Genetics and Genomics Commons^™

Long-Term Environmental Effects Of Conifer Removal To Achieve Aspen Release In Near-Stream Areas Within The Northern Sierras, Kenneth W. Tate, Bobette Jones, Melanie Mcfarland, Tom Rickman, Al Vasquez

Aspen Bibliography

The advanced state of conifer encroachment in aspen stands in the Sierra Nevada and southern Cascades is retarding aspen regeneration, putting an estimated 70 plus percent of stands at immediate risk of extinction with a significant percentage of stands already lost.

Executive Summary The Role Of Ungulate Herbivory And Management On Ecosystem Patterns And Processes: A Problem Analysis, John G. Kie, Martin Vavra

Aspen Bibliography

No abstract provided.

National Pork Producers Council Maternal Line Genetic Evaluation: A Comparison Of Growth And Carcass Traits In Terminal Progeny, J. D. Cassady, O. W. Berg, Rodger K. Johnson, J. W. Mabry, L. L. Christian, M. D. Tokach, R. K. Miller, R. N. Goodwin

Department of Animal Science: Faculty Publications

The objective of this study was to compare growth and carcass traits of 1,252 progeny of six commercially available dam lines included in the National Pork Producers Council Maternal Line Evaluation Project. Lines compared included one maternal line supplied by each of American Diamond Swine Genetics (ADSG), Danbred NA (DB), two lines supplied by Monsanto Choice Genetics (DK and GPK347), Newsham Hybrids (NH), and Landrace × Large White females supplied by the National Swine Registry (NSR). All females were mated to DB, Duroc-Hampshire terminal sires. Traits analyzed were ADG from 56 to 115 kg live weight, days to 115 kg, …

Glycosyltransferases Encoded By Viruses, Nicolas Markine-Goriaynoff, Laurent Gillet, James L. Van Etten, Haralambos Korres, Naresh Verma, Alain Vanderplasschen

James Van Etten Publications

Studies of cellular biology in recent decades have highlighted the crucial roles of glycans in numerous important biological processes, raising the concept of glycomics that is now considered as important as genomics, transcriptomics and proteomics. For millions of years, viruses have been co-evolving with their hosts. Consequently, during this co-evolution process, viruses have acquired mechanisms to mimic, hijack or sabotage host processes that favour their replication, including mechanisms to modify the glycome. The importance of the glycome in the regulation of host–virus interactions has recently led to a new concept called ‘glycovirology’. One fascinating aspect of glycovirology is the study …

Hsp70 Promotes Tnf-Mediated Apoptosis By Binding Ikkγ And Impairing Nf-Κb Survival Signaling, Ruiqiong Ran, Aigang Lu, Lu Zhang, Yang Tang, Hongyan Zhu, Huichun Xu, Benjamin Feng, Chun Han, Guoping Zhou, Alan C. Rigby, Frank R. Sharp

Peer Reviewed Articles

The major heat shock protein, Hsp70, can protect against cell death by directly interfering with mitochondrial apoptosis pathways. However, Hsp70 also sensitizes cells to certain apoptotic stimuli like TNF. Little is known about how Hsp70 enhances apoptosis. We demonstrate here that Hsp70 promotes TNF killing by specifically binding the coiled-coil domain of IκB kinase γ (IKKγ) to inhibit IKK activity and consequently inhibit NF-κB-dependent antiapoptotic gene induction. An IKKγ mutant, which interacts with Hsp70, competitively inhibits the Hsp70–IKKγ interaction and relieves heat-mediated NF-κB suppression. Depletion of Hsp70 expression with RNA interference rescues TNF-mediated cell death. Although TNF may or may …

Computational Protein Biomarker Prediction: A Case Study For Prostate Cancer, Michael Wagner, Dayanand N. Naik, Alex Pothen, Srinivas Kasukurti, Raghu Ram Devineni, Bao-Ling Adam, O. John Semmes, George L. Wright Jr.

Mathematics & Statistics Faculty Publications

Background: Recent technological advances in mass spectrometry pose challenges in computational mathematics and statistics to process the mass spectral data into predictive models with clinical and biological significance. We discuss several classification-based approaches to finding protein biomarker candidates using protein profiles obtained via mass spectrometry, and we assess their statistical significance. Our overall goal is to implicate peaks that have a high likelihood of being biologically linked to a given disease state, and thus to narrow the search for biomarker candidates.

Results: Thorough cross-validation studies and randomization tests are performed on a prostate cancer dataset with over 300 patients, obtained …

Morphological Characteristics And Species Separation Of Hawaiian Postlarval Amphidromous Fishes, M. Eric Benbow, Albert J. Burky, Carl M. Way

Biology Faculty Publications

There are five Hawaiian amphidromous fishes (Gobiidae: Lentipes concolor, Awaous guamensis, Sicyopterus stimpsoni, Stenogobius hawaiiensis; Eleotridae: Eleotris sandwicensis). Amphidromous adults deposit eggs on the stream bottom. After hatching, larvae drift to the ocean for growth followed by postlarval migration back into the streams. Postlarvae were collected to construct a dichotomous identification key based on 12 morphological measures and ray counts from four fins. Overall, the presense of fused pelvic fins, standard length (SL), and fin ray numbers were the most useful in species separation. Gobies were separated from the eleotrid by the former having fused …

Human Genetic Variation And Health: New Assessment Approaches Based On Ethnogenetic Layering, Fatimah Linda Collier Jackson

Department of Biology Faculty Publications

Human genetic variation is often biologically relevant, particularly when it influences (or is influenced by) health outcomes. For example, human genetic variation can modulate disease aetiology as in the case ofhomozygous beta sickle gene (βS/βS or sickle cell) pathology. Conversely, health outcomes, such as the frequency and duration of homozygous sickle cell pathology, can change affected group gene frequencies by selectively targeting and culling specific genotypes in a group, such as clinically more severe βS Bantu/βS Bantu versions of the βS gene, thereby changing future patterns of genetic variation in this gene.

Demographic Estimates From Y Chromosome Microsatellite Polymorphisms: Analysis Of A Worldwide Sample, J. Michael Macpherson, Sohini Ramachandran, Lisa Diamond, Marcus W. Feldman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Polymorphisms in microsatellites on the human Y chromosome have been used to estimate important demographic parameters of human history. We compare two coalescent-based statistical methods that give estimates for a number of demographic parameters using the seven Y chromosome polymorphisms in the HGDP-CEPH Cell Line Panel, a collection of samples from 52 worldwide populations. The estimates for the time to the most recent common ancestor vary according to the method used and the assumptions about the prior distributions of model parameters, but are generally consistent with other global Y chromosome studies. We explore the sensitivity of these results to assumptions …

A Role For Tbx5 In Proepicardial Cell Migration During Cardiogenesis, Cathy J. Hatcher, Nata Diman, Minsu Kim, David Pennisi, Yan Song, Marsha M. Goldstien, Takashi Mikawa, Craig T. Basson

PCOM Scholarly Works

Transcriptional regulatory cascades during epicardial and coronary vascular development from proepicardial progenitor cells remain to be defined. We have used immunohistochemistry of human embryonic tissues to demonstrate that the TBX5 transcription factor is expressed not only in the myocardium, but also throughout the embryonic epicardium and coronary vasculature. TBX5 is not expressed in other human fetal vascular beds. Furthermore, immunohistochemical analyses of human embryonic tissues reveals that unlike their epicardial counterparts, delaminating epicardial-derived cells do not express TBX5 as they migrate through the subepicardium before undergoing epithelial-mesenchymal transformation required for coronary vasculogenesis. In the chick, Tbx5 is expressed in the …

Cd46-Mediated Transduction Of A Species D Adenovirus Vaccine Improves Mucosal Vaccine Efficacy, Zenaido T. Camacho, Mallory A. Turner, Michael A. Barry, Eric A. Weaver

Nebraska Center for Virology: Faculty Publications

The high levels of preexisting immunity against Adenovirus type 5 (Ad5) have deemed Ad5 unusable for translation as a human vaccine vector. Low seroprevalent alternative viral vectors may be less impacted by preexisting immunity, but they may also have significantly different phenotypes from that of Ad5. In this study we compare species D Ads (26, 28, and 48) to the species C Ad5. In vitro transduction studies show striking differences between the species C and D viruses. Most notably, Ad26 transduced human dendritic cells much more effectively than Ad5. In vivo imaging studies showed strikingly different transgene expression profiles. The …

Phylogenetic Analyses Of Texas Isolates Indicate An Evolving Subtype Of The Clade B Feline Immunodeficiency Viruses, Eric A. Weaver, Ellen W. Collisson, Margaret Slater, Guan Zhu

Nebraska Center for Virology: Faculty Publications

Rigorous phylogenetic analyses were used to compare the nucleotide sequences of feline immunodeficiency virus strains isolated from Texas and throughout the world. The envelope V3-V4 sequences and capsid gene of the Texas isolates formed a cluster between subtypes B and E. Statistical comparisons with other published sequences confirmed that the Texas group is a unique cluster, possibly a new subtype, arising from subtype B.

Detection Of Five Common Cftr Mutations By Rapid-Cycle Real Time Amplification Refractory Mutation System Pcr., Eugene Dempsey, David Barton, Fergus Ryan

Articles

No abstract provided.

Impaired Antigen Receptor Induced Calcium Mobilization In A Phospholipase C-Gamma1 Deficient B Cell Line., Natarajan Muthusamy, Do Joon Park, Hei-Won Rho, Sue Goo Rhee, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

B lymphocytes express phospholipase C-gamma(1) (PLC-gamma(1)) and phospholipase C-gamma(2) (PLC-gamma(2)) isozymes. However, the relative importance of these two isozymes in B cell signaling is not known. We report here the identification and analysis of a B cell line deficient in PLC-gamma(1). Mature splenic B lymphocytes and a panel of cell lines representing pre-B, immature and mature B cell stages expressed phospholipase C-gamma (PLC-gamma), but not the beta or delta isoforms of phospholipase C (PLC). While all the tested B cell lines and primary splenic B cells expressed PLC-gamma(1) and PLC-gamma(2) isozymes, the L1.2 B cell line exclusively expressed PLC-gamma(2), but …

Loss-Based Estimation With Cross-Validation: Applications To Microarray Data Analysis And Motif Finding, Sandrine Dudoit, Mark J. Van Der Laan, Sunduz Keles, Annette M. Molinaro, Sandra E. Sinisi, Siew Leng Teng

U.C. Berkeley Division of Biostatistics Working Paper Series

Current statistical inference problems in genomic data analysis involve parameter estimation for high-dimensional multivariate distributions, with typically unknown and intricate correlation patterns among variables. Addressing these inference questions satisfactorily requires: (i) an intensive and thorough search of the parameter space to generate good candidate estimators, (ii) an approach for selecting an optimal estimator among these candidates, and (iii) a method for reliably assessing the performance of the resulting estimator. We propose a unified loss-based methodology for estimator construction, selection, and performance assessment with cross-validation. In this approach, the parameter of interest is defined as the risk minimizer for a suitable …

Determination Of The Optimal Form Of A Dna Vaccine To Induce An Effective Immune Response Against A Murine B-Cell Lymphoma, Deepti Aurora

All-Inclusive List of Electronic Theses and Dissertations

Tumor vaccines are a promising alternative to chemotherapy for the treatment of cancer. To be effective and safe, a cancer vaccine should specifically target antigens expressed only on tumor cells. The B-cell tumor-derived Ig receptor may be considered a model tumor antigen for cancer vaccine development. Specifically the immunoglobulin idiotype (ld) encoded by the variable region genes (VH and VL) provides a target antigen. Promising results have been obtained in clinical studies of ld vaccination using ld proteins. However, ld protein is laborious and time-consuming to produce. Gene-based vaccines, on the other hand, are inexpensive and offer ease of manipulation …

Initial State Of The Drosophila Eye Before Dorsoventral Specification Is Equivalent To Ventral, Amit Singh, Kwang-Wook Choi

Biology Faculty Publications

Dorsoventral (DV) patterning is crucial for eye development in invertebrates and higher animals. DV lineage restriction is the primary event in undifferentiated early eye primordia of Drosophila. InDrosophila eye disc, a dorsal-specific GATA family transcription factor pannier (pnr) controls Iroquois-Complex (Iro-C) genes to establish the dorsal eye fate whereas Lobe (L), which is involved in controlling a Notch ligand Serrate (Ser), is specifically required for ventral growth. However, fate of eye disc cells before the onset of dorsal expression of pnr and Iro-C is not known. We show that L/Ser …

Comprehensive Analysis Of Class I And Class Ii Hla Antigens And Chronic Hepatitis B Virus Infection, Chloe L. Thio, David L. Thomas, Peter Karacki, Xiaojiang Gao, Darlene Marti, Richard A. Kaslow, James J. Goedert, Margaret Hilgartner, Steffanie A. Strathdee, Priya Duggal, Stephen J. O'Brien, Jacquie Astemborski, Mary Carrington

Biology Faculty Articles

Following an acute hepatitis B virus (HBV) infection, clearance or persistence is determined in part by the vigor and breadth of the host immune response. Since the human leukocyte antigen system (HLA) is an integral component of the immune response, we hypothesized that the highly polymorphic HLA genes are key determinants of viral clearance. HLA class I and II genes were molecularly typed in 194 Caucasian individuals with viral persistence and 342 matched controls who had cleared the virus. A single class I allele, A*0301 (odds ratio [OR], 0.47; 95% confidence interval [CI], 0.30 to 0.72; P = 0.0005) was …

Reconstructing The Genomic Architecture Of Mammalian Ancestors Using Multispecies Comparative Maps, William J. Murphy, Guillaume Bourque, Glenn Tesler, Pavel Pevzner, Stephen J. O'Brien

Biology Faculty Articles

Rapidly developing comparative gene maps in selected mammal species are providing an opportunity to reconstruct the genomic architecture of mammalian ancestors and study rearrangements that transformed this ancestral genome into existing mammalian genomes. Here, the recently developed Multiple Genome Rearrangement (MGR) algorithm is applied to human, mouse, cat and cattle comparative maps (with 311-470 shared markers) to impute the ancestral mammalian genome. Reconstructed ancestors consist of 70-100 conserved segments shared across the genomes that have been exchanged by rearrangement events along the ordinal lineages leading to modern species genomes. Genomic distances between species, dominated by inversions (reversals) and translocations, are …

Unification Of Variance Components And Haseman-Elston Regression For Quantitative Trait Linkage Analysis, Wei-Min Chen, Karl W. Broman, Kung-Yee Liang

Johns Hopkins University, Dept. of Biostatistics Working Papers

Two of the major approaches for linkage analysis with quantitative traits in humans include variance components and Haseman-Elston regression. Previously, these have been viewed as quite separate methods. We describe a general model, fit by use of generalized estimating equations (GEE), for which the variance components and Haseman-Elston methods (including many of the extensions to the original Haseman-Elston method) are special cases, corresponding to different choices for a working covariance matrix. We also show that the regression-based test of Sham et al.(2002) is equivalent to a robust score statistic derived from our GEE approach. These results have several important implications. …

Bioethics: Everything You Wanted To Know About Life Or Death, But Were Afraid To Ask, St Mary's University

President's Peace Commission - Programs

The President’s Peace Commission existed from 1984 to 2013 at St. Mary's University. The Commission fostered an ethical commitment to participate in the establishment of world peace and social justice.

This program is about genetic technologies, ethical issues in human and animal experimentation and physician assisted suicide.

A Nested Unsupervised Approach To Identifying Novel Molecular Subtypes, Elizabeth Garrett, Giovanni Parmigiani

Johns Hopkins University, Dept. of Biostatistics Working Papers

In classification problems arising in genomics research it is common to study populations for which a broad class assignment is known (say, normal versus diseased) and one seeks to find undiscovered subclasses within one or both of the known classes. Formally, this problem can be thought of as an unsupervised analysis nested within a supervised one. Here we take the view that the nested unsupervised analysis can successfully utilize information from the entire data set for constructing and/or selecting useful predictors. Specifically, we propose a mixture model approach to the nested unsupervised problem, where the supervised information is used to …

The Hyperthermophilic Archaeon Sulfolobus: From Exploration To Exploitation, Stan J.J. Brouns, Thijs J.G. Ettema, Kenneth M. Stedman, Jasper Walther, Hauke Smith, Ambrosius P.L. Snijders, Mark Young, Rolf Bernander, Phillip C. Wright, Betina Siebers, John Van Der Oost

Biology Faculty Publications and Presentations

In the early 1970s, Sulfolobus was first isolated by Thomas Brock and co-workers from sulfur-rich acidic hot springs in Yellowstone National Park. Sulfolobus became one of the model organisms of Archaea in general, and of Crenarchaea in particular. Many of its unusual physiological characteristics have been investigated, and several of its thermostable enzymes have been studied in considerable detail. For fundamental reasons, and because of its potential for industrial applications, Sulfolobus has been selected for a genome sequence project. The recent completion of the Sulfolobus solfataricus genome has set the stage for a series of postgenome research lines that will …

On Nancy Ordover's American Eugenics: Race, Queer Anatomy, And The Science Of Nationalism, Markus Rheindorf

Reconstruction: Studies in Contemporary Culture

[First paragraph]

Nancy Ordover's American Eugenics is a very personal book, not so much in terms of its content, but because of the convictions and a deep-felt sense of injustice that have inspired it. And while the author is straightforward in acknowledging her personal motivations, this is not to suggest that American Eugenics ever lapses into personal anecdote or polemic; far from it, the book is a serious and tightly argued attempt to grasp, in Ordover's words the resiliency of this often discredited but never dormant philosophy (xvi). In order to do this, Ordover goes on to argue in her …

Human Rights And Genetic Discrimination: Protecting Genomics' Promise For Public Health, Anita Silvers, Michael Ashley Stein

Faculty Publications

No abstract provided.

Tree-Based Multivariate Regression And Density Estimation With Right-Censored Data , Annette M. Molinaro, Sandrine Dudoit, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

We propose a unified strategy for estimator construction, selection, and performance assessment in the presence of censoring. This approach is entirely driven by the choice of a loss function for the full (uncensored) data structure and can be stated in terms of the following three main steps. (1) Define the parameter of interest as the minimizer of the expected loss, or risk, for a full data loss function chosen to represent the desired measure of performance. Map the full data loss function into an observed (censored) data loss function having the same expected value and leading to an efficient estimator …

Fisheries Research Contract Report No. 3 - Early Life History Of Abalone (Haliotis Rubra, H. Laevigata): Settlement, Survival And Early Growth. Final Report For Frdc Project 1998/306, Dr Sabine Daume

Fisheries Research Contract Reports

Australian abalone fisheries produce a high value, export-orientated products that provided 60% of the world supply in 1994 (Fleming, 2000). With wild abalone fisheries declining in countries worldwide, the interest in aquaculture products has increased substantially. The world production of abalone from aquaculture in 1999 was approximately 7,775 tonnes with only 89 tonnes (ca. 1%) being produced in Australia (Fleming, 2000). Abalone farming is expected to develop into a major industry and is a significant investment opportunity (McNamara, Victorian Aquaculture Strategy, May 1997). Future production from the numerous farms and sites either established, under construction or approved in Australia, could …

Sheep Updates 2003 - Wool, Richard Coole, Stephen Gherardi, Chris Oldham, K. Curtis, J. Stanton, Johan Greeff, Chris Oldham, Mike Hyder, Beth Pagamoni, Andrew Thompson, Tom Plaisted, Kazue Tanaka, Mike Ferguson, Darren Gordon, Andrew Peterson, Peter Sommerville

Sheep Updates

This session covers six papers from different authors:1.‘Pastures from space’ - an opportunity to increase the profitability of sheep production Richard Coole Farmer Kojonup W.A. Stephen Gherardi Chris Oldham Department of Agriculture Western Australia 2. K. Curtis Department of Agriculture WA J. Stanton Department of Agriculture WA and Curtin University 3. Is selection of ewe hogget replacement on measurement profitable? Johan Greeff Department of Agriculture of Western Australia 4. Optimising the nutrition/grazing management of ewe flocks Chris Oldham Mike Hyder Beth Paganoni Department of Agriculture of Western Australia Andrew Thompson Department of Primary Industries, Hamilton, Victoria Tom Plaisted Kazue Tanaka …

Sheep Updates 2003 - Husbandry, Paul Barrett, Kevin Bell, J Greeff, L. Butler, S. Brown, K. Hart, A. Gray, John Karlsson, Paula Coombe, Ron Mctarrart, David Scobie, Sandy White

Sheep Updates

This session covers seven papers from different authors:1. Setting up a successful, low input feedlot Paul Barrett, ‘Bimberdong’ Jerramungup 2. Effective mineral supplementation of sheep Kevin Bell, Sheep Management and Production Consultants, Kojonup, WA 3. Genetic benchmarking for WA sheep producers J. Greeff, L. Butler, S. Brown, K. Hart and A. Gray Department of Agriculture Western Australia 4. Does selecting sheep for low WEC reduce scouring? John Karlsson, Johan Greeff and Paula Coombe, Department of Agriculture Western Australia 5. Summer quarters for sheep - stubbles Ron McTaggart, Department of Agriculture Western Australia, Albany 6. Thinking about breeding Easy Care Sheep? …

Sheep Updates 2003 - Plenaries, Ashley Mercy, David Scobie, Neil Buchanan, Kevin Bell, John Milton, Graeme Martin, Bob Hall, Maurie Stephen, Rob Woodgate

Sheep Updates

This session covers eight papers from different authors:1. Biosecurity in the sheep industry will improve production and profits Ashley Mercy, Department of Agriculture, Western Australia 2. Easy care sheep David Scobie, AgResearch, PO Box 60 Lincoln, 8152, New Zealand 3. Targeting the market’s requirements - live sheep exports Neil Buchanan, Manager Animal Health Operations, Primary Industries & Resources, South Australia 4. Setting flock breeding objectives Kevin Bell, Sheep Management and Production Consultants, Kojonup WA 5. Future feeding of sheep in Western Australia John Milton and Graeme Martin, The University of Western Australia 6. Recipe for getting back into Sheep Bob …