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A Generalized Approach For Testing The Association Of A Set Of Predictors With An Outcome: A Gene Based Test, Benjamin A. Goldstein, Alan E. Hubbard, Lisa F. Barcellos

U.C. Berkeley Division of Biostatistics Working Paper Series

In many analyses, one has data on one level but desires to draw inference on another level. For example, in genetic association studies, one observes units of DNA referred to as SNPs, but wants to determine whether genes that are comprised of SNPs are associated with disease. While there are some available approaches for addressing this issue, they usually involve making parametric assumptions and are not easily generalizable. A statistical test is proposed for testing the association of a set of variables with an outcome of interest. No assumptions are made about the functional form relating the variables to the …

Structuring An Efficient Organic Wheat Breeding Program, P. Stephen Baenziger, Ibrahim Salah, Richard S. Little, Dipak K. Santra, Teshome Regassa, Meng Yuan Wang

Department of Agronomy and Horticulture: Faculty Publications

Our long-term goal is to develop wheat cultivars that will improve the profitability and competitiveness of organic producers in Nebraska and the Northern Great Plains. Our approach is to select in early generations for highly heritable traits that are needed for both organic and conventional production (another breeding goal), followed by a targeted organic breeding effort with testing at two organic locations (each in a different ecological region) beginning with the F₆ generation. Yield analyses from replicated trials at two organic breeding sites and 7 conventional breeding sites from F₆ through F₁₂ nurseries revealed, using analyses of …

The Scientific Classification Of Wolves: Canis Lupus Soupus, L. David Mech

United States Geological Survey, Northern Prairie Wildlife Research Center: Publications

Gray wolf, timber wolf, red wolf, eastern wolf, brush wolf, arctic wolf, Mexican wolf, maned wolf, Ethiopian wolf, etc., etc. How many kinds of wolves are there? And what are the differences? This is a really good question, and the answer is getting more complicated all the time. Let us start by going back a few years to the way science looked at wolves more traditionally— before the days of the new field of molecular genetics. Molecular genetics examines the actual DNA of animals and tries to classify them according to genetic similarities. ...

What does all this mean in …

A Novel Correlation Networks Approach For The Identification Of Gene Targets, Kathryn Dempsey Cooper, Stephen Bonasera, Dhundy Raj Bastola, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

Correlation networks are emerging as a powerful tool for modeling temporal mechanisms within the cell. Particularly useful in examining coexpression within microarray data, studies have determined that correlation networks follow a power law degree distribution and thus manifest properties such as the existence of “hub” nodes and semicliques that potentially correspond to critical cellular structures. Difficulty lies in filtering coincidental relationships from causative structures in these large, noise-heavy networks. As such, computational expenses and algorithm availability limit accurate comparison, making it difficult to identify changes between networks. In this vein, we present our work identifying temporal relationships from microarray data …

A Retinoic Acid–Dependent Checkpoint In The Development Of Cd4+ T Cell–Mediated Immunity, Karina Pino-Lagos, Yanxia Guo, Chrysothemis Brown, Matthew P. Alexander, Raúl Elgueta, Kathryn A. Bennett, Victor De Vries, Elizabeth Nowak, Rune Blomhoff, Shanthini Sockanathan, Roshantha A. Chandraratna, Ethan Dmitrovsky, Randolph J. Noelle

Dartmouth Scholarship

It is known that vitamin A and its metabolite, retinoic acid (RA), are essential for host defense. However, the mechanisms for how RA controls inflammation are incompletely understood. The findings presented in this study show that RA signaling occurs concurrent with the development of inflammation. In models of vaccination and allogeneic graft rejection, whole body imaging reveals that RA signaling is temporally and spatially restricted to the site of inflammation. Conditional ablation of RA signaling in T cells significantly interferes with CD4⁺ T cell effector function, migration, and polarity. These findings provide a new perspective of the role of …

Genetic Variation And Inheritance Of Diapause Induction In Two Distinct Voltine Ecotypes Of Ostrinia Nubilalis (Lepidoptera: Crambidae), Cengis Ikten, Steven R. Skoda, Thomas E. Hunt, Jaime Molina-Ochoa, John E. Foster

Department of Entomology: Faculty Publications

European corn borer, Ostrinia nubilalis (Hübner) (Lepidoptera: Crambidae), displays a larval diapause in response to short photoperiods and is adapted to a variety of local conditions throughout North America. Hence, the effective photoperiod inducing larval diapause will differ among geographic ecotypes. This study considers the inheritance of photoperiodic larval diapause induction by hybridization and backcrossing two latitudinally distinct ecotypes of the European corn borer collected between 41° N, 96° W and 48° N, 96° W and under a range of photoperiods representative of their respective locations: from 14:10 to 16:8 (L:D) h. The ecotype adapted to a bivoltine habitat (southeastern …

The Genetic Basis Of Creativity And Ideational Fluency The Genetic Basis Of Creativity And Ideational Fluency, Mark A. Runco, Ernest P. Noble, Roni Reiter-Palmon, Selcuk Acar, Terry Ritchie, Justin M. Yurkovich

Psychology Faculty Publications

Reuter, Roth, Holve, & Hennig (2006) described what they called the first candidate gene for creativity. This study replicated and extended their work for a more careful analysis of five candidate genes: Dopamine Transporter (DAT), Catechol-O-Methyltransferase (COMT), Dopamine Receptor D4 (DRD4), D2 Dopamine Receptor (DRD2), and Tryptophane Hydroxylase (TPH1). Participants were 147 college students who received a battery of tests of creative potential. Multivariate analyses of variance indicated that ideational fluency scores were significantly associated with several genes (DAT, COMT, DRD4, and TPH1). This was apparent in both verbal and figural fluency ideation scores, before and after controlling general …

Help3 Directly Modulates The Expression Of Hsp70 Gene In Hela Cells Via Hat Activity, Fen Li, Jixian Ma, Yu Ma, Yanyan Hu, Shuhuan Tian, Richard E. White, Guichun Han

PCOM Scholarly Works

Human Elongator complex, which plays a key role in transcript elongation in vitro assay, is incredibly similar in either components or function to its yeast counterpart. However, there are only a few studies focusing on its target gene characterization in vivo. We studied the effect of down-regulation of the human elongation protein 3 (hELP3) on the expression of HSP70 through antisense strategy. Transfecting antisense plasmid p1107 into HeLa cells highly suppressed hELP3 expression, and substantially reduced expression of HSP70 mRNA and protein. Furthermore, chromatin immunoprecipitation assay (ChIP Assay) revealed that hElp3 participates in the transcription elongation of HSPA1A in HeLa …

Β-Lactams Interfering With Pbp1 Induce Panton-Valentine Leukocidin Expression By Triggering Sara And Rot Global Regulators Of Staphylococcus Aureus, Oana Dumitrescu, Priya Choudhury, Sandrine Boisset, Cedric Badiou, Michele Bes, Yvonne Benito, Christiane Wolz, Francois Vandenesch, Jerome Etienne, Ambrose L. Cheung

Dartmouth Scholarship

Previous articles reported that beta-lactam antibiotics increase the expression of Staphylococcus aureus Panton-Valentine leukocidin (PVL) by activating its transcription. We investigated the mechanisms underlying the inductor effect of beta-lactams on PVL expression by determining targets and regulatory pathways possibly implicated in this process. We measured PVL production in the presence of oxacillin (nonselective), imipenem (penicillin-binding protein 1 [PBP1] selective), cefotaxime (PBP2 s

Maternal Effects On Ethanol Teratogenesis In A Cross Between A/J And C57bl/6j Mice, David Gilliam, Nate Valdez, Scott Branson, Ashley Dixon, Chris Downing

SPS Faculty Publications

Genetic factors influence adverse pregnancy outcome in both humans and animal models. Animal research reveals both the maternal and fetal genetic profiles are important for determining the risk of physical birth defects and prenatal mortality. Using a reciprocal-cross breeding design, we investigated whether the mother’s genes may be more important than fetal genes in determining risk for ethanol teratogenesis. Examination of possible synergistic genetic effects on ethanol teratogenesis was made possible by using two mouse strains known to be susceptible to specific malformations. Inbred A/J (A) and C57BL/6J (B6) mice were mated to produce four fetal genotype groups: the true-bred …

Five Blood Pressure Loci Identified By An Updated Genome-Wide Linkage Scan: Meta-Analysis Of The Family Blood Pressure Program, Jeannette Simino, Gang Shi, Rezart Kume, Karen Schwander, Michael A. Province, C. Charles Gu, Sharon Kardia, Aravinda Chakravarti, Georg Ehret, Richard A. Olshen, Stephen T. Turner, Low Tone Ho, Xiaofeng Zhu, Cashell Jaquish, Dina Paltoo, Richard S. Cooper, Alan Weder, J. David Curb, Eric Boerwinkle, Steven C. Hunt, Dabeeru C. Rao

Faculty Publications

Background A preliminary genome-wide linkage analysis of blood pressure in the Family Blood Pressure Program (FBPP) was reported previously. We harnessed the power and ethnic diversity of the final pooled FBPP dataset to identify novel loci for blood pressure thereby enhancing localization of genes containing less common variants with large effects on blood pressure levels and hypertension.MethodsWe performed one overall and 4 race-specific meta-analyses of genome-wide blood pressure linkage scans using data on 4,226 African-American, 2,154 Asian, 4,229 Caucasian, and 2,435 Mexican-American participants (total N = 13,044). Variance components models were fit to measured (raw) blood pressure levels and two …

The Last Shall Be First: Human Potential In Genetic And Theological Perspectives, M. Therese Lysaught

Theology Faculty Research and Publications

The notion of “human potential” provides a fruitful window through which to explore the competing conceptual frameworks of contemporary genetics and Christianity. The contemporary cultural frame of genetics conceives of human potential in a broadly positive manner: the source of personal and societal flourishing is located within individual bodies, waiting to be identified and unleashed by genetic science and medicine for the good of persons and society. In the Judeo-Christian narrative, human individual, biological potential is far less relevant—and, in fact, may be construed as an impediment to the achievement of personal and social flourishing. Implications for the dialogue between …

Scientific Inquiry In The Genetics Laboratory: Biologists And University Science Teacher Educators Collaborating To Increase Engagements In Science Processes., Todd Campbell, P. G. Wolf, J. P. Der, E. Packenham, N. Abd-Hamid

Teacher Education and Leadership Faculty Publications

No abstract provided.