Genetics and Genomics Commons^™

Cd5 Plays An Inhibitory Role In The Suppressive Function Of Murine Cd4+ Cd25+ TReg Cells, Trivikram Dasu, Joseph E. Qualls, Halide Tuna, Chander Raman, Donald A. Cohen, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

A subset of CD4⁺ T cells, the CD4⁺ CD25⁺ regulatory T (T_reg) cells in the lymphoid organs and peripheral blood are known to possess suppressive function. Previous in vitro and in vivo studies have indicated that T cell receptor (TCR) signal is required for development of such ‘natural regulatory (T_reg) cells’ and for activation of the effector function of CD4⁺ CD25⁺ regulatory T cells. CD5 is a cell surface molecule present on all T cells and a subtype of B lymphocytes, the B-1 cells, primarily localized to coelomic cavities, Peyer's patches, …

Gene Expression And Phenotype Response Of Drosophila Melanogaster To Selection., Kenneth W. Mcdonald

Electronic Theses and Dissertations

The evolution of phenotypic plasticity is currently a topic of paramount interest in a diverse field of sub-disciplines. Salience is placed by all fields in describing the interaction of selection and phenotypic plasticity and the consequence of this interaction more broadly on evolution. Lacking in the discussion is substantial empirical description of genotype/phenotype interactions that by definition constitute the plastic response to novel and stressful environments. Here, I present empirical observations that bring the interaction of genotype and phenotype into focus. Drosophila melanogaster populations subjected to selection for tolerance to low food or high alcohol conditions each exhibited an enhancement …

Investigation Of Gene And Protein Expression Based On Honey Bee (Apis Mellifera) Aging, Flight Experience, And Behavior, Azucena A. Benito, G. E. Mancinelli, A. Ammons, Michelle M. Elekonich

Undergraduate Research Opportunities Program (UROP)

Honeybees undergo a process of adult behavioral development, spending their first 2-3 weeks working inside the constant environment of the hive. At about 3 weeks of age workers leave the hive as foragers who gather pollen and nectar. Previous research found that bees show an enormous decline in immunity as a result of their transition from regular hive jobs to more difficult foraging activities. Foragers can be forced to go back into hive-tasks, thus becoming “reverted nurses” which may also allow a reversal of immunosenescence. Understanding how this happens could prove to be useful because if there is flexibility in …

Expression Of Thor Does Not Increase Desiccation Resistance In Drosophila Melanogaster, Robert L. Kobey, Deborah K. Hoshizaki, Allen G. Gibbs

Undergraduate Research Opportunities Program (UROP)

Using microarray analysis of Drosophila melanogaster, the Gibbs lab has identified several hundred candidate genes that may be involved in desiccation resistance. One of these genes is Thor, an important downstream target of the TOR/insulin signaling pathway. Preliminary results confirm that Thor plays a role in desiccation resistance. Further research will be needed to verify these results and understand the mechanism by which Thor increases desiccation resistance. This research will also serve as a proof-of-principle for testing microarray-derived hypotheses.

A previous microarray analysis found evidence that down-regulation of protein synthesis might be a cellular response to desiccation through the up-regulation …

Construction Of A Thif Genetic Disruption In Bacillus Subtilis, Kathleen Bradley, Christine Pybus, Ronald Yasbin, Eduardo Robleto

Undergraduate Research Opportunities Program (UROP)

The goal of our research is to determine whether the level of transcription of a gene is correlated with the level of mutation in that gene. One factor involved in the mutability of a transcribed gene is the ability of the single stranded DNA to form secondary stem loop structures (SLS), in the wake of the transcription bubble, that contain unpaired mutable bases. We are interested in correlating the levels of mutation with transcription in the thiF gene, which is predicted by bioinformatic analysis to be highly mutable. To achieve this goal, Kathleen will first construct a non-polar thiF genetic …

Constructing An Argf- Strain Of Bacillus Subtilis, Allison Faucher, Christine Pybus, Ronald E. Yasbin, Eduardo A. Robleto

Undergraduate Research Opportunities Program (UROP)

The goal of our research is to determine whether the level of transcription of a gene is correlated with the level of mutation in that gene. One factor involved in the mutability of a transcribed gene is the ability of the single stranded DNA to form secondary stem loop structures (SLS), in the wake of the transcription bubble, that contain unpaired mutable bases. We are interested in correlating the levels of mutation with transcription in the argF gene, which is predicted by bioinformatic analysis to be highly mutable. To achieve this goal, Allison will first construct a non-polar argF genetic …

The Regulation Of The Icsp Promoter Of Shigella Flexneri By The Virulence Factor Virb, Maria Castellanos, Dustin Harrison, Helen Wing

Undergraduate Research Opportunities Program (UROP)

Shigella flexneri is a pathogenic bacterium that causes severe dysentery in humans commonly known as shigellosis. Shigella encodes an outer membrane protease called IcsP. The regulation of icsP expression is under direct control of a transcriptional factor called VirB, which controls the expression of many virulence genes in Shigella. Previous work has shown through deletion analysis of the icsP promoter region that sequences as far as 1368 base pairs upstream of the transcription starting site are important for the regulation of the icsP gene by VirB. However, it is still unclear whether VirB activation requires sequences within the icsP promoter …

Genomic Foundations Of Carbon Fixation In Bacteria Living In Hot Springs, Rachel K. Skinner, Brian P. Hedlund, Jeremy A. Dodsworth

Undergraduate Research Opportunities Program (UROP)

Photosynthesis does not occur above 73°C, so organisms living above this temperature must obtain useable carbon by some other mechanism. It is generally assumed that carbon is fixed by thermophiles through the process of chemolithoautotrophy; however, primary production has never been demonstrated to occur in hot springs >73°C. We have shown that two organisms, Thermocrinis and Pyrobaculum, make up more than 90% of the cells in an 80°C Great Basin hot spring, Great Boiling Spring. We hypothesize that these organisms fix carbon in the hot spring via the reverse tricarboxylic acid (rTCA) cycle. To test this hypothesis we will: i) …

Decoding The Protein Interaction Network - An Approach Integrating Biology And Math, Ryan Huang, Lingkun Gu, Qingxi J. Shen

Undergraduate Research Opportunities Program (UROP)

The WRKY super family is known to play a major role during the plant stress response and development. My project focuses on the protein-protein interaction of an Oryzasativa (rice) transcription factor, OsWRKY71 which functions as the repressor of gibberellins signaling pathway. Previous literature revealed that OsWRKY71 can interact with itself or OsWRKY51 to form dimmers by using bimolecular fluorescence complementation (BiFC). To confirm this result, we use yeast two-hybrid system. As our data showed, OsWRKY71 seems to suppress the reporter gene expression of the conventional yeast two-hybrid system, so we use a modified yeast two-hybrid, Mating-based Split Ubiquitin System (MbSUS). …

An Evolutionary Expressed Sequence Tag Analysis Of Drosophila Spermatheca Genes, Adrianne Prokupek, Federico G. Hoffmann, Seong-Il Eyun, Etsuko N. Moriyama, Min Zhou, Lawrence G. Harshman

Papers in Genetics

This study investigates genes enriched for expression in the spermatheca, the long-term sperm storage organ (SSO) of female Drosophila. SSO genes are likely to play an important role in processes of sexual selection such as sperm competition and cryptic female choice. Although there is keen interest in the mechanisms of sexual selection at the molecular level, very little is known about the female genes that are involved. In the present study, a high proportion of genes enriched for expression in the spermatheca are evolving rapidly. Most of the rapidly evolving genes are proteases and genes of unknown function that …

Mitochondrial Genomes Reveal An Explosive Radiation Of Extinct And Extant Bears Near The Miocene-Pliocene Boundary, Johannes Krause, Tina Unger, Aline Nocon, Anna-Sapfo Malaspinas, Sergios-Orestis Kolokotronis, Mathias Stiller, Leopoldo Soibelzon, Helen Spriggs, Paul H. Dear, Adrian W. Briggs, Sarah C. E. Bray, Stephen J. O'Brien, Gernot Rabeder, Paul Matheus, Alan Cooper, Montgomery Slatkin, Svante Paabo, Michael Hofreiter

Biology Faculty Articles

Background: Despite being one of the most studied families within the Carnivora, the phylogenetic relationships among the members of the bear family (Ursidae) have long remained unclear. Widely divergent topologies have been suggested based on various data sets and methods.

Results: We present a fully resolved phylogeny for ursids based on ten complete mitochondrial genome sequences from all eight living and two recently extinct bear species, the European cave bear (Ursus spelaeus) and the American giant short-faced bear (Arctodus simus). The mitogenomic data yield a well-resolved topology for ursids, with the sloth bear at the basal …

Computational Design Of Orthogonal Ribosomes, Lon Chubiz, Christopher Rao

Biology Department Faculty Works

Orthogonal ribosomes (o-ribosomes), also known as specialized ribosomes, are able to selectively translate mRNA not recognized by host ribosomes. As a result, they are powerful tools for investigating translational regulation and probing ribosome structure. To date, efforts directed towards engineering o-ribosomes have involved random mutagenesisbased approaches. As an alternative, we present here a computational method for rationally designing o-ribosomes in bacteria. Working under the assumption that base-pair interactions between the 16S rRNA and mRNA serve as the primary mode for ribosome binding and translational initiation, the algorithm enumerates all possible extended recognition sequences for 16S rRNA and then chooses those …

African Genetic Diversity: Implications For Human Demographic History, Modern Human Origins, And Complex Disease Mapping, Michael Campbell, Sarah Tishkoff

Department of Biology Faculty Publications

Comparative studies of ethnically diverse human populations, particularly in Africa, are important for reconstructing human evolutionary history and for understanding the genetic basis of phenotypic adaptation and complex disease. African populations are characterized by greater levels of genetic diversity, extensive population substructure, and less linkage disequilibrium (LD) among loci compared to non-African populations. Africans also possess a number of genetic adaptations that have evolved in response to diverse climates and diets, as well as exposure to infectious disease. This review summarizes patterns and the evolutionary origins of genetic diversity present in African populations, as well as their implications for the …

Promoter Library Designed For Fine-Tuned Gene Expression In Pichia Pastoris, Franz S. Hartner, Claudia Ruth, David Langenegger, Sabrina N. Johnson, Petr Hyka, Geoff P. Lin-Cereghino, Joan Lin-Cereghino, Karin Kovar, James Cregg, Anton Glieder

College of the Pacific Faculty Articles

Although frequently used as protein production host, there is only a limited set of promoters available to drive the expression of recombinant proteins in Pichia pastoris. Fine-tuning of gene expression is often needed to maximize product yield and quality. However, for efficient knowledge-based engineering, a better understanding of promoter function is indispensable. Consequently, we created a promoter library by deletion and duplication of putative transcription factor-binding sites within the AOX1 promoter (P_AOX1) sequence. This first library initially spanned an activity range between ∼6% and >160% of the wild-type promoter activity. After characterization of the promoter library employing …

Corn Distillers Dried Grains (Ddgs) For Growing-Finishing Swine, Phillip S. Miller

Department of Animal Science: Faculty Publications

Two-hundred and forty pigs growing-finishing pigs were used to evaluate the feeding value of distillers dried grains with solubles (DDGS). Treatments consisted of 0, 5, 10 and 15% dietary DDGS inclusion. Treatments did not affect average daily gain (ADG), average daily feed intake (ADFI) or gain:feed (G:F) during the grower 1 period (P > 0.05). During the grower 2 period ADG and ADFI linearly decreased as DDGS increased (P < 0.05). No differences among treatments were detected throughout the feeding phase finisher 1 for ADG, ADFI, and G:F (P > 0.05). During the finisher 2 feeding phase, there was a linear reduction in ADG and ADFI in response to dietary DDGS inclusion (P = 0.01). Overall, linear reductions …

Sheep Updates 2008 - Part 3, L. J. E. Karlsson, J. C. Greeff, L. Slocombe, K. Jones, N. Underwood, Fred Wilkinson, W. D. Hoffman, W. A. Mckiernan, V. H. Oddy, M. J. Mcphee, B. L. Mcintyre, P. F. Parnell, R. A. Clark, J. Timms, G. Griffith, C. Mulholland, P. Hyland, Danielle England, Fiona Jones, John Lucey, Martin Staines, Richard Morris, Megan Abrahams, Caroline Peek, Dennis Van Gool, Daniel Gardiner, Kari-Lee Falconer, Sandra Prosser, Mario D'Antuono, John Young, Andrew Thompson, Chris Oldham, Brown Besier, Angus Campbell, Ralph Behrendt

Sheep Updates

This session covers fiveteen papers from different authors:

CONTROLLING FLY STRIKE

1. Breeding for Blowfly Resistance - Indicatoe Traits, LJE Karlsson, JC Greeff, L Slocombe, Department of Agriculture & Food, Western Australia

2.A practical method to select for breech strike resistance in non-pedigreed Merino flocks, LJE Karlsson, JC Greeff, L Slocombe, K. Jones, N. Underwood, Department of Agriculture & Food, Western Australia

3. Twice a year shearing - no mulesing, Fred Wilkinson, Producer, Brookton WA

BEEF

4. Commercial testing of a new tool for prediction of fatness in beef cattle, WD Hoffman^A, WA McKiernan^A, VH Oddy …

Estimation And Testing For The Effect Of A Genetic Pathway On A Disease Outcome Using Logistic Kernel Machine Regression Via Logistic Mixed Models, Dawei Liu, Debashis Ghosh, Xihong Lin

Harvard University Biostatistics Working Paper Series

No abstract provided.

A Powerful And Flexible Multilocus Association Test For Quantitative Traits, Lydia Coulter Kwee, Dawei Liu, Xihong Lin, Debashis Ghosh, Michael P. Epstein

Harvard University Biostatistics Working Paper Series

No abstract provided.

Model-Based Clustering Of Methylation Array Data: A Recursive-Partitioning Algorithm For High-Dimensional Data Arising As A Mixture Of Beta Distributions, E. Andres Houseman, Brock C. Christensen, Ru-Fang Yeh, Carmen J. Marsit, Margaret R. Karagas, Margaret Wrensch, Heather H. Nelson, Joseph Wiemels, Shichun Zheng, John K. Wiencke, Karl T. Kelsey

Harvard University Biostatistics Working Paper Series

No abstract provided.

Comparison Of Dna Pyrosequencing With Alternative Methods For Identification Of Mycobacteria, Loree C. Heller, Michael Jones, Ray H. Widen

Bioelectrics Publications

Identification of mycobacterial clinical isolates by pyrosequencing within the hypervariable A region of the 16S rRNA gene was compared to other identification methods. For >90% of isolates, these identifications correlated to the level of complex or species. For identification of many mycobacteria, pyrosequencing offers an inexpensive alternative to traditional sequencing.

Transmembrane Domain Length Of Viral K+ Channels Is A Signal For Mitochondria Targeting, Jorg Balss, Panagiotis Papatheodorou, Mario Mehmel, Dirk Baumeister, Brigitte Hertel, Nicolas Delaroque, Frank C. Chatelain, Daniel L. Minor Jr., James L. Van Etten, Joachim Rassow, Anna Moroni, Gerhard Thiel

James Van Etten Publications

K⁺ channels operate in the plasma membrane and in membranes of organelles including mitochondria. The mechanisms and topogenic information for their differential synthesis and targeting is unknown. This article describes 2 similar viral K⁺ channels that are differentially sorted; one protein (Kesv) is imported by the Tom complex into the mitochondria, the other (Kcv) to the plasma membrane. By creating chimeras we discovered that mitochondrial sorting of Kesv depends on a hierarchical combination of N- and C-terminal signals. Crucial is the length of the second transmembrane domain; extending its C terminus by >2 hydrophobic amino acids redirects Kesv …

Sequences, Annotation And Single Nucleotide Polymorphism Of The Major Histocompatibility Complex In The Domestic Cat, Naoya Yuhki, James C. Mullikin, Thomas W. Beck, Robert M. Stephens, Stephen J. O'Brien

Biology Faculty Articles

Two sequences of major histocompatibility complex (MHC) regions in the domestic cat, 2.976 and 0.362 Mbps, which were separated by an ancient chromosome break (55–80 MYA) and followed by a chromosomal inversion were annotated in detail. Gene annotation of this MHC was completed and identified 183 possible coding regions, 147 human homologues, possible functional genes and 36 pseudo/unidentified genes) by GENSCAN and BLASTN, BLASTP RepeatMasker programs. The first region spans 2.976 Mbp sequence, which encodes six classical class II antigens (three DRA and three DRB antigens) lacking the functional DP, DQ regions, nine antigen processing molecules (DOA/DOB, DMA/DMB, TAPASIN, and …

Oxidative Stress-Mediated Anticancer Activity Of Novel Ahr Modulators Af & 5f203, Lancelot S. Mclean

Loma Linda University Electronic Theses, Dissertations & Projects

Estrogen receptor positive (ER+) breast cancer tends to respond to anti-estrogen agents such as Tamoxifen. Approximately 40% of ER+ breast cancer is resistant to these agents and those that initially respond often acquire resistance. Estrogen receptor negative (ER-) breast cancer remains largely unresponsive to these agents. It is therefore vital to discover drugs that are potent in both forms of breast cancer. Aminoflavone, (5-amino-2, 3-fluorophenyl)-6,8-difluoro-7-methyl-4H-l-benzopyran-4-one; AF; NSC 686288) and 5F203, (2-[-Amino-3-methy phenyl]-5-flurobenzothiazole) are novel anticancer candidate agents that display potent in vitro and in vivo anti-proliferative activity against select human tumor cells with a unique anticancer activity profile in the …

Novel Binding Domains Mediate Binding Of Hpv 16 E6 To Fadd And Procaspase 8, Sandy S. Tungteakkhun

Loma Linda University Electronic Theses, Dissertations & Projects

To evade the host response to infection, viruses have developed means to survive and propagate. HPV 16, a causative agent of cervical cancer and of some cases of oropharyngeal cancers, is one example. We have reported that the early viral protein E6 binds to proteins necessary for propagation of the apoptotic signal following receptor/ligand interactions, such as those mediated by FADD DED and procaspase 8 DED. E6 expression leads to the dose-dependent accelerated degradation of FADD and the protection of E6-expressing cells from Fas-induced apoptosis. Surprisingly, the splice isoforms of E6, E6_large and E6*, affect the stability of procaspase …

Mechanisms Of T Helper Cell Modulation In A Simulated Space Radiation Environment, Asma Rizvi

Loma Linda University Electronic Theses, Dissertations & Projects

Exposure to solar particle events (SPEs) poses the most serious threat to astronaut health. Due to this radiation environment, exploration of the solar system beyond Earth’s orbit entails many risks for the crew on these deep space missions. Depression or dysfunction of the immune system is a major concern due to its high radio-sensitivity; potential consequences include overwhelming infection, development of cancer, fibrosis, and poor wound healing. Astronauts are also exposed to low dose/low dose rate (LDR) radiation. A three month stay at the international space station exposes them to ~ 0.05 Gy of radiation.

C57BL/6 mice received LDR gamma-radiation …

Novel Candidate Genes Identified In The Brain During Nociception In Common Carp (Cyprinus Carpio) And Rainbow Trout (Oncorhynchus Mykiss), Siobhan C. Reilly, John P. Quinn, Andrew R. Cossins, Lynne U. Sneddon

Veterinary Science and Medicine Collection

Recent studies have demonstrated that teleost fish possess nociceptors that detect potentially painful stimuli and that the physiological properties of these fibres are markedly similar to those found in mammals. This finding led to suggestions of possible pain perception in fish, contrary to the view that the sensory response in these animals is limited to the spinal cord and hindbrain and as such is reflexive. Therefore, the aim of this study was to determine if the brain is active at the molecular level by using a microarray analysis of gene expression in the forebrain, midbrain and hindbrain of two fish …

Genomic Imprinting Of Igf2 In Marsupials Is Methylation Dependent, Betty R. Lawton, Benjamin R. Carone, Craig J. Obergfell, Gianni C. Ferreri, Christina M. Gondolphi, John L. Vandeberg, Ikhide Imumorin, Rachel J. O'Neill, Michael J. O'Neill

College of Science & Mathematics Departmental Research

Background-: Parent-specific methylation of specific CpG residues is critical to imprinting in eutherian mammals, but its importance to imprinting in marsupials and, thus, the evolutionary origins of the imprinting mechanism have been the subject of controversy. This has been particularly true for the imprinted Insulin-like Growth Factor II (IGF2), a key regulator of embryonic growth in vertebrates and a focal point of the selective forces leading to genomic imprinting. The presence of the essential imprinting effector, DNMT3L, in marsupial genomes and the demonstration of a differentially methylated region (DMR) in the retrotransposon-derived imprinted gene, PEG10, in tammar wallaby argue …

The Complete Plastid Genome Sequence Of Welwitschia Mirabilis: An Unusually Compact Plastome With Accelerated Divergence Rates, Skip R. Mccoy, Jennifer V. Kuehl, Jeffrey L. Boore, Linda A. Raubeson

All Faculty Scholarship for the College of the Sciences

Background

Welwitschia mirabilis is the only extant member of the family Welwitschiaceae, one of three lineages of gnetophytes, an enigmatic group of gymnosperms variously allied with flowering plants or conifers. Limited sequence data and rapid divergence rates have precluded consensus on the evolutionary placement of gnetophytes based on molecular characters. Here we report on the first complete gnetophyte chloroplast genome sequence, from Welwitschia mirabilis, as well as analyses on divergence rates of protein-coding genes, comparisons of gene content and order, and phylogenetic implications.

Results

The chloroplast genome of Welwitschia mirabilis [GenBank: EU342371] is comprised of 119,726 base pairs and exhibits …

Dna Methylation And Promoter Sequence Analysis Of Colon Cancer Genes, Fang Wang

All Theses

Aberrant DNA methylation in the genome is associated with human cancers. Tumor cells can undergo an overall loss of DNA methylation in non-coding repetitive regions (including the Alu elements) and at the same time maintain hypermethylation in the CpG islands in promoter region of multiple genes. We are interested in understanding the pattern of DNA methylation in the promoters of genes that may mediate the tumor genesis in colon cells. Recent literature survey suggested that about two dozens of genes, when mutated or undergone changes in DNA methylation, can directly promote the development of colon cancers. We downloaded the promoter …

Marketing Of Forest Reproductive Material: The Use Of Microsatellites For Identification Of Registered Tree Clones In Finland, Leena Koviuranta, Kari Leinonen, Pertti Pulkkinen

Aspen Bibliography

According to the current legislation on the marketing of forest reproductive material, tree clones marketed in the EU must have certain traits which make them identifiable, and these traits must have been accepted and registered by an official body. Due to this obligation, there is a need for reliable, functional and practicable methods for specifying these distinctive characters. We have developed a clone identification method for European and hybrid aspens and curly birch, based on nuclear microsatellites, which can be used for determining the distinctive characters mentioned in the directive. For aspens, we have used 18 loci, of which nine …