Genetics and Genomics Commons^™

Tracing Evolutionary Footprints To Identify Novel Gene Functional Linkages., Yong Chen, Li Yang, Yunfeng Ding, Shuyan Zhang, Tong He, Fenglou Mao, Congyan Zhang, Huina Zhang, Chaoxing Huo, Pingsheng Liu

College of Science & Mathematics Departmental Research

Systematic determination of gene function is an essential step in fully understanding the precise contribution of each gene for the proper execution of molecular functions in the cell. Gene functional linkage is defined as to describe the relationship of a group of genes with similar functions. With thousands of genomes sequenced, there arises a great opportunity to utilize gene evolutionary information to identify gene functional linkages. To this end, we established a computational method (called TRACE) to trace gene footprints through a gene functional network constructed from 341 prokaryotic genomes. TRACE performance was validated and successfully tested to predict enzyme …

The Effect Of Soluble Uterine Factors On Porcine Embryo Development Within A Three-Dimensional Alginate Matrix System, Catherine Sargus-Patino, Elane C. Wells, Jeremy R. Miles, Angela K. Pannier

Department of Animal Science: Faculty Publications

Between day 10 and 12 of gestation in the pig, the embryo undergoes a dramatic morphological change, known as elongation. During elongation the embryo produces and secretes estrogen, which serves as a key signal for maternal recognition of pregnancy. The uterine environment prepares for embryo elongation and implantation by releasing nutrients, metabolites, and hormones in a time-dependent manner relative to paracrine signals from the conceptus (i.e., estrogen) and endocrine/paracrine signals within the endometrium (i.e., progesterone). Despite advances in identification of specific uterine factors present throughout pregnancy in the pig, little is known about the exact mechanisms by which porcine embryos …

Afraid To Help: Social Anxiety Partially Mediates The Association Between 5-Httlpr Triallelic Genotype And Prosocial Behavior, Scott F. Stoltenberg, Christa C. Christ, Gustavo Carlo

Department of Psychology: Faculty Publications

There is growing evidence that the serotonin system influences prosocial behavior. We examined whether anxiety mediated the association between variation in the serotonin transporter gene regulatory region (5-HTTLPR) and prosocial behavior. We collected self-reported tendencies to avoid certain situations and history of helping others using standard instruments and buccal cells for standard 5-HTTLPR genotyping from 398 undergraduate students. Triallelic 5-HTTLPR genotype was significantly associated with prosocial behavior and the effect was partially mediated by social anxiety, such that those carrying the S′ allele reported higher levels of social avoidance and lower rates of helping others. These results are consistent with …

Genomics Of A Metamorphic Timing Qtl: Met1 Maps To A Unique Genomic Position And Regulates Morph And Species-Specific Patterns Of Brain Transcription, Robert B. Page, Meredith A. Boley, D. Kevin Kump, S. Randal Voss

Biology Faculty Publications

Very little is known about genetic factors that regulate life history transitions during ontogeny. Closely related tiger salamanders (Ambystoma species complex) show extreme variation in metamorphic timing, with some species foregoing metamorphosis altogether, an adaptive trait called paedomorphosis. Previous studies identified a major effect QTL (met1) for metamorphic timing and expression of paedomorphosis in hybrid crosses between the biphasic Eastern tiger salamander (Ambystoma tigrinum tigrinum) and the paedomorphic Mexican axolotl (Ambystoma mexicanum). We used existing hybrid mapping panels and a newly created hybrid cross to map the met1 genomic region and determine the …

Assessment Of Genetic Diversity In Peruvian Amaranth (Amaranthus Caudatus And A. Hybridus) Germplasm Using Single Nucleotide Polymorphism Markers [Abstract], Felix Jimenez, Peter J. Maughan, Aquilino Alvarez, Kiel D. Kielinski, Scott M. Smith, Donald B. Pratt, David B. Elzinga, Eric N. Jellen

Faculty Publications

No abstract provided.

Certified Angus, Certified Patriot: Breeding, Bodies, And Pedigree Practices, Scout Calvert

University of Nebraska-Lincoln Libraries: Faculty Publications

The pedigree chart is a cornerstone technology for producing bodies and value in livestock pure breeding. It organizes a cluster of processes, technologies, and discourses gathered under the rubric “pedigree practices.” Angus breeders commonly use artificial insemination to import performance “genetics” into their herds, using the “expected progeny differences” predicted by massive pedigree databases that now also contain phenotype data reported by cattle growers. Discourses of biological inheritance, good breeding, and pedigrees arose in the eighteenth century, concomitant with a fascination with races, species, and other biological kinds. A case study from Angus cattle breeding illustrates pedigree practices and the …

The Role Of Cardiolipin In Iron Homeostasis And Glutathione Metabolism, Vinay A. Patil

Wayne State University Dissertations

Cardiolipin (CL) is the signature phospholipid of mitochondrial membranes, where it is synthesized locally and plays a critical role in mitochondrial bioenergetic functions. Inside the mitochondria, CL is a critical target of mitochondrial generated reactive oxygen species (ROS) and regulates signaling events related to apoptosis and aging. CL deficiency causes perturbation of signaling pathways outside the mitochondria, including the PKC-Slt2 cell integrity pathway and the high osmolarity glycerol (HOG) pathway, and is a key player in the cross-talk between the mitochondria and the vacuole. The importance of CL in human health is underscored by the observation that perturbation of CL …

Development Of 11 Polymorphic Microsatellite Markers For Xylocarpus Granatum (Meliaceae) Using Next-Generation Sequencing Technology, Yuki Tomizawa, Yoshimi Shinmura, Alison K S Wee, Koji Takayama, Takeshi Asakawa, Orlex Baylen Yllano, Severino G. Salmo Iii, Erwin Riyanto Ardli, Nguyen Xuan Tung, Norhaslinda Binti Malekal, Onrizal Onrizal, Sankararamasubramanian H. Meenakshisundaram, Sarawood Sungkaew, Mohd Nazre Saleh, Bayu Adjie, Khin Khin Soe, Emiko Oguri, Noriaki Murakami, Yasuyuki Watano, Shigeyuki Baba, Edward L. Webb, Tadashi Kajita

Environmental Science Faculty Publications

Human impacts have seriously damaged mangroves, and conservation of mangroves will require information on local and regional population genetic structures. Here, we report the development and polymorphism of eleven novel microsatellite markers, developed using next- generation sequencing on 56 samples of widespread man- grove species Xylocarpus granatum (Meliaceae) from nine populations across the Indo-West Pacific region. All loci were found to be polymorphic, with the number of alleles per locus ranging from four to 19. In a population from Sabah (Malaysia), the mean observed and expected heterozygosity per locus was 0.59 and 0.58, respectively. No null allele, significant linkage disequilibrium …

Genetic Diversity In The Modern Horse Illustrated From Genome-Wide Snp Data, Jessica Lynn Petersen, James R. Mickelson, E. Gus Cothran, Lisa S. Andersson, Jeanette Axelsson, Ernie Bailey, Danika L. Bannasch, Matthew M. Binns, Alexandre S. Borges, Pieter Brama, Artur Da Câmaro Machado, Ottmar Distl, Michela Felicetti, Laura Fox-Clipsham, Kathryn T. Graves, Gérard Guérin, Bianca Haase, Telhisa Hasegawa, Karin Hemmann, Emmeline W. Hill, Tosso Leeb, Gabriella Lindgren, Hannes Lohi, Maria Susana Lopes, Beatrice A. Mcgivney, Sofia Mikko, Nicholas Orr, M. Cecilia T. Penedo, Richard J. Piercy, Marja Raekallio, Stefan Rieder, Knut H. Røed, Maurizio Silvestrelli, June Swinburne, Teruaki Tozaki, Mark Vaudin, Claire M. Wade, Molly E. Mccue

Department of Animal Science: Faculty Publications

Horses were domesticated from the Eurasian steppes 5,000–6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. F_ST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely …

Genome-Wide Analysis Reveals Selection For Important Traits In Domestic Horse Breeds, Jessica Lynn Petersen, James R. Mickelson, Aaron K. Rendahl, Stephanie K. Valberg, Lisa S. Andersson, Ernie Bailey, Danika L. Bannasch, Matthew M. Binns, Alexandre S. Borges, Pieter Brama, Artur Da Câmara Machado, Stefano Capomaccio, Katia Cappelli, E. Gus Cothran, Ottmar Distl, Laura Fox-Clipsham, Kathryn T. Graves, Gérard Guérin, Bianca Haase, Telhia Hasegawa, Karin Hemmann, Emmeline W. Hill, Tosso Leeb, Gabriella Lindgren, Hannes Lohi, Maria Susana Lopes, Beatrice A. Mcgivney, Sofia Mikko, Nicholas Orr, M. Cecilia T. Penedo, Richard J. Piercy, Marja Raekallio, Stefan Rieder, Knut H. Røed, June Swinburne, Teruaki Tozaki, Mark Vaudin, Claire M. Wade, Molly E. Mccue

Department of Animal Science: Faculty Publications

Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an F_ST-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were …

Genetic Interaction Influenced By Fluvastatin And Tgfb, Rebekah Rifareal

AUCTUS: The Journal of Undergraduate Research and Creative Scholarship

I was looking for an opportunity to network with researchers at VCU and found this program that would provide the perfect atmosphere to do so. The added benefit of HERO was that I also got the opportunity to network with other undergraduates interested in research from VCU as well as other institutions.

The Role Of Retrotransposons In Gene Family Expansions: Insights From The Mouse Abp Gene Family, Václav Janoušek, Robert C. Karn, Christina M. Laukaitis

Scholarship and Professional Work - LAS

Background: Retrotransposons have been suggested to provide a substrate for non-allelic homologous recombination (NAHR) and thereby promote gene family expansion. Their precise role, however, is controversial. Here we ask whether retrotransposons contributed to the recent expansions of the Androgen-binding protein (Abp) gene families that occurred independently in the mouse and rat genomes. Results: Using dot plot analysis, we found that the most recent duplication in the Abp region of the mouse genome is flanked by L1Md_T elements. Analysis of the sequence of these elements revealed breakpoints that are the relicts of the recombination that caused the duplication, confirming that the …

Characterization And Distribution Of Novel Non-Ltr Retroelements Driving High Telomere Rflp Diversity In Clonal Lines Of Magnaporthe Oryzae, John H. Starnes

Theses and Dissertations--Plant Pathology

The filamentous ascomycete fungus Magnaporthe oryzae is a pathogen of over 50 genera of grasses. Two important diseases it can cause are gray leaf spot in Lolium perenne (perennial ryegrass) and blast in Oryza sativa (rice). The telomeres of M. oryzae isolates causing gray leaf spot are highly variable, and can spontaneously change during fungal culture. In this dissertation, it is shown that a rice-infecting isolate is much more stable at the telomeres than an isolate from gray leaf spot. To determine the molecular basis of telomere instability several gray leaf spot isolates telomeres were cloned, which revealed two non-LTR …

Diversification Under Sexual Selection: The Relative Roles Of Mate Preference Strength And The Degree Of Divergence In Mate Preferences, Rafael L. Rodríguez, Janette W. Boughman, David A. Gray, Eileen A. Hebets, Gerlinde Höbel, Laurel B. Symes

Eileen Hebets Publications

The contribution of sexual selection to diversification remains poorly understood after decades of research. This may be in part because studies have focused predominantly on the strength of sexual selection, which offers an incomplete view of selection regimes. By contrast, students of natural selection focus on environmental differences that help compare selection regimes across populations. To ask how this disparity in focus may affect the conclusions of evolutionary research, we relate the amount of diversification in mating displays to quantitative descriptions of the strength and the amount of divergence in mate preferences across a diverse set of case studies of …

Reconstruction Of Family-Level Phylogenetic Relationships Within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes, Malcolm Hill, April L. Hill, Et. Al.

Biology Faculty Publications

Background: Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges.

Methodology/Principal Findings: We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosa^p, Myxospongiae …

Next-Peak: A Normal-Exponential Two-Peak Model For Peak-Calling In Chip-Seq Data, Nak-Kyeong Kim, Rasika V. Jayatillake, John L. Spouge

Mathematics & Statistics Faculty Publications

Background: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) can locate transcription factor binding sites on genomic scale. Although many models and programs are available to call peaks, none has dominated its competition in comparison studies.

Results: We propose a rigorous statistical model, the normal-exponential two-peak (NEXT-peak) model, which parallels the physical processes generating the empirical data, and which can naturally incorporate mappability information. The model therefore estimates total strength of binding (even if some binding locations do not map uniquely into a reference genome, effectively censoring them); it also assigns an error to an estimated binding location. The comparison study …

Comparison Of Th1 Cytokines And T Cell Markers Gene Expressions Between Virulent And An Attenuated Eiav Vaccine Strain, Talia R. Henkle

Lewis Honors College Capstone Collection

The equine infectious anemia virus (EIAV) is closely related to HIV and has been used as a model to identify protective mechanisms against lentivirus infection. In horses, EIA infection progresses for about a year before infected horses manage to control virus replication. This naturally-gained protection is absolutely dependent on active immune responses as evidenced by the fact that immunosuppressive drugs can induce the recurrence of disease. As the resolution of initial viremia correlates with the appearance of virus specific cytotoxic T lymphocytes (CTL), we believe that cellular immune responses play a key role in controlling EIAV in the horse. In …

Molecular Architecture Of The Uncleaved Hiv-1 Envelope Glycoprotein Trimer, Youdong Mao, Luis Castillo-Menendez, Liping Wang, Christopher Gu, Alon Herschhorn, Anik Désormeaux, Andrés Finzi, Shi-Hua Xiang, Joseph Sodroski

Nebraska Center for Virology: Faculty Publications

The human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer, a membrane-fusing machine, mediates virus entry into host cells and is the sole virusspecific target for neutralizing antibodies. Binding the receptors, CD4 and CCR5/CXCR4, triggers Env conformational changes from the metastable unliganded state to the fusion-active state. We used cryo-electron microscopy to obtain a 6-Å structure of the membranebound, heavily glycosylated HIV-1 Env trimer in its uncleaved and unliganded state. The spatial organization of secondary structure elements reveals that the unliganded conformations of both gp120 and gp41 subunits differ from those induced by receptor binding. The gp120 trimer association domains, which …

Variations In The Biological Functions Of Hiv-1 Clade C Envelope In A Shiv-Infected Rhesus Macaque During Disease Progression, For Yue Tso, Levon Abrahamyan, Shiu-Lok Hu, Ruth M. Ruprecht, Charles Wood

Nebraska Center for Virology: Faculty Publications

A better understanding of how the biological functions of the HIV-1 envelope (Env) changes during disease progression may aid the design of an efficacious anti-HIV-1 vaccine. Although studies from patient had provided some insights on this issue, the differences in the study cohorts and methodology had make it difficult to reach a consensus of the variations in the HIV-1 Env functions during disease progression. To this end, an animal model that can be infected under controlled environment and reflect the disease course of HIV-1 infection in human will be beneficial. Such an animal model was previously demonstrated by the infection …

Kaposi’S Sarcoma-Associated Herpesvirus Transactivator Rta Induces Cell Cycle Arrest In G0/G1 Phase By Stabilizing And Promoting Nuclear Localization Of P27Kip, Pankaj Kumar, Charles Wood

Nebraska Center for Virology: Faculty Publications

The Kaposi’s sarcoma-associated herpesvirus (KSHV) immediate-early gene, replication, and transcription activator (KRta) is a key viral protein that serves as the master regulator for viral lytic replication. In this study, we investigated the role of K-Rta in cell cycle regulation and found that the expression of K-Rta in doxycycline (Dox)-inducible BJAB cells induced cell cycle arrest in G₀/G₁ phase. Western blot analysis of key cell cycle regulators revealed that K-Rta-mediated cell cycle arrest was associated with a decrease in cyclin A and phosphorylated Rb (pS807/pS811) protein levels, both markers of S phase progression, and an increase in …