illa-Berenguer, Nathan K. Taitano, M. J. Gonzalo, Aurora Díaz, Yupeng Pan, Courtney P. Leisner, Dennis Halterman, C. Robin Buell, Yiqun Weng, Shelley H. Jansky, Herman Van Eck, Johan Willemsen, Antonio J Monforte, Tea Meulia, Esther Van Der Knaap

Plant and Soil Sciences Faculty Publications

Shapes of edible plant organs vary dramatically among and within crop plants. To explain and ultimately employ this variation towards crop improvement, we determined the genetic, molecular and cellular bases of fruit shape diversity in tomato. Through positional cloning, protein interaction studies, and genome editing, we report that OVATE Family Proteins and TONNEAU1 Recruiting Motif proteins regulate cell division patterns in ovary development to alter final fruit shape. The physical interactions between the members of these two families are necessary for dynamic relocalization of the protein complexes to different cellular compartments when expressed in tobacco leaf cells. Together with data …

Embryonic Origin And Genetic Basis Of Cave Associated Phenotypes In The Isopod Crustacean Asellus Aquaticus., Hafasa Mojaddidi, Franco Fernandez, Priscilla A. Erickson, Meredith E. Protas

Natural Sciences and Mathematics | Faculty Scholarship

Characteristics common to animals living in subterranean environments include the reduction or absence of eyes, lessened pigmentation and enhanced sensory systems. How these characteristics have evolved is poorly understood for the majority of cave dwelling species. In order to understand the evolution of these changes, this study uses an invertebrate model system, the freshwater isopod crustacean, Asellus aquaticus, to examine whether adult differences between cave and surface dwelling individuals first appear during embryonic development. We hypothesized that antennal elaboration, as well as eye reduction and pigment loss, would be apparent during embryonic development. We found that differences in pigmentation, eye …

How Does Antibiotic Resistance Spread In Tuberculosis?, Julie A. Spencer

Shared Knowledge Conference

The ancient bacterial disease of tuberculosis (TB) is curable with antibiotics, but according to the World Health Organization, in 2016 over 10 million people became infected with the disease. 600,000 of these cases were resistant to antibiotics, yet the worldwide treatment success rate for drug resistant TB is only 54%. Furthermore, strains exist now that are resistant to all known antibiotics. In the current environment of global travel, this poses a risk for emergent epidemics of drug resistant TB. In this study, I asked: after an antibiotic resistant strain has evolved in someone’s lungs, how does it spread? It is …

Mechanisms For The Spread Of Antibiotic Resistance In Tuberculosis, Julie Allison Spencer

Shared Knowledge Conference

Tuberculosis (TB) is currently the ninth leading cause of death for humans worldwide, causing 10.4 million new infections in 2016. According to the World Health Organization, of these infections, 600,000 were antibiotic resistant. However, the treatment success rate for resistant TB was only 54%. The potential for emergent epidemics of drug resistant TB highlights the need to understand the mechanisms for the spread of resistance. Mycobacterium tuberculosis, the bacterium that causes TB, evolves resistant strains within individuals who are being treated with antibiotics. It has been assumed previously that the resistant characteristics of these strains are spread primarily by the …

Molecular Structure Of Promoter-Bound Yeast Tfiid., Olga Kolesnikova, Adam Ben-Shem, Jie Luo, Jeff Ranish, Patrick Schultz, Gabor Papai

Articles, Abstracts, and Reports

Transcription preinitiation complex assembly on the promoters of protein encoding genes is nucleated in vivo by TFIID composed of the TATA-box Binding Protein (TBP) and 13 TBP-associate factors (Tafs) providing regulatory and chromatin binding functions. Here we present the cryo-electron microscopy structure of promoter-bound yeast TFIID at a resolution better than 5 Å, except for a flexible domain. We position the crystal structures of several subunits and, in combination with cross-linking studies, describe the quaternary organization of TFIID. The compact tri lobed architecture is stabilized by a topologically closed Taf5-Taf6 tetramer. We confirm the unique subunit stoichiometry prevailing in TFIID …

South American Leaf-Cutter Bees (Genus Megachile) Of The Subgenera Rhyssomegachile And Zonomegachile, With Two New Subgenera (Hymenoptera: Megachilidae), Víctor H. González, Terry Griswold, Michael S. Engel

All PIRU Publications

Leaf-cutter bees (genus Megachile Latreille) are among the most common and diverse group of bees. However, the identity and taxonomic placement of many species are problematic and species identification is often difficult. Some species are known only from a single specimen or from one of the sexes, and identification keys are not available for many groups. We address these taxonomic issues for the subgenera Rhyssomegachile Mitchell and Zonomegachile Mitchell, two poorly known South American lineages of leaf-cutter bees. We provide comparative diagnoses, redescriptions, illustrated identification keys, new geographical records, and designate needed neotypes for Megachile cara Mitchell, M. gigas Schrottky, …

The Impact Of Selective Genotyping On The Response To Selection Using Single-Step Genomic Best Linear Unbiased Prediction, Jeremy T. Howard, Thomas A. Rathje, Caitlyn E. Bruns, Danielle F. Wilson-Wells, Stephen D. Kachman, Matthew L. Spangler

Department of Animal Science: Faculty Publications

Across the majority livestock species, routinely collected genomic and pedigree information has been incorporated into evaluations using single-step methods. As a result, strategies that reduce genotyping costs without reducing the response to selection are important as they could have substantial economic impacts on breeding programs. Therefore, the objective of the current study was to investigate the impact of selectively genotyping selection candidates on the selection response using simulation. Populations were simulated to mimic the genome and population structure of a swine and cattle population undergoing selection on an index comprised of the estimated breeding values (EBV) for 2 genetically correlated …

Population Genetics Of The Eastern Subterranean Termite, Reticulitermes Flavipes, In The Southern Appalachian Mountains, Lee Ann Passarella

Honors Theses

As an area rich in biodiversity, the Appalachian Mountains are an ideal place for biological research. The pronounced impacts of Pleistocene climatic cycles on forest distributions over time have shaped the evolutionary history of animals that depend on these habitats, underpinning the research that is presented here. The present study on the eastern subterranean termite, Reticulitermes flavipes, was conducted to better understand the spatial distribution of genetic diversity within and among populations of this species in the context of the aforementioned historical climatic changes in the southern Appalachian Mountain region. I hypothesized that there would be geographically localized, distinct genetic …

Genetic Variants In The Sirt6 Transcriptional Regulatory Region Affect Gene Activity And Carcass Quality Traits In Indigenous Chinese Beef Cattle (Bos Taurus), Lin-Sheng Gui, Sayed Haidar Abbas Raza, Matthew Garcia, Yong-Gang Sun, Irfan Ullah, Yin-Cang Han

Animal, Dairy, and Veterinary Science Faculty Publications

Background: The aim of this study was to analyze potential influences of polymorphisms within the regulatory region of the bovine SIRT6 gene on carcass quality traits. Expression analyses suggested that SIRT6 gene is predominately expressed in kidney, compared with other tissues. In 535 indigenous Chinese beef cattle, two novel single nucleotide polymorphisms (SNPs) were identified within the promoter region of the SIRT6 gene.

Results: Association analysis indicated that G allele of the c.-1100 A > G had a positive effect on fat deposition, and the Hap4/4 diplotype had more favourable results than other dipoltypes with respect to the evaluation of carcass …

Kaposi’S Sarcoma-Associated Herpesvirus Seropositivity Is Associated With Type 2 Diabetes Mellitus: A Case–Control Study In Xinjiang, China, Meng Cui, Qiwen Fang, Jun Zheng, Zhanjun Shu, Yin Chen, Yage Fan, Juan Zhao, Charles Wood, Tiejun Zhang, Yan Zeng

Nebraska Center for Virology: Faculty Publications

Objective: To assess the potential relationship between Kaposi’s sarcoma-associated herpesvirus (KSHV) infection and type 2 diabetes mellitus (DM-2) in Xinjiang, China.

Methods: A case–control study of consecutively included DM-2 patients and normal controls was conducted among the Uygur and Han populations in Xinjiang Uygur Autonomous Region, China. Blood samples were collected and KSHV seroprevalence, antibody titers, and viral load were investigated. Logistic regression analysis and multiple linear regression analysis were applied to explore determinants of the main outcome measures.

Results: A total of 324 patients with DM-2 and 376 normal controls were included. The seroprevalence of KSHV was 49.1% (95% …

A Novel Tetracycline-Responsive Transgenic Mouse Strain For Skeletal Muscle-Specific Gene Expression, Masahiro Iwata, Davis A. Englund, Yuan Wen, Cory M. Dungan, Kevin A. Murach, Ivan J. Vechetti Jr., Christopher B. Mobley, Charlotte A. Peterson, John J. Mccarthy

Center for Muscle Biology Faculty Publications

Background: The tetracycline-responsive system (Tet-ON/OFF) has proven to be a valuable tool for manipulating gene expression in an inducible, temporal, and tissue-specific manner. The purpose of this study was to create and characterize a new transgenic mouse strain utilizing the human skeletal muscle α-actin (HSA) promoter to drive skeletal muscle-specific expression of the reverse tetracycline transactivator (rtTA) gene which we have designated as the HSA-rtTA mouse.

Methods: To confirm the HSA-rtTA mouse was capable of driving skeletal muscle-specific expression, we crossed the HSA-rtTA mouse with the tetracycline-responsive histone H2B-green fluorescent protein (H2B-GFP) transgenic mouse in order to label myonuclei.

Results: …

The Mitochondrial Genome Of The Endemic Brazilian Paradoxial Frog Pseudis Tocantins (Hylidae), Kaleb Pretto Gatto, Jeramiah J. Smith, Luciana Bolsoni Lourenço

Biology Faculty Publications

In this work, we present for the first time the mitochondrial genome of a paradoxical frog (Pseudis tocantins). This genome is 15.56 kb, excluding the control region, and is similar in gene content to other hylid mitogenomes. Maximum likelihood analysis, using the mitogenomes of several anurans, indicated P. tocantins as closely related to other hylid species.

Integrating Multiple Genetic Detection Methods To Estimate Population Density Of Social And Territorial Carnivores, Sean M. Murphy, Ben C. Augustine, Jennifer R. Adams, Lisette P. Waits, John J. Cox

Forestry and Natural Resources Faculty Publications

Spatial capture–recapture models can produce unbiased estimates of population density, but sparse detection data often plague studies of social and territorial carnivores. Integrating multiple types of detection data can improve estimation of the spatial scale parameter (σ), activity center locations, and density. Noninvasive genetic sampling is effective for detecting carnivores, but social structure and territoriality could cause differential detectability among population cohorts for different detection methods. Using three observation models, we evaluated the integration of genetic detection data from noninvasive hair and scat sampling of the social and territorial coyote (Canis latrans). Although precision of estimated density was …

Repeat Elements Organise 3d Genome Structure And Mediate Transcription In The Filamentous Fungus Epichloë Festucae, David J. Winter, Austen R. D. Ganley, Carolyn A. Young, Ivan Liachko, Christopher L. Schardl, Pierre-Yves Dupont, Daniel Berry, Arvina Ram, Barry Scott, Murray P. Cox

Plant Pathology Faculty Publications

Structural features of genomes, including the three-dimensional arrangement of DNA in the nucleus, are increasingly seen as key contributors to the regulation of gene expression. However, studies on how genome structure and nuclear organisation influence transcription have so far been limited to a handful of model species. This narrow focus limits our ability to draw general conclusions about the ways in which three-dimensional structures are encoded, and to integrate information from three-dimensional data to address a broader gamut of biological questions. Here, we generate a complete and gapless genome sequence for the filamentous fungus, Epichloë festucae. We use Hi-C …

Identification And Heterologous Reconstitution Of A 5-Alk(En)Ylresorcinol Synthase From Endophytic Fungus Shiraia Sp. Slf14, Huiwen Yan, Lei Sun, Jinge Huang, Yixing Qiu, Fuchao Xu, Riming Yan, Du Zhu, Wei Wang, Jixun Zhan

Biological Engineering Faculty Publications

A new type III polyketide synthase gene (Ssars) was discovered from the genome of Shiraia sp. Slf14, an endophytic fungal strain from Huperzia serrata. The intron-free gene was cloned from the cDNA and ligated to two expression vectors pET28a and YEpADH2p-URA3 for expression in Escherichia coli BL21(DE3) and Saccharomyces cerevisiae BJ5464, respectively. SsARS was efficiently expressed in E. coli BL21(DE3), leading to the synthesis of a series of polyketide products. Six major products were isolated from the engineered E. coli and characterized as 1,3-dihydroxyphenyl-5-undecane, 1,3-dihydroxyphenyl-5-cis-6'-tridecene,1,3-dihydroxyphenyl-5-tridecane, 1,3-dihydroxyphenyl-5-cis-8'-pentadecene, 1,3-dihydroxyphenyl-5-pentadecane and 1,3-dihydroxyphenyl-5-cis-10'-heptadecene, respectively, …

Genome Wide Association Studies For Identification Of Markers Linked To Sucrose Traits In Sugarcane, Nathanael Darrell Fickett

LSU Doctoral Dissertations

Sugarcane, being a complex aneu-polyploid, poses unique challenges to fine mapping of quantitative trait loci (QTL) controlling agronomic traits of interest. Genome-wide association studies (GWAS) could be a better alternative to identify molecular markers associated with specific traits due to high linkage disequilibrium in sugarcane. In the first study, marker-trait associations (MTAs) were evaluated for three sucrose traits, Brix, total recoverable sugar (TRS), and percent sucrose on 48 elite and historic Louisiana breeding clones using 1,062 alleles. These sucrose traits were highly correlated (P-value < 0.0001) at >0.96. TASSEL 5.1 and JMP Genomics 8.0 were compared with eight models run in each program. …

Synergistic Effects Of Temperature And Salinity On The Gene Expression And Physiology Of Crassostrea Virginica, Hollis Jones

LSU Master's Theses

Crassostrea virginica, the eastern oyster, forms reefs that provide critical services and benefits to the resiliency of the surrounding ecosystem. Changes in environmental conditions, including salinity and temperature, can dramatically alter the services oysters provide by affecting their population dynamics. Climate warming may further exacerbate the effects of salinity changes as precipitation events increase in frequency, intensity, and duration. Temperature and salinity independently and synergistically influence gene expression and physiology in marine organisms. We used comparative transcriptomics, physiology, and a field assessment experiment to investigate whether Louisianan oyster are changing their phenotypes to cope with increased temperature and salinity …

Hominoid Intraspecific Cranial Variation Mirrors Neutral Genetic Diversity, Julia M. Zichello, Karen L. Baab, Kieran P. Mcnulty, Christopher J. Raxworthy, Michael E. Steiper

Publications and Research

Natural selection, developmental constraint, and plasticity have all been invoked as explanations for intraspecific cranial variation in humans and apes. However, global patterns of human cranial variation are congruent with patterns of genetic variation, demonstrating that population history has influenced cranial variation in humans. Here we show that this finding is not unique to Homo sapiens but is also broadly evident across extant ape species. Specifically, taxa that exhibit greater intraspecific cranial shape variation also exhibit greater genetic diversity at neutral autosomal loci. Thus, cranial shape variation within hominoid taxa reflects the population history of each species. Our results suggest …

Gene Gangs Of The Chloroviruses: Conserved Clusters Of Collinear Monocistronic Genes, Phillip Seitzer, Adrien Jeanniard, Fangrui Ma, James L. Van Etten, Marc T. Facciotti, David D. Dunigan

Nebraska Center for Virology: Faculty Publications

Chloroviruses (family Phycodnaviridae) are dsDNA viruses found throughout the world’s inland waters. The open reading frames in the genomes of 41 sequenced chloroviruses (330 + 40 kbp each) representing three virus types were analyzed for evidence of evolutionarily conserved local genomic “contexts”, the organization of biological information into units of a scale larger than a gene. Despite a general loss of synteny between virus types, we informatically detected a highly conserved genomic context defined by groups of three or more genes that we have termed “gene gangs”. Unlike previously described local genomic contexts, the definition of gene gangs requires only …

Seqothello: Querying Rna-Seq Experiments At Scale, Ye Yu, Jinpeng Liu, Xinan Liu, Yi Zhang, Eamonn Magner, Erik Lehnert, Chen Qian, Jinze Liu

Computer Science Faculty Publications

We present SeqOthello, an ultra-fast and memory-efficient indexing structure to support arbitrary sequence query against large collections of RNA-seq experiments. It takes SeqOthello only 5 min and 19.1 GB memory to conduct a global survey of 11,658 fusion events against 10,113 TCGA Pan-Cancer RNA-seq datasets. The query recovers 92.7% of tier-1 fusions curated by TCGA Fusion Gene Database and reveals 270 novel occurrences, all of which are present as tumor-specific. By providing a reference-free, alignment-free, and parameter-free sequence search system, SeqOthello will enable large-scale integrative studies using sequence-level data, an undertaking not previously practicable for many individual labs.

Antibody Epitope Specificity For Dsdna Phosphate Backbone Is An Intrinsic Property Of The Heavy Chain Variable Germline Gene Segment Used, Tatjana Srdic-Rajic, Heinz Kohler, Vladimir Jurisic, Radmila Metlas

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Analysis of protein sequences by the informational spectrum method (ISM) enables characterization of their specificity according to encoded information represented with defined frequency (F). Our previous data showed that F(0.367) is characteristic for variable heavy chain (VH) domains (a combination of variable (V), diversity (D) and joining (J) gene segments) of the anti-phosphocholine (PC) T15 antibodies and mostly dependent on the CDR2 region, a site for PC phosphate group binding. Because the T15 dsDNA-reactive U4 mutant also encodes F(0.367), we hypothesized that the same frequency may also be characteristic for anti-DNA antibodies. Data obtained from an analysis of 60 spontaneously …

Genome-Wide Screening Identifies Genes And Biological Processes Implicated In Chemoresistance And Oncogene-Induced Apoptosis, Tengyu Ko

LSU Doctoral Dissertations

Anti-proliferative responses such as senescence and apoptosis are often used by normal cells to combat oncogenic insults and to prevent tumorigenesis. However, oncogenic mutations are frequently found in cancers, suggesting that additional mutations may occur to facilitate the bypass of these anti-proliferative responses. It is believed that some of these additional mutations may also contribute to the chemoresistance of cancers. This dissertation focused on identifying novel genes and biological processes implicated in chemoresistance and tumorigenesis.

Cisplatin-based chemotherapeutic regimens are frequently used for treatments of solid tumors. However, tumor cells may have inherent or acquired resistance to cisplatin, and the underlying …

Myc Distant Enhancers Underlie Ovarian Cancer Susceptibility At The 8q24.21 Locus, Anxhela Gjyshi Gustafson

USF Tampa Graduate Theses and Dissertations

Ovarian cancer is a leading cause of death among women diagnosed with cancer. Mortality rate is high because an overwhelming majority of new cases are diagnosed with late-stage disease when the survival statistics are very poor with an overall 5-year survival rate of less than 40%. Despite the large burden of disease, the etiology of ovarian cancer is not well understood. In addition to linkage studies that have identified highly penetrant cancer susceptibility genes such as BRCA1 and BRCA2, the emergence of Genome Wide Association Studies (GWAS) in the last decade has facilitated the identification of common genetic variants with …

Re-Thinking Alzheimer's Disease Therapeutic Targets Using Gene-Based Tests, Man Ki Kwok, Shi Lin Lin, C Mary Schooling

Publications and Research

Background: Alzheimer's disease (AD) is a devastating condition with no known effective drug treatments. Existing drugs only alleviate symptoms. Given repeated expensive drug failures, we assessed systematically whether approved and investigational AD drugs are targeting products of genes strongly associated with AD and whether these genes are targeted by existing drugs for other indications which could be re-purposed.

Methods: We identified genes strongly associated with late-onset AD fromthe loci of genetic variants associated with AD at genome-wide-significance and from a gene-based test applied to the most extensively genotyped late-onset AD case (n=17,008)-control (n=37,154) study, the International Genomics of Alzheimer's Project. …

A Review Of Current Knowledge Concerning The Breeding And Summer Distribution Of The Cordilleran Flycatcher (Empidonax Occidentalis) In Mexico, Harold F. Greeney, Matthew J. Miller, Charles Van Riper Iii

Occasional Papers of the Museum of Natural Science, Louisiana State University

The Cordilleran Flycatcher (Empidonax occidentalis) is one of many North American birds whose distribution crosses the US–Mexican border and for which little is presently known about summer distribution and breeding biology south of this border. In addition, the Cordilleran Flycatcher presents ornithologists with a number of challenging questions surrounding its taxonomy, migration, distribution, population structure, and species limits. In particular, there remains a good deal of uncertainty concerning the species-level relationships, seasonal movements, and the wintering and breeding distributions of both recognized subspecies of Cordilleran Flycatcher in Mexico. Using field observations, a thorough review of the literature, and …

Stochastic Difference Model For Evolutional Dynamics Of Large Antigen Repertoires In African Trypanosomes, Fan Yu

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

The Future Of Biodiversity Assessment: Using Environmental Dna And Next-Generation Sequencing To Characterize Biological Communities In The Central Highlands Of Arizona, Courtney Turner-Rathbone

Undergraduate Research Symposium - Prescott

Historically ecological surveys require significant man hours in the field, utilizing methods which can stress species being observed. In using environmental DNA (eDNA) gathered from air, soil, and water, traditional methods may be supplemented or reduced in order to more efficiently utilize funding and reduce or eliminate stress on surveyed species. Water was collected in replicates using aseptic technique from two different sites, 60 miles apart, along the Verde River. Samples were vacuum filtered within 24 hours through 0.45 μm cellulose nitrate (CN) filters to collect eDNA. DNA extraction from the filters was performed. The polymerase chain reaction (PCR) was …

Genotype Fingerprints Enable Fast And Private Comparison Of Genetic Testing Results For Research And Direct-To-Consumer Applications., Max Robinson, Gustavo Glusman

Articles, Abstracts, and Reports

Genetic testing has expanded out of the research laboratory into medical practice and the direct-to-consumer market. Rapid analysis of the resulting genotype data now has a significant impact. We present a method for summarizing personal genotypes as 'genotype fingerprints' that meets these needs. Genotype fingerprints can be derived from any single nucleotide polymorphism-based assay, and remain comparable as chip designs evolve to higher marker densities. We demonstrate that these fingerprints support distinguishing types of relationships among closely related individuals and closely related individuals from individuals from the same background population, as well as high-throughput identification of identical genotypes, individuals in …

Complete Genome Sequences Of 18 Paenibacillus Larvae Phages From The Western United States, Bryan D. Merrill, Christopher P. Fajardo, Jared A. Hilton, Ashley M. Payne, Andy T. Ward, Jamison K. Walker, Aziza Dhalai, Cameron Imahara, James Mangohig, Josh Monk, Cristian Pascacio, Padmani Rai, Alicia Salisbury, Kathie Velez, Travis J. Bloomfield, Brett Buhler, Steven G. Duncan, David A. Fuhriman, Josil George, Kiel Graves, Karli Graves, Hunter L. Hill, Michelle Kim, Bradley K. Knabe, Devin B. Ririe, Spencer L. Rogers, Casey Stamereilers, Michael B. Stephenson, Brittian K. Usher, Colton S. Ward, Jacob M. Withers

Life Sciences Faculty Research

We present here the complete genomes of 18 phages that infect Paenibacillus larvae, the causative agent of American foulbrood in honeybees. The phages were isolated between 2014 and 2016 as part of an undergraduate phage discovery course at Brigham Young University. The phages were isolated primarily from bee debris and lysogens.

8th Annual Postdoctoral Science Symposium, University Of Texas Md Anderson Cancer Center Postdoctoral Association

Annual Postdoctoral Science Symposium Abstracts

The mission of the Annual Postdoctoral Science Symposium (APSS) is to provide a platform for talented postdoctoral fellows throughout the Texas Medical Center to present their work to a wider audience. The MD Anderson Postdoctoral Association convened its inaugural Annual Postdoctoral Science Symposium (APSS) on August 4, 2011.

The APSS provides a professional venue for postdoctoral scientists to develop, clarify, and refine their research as a result of formal reviews and critiques of faculty and other postdoctoral scientists. Additionally, attendees discuss current research on a broad range of subjects while promoting academic interactions and enrichment and developing new collaborations.