Use Of A Complete-Feed Diet (Ramp) In Grain Adaptation Programs Compared To Traditional Grain Adaptation Programs, C. J. Schneider, Brandon L. Nuttelman, Kelsey M. Rolfe Rolfe, William A. Griffin, Terry J. Klopfenstein, Galen E. Erickson

Department of Animal Science: Faculty Publications

A study evaluated using RAMP to adapt cattle to a high grain finishing diet. Yearling crossbred steers (n = 229; BW = 397 ± 28.4 kg) were consecutively weighed over 2 d, stratified by BW, and assigned randomly within strata to 18 feedlot pens, with 12 or 13 steers per pen. Treatments were imposed during grain adaptation (22 d) by decreasing RAMP (100 to 0%) and increasing finishing diet (0 to 100%). RAMP was fed either as a blend in a 1-diet system which was delivered twice daily (RAMP-1RS) or as 2 daily diets where RAMP was delivered in one …

Pseudoscorpion Mitochondria Show Rearranged Genes And Genome-Wide Reductions Of Rna Gene Sizes And Inferred Structures, Yet Typical Nucleotide Composition Bias, Sergey Ovchinnikov, Susan E. Masta

Biology Faculty Publications and Presentations

Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes.

We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do …

Spatial Genetic Variation Among Spodoptera Frugiperda (Lepidoptera: Noctuidae) Sampled From The United States, Puerto Rico, Panama, And Argentina, Difabachew K. Belay, Pete L. Clark, Steven R. Skoda, David J. Isenhour, Jaime Molina-Ochoa, Claudia Gianni, John E. Foster

Department of Entomology: Faculty Publications

Spatial genetic variability of the fall armyworm, Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae), was studied by collecting samples from 31 locations in the United States, Argentina, Panama, and Puerto Rico, and then using amplified fragment length polymorphism to detect genetic variation. Analysis of molecular variance showed significant genetic variation in fall armyworm among all (28%) sample locations and individuals within (71%) sample locations; genetic variation of fall armyworm was minimal between sample locations grouped into regions. The pairwise fixation index (F_ST) comparisons showed significant genetic differentiation (0.288) among the 31 locations. However, dendrograms of results from cluster …

Akirin Links Twist-Regulated Transcription With The Brahma Chromatin Remodeling Complex During Embryogenesis, Scott J. Nowak, Hitoshi Aihara, Katie Gonzalez, Yutaka Nibu, Mary K. Baylies

Faculty Articles

The activities of developmentally critical transcription factors are regulated via interactions with cofactors. Such interactions influence transcription factor activity either directly through protein–protein interactions or indirectly by altering the local chromatin environment. Using a yeast double-interaction screen, we identified a highly conserved nuclear protein, Akirin, as a novel cofactor of the key Drosophila melanogaster mesoderm and muscle transcription factor Twist. We find that Akirin interacts genetically and physically with Twist to facilitate expression of some, but not all, Twist-regulated genes during embryonic myogenesis. akirin mutant embryos have muscle defects consistent with altered regulation of a subset of Twistregulated genes. To …

Will Gene Patents Impede Whole Genome Sequencing?: Deconstructing The Myth That 20% Of The Human Genome Is Patented, Christopher M. Holman

IP Theory

No abstract provided.

Sparse Integrative Clustering Of Multiple Omics Data Sets, Ronglai Shen, Sijian Wang, Qianxing Mo

Memorial Sloan-Kettering Cancer Center, Dept. of Epidemiology & Biostatistics Working Paper Series

High resolution microarrays and second-generation sequencing platforms are powerful tools to investigate genome-wide alterations in DNA copy number, methylation, and gene expression associated with a disease. An integrated genomic profiling approach measuring multiple omics data types simultaneously in the same set of biological samples would render an integrated data resolution that would not be available with any single data type. In a previous publication (Shen et al., 2009), we proposed a latent variable regression with a lasso constraint (Tibshirani, 1996) for joint modeling of multiple omics data types to identify common latent variables that can be used to cluster patient …

Genes And Plays: Bringing Elsi Issues To Life, Karen H. Rothenberg, Lynn W. Bush

Faculty Scholarship

Ethical complexities surround the promise of genomic technology and the power of genetic information as they alter conceptions of identity and dynamics within personal and professional relationships. Creative approaches such as dramatic vignettes offer a unique analytical stage for imagining the bioethical past and future. Dramatic narratives can bring to life images of differing perspectives and values when experiencing innovations in medicine. Although the scientific landscape shifts, concerns expressed in theatre from 50 years ago parallel many contemporary ELSI (ethical, legal and social implications) issues, highlighting the ongoing struggle to appreciate the impact of emerging genetic technologies on relationships. To …

Cranial Variation And The Transition To Agriculture In Europe, Ron Pinhasi, Noreen Von Cramon-Taubadel

Human Biology Open Access Pre-Prints

Debates surrounding the nature of the Neolithic demographic transition in Europe have historically centred on two opposing models; a 'demic' diffusion model whereby incoming farmers from the Near East and Anatolia effectively replaced or completely assimilated indigenous Mesolithic foraging communities and an 'indigenist' model resting on the assumption that ideas relating to agriculture and animal domestication diffused from the Near East, but with little or no gene flow. The extreme versions of these dichotomous models have been heavily contested primarily on the basis of archaeological and modern genetic data. However, in recent years there has been a growing acceptance of …

The Y-Chromosome C3* Star-Cluster Attributed To Genghis Khan's Descendants Is Present At High Frequency In The Kerey Clan From Kazakhstan, Serikbai Abilev, Boris Malyarchuk, Miroslava Derenko, Marcin Wozniak, Tomasz Grzybowski, Ilya Zakharov

Human Biology Open Access Pre-Prints

In order to verify the possibility that the Y-chromosome C3* star-cluster attributed to Genghis Khan and his patrilineal descendants is relatively frequent in the Kereys, who are the dominant clan in Kazakhstan and in Central Asia as a whole, polymorphism of the Y-chromosome was studied in Kazakhs, represented mostly by members of the Kerey clan. The Kereys showed the highest frequency (76.5%) of individuals carrying the Y-chromosome variant known as C3* star-cluster ascribed to the descendants of Genghis Khan. C3* star-cluster haplotypes were found in two sub-clans, Abakh-Kereys and Ashmaily-Kereys, diverged about 20-22 generations ago according to the historical data. …

Pten Regulation Of Local And Long-Range Connections In Mouse Auditory Cortex, Qiaojie Xiong, Hysell V. Oviedo, Lloyd C. Trotman, Anthony M. Zador

Publications and Research

Autism spectrum disorders (ASDs) are highly heritable developmental disorders caused by a heterogeneous collection of genetic lesions. Here we use a mouse model to study the effect on cortical connectivity of disrupting the ASD candidate gene PTEN (phosphatase and tensin homolog deleted on chromosome 10). Through Cre-mediated recombination, we conditionally knocked out PTEN expression in a subset of auditory cortical neurons. Analysis of long-range connectivity using channelrhodopsin-2 revealed that the strength of synaptic inputs from both the contralateral auditory cortex and from the thalamus onto PTEN-cko neurons was enhanced compared with nearby neurons with normal PTEN expression. Laser-scanning photostimulation showed …

Structural Characterization Of Human Uch37, E. S. Burgie, C. Bingman, Ameet Soni, G. N. Phillips Jr.

Computer Science Faculty Works

Uch37 is a de-ubiquitylating enzyme that is functionally linked with the 26S proteasome via Rpn13, and is essential for metazoan development. Here, we report the X-ray crystal structure of full-length human Uch37 at 2.95 Å resolution. Uch37's catalytic domain is similar to those of all UCH enzymes characterized to date. The C-terminal extension is elongated, predominantly helical and contains coiled coil interactions. Additionally, we provide an initial characterization of Uch37's oligomeric state and identify a systematic error in previous analyses of Uch37 activity. Taken together, these data provide a strong foundation for further analysis of Uch37's several functions.

Probabilistic Ensembles For Improved Inference In Protein-Structure Determination, Ameet Soni, J. Shavlik

Computer Science Faculty Works

Protein X-ray crystallography — the most popular method for determining protein structures — remains a laborious process requiring a great deal of manual crystallographer effort to interpret low-quality protein images. Automating this process is critical in creating a high-throughput protein-structure determination pipeline. Previously, our group developed ACMI, a probabilistic framework for producing protein-structure models from electron-density maps produced via X-ray crystallography. ACMI uses a Markov Random Field to model the three-dimensional (3D) location of each non-hydrogen atom in a protein. Calculating the best structure in this model is intractable, so ACMI uses approximate inference methods to estimate the optimal structure. …

Vegfa Family Isoforms Regulate Spermatogonial Stem Cell Homeostasis In Vivo, Kyle C. Caires, Jeanene M. Clopton, Andrea S. Cupp, Derek J. Mclean

Department of Animal Science: Faculty Publications

The objective of the present study was to investigate vascular endothelial growth factor A (VEGFA) isoform regulation of cell fate decisions of spermatogonial stem cells (SSC) in vivo. The expression pattern and cell-specific distribution of VEGF isoforms, receptors, and coreceptors during testis development postnatal d 1–180 suggest a nonvascular function for VEGF regulation of early germ cell homeostasis. Populations of undifferentiated spermatogonia present shortly after birth were positive for VEGF receptor activation as demonstrated by immunohistochemical analysis. Thus, we hypothesized that proangiogenic isoforms of VEGF (VEGFA₁₆₄) stimulate SSC self-renewal, whereas antiangiogenic isoforms of VEGF (VEGFA₁₆₅b) …

Emerging Viruses In The Felidae: Shifting Paradigms, Stephen J. O'Brien, Jennifer L. Troyer, Meredith Brown, Warren E. Johnson, Agostinho Antunes, Melody E. Roelke, Jill Pecon-Slattery

Biology Faculty Articles

The domestic cat is afflicted with multiple viruses that serve as powerful models for human disease including cancers, SARS and HIV/AIDS. Cat viruses that cause these diseases have been studied for decades revealing detailed insight concerning transmission, virulence, origins and pathogenesis. Here we review recent genetic advances that have questioned traditional wisdom regarding the origins of virulent Feline infectious peritonitis (FIP) diseases, the pathogenic potential of Feline Immunodeficiency Virus (FIV) in wild non-domestic Felidae species, and the restriction of Feline Leukemia Virus (FeLV) mediated immune impairment to domestic cats rather than other Felidae species. The most recent interpretations indicate important …

Genome-Wide Analysis Of Syntenic Gene Deletion In The Grasses, James C. Schnable, Michael Freeling, Eric Lyons

Department of Agronomy and Horticulture: Faculty Publications

The grasses, Poaceae, are one of the largest and most successful angiosperm families. Like many radiations of flowering plants, the divergence of the major grass lineages was preceded by a whole-genome duplication (WGD), although these events are not rare for flowering plants. By combining identification of syntenic gene blocks with measures of gene pair divergence and different frequencies of ancient gene loss, we have separated the two subgenomes present in modern grasses. Reciprocal loss of duplicated genes or genomic regions has been hypothesized to reproductively isolate populations and, thus, speciation. However, in contrast to previous studies in yeast and teleost …

Heterogeneity In Mitochondrial Morphology And Membrane Potential Is Independent Of The Nuclear Division Cycle In Multinucleate Fungal Cells, John P. Gerstenberger, Patricia Occhipinti, Amy S. Gladfelter

Dartmouth Scholarship

In the multinucleate filamentous fungus Ashbya gossypii, nuclei divide asynchronously in a common cytoplasm. We hypothesize that the division cycle machinery has a limited zone of influence in the cytoplasm to promote nuclear autonomy. Mitochondria in cultured mammalian cells undergo cell cycle-specific changes in morphology and membrane potential and therefore can serve as a reporter of the cell cycle state of the cytoplasm. To evaluate if the cell cycle state of nuclei in A. gossypii can influ

Desert Hedgehog Is A Mammal-Specific Gene Expressed During Testicular And Ovarian Development In A Marsupial, William A. O'Hara

Master's Theses

Desert hedgehog (DHH) belongs to the hedgehog gene family that act as secreted intercellular signal transducers. DHH is an essential morphogen for normal testicular development and function in both mice and humans but is not present in the avian lineage. Like other hedgehog proteins, DHH signals through the patched (PTCH) receptors 1 and 2. Here we examine the expression and protein distribution of DHH, PTCH1 and PTCH2 in the developing testes of a marsupial mammal (the tammar wallaby) to determine whether DHH signalling is a conserved factor in gonadal development in all therian mammals.

Tumor Suppression By Cell Competition Through Regulation Of The Hippo Pathway, Chiao-Lin Chen, Molly C. Schroeder, Madhuri Kango-Singh, Chunyao Tao, Georg Halder

Biology Faculty Publications

Homeostatic mechanisms can eliminate abnormal cells to prevent diseases such as cancer. However, the underlying mechanisms of this surveillance are poorly understood. Here we investigated how clones of cells mutant for the neoplastic tumor suppressor gene scribble (scrib) are eliminated from Drosophila imaginal discs. When all cells in imaginal discs are mutant for scrib, they hyperactivate the Hippo pathway effector Yorkie (Yki), which drives growth of the discs into large neoplastic masses. Strikingly, when discs also contain normal cells, the scrib− cells do not overproliferate and eventually undergo apoptosis through JNK-dependent mechanisms. However, induction of apoptosis does …

Increased Variability Of Microbial Communities In Restored Salt Marshes Nearly 30 Years After Tidal Flow Restoration, Anne E. Bernhard, David Marshall, Lazaros Yiannos

Biology Faculty Publications

We analyzed microbial diversity and community composition from four salt marsh sites that were impounded for 40–50 years and subsequently restored and four unimpounded sites in southeastern Connecticut over one growing season. Community composition and diversity were assessed by terminal restriction fragment length polymorphism (TRFLP) and sequence analysis of 16S ribosomal RNA (rRNA) genes. Our results indicated diverse communities, with sequences representing 14 different bacterial divisions. Proteobacteria, Bacteroidetes, and Planctomycetes dominated clone libraries from both restored and unimpounded sites. Multivariate analysis of the TRFLP data suggest significant site, sample date, and restoration status effects, but the exact causes of these …

Parenting As Phenotype: A Behavioral Genetic Approach To Understanding Parenting, Shirley Mcguire, Nancy Segal, S. Hershberger

Psychology

This article discusses the behavioral genetic (BG) approach to parenting. Parenting is considered a phenotype that can be influenced by nature and nurture. Genetic contributions to parenting are conceptualized as evidence of genotype–environment correlation (rGE). Early BG studies focused on demonstrating that some parenting dimensions were heritable due to passive and evocative rGE processes. Current studies are investigating moderators and mediators of genetic and environmental contributions to parenting. The paper uses parent and child report data on parental warmth from the Twins, Adoptees, Peers, and Siblings study to illustrate the BG approach. Results show that heritability is …

Comparative Analysis Of Grapevine Whole-Genome Gene Predictions, Functional Annotation, Categorization And Integration Of The Predicted Gene Sequences, Jerome Grimplet, John Van Hemert, Pablo Carbonell-Bejerano, Jose Diaz-Riquelme, Julie Dickerson, Anne Fennell Dr, Mario Pezzotti, Jose M. Martinez-Zapater

Agronomy, Horticulture and Plant Science Faculty Publications

Background: The first draft assembly and gene prediction of the grapevine genome (8X base coverage) was made available to the scientific community in 2007, and functional annotation was developed on this gene prediction. Since then additional Sanger sequences were added to the 8X sequences pool and a new version of the genomic sequence with superior base coverage (12X) was produced.
Results: In order to more efficiently annotate the function of the genes predicted in the new assembly, it is important to build on as much of the previous work as possible, by transferring 8X annotation of the genome to the …

Cell-Free Circulating Mirna Biomarkers In Cancer., Meng-Hsuan Mo, Liang Chen, Yebo Fu, Wendy Wang, Sidney W. Fu

Microbiology, Immunology, and Tropical Medicine Faculty Publications

Considerable attention and an enormous amount of resources have been dedicated to cancer biomarker discovery and validation. However, there are still a limited number of useful biomarkers available for clinical use. An ideal biomarker should be easily assayed with minimally invasive medical procedures but possess high sensitivity and specificity. Commonly used circulating biomarkers are proteins in serum, most of which require labor-intensive analysis hindered by low sensitivity in early tumor detection. Since the deregulation of microRNA (miRNA) is associated with cancer development and progression, profiling of circulating miRNAs has been used in a number of studies to identify novel minimally …

Phylogenetic Search Through Partial Tree Mixing., Kenneth Sundberg, Mark Clement, Quinn Snell, Dan Ventura, Michael Whiting, Keith Crandall

Computational Biology Institute

BACKGROUND: Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques.

RESULTS: When compared to popular phylogenetic search algorithms, better trees are found much more quickly for large data sets. These algorithms are incorporated in the PSODA application available at http://dna.cs.byu.edu/psoda

CONCLUSIONS: The use of Partial Tree Mixing …

Pomc Is Expressed In Pancreatic Alpha Cells, Samia M.M Farrara

Electronic Theses and Dissertations

Pancreatic alpha cells secrete glucagon to increase blood glucose during hypoglycemia. Currently, the mechanisms that initiate glucagon secretion are not well understood. This study investigates the expression of pro-opiomelanocortin (POMC), a potent regulator of glucagon secretion, in alpha cells.

Insulin tolerance tests in mice lacking the POMC gene showed a correlation between alpha MSH, and glucagon secretion from alpha cells (Hochgeschwender et al. 2003). Results from a previous study showed that the POMC product, melanocortin á-MSH, acts through a melanocortin receptor 4 (MC4R) at the surface of the alpha cells to trigger the release of glucagon [Angleson, unpublished data, Lumsden …

Novel Report Of Expression And Function Of Cd97 In Malignant Gliomas: Correlation With Wilms Tumor 1 Expression And Glioma Cell Invasiveness Laboratory Investigation, Archana Chidambaram, Helen L. Fillmore, Timothy E. Van Meter, Catherine I. Dumur, William C. Broaddus

Division of Research and Economic Development Faculty & Staff Publications

Object. The Wilms tumor 1 (WT1) protein—a developmentally regulated transcription factor—is aberrantly expressed in gliomas and promotes their malignant phenotype. However, little is known about the molecular allies that help it mediate its oncogenic functions in glioma cells.

Methods. The authors used short interfering RNA (siRNA) to suppress WT1 expression in glioblastoma (GBM) cells and evaluated the effect of this on GBM cell invasiveness. Gene expression analysis was then used to identify the candidate genes that were altered as a result of WT1 silencing. One candidate target, CD97, was then selected for further investigation into its role by suppressing …

Inheritance Of Humeral Spotting In The Croaking Gourami (Osphronemidae: Trichopsis Vittatus), Jack Frankel, Lisa Alder-Golden, Andre Porter

Department of Biology Faculty Publications

The croaking gourami (Trichopsis vittatus) exhibits two phenotypes associated with humeral spotting. Fish possess a prominent, dark humeral patch or spot located behind the operculum or lack this spotting pattern. Segregation patterns observed from the progenies of eleven different crosses support the hypothesis that the inheritance of humeral spotting in T. vittatus is controlled by the action of a single autosomal locus, with complete dominance of the allele controlling the spotted phenotype.

Effects Of Feeding Field Peas In Combination With Distillers Grains Plus Solubles In Finishing And Growing Diets On Cattle Performance And Carcass Characteristics, A. C. Pesta, A. H. Titlow, J. A. Hansen, A. L. Berger, S. A. Furman, Matt K. Luebbe, G. E. Erickson, K. H. Jenkins

Department of Animal Science: Faculty Publications

Two studies were conducted to evaluate field peas and wet or dry corn distillers grains with solubles (WDGS and DDGS, respectively) in finishing and growing diets. In Exp. 1, British crossbred steers (n = 352, initial BW 356 ± 27 kg) were used in a randomized block design with factors being 0 or 20% field peas and 0 or 30% WDGS in dry-rolled corn (DRC) based finishing diets (DM basis). There was an interaction (P < 0.01) for DMI and G:F. Feeding WDGS increased ADG (P < 0.01), whereas peas had no effect on ADG (P = 0.33). Including WDGS increased G:F in diets without peas (P < 0.01), but had no impact (P = 0.12) in diets containing peas. Peas increased G:F (P = 0.04) in diets without WDGS, but decreased G:F (P = 0.03) with WDGS. Feeding WDGS increased HCW (P < 0.01). In Exp. 2, Continental crossbred heifers (yr. 1; n = 108, initial BW 338 ± 14 kg) and British crossbred steers (yr. 2; n = 90, initial BW 321 ± 10 kg) were assigned randomly to 1 of 9 pastures. Treatments were supplementation with loose DDGS meal on the ground (GROUND), in a bunk (BUNK) or a 25% field peas, 75% DDGS cube on the ground (CUBE) at equal CP. Final BW and ADG were less (P < 0.01) for GROUND than for CUBE and BUNK, which were similar. These data indicate up to 50% DRC could be replaced by peas and WDGS, and peas are an acceptable binder for DDGS range cubes.

A Systematic Genetic Screen To Dissect The Microrna Pathway In Drosophila, Sigal Pressman, Catherine A. Reinke, Xiaohong Wang, Richard W. Carthew

Faculty Publications

A central goal of microRNA biology is to elucidate the genetic program of miRNA function and regulation. However, relatively few of the effectors that execute miRNA repression have been identified. Because such genes may function in many developmental processes, mutations in them are expected to be pleiotropic and thus are discarded in most standard genetic screens. Here, we describe a systematic screen designed to identify all Drosophila genes in ~40% of the genome that function in the miRNA pathway. To identify potentially pleiotropic genes, the screen analyzed clones of homozygous mutant cells in heterozygous animals. We identified 45 mutations representing …

Testing Phylogenetic Hypotheses Of The Subgenera Of The Freshwater Crayfish Genus Cambarus (Decapoda: Cambaridae)., Jesse W Breinholt, Megan L Porter, Keith A Crandall

Computational Biology Institute

BACKGROUND: The genus Cambarus is one of three most species rich crayfish genera in the Northern Hemisphere. The genus has its center of diversity in the Southern Appalachians of the United States and has been divided into 12 subgenera. Using Cambarus we test the correspondence of subgeneric designations based on morphology used in traditional crayfish taxonomy to the underlying evolutionary history for these crayfish. We further test for significant correlation and explanatory power of geographic distance, taxonomic model, and a habitat model to estimated phylogenetic distance with multiple variable regression.

METHODOLOGY/PRINCIPAL FINDINGS: We use three mitochondrial and one nuclear gene …

A Genomic Island In Salmonella Enterica Ssp. Salamae Provides New Insights On The Genealogy Of The Locus Of Enterocyte Effacement., P Scott Chandry, Simon Gladman, Sean C Moore, Torsten Seemann, Keith A Crandall, Narelle Fegan

Computational Biology Institute

The genomic island encoding the locus of enterocyte effacement (LEE) is an important virulence factor of the human pathogenic Escherichia coli. LEE typically encodes a type III secretion system (T3SS) and secreted effectors capable of forming attaching and effacing lesions. Although prominent in the pathogenic E. coli such as serotype O157:H7, LEE has also been detected in Citrobacter rodentium, E. albertii, and although not confirmed, it is likely to also be in Shigella boydii. Previous phylogenetic analysis of LEE indicated the genomic island was evolving through stepwise acquisition of various components. This study describes a new LEE region from two …