Genetics and Genomics Commons^™

Judging Genes: Implications Of The Second Generation Of Genetic Tests In The Courtroom, Diane E. Hoffmann, Karen H. Rothenberg

Faculty Scholarship

The use of DNA tests for identification has revolutionized court proceedings in criminal and paternity cases. Now, requests by litigants to admit or compel a second generation of genetic tests – tests to confirm or predict genetic diseases and conditions – threaten to affect judicial decision-making in many more contexts. Unlike DNA tests for identification, these second generation tests may provide highly personal health and behavioral information about individuals and their relatives and will pose new challenges for trial court judges. This article reports on an original empirical study of how judges analyze these requests and uses the study results …

Mutations Affecting A Putative Mutla Endonuclease Motif Impact Multiple Dna Mismatch Repair Functions, Naz Erdeniz, Megan Nguyen, Suzanne M. Deschênes, R. Michael Liskay

Biology Faculty Publications

Mutations in DNA mismatch repair (MMR) lead to increased mutation rates and higher recombination between similar, but not identical sequences, as well as resistance to certain DNA methylating agents. Recently, a component of human MMR machinery, MutLα, has been shown to display a latent endonuclease activity. The endonuclease active site appears to include a conserved motif, DQHA(X)₂E(X)₄E, within the COOH-terminus of human PMS2. Substitution of the glutamic acid residue (E705) abolished the endonuclease activity and mismatch-dependent excision in vitro. Previously, we showed that the PMS2-E705K mutation and the corresponding mutation in Saccharomyces cerevisiae were …

Fully Codon-Optimized Luciferase Uncovers Novel Temperature Characteristics Of The Neurospora Clock, Van D. Gooch, Arun Mehra, Luis F. Larrondo, Julie Fox, Melissa Touroutoutoudis, Jennifer J. Loros, Jay C. Dunlap

Dartmouth Scholarship

We report the complete reconstruction of the firefly luciferase gene, fully codon optimized for expression in Neurospora crassa. This reporter enhances light output by approximately 4 log orders over that with previously available versions, now producing light that is visible to the naked eye and sufficient for monitoring the activities of many poorly expressed genes. Time lapse photography of strains growing in race tubes, in which the frq or eas/ccg-2 promoter is used to drive luciferase, shows the highest levels of luciferase activity near the growth front and newly formed conidial bands. Further, we have established a sorbose medium colony …

Chloroplast Comparative Genomics: Implications For Phylogeny, Evolution, And Biotechnology, Christopher Saski

All Dissertations

Lack of complete chloroplast genome sequences is still a limiting factor determining phylogenetic relationships, discerning evolutionary forces, and extending chloroplast genetic engineering to useful crops. Therefore, the chloroplast genomes from six economically important crops were isolated and sequenced. The results will have an impact on chloroplast biology and biotechnology.
The complete soybean chloroplast genome was compared to the other completely sequenced legumes, Lotus and Medicago. The rpl22 gene was found to be missing from all three legumes, a very informative phylogenetic marker. There is a single, large inversion changing the gene order in the legumes from the typical order found …

Functional Characterization Of Ectodysplasin-1 And Identification Of Novel Candidate Genes For Ectodermal Dysplasias And Associated Clinical Features, Bradley Griggs

All Dissertations

Ectodermal dysplasias (ED) are a group of developmental disorders in which ectodermally derived structures are abnormally formed or absent entirely. The molecular signaling pathway controlling the differentiation of ectodermal appendages has been well documented in recent years. However, questions remain concerning the key signaling molecule of this pathway, ectodysplasin-1 (EDA), the identity of the EDA signaling pathway's target genes, and the presence of additional phenotypes observed in some patients.
Despite the intensive study of EDA in recent years, the functional significance of the N-terminal intracellular domain of ectodysplasin-1 (N-EDA) has remained elusive. The yeast two-hybrid system was employed to further …

Functional Genomics Of The Angiotensin Ii Type 2 Receptor In The Developing Brain, Traci Pawlowski

All Dissertations

The mammalian brain expresses two angiotensin II specific receptors, the angiotensin II type 1 (AGTR1) and type 2 (AGTR2). Studies in humans and mice indicate a possible role for AGTR2 in learning, memory and behavior. However, AGTR2 gene function in the brain, and the molecular mechanisms by which AGTR2 exerts its physiological action, remains elusive. This study examines the possible role of AGTR2 in the developing brain and in brain function by employing three different approaches.
To identify genes in the developing brain that depend on AGTR2 function, a microarray analysis was conducted that compared the gene expression of Agtr2-/y …

Australian Temperate Strawberry Breeding Program (Albany Western Australia) Screening Of Advance And New Selections For Albany Western Australia - 2006/2007, Shane Trainer, Dennis Phillips, Hal

Horticulture research reports

Fourteen intermediate day neutral selections from the Australian temperate breeding program were compared in a June trial planting on a commercial property in the Albany region. Intermediate selections were derived from crosses made between 1999 and 2002. Three advanced 'short day' selections were compared for yield, both as trial plots (10 plants) and as large plot demonstrations of up to 500 plants. Accompanying these selections, six named day neutral, three short day and four Queensland cultivars of different runner origins were compared. Camarosa, Selva and Diamante were included as commercial controls.

Day neutral selections 02-083-24 and 02-83-311 were potentially superior …

Sheep Updates 2007 - Part 5, Bindi Murray, John Karlsson, Johan Greeff, Carolina Viñoles Gil, B. L. Paganoni, K. M. M. Glover, J. T. B. Milton, G. B. Martin, Hugh Dove, Bill Mckiernan, John Wilkins, Paul Greenwood, Linda Cafe

Sheep Updates

This session covers six papers from different authors:

GENETIC IMPROVEMENT

1. Breech Strike Resistance: Selecting for resistance traits reduces breech strike, Bindi Murray, John Karlsson, Johan Greeff, Department of Agriculture and Food, Western Australia

2. Breeding Merino Sheep for Worm Resistance increases profit in a Mediterranean Environment, John Karlsson and Johan Greeff Department of Agriculture and Food, Western Australia

FEEDING

3. Embryo lasses were not increased when Merino ewes that had lost weight were supplemented with lupins, C. Viñoles Gil, B.L. Paganoni, K.M.M. Glover, J.T.B. Milton & G.B. Martin, School of Animal Biology, Faculty of Natural and Agricultural Sciences, …

Sheep Updates 2007 - Part 2, Ian Mcfarland, Catherine Stockman, Anne Barnes, David Pethick, Jenny Davis, Brett Thompson, Ron Leng, Sally Pieruzzini, Elizabeth Jackson, Mohammed Quaddus, Nazrul Islam, John Stanton, Melanie Dowling

Sheep Updates

This session covers six papers from different authors:

CONCURRENT SESSIONS

FINISHING LAMB AND BEEF

1. Precision Feedlot Lamb, Ian McFarland, Department of Agriculture and Food, Western Australia

2. Feeding sheep under high heat load did not decrease intake of feedlot rations, Catherine Stockman, Department of Agriculture and Food, Western Australia & Murdoch University, Anne Barnes, Murdoch University David Pethick, Murdoch University

3. Taking the stress out of fifishing lambs and cattle - EasyFeed solutions, Jenny Davis, Brett Thomson, Milne AgriGroup, Welshpool WA, Ron Leng, Emeritus Professor, University of New England, Armidale, NSW

WOOL

4. DAFWA …

Assessment Of A Cgh-Based Genetic Instability, David A. Engler, Yiping Shen, J F. Gusella, Rebecca A. Betensky

Harvard University Biostatistics Working Paper Series

No abstract provided.

Survival Analysis With Large Dimensional Covariates: An Application In Microarray Studies, David A. Engler, Yi Li

Harvard University Biostatistics Working Paper Series

Use of microarray technology often leads to high-dimensional and low- sample size data settings. Over the past several years, a variety of novel approaches have been proposed for variable selection in this context. However, only a small number of these have been adapted for time-to-event data where censoring is present. Among standard variable selection methods shown both to have good predictive accuracy and to be computationally efficient is the elastic net penalization approach. In this paper, adaptation of the elastic net approach is presented for variable selection both under the Cox proportional hazards model and under an accelerated failure time …

Comparative Functional Analysis Of Aquaporins/Glyceroporins In Mammals And Anurans, Carissa M. Krane, David L. Goldstein

Biology Faculty Publications

Maintenance of fluid homeostasis is critical to establishing and maintaining normal physiology. The landmark discovery of membrane water channels (aquaporins; AQPs) ushered in a new area in osmoregulatory biology that has drawn from and contributed to diverse branches of biology, from molecular biology and genomics to systems biology and evolution, and from microbial and plant biology to animal and translational physiology. As a result, the study of AQPs provides a unique and integrated backdrop for exploring the relationships between genes and genome systems, the regulation of gene expression, and the physiologic consequences of genetic variation. The wide species distribution of …

A Genome-Wide Association Study Of Type 2 Diabetes In Finns Detects Multiple Susceptibility Variants, Laura J. Scott, Karen L. Mohlke, Lori L. Bonnycastle, Cristen J. Willer, Randall J. Pruim

University Faculty Publications and Creative Works

Identifying the genetic variants that increase the risk of type 2 diabetes (T2D) in humans has been a formidable challenge. Adopting a genome-wide association strategy, we genotyped 1161 Finnish T2D cases and 1174 Finnish normal glucose-tolerant (NGT) controls with >315,000 single-nucleotide polymorphisms (SNPs) and imputed genotypes for an additional >2 million autosomal SNPs. We carried out association analysis with these SNPs to identify genetic variants that predispose to T2D, compared our T2D association results with the results of two similar studies, and genotyped 80 SNPs in an additional 1215 Finnish T2D cases and 1258 Finnish NGT controls. We identify T2D-associated …

Coordinated Regulation Of Myc Trans-Activation Targets By Polycomb And The Trithorax Group Protein Ash1, Julie M. Goodliffe, Michael D. Cole, Eric Wieschaus

Dartmouth Scholarship

The Myc oncoprotein is a transcriptional regulator whose function is essential for normal development. Myc is capable of binding to 10% of the mammalian genome, and it is unclear how a developing embryo controls the DNA binding of its abundant Myc proteins in order to avoid Myc's potential for inducing tumorigenesis.To identify chromatin binding proteins with a potential role in controlling Myc activity, we established a genetic assay for dMyc activity in Drosophila. We conducted a genome-wide screen using this assay, and identified the Trithorax Group protein Ash1 as a modifier of dMyc activity. Ash1 is a histone methyltransferase known …

The E705k Mutation In Hpms2 Exerts Recessive, Not Dominant, Effects On Mismatch Repair, Suzanne M. Deschênes, Guy Tomer, Megan Nguyen, Naz Erdeniz, Nicole C. Juba, Natalia Sepúlveda, Jenna E. Pisani, R. Michael Liskay

Biology Faculty Publications

The hPMS2 mutation E705K is associated with Turcot syndrome. To elucidate the pathogenesis of hPMS2-E705K, we modeled this mutation in yeast and characterized its expression and effects on mutation avoidance in mammalian cells. We found that while hPMS2-E705K (pms1-E738K in yeast) did not significantly affect hPMS2 (Pms1p in yeast) stability or interaction with MLH1, it could not complement the mutator phenotype in MMR-deficient mouse or yeast cells. Furthermore, hPMS2-E705K/pms1-E738K inhibited MMR in wild-type (WT) mammalian cell extracts or yeast cells only when present in excess amounts relative to WT PMS2. Our results strongly suggest that hPMS2-E705K is a …

A Simple And Improved Pcr-Based Technique For White-Tailed Deer (Odocoileus Virginianus) Sex Identification, Alec R. Lindsay Ph. D., Jerrold L. Belant

Faculty Works

We describe a simple single-reaction technique for identifying the sex of white-tailed deer (Odocoileus virginianus) based on the PCR amplification of a zinc-finger intron using one pair of primers. Although Sry-coamplification confirmed sex identities, use of the Sry marker was unnecessary due to dimorphic alleles on the X and Y chromosomes at the zinc-finger locus. Insertions in intron 7 of the Y-linked allele (417 bp) make it nearly twice as long as the X-linked allele (236 bp) and thus the amplification products are easily discernable by simple agarose gel electrophoresis. The relatively short size of these products makes them useful …

Single-Stranded Dna-Binding Proteins Regulate The Abundance Of Lim Domain And Lim Domain-Binding Proteins, Zhixiong Xu, Xianzhang Meng, Ying Cai, Hong Liang, Lalitha Nagarajan, Stephen J Brandt

Faculty, Staff and Student Publications

The LIM domain-binding protein Ldb1 is an essential cofactor of LIM-homeodomain (LIM-HD) and LIM-only (LMO) proteins in development. The stoichiometry of Ldb1, LIM-HD, and LMO proteins is tightly controlled in the cell and is likely a critical determinant of their biological actions. Single-stranded DNA-binding proteins (SSBPs) were recently shown to interact with Ldb1 and are also important in developmental programs. We establish here that two mammalian SSBPs, SSBP2 and SSBP3, contribute to an erythroid DNA-binding complex that contains the transcription factors Tal1 and GATA-1, the LIM domain protein Lmo2, and Ldb1 and binds a bipartite E-box-GATA DNA sequence motif. In …

Shark Bay Prawn And Scallop Fisheries. Draft Review Report, Department Of Fisheries Western Australia

Fisheries Management Papers

In recent times, the Department of Fisheries has received representations from both sectors about the ongoing interaction of the fisheries and their respective management settings. As a result, a decision was made to comprehensively review the fisheries, taking into account matters of fishery sustainability and gear interactions, together with industry economics and market considerations. The review has also addressed research requirements to ensure an appropriate scientific basis for decision-making into the future.

Statistical Evaluation Of Evidence For Clonal Allelic Alterations In Array-Cgh Experiments, Colin B. Begg, Kevin Eng, Adam Olshen, E S. Venkatraman

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

In recent years numerous investigators have conducted genetic studies of pairs of tumor specimens from the same patient to determine whether the tumors share a clonal origin. These studies have the potential to be of considerable clinical significance, especially in clinical settings where the distinction of a new primary cancer and metastatic spread of a previous cancer would lead to radically different indications for treatment. Studies of clonality have typically involved comparison of the patterns of somatic mutations in the tumors at candidate genetic loci to see if the patterns are sufficiently similar to indicate a clonal origin. More recently, …

Sequential Quantitative Trait Locus Mapping In Experimental Crosses, Jaya M. Satagopan, Saunak Sen, Gary A. Churchill

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

The etiology of complex diseases is heterogeneous. The presence of risk alleles in one or more genetic loci affects the function of a variety of intermediate biological pathways, resulting in the overt expression of disease. Hence, there is an increasing focus on identifying the genetic basis of disease by sytematically studying phenotypic traits pertaining to the underlying biological functions. In this paper we focus on identifying genetic loci linked to quantitative phenotypic traits in experimental crosses. Such genetic mapping methods often use a one stage design by genotyping all the markers of interest on the available subjects. A genome scan …

Improved Performance Of Marron Using Genetic And Pond On Using Genetic And Pond Management Strategies, Craig Lawrence Dr

Fisheries Research Contract Reports

Marron (Cherax tenuimanus) are the highest valued freshwater crayfish farmed in Australia. This project addressed the need to increase the profitability of commercial marron farms by improving growth rates and pond management strategies.

The Carnegie Protein Trap Library: A Versatile Tool For Drosophila Developmental Studies, Anna Allen

Department of Biology Faculty Publications

Metazoan physiology depends on intricate patterns of gene expression that remain poorly known. Using transposon mutagenesis in Drosophila, we constructed a library of 7404 protein trap and enhancer trap lines, the Carnegie collection, to facilitate gene expression mapping at single-cell resolution. By sequencing the genomic insertion sites, determining splicing patterns downstream of the enhanced green fluorescent protein (EGFP) exon, and analyzing expression patterns in the ovary and salivary gland, we found that 600-900 different genes are trapped in our collection. A core set of 244 lines trapped different identifiable protein isoforms, while insertions likely to act as GFP-enhancer traps were …

Multiple Diseases In Carrier Probability Estimation: Accounting For Surviving All Cancers Other Than Breast And Ovary In Brcapro, Hormuzd A. Katki, Amanda Blackford, Sining Chen, Giovanni Parmigiani

Johns Hopkins University, Dept. of Biostatistics Working Papers

Mendelian models can predict who carries an inherited deleterious mutation of known disease genes based on family history. For example, the BRCAPRO model is commonly used to identify families who carry mutations of BRCA1 and BRCA2, based on familial breast and ovarian cancers. These models incorporate the age of diagnosis of diseases in relatives and current age or age of death. We develop a rigorous foundation for handling multiple diseases with censoring. We prove that any disease unrelated to mutations can be excluded from the model, unless it is sufficiently common and dependent on a mutation-related disease time. Furthermore, if …

Power Boosting In Genome-Wide Studies Via Methods For Multivariate Outcomes, Mary J. Emond

UW Biostatistics Working Paper Series

Whole-genome studies are becoming a mainstay of biomedical research. Examples include expression array experiments, comparative genomic hybridization analyses and large case-control studies for detecting polymorphism/disease associations. The tactic of applying a regression model to every locus to obtain test statistics is useful in such studies. However, this approach ignores potential correlation structure in the data that could be used to gain power, particularly when a Bonferroni correction is applied to adjust for multiple testing. In this article, we propose using regression techniques for misspecified multivariate outcomes to increase statistical power over independence-based modeling at each locus. Even when the outcome …

Optimization Of Cutaneous Electrically Mediated Plasmid Dna Delivery Using Novel Electrode, L. C. Heller, M. J. Jaroszeski, D. Coppola, A. N. Mccray, J. Hickey, R. Heller

Bioelectrics Publications

The easy accessibility of skin makes it an excellent target for gene transfer protocols. To take advantage of skin as a target for gene transfer, it is important to establish an efficient and reproducible delivery system. Electroporation is an established technique for enhancing plasmid delivery to many tissues in vivo. A critical component of this technique is the electrode configuration. Electroporation parameters were optimized for transgene expression with minimal tissue damage with a novel electrode. The highest transgene expression and efficiency of individual cell transformation with minimal damage was produced with eight 150 ms pulses at field strength of …

The Yeast Orthologue Of Grasp65 Forms A Complex With A Coiled-Coil Protein That Contributes To Er To Golgi Traffic, Rudy Behnia, Francis A. Barr, John J. Flanagan, Charles Barlowe, Sean Munro

Dartmouth Scholarship

The mammalian Golgi protein GRASP65 is required in assays that reconstitute cisternal stacking and vesicle tethering. Attached to membranes by an N-terminal myristoyl group, it recruits the coiled-coil protein GM130. The relevance of this system to budding yeasts has been unclear, as they lack an obvious orthologue of GM130, and their only GRASP65 relative (Grh1) lacks a myristoylation site and has even been suggested to act in a mitotic checkpoint. In this study, we show that Grh1 has an N-terminal amphipathic helix that is N-terminally acetylated and mediates association with the cis-Golgi. We find that Grh1 forms a complex with …

Following Temperature Stress, Export Of Heat Shock Mrna Occurs Efficiently In Cells With Mutations In Genes Normally Important For Mrna Export, Christiane Rollenhagen, Christine A. Hodge, Charles N. Cole

Dartmouth Scholarship

Heat shock leads to accumulation of polyadenylated RNA in nuclei of Saccharomyces cerevisiae cells, transcriptional induction of heat shock genes, and efficient export of polyadenylated heat shock mRNAs. These studies were conducted to examine the requirements for export of mRNA following heat shock. We used in situ hybridization to detect SSA4 mRNA (encoding Hsp70) and flow cytometry to measure the amount of Ssa4p-green fluorescent protein (GFP) produced following heat shock. Npl3p and Yra1p are mRNA-binding proteins recruited to nascent mRNAs and are essential for proper mRNA biogenesis and export. Heat shock mRNA was exported efficiently in temperature-sensitive npl3, yra1 …

A Proposal For Robust Temperature Compensation Of Circadian Rhythms, Christian I. Hong, Emery D. Conrad, John J. Tyson

Dartmouth Scholarship

The internal circadian rhythms of cells and organisms coordinate their physiological properties to the prevailing 24-h cycle of light and dark on earth. The mechanisms generating circadian rhythms have four defining characteristics: they oscillate endogenously with period close to 24 h, entrain to external signals, suffer phase shifts by aberrant pulses of light or temperature, and compensate for changes in temperature over a range of 10°C or more. Most theoretical descriptions of circadian rhythms propose that the underlying mechanism generates a stable limit cycle oscillation (in constant darkness or dim light), because limit cycles quite naturally possess the first three …

Structure And Temperature Regulated Expression Of A Cysteine Proteinase Gene In Pachysandra Terminalis Sieb. & Zucc., Suping Zhou, Roger Sauve, Fur-Chi Chen

Agricultural and Environmental Sciences Faculty Research

A cysteine proteinase gene (DQ403257) with an open reading frame of 1125 base pairs was isolated from Pachysdandra terminalis. The primary translated peptide has a predicted length of 374 amino acids, pI (isoelectric point) of 5.70, and molecular mass of 40.9 kDa. The Peptidase_C1 domain is between residue 141 and 367. The proteinase has a conserved motif Gly-Xaa-Thy-Xaa-Phe-Xaa-Asn in the pro region. Sequence comparison shows that the deduced peptide shares 82% identity with the cysteine proteinase RD19a precursor (RD19) (accession P43296) from Arabidopsis thaliana (L.) Heynh. Real-time quantitative reverse-transcriptase–polymerase chain reaction revealed that the gene is induced by treatments of …

Australian Temperate Strawberry Breeding Program (Western Australia) Selection Of New And Advanced Short Day Breeding Lines And Cultivars In Western Australia - 2006/2007, Aileen Reid, Dennis Phillips, Hal

Horticulture research reports

Thirty-two ‘Stage 4’ numbered selections (2004 crosses) from the Australian Temperate Strawberry Breeding Program were evaluated in unreplicated plots on a commercial property in Wanneroo for their potential under WA conditions. Seven of these have been selected as worthy of further testing. The priority selection among these was 04- 021-263, and the other six included 04-021-467, 04-037-102, 04-021-241, 04-021-172, 04-021-475 and 04-029-211.

In addition, 21 advanced numbered selections (Stages 5, 6 and 7) were also evaluated on the same grower’s property. Three of those were substantially larger plots and a later planting date. Of the first group of 18 selections, …