Genetics and Genomics Commons^™

Editor's Note, Padraig O'Malley

New England Journal of Public Policy

This issue of the journal can be summed up in one word: provocative. At least two articles break new ground. Anthony Robbins and Phyllis Freeman explore the ways in which environmentally oriented public health is uniquely suited to help organized medical care in providing health and in restraining expenditures. Janet Farrell Smith challenges policymakers to look at what will soon become a hot issue — the medical use of genetic information. The genetic testing of children, now becoming prevalent in the foster care and pre-adoptive stage in order to facilitate placement and satisfy prospective parents’ “need to know,” is already …

Genetic Testing: A Cautionary Tale Of Foster And Pre-Adoptive Children, Janet Farrell Smith

New England Journal of Public Policy

Genetic testing of children in the foster care and pre-adoptive stage may be thought to facilitate child placement and satisfy prospective parents’ need to know. But, the policy analysis in this paper recommends great caution, especially given eugenic attitudes in the history of adoption and the risk of creating a second tier of un-adoptable children. Testing should be done only when two conditions are satisfied: test information is medically useful for childhood onset diseases; test information supports and does not diminish the child’s access to present and future healthcare (or the child’s future insurability). Public policy needs to make a …

Genomic Microsatellites As Evolutionary Chronometers: A Test In Wild Cats, Carlos A. Driscoll, Marilyn Menotti-Raymond, George Nelson, David Goldstein, Stephen J. O'Brien

Biology Faculty Articles

Nuclear microsatellite loci (2- to 5-bp tandem repeats) would seem to be ideal markers for population genetic monitoring because of their abundant polymorphism, wide dispersal in vertebrate genomes, near selective neutrality, and ease of assessment; however, questions about their mode of generation, mutation rates and ascertainment bias have limited interpretation considerably. We have assessed the patterns of genomic diversity for ninety feline microsatellite loci among previously characterized populations of cheetahs, lions and pumas in recapitulating demographic history. The results imply that the microsatellite diversity measures (heterozygosity, allele reconstitution and microsatellite allele variance) offer proportionate indicators, albeit with large variance, of …

Neurospora Clock-Controlled Gene 9 (Ccg-9) Encodes Trehalose Synthase: Circadian Regulation Of Stress Responses And Development, Mari L. Shinohara, Alejandro Correa, Deborah Bell-Pedersen, Jay C. Dunlap, Jennifer J. Loros

Dartmouth Scholarship

The circadian clock of Neurospora crassa regulates the rhythmic expression of a number of genes encoding diverse functions which, as an ensemble, are adaptive to life in a rhythmic environment of alternating levels of light and dark, warmth and coolness, and dryness and humidity. Previous differential screens have identified a number of such genes based solely on their cycling expression, including clock-controlled gene 9 (ccg-9). Sequence analysis now shows the predicted CCG-9 polypeptide to be homologous to a novel form of trehalose synthase; as such it would catalyze the synthesis of the disaccharide trehalose, which plays an important …

A New Partitioning Around Medoids Algorithm, Mark J. Van Der Laan, Katherine S. Pollard, Jennifer Bryan

U.C. Berkeley Division of Biostatistics Working Paper Series

Kaufman & Rousseeuw (1990) proposed a clustering algorithm Partitioning Around Medoids (PAM) which maps a distance matrix into a specified number of clusters. A particularly nice property is that PAM allows clustering with respect to any specified distance metric. In addition, the medoids are robust representations of the cluster centers, which is particularly important in the common context that many elements do not belong well to any cluster. Based on our experience in clustering gene expression data, we have noticed that PAM does have problems recognizing relatively small clusters in situations where good partitions around medoids clearly exist. In this …

An Equity Paradigm For Preventing Genetic Discrimination, Anita Silvers, Michael Ashley Stein

Faculty Publications

No abstract provided.

Registration Of N547 Maize Germplasm Line, Nora E. D'Croz-Mason, John E. Foster, Stephen C. Mason

Department of Entomology: Faculty Publications

N547 germplasm line (Reg. no. GP-367, PI 615526) was released by the Agriculture Research Division, Institute of Agriculture and Natural Resources, University of Nebraska, on 24 Aug. 1999. N547 is a yellow endosperm maize inbred germplasm with resistance to stalk and shank tunneling damage caused by the second generation of the European corn borer (ECB) Ostrinia nubilalis (Hubner).

N547 was derived by selfing a selected full-sib family from MBITA, a tropical population developed by CIMMYT, Mexico. MBITA was created to recombine sources of resistance to temperate and subtropical stalk borers. These insects included ECB, southwestern corn borer (SWCB) Diatraea grandiosella …

Application Of Fuzzy-Neural Network In Classification Of Soils Using Ground-Penetrating Radar Imagery, Lameck O. Odhiambo, Robert S. Freeland, Ronald E. Yoder, J. Wesley Hines

Department of Animal Science: Faculty Publications

Errors associated with visual inspection and interpretation of radargrams often inhibits the intensive surveying of widespread areas using ground-penetrating radar (GPR). To automate the interpretive process, this paper presents an application of a fuzzy-neural network (F-NN) classifier for unsupervised clustering and classification of soil profile using GPR imagery. The classifier clusters and classifies soil profiles strips along a traverse based on common pattern similarities that can relate to physical features of the soil (e.g., number of horizons; depth, texture and structure of the horizons; and relative arrangement of the horizons, etc). This paper illustrates this classification procedure by its application …

Rapid Communication: Mapping Of The Beta Tropomyosin (Tpm2) Gene To Pig Chromosome 1, J. Sherwood, Daniel C. Gill, M. F. Rothschild

Department of Animal Science: Faculty Publications

Locus. Pig Tropomyosin beta (TPM2) gene.

Genus and Species. Sus Scrofa.

Source and Description of Primers. Primers were derived by using well-conserved regions of published human and mouse sequence (GenBank accession nos. AF209746 and NM_009416). The primers were used to amplify a 1.4-kp fragment of the porcine TPM2 gene covering exons 3 through 8. The porcine cDNA sequence (GenBank accession no. AF420022) showed 95% exonic identity (325 bp) at the nucleotide level to the human skeletal muscle beta tropomyosin (GenBank accession no. X06825). Additionally, pig specific primers were designed to amplify a 246-bp piece that spans exons 3 to …

Rapid Communication: Physical And Linkage Mapping Of The Porcine Calcitonin (Calc) Gene, J. E. Neil, S. E. Zhang, J. M. Helm, Daniel C. Ciobanu, M. F. Rothschild

Department of Animal Science: Faculty Publications

Genus and Species. Sus scrofa.

Locus. Porcine calcitonin (CALC) gene.

Source and Description of Primers. Primers, CCA1F and CCA1R, were designed from canine calcitonin sequence (GenBank Accession no. AJ271090) to amplify genomic porcine DNA. Using sequence obtained from the amplified PCR product, additional pig-specific primers (CIPBF, CIPBR, CIPCF, CIPCR) were designed.

Primer Sequences. CCA1F: 5′-CAC TTT GGA TTG GCC GCG C-3′; CCA1R: 5′-ACC AGG GCA GCC AGC AGG A-3′; CIPBF: 5′-AAC TTC CCA CTC TGC ACA CT-3′; CIPBR: 5′-AGA CCA AAC TTC AGC AGG AT- 3′; CIPCF: 5′-TTC TCC TTC CTC TGC TTC TG-3′; CIPCR: 5′-GCA AAC CCA ATA …

Methods And Compositions To Enhance Tenderness And Value Of Meat, Chris R. Calkins, Jesus Pablo Velazco De La Garcia, Nancy Coromoto Jerez-Timaure

Department of Animal Science: Faculty Publications

A method of enhancing the tenderness of meat for animal or human consumption by treatment of pre-rigor muscle with the compositions of the invention. It has been found that other quality meat traits can also be enhanced with the method of the invention.

Variability Of Placental Expression Of Cyclin E Low Molecular Weight Variants, A Bukovsky, Maria Cekanova Ms, Rndr, Phd, Mr Caudle, J Wimalasena, Js Foster, Ja Keenan, Rf Elder

Faculty Publications and Other Works -- Biochemistry, Cellular and Molecular Biology

No abstract provided.

Compensation For Herbivory In Wild Sunflower: Response To Simulated Damage By The Head-Clipping Weevil, Diana Pilson, Karin L. Decker

Diana Pilson Publications

Herbivore damage is generally detrimental to plant fitness, and the evolutionary response of plant populations to damage can involve either increased resistance or increased tolerance. While characters that contribute to resistance, such as secondary chemicals and trichomes, are relatively well understood, characters that contribute to a plant’s ability to tolerate damage have received much less attention. Using Helianthus annuus (wild sunflower) and simulated damage of Haplorhynchites aeneus (head-clipping weevil) as a model system, we examined morphological characters and developmental processes that contribute to compensatory ability. We performed a factorial experiment that included three levels of damage (none, the first two, …

Mouse Ribonuclease Iii. Cdna Structure, Expression Analysis, And Chromosomal Location, Kristine R. Fortin, Rhonda H. Nicholson, Allen W. Nicholson

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Members of the ribonuclease III superfamily of double-stranded(ds)-RNA-specific endoribonucleases participate in diverse RNA maturation and decay pathways in eukaryotic and prokaryotic cells. A human RNase III orthologue has been implicated in ribosomal RNA maturation. To better understand the structure and mechanism of mammalian RNase III and its involvement in RNA metabolism we determined the cDNA structure, chromosomal location, and expression patterns of mouse RNase III.

Results

The predicted mouse RNase III polypeptide contains 1373 amino acids (~160 kDa). The polypeptide exhibits a single C-terminal dsRNA-binding motif (dsRBM), tandem catalytic domains, a proline-rich region (PRR) and an RS domain. …

Variability Of Placental Expression Of Cyclin E Low Molecular Weight Variants, A Bukovsky, Maria Cekanova Ms, Rndr, Phd, Mr Caudle, J Wimalasena, Js Foster, Ja Keenan, Rf Elder

Maria Cekanova MS, RNDr, PhD

No abstract provided.

The Unblazed Trail: Bioinformatics And The Protection Of Genetic Knowledge, Lawrence M. Sung

Faculty Scholarship

No abstract provided.

Human Genomics Of Biotechnology, Brian Bluelake, Bob Wang, Serin Hudson, Fatih Ersan, Aaron Freier

Engineering and Technology Management Student Projects

Biotechnology is the term for the techniques of managing biological systems for human benefit. A biological system can range from a single cell organism to different types of plants, animals, and to the very complicated human being. Biotechnology includes a great range of scientific and technological disciplines and has a great variety of important applications in biology, medicine, agriculture, and various industries. In our report, we shall only focus on one of the most active frontiers of today's biotechnology-human genomics.

A Note On Cascade Climbing Of Migrating Goby And Shrimp Postlarvae In Two Maui Streams, M. Eric Benbow, Leslie Luchar Orzetti, Mollie D. Mcintosh, Albert J. Burky

Biology Faculty Publications

In this study, we documented cascade climbing rates of 133 and 230 postlarvae of Lentipes concolor (O‘opu alamo‘o) and Atyoida bisulcata (Opae kahaole), respectively, from two streams on the island of Maui, Hawaii. Climbing measurements and observations were made of postlarvae at the water-substrate interface in cascade habitats of constricted water flow. Both species were observed to move in short bursts of forward progression within or above the pulsing water-substrate interface. Goby postlarval climbing rates ranged from 0.04 – 1.50 cm s–1 and were slower than shrimp rates which ranged from 0.30 – 3.06 cm s–1. The high variability is …

Multiple Immuno-Regulatory Defects In Type-1 Diabetes, Anjli Kukreja, Giulia Cost, John Marker, Chenhui Zhang, Karen Lin-Su, Zhong Sun, Svetlana Ten, Maureen M. Sanz, Mark Exley, Brian Wilson, Steven Porcelli

Faculty Works: Biology, Chemistry, and Environmental Studies

Susceptibility to immune-mediated diabetes (IMD) in humans and NOD mice involves their inherently defective T cell immunoregulatory abilities. We have followed natural killer (NK) T cell numbers in patients with IMD, both by flow cytometry using mAbs to the characteristic junctions found in the T cell receptors of this cell subtype, and by semiquantitative RT-PCR for the corresponding transcripts. Both before and after clinical onset, the representation of these cells in patients’ PBMCs is reduced. We also report low numbers of resting CD4+ CD25+ T cells in IMD patients, a subset of T cells shown to have important immunoregulatory functions …

Life History Response Of Mediterranean Fruit Flies To Dietary Restriction, James R. Carey, Pablo Liedo, Lawrence G. Harshman, Ying Zhang, Hans-Georg Müller, Linda Partridge, Jane-Ling Wang

Lawrence G. Harshman Publications

The purpose of this study was to investigate medfly longevity and reproduction across a broad spectrum of diet restriction using a protocol similar to those applied in most rodent studies. Age-specific reproduction and age of death were monitored for 1,200 adult males and 1,200 females, each individually maintained on one of 12 diets from ad libitum to 30% of ad libitum. Diet was provided in a fixed volume of solution that was fully consumed each day, ensuring control of total nutrient consumption for every fly. Contrary to expectation and precedence, increased longevity was not observed at any level of …

Rapid Communication: Mapping Of The Ca2+ Atpase Of Fast Twitch 1 Skeletal Muscle Sarcoplasmic Reticulum (Atp2a1) Gene To Porcine Chromosome 3, Daniel C. Ciobanu, Y. Ciobanu, M. F. Rothschild

Department of Animal Science: Faculty Publications

Locus Name. Ca²⁺ ATPase of fast twitch 1 skeletal muscle sarcoplasmic reticulum.

Species. Sus scrofa.

Locus Symbol. ATP2A1.

Source of Primers. Two sets of PCR primers were designed based on human ATP2A1 sequences (Gen- Bank accession numbers U96773 and U96777) available in the GenBank database. Using pig genomic DNA as a template we used set A primers to amplify approximately 1,100 bp spanning exon 1 to exon 2 and set B primers to amplify 1,200 bp gene segment covering some of exon 8 through part of exon 9. These sequences were deposited in GenBank, accession number AY027797-AY027799.

Small Glutamine-Rich Protein/Viral Protein U–Binding Protein Is A Novel Cochaperone That Affects Heat Shock Protein 70 Activity, Peter C. Angeletti, Doriann Walker, Antonito T. Panganiban

Nebraska Center for Virology: Faculty Publications

Molecular chaperone complexes containing heat shock protein (Hsp) 70 and Hsp90 are regulated by cochaperones, including a subclass of regulators, such as Hsp70 interacting protein (Hip), C-terminus of Hsp70 interacting protein (CHIP), and Hsp70-Hsp90 organizing factor (Hop), that contain tetratricopeptide repeats (TPRs), where Hsp70 refers to Hsp70 and its nearly identical constitutive counterpart, Hsc70, together. These proteins interact with the Hsp70 to regulate adenosine triphosphatase (ATPase) and folding activities or to generate the chaperone complex. Here we provide evidence that small glutamine-rich protein/viral protein U–binding protein (SGT/UBP) is a cochaperone that negatively regulates Hsp70. By “Far-Western” and pull-down assays, SGT/UBP …

Il-12 Plasmid Delivery By In Vivo Electroporation For The Successful Treatment Of Established Subcutaneous B16.F10 Melanoma, M. Lee Lucus, Loree Heller, Domenico Coppola, Richard Heller

Bioelectrics Publications

Interleukin-12 (IL-12) has been used in numerous immunotherapy protocols against melanoma. However, delivery of IL-12 in the form of recombinant protein can result in severe toxicity, and gene therapy has had limited success against B16.F10 murine melanoma. The purpose of this study was to examine the effectiveness of in vivo electroporation for the delivery of plasmid DNA encoding IL-12 as an antitumor agent against B16.F10 melanoma. We treated mice bearing established B16.F10 melanoma tumors with intratumoral (i.t.) or intramuscular (i.m.) injections of a plasmid encoding IL-12, followed by in vivo electroporation. For i.t. treatments, we used an applicator containing six …

Molecular And Morphological Evolution Of The Amphipod Radiation Of Lake Baikal, Kenneth S. Macdonald Iii

Dissertations, Theses, and Masters Projects

The amphipods of Lake Baikal, Russia, are a taxonomically and morphologically diverse group, and have been cited as a classic example of adaptive radiation. An unfortunate consequence of this diversity has been an instability of Baikal amphipod classification, with frequent revisions spurred by differing opinions about the phylogenetic utility of different characters. Classifications have never been based on a rigorous phylogenetic analysis of morphological data and only recently has the phylogeny of Lake Baikal's amphipods been examined using molecular tools. Unfortunately, most of these studies have led to a limited expansion of our understanding of Baikal amphipod systematics. Phylogenetic relationships …

Genetic Stock Structure Of The Sailfish, Istiophorus Platypterus, Based On Nuclear And Mitochondrial Dna, Jan Renee Mcdowell

Dissertations, Theses, and Masters Projects

The results of life history studies involving the sailfish, Istiophorus platypterus, from the Atlantic, Pacific, and Indian oceans were reviewed. Results of studies agree on several aspects of sailfish biology; sailfish exhibit opportunistic feeding behavior, follow the 28??C isotherm, spawn in summer mature at approximately age 3, and are the least migratory of the billfishes. However, results are in conflict concerning sex ratio and whether sailfish are single or multiple spawners. Although many researchers have reported that sailfish are sexually dimorphic, their fragile otoliths make them difficult to age, aging studies have not been validated, and sexual dimorphism has not …

Cases And Guidelines In Genetics, Roger B. Dworkin

Articles by Maurer Faculty

No abstract provided.

Functional Requirement Of Aquaporin-5 In Plasma Membranes Of Sweat Glands, Lene N. Nejsum, Tae-Hwan Kwon, Uffe B. Jensen, Ornella Fumagalli, Jørgen Frøkiaer, Carissa M. Krane, Anil G. Menon, Landon S. King, Peter C. Agre, Søren Nielsen

Biology Faculty Publications

The distribution and function of aquaporins (AQPs) have not previously been defined in sweat glands. In this study, AQP1, AQP3, and AQP5 mRNA were demonstrated in rat paw by reverse transcription (RT)–PCR, but AQP2 and AQP4 were not. AQP1, AQP3, and AQP5 protein were confirmed in these tissues by immunoblotting. AQP1 was identified in capillary endothelial cells by immunohistochemical labeling, but not in sweat glands or epidermis. Abundant AQP3 expression was seen in basal levels of epidermis, but not in sweat glands. AQP2 and AQP4 were not observed in either skin or sweat glands. Immunohistochemical labeling revealed abundant AQP5 in …

Mitochondrial Dna And Microsatellite Genetic Variation Of Dollar Sunfish (Lepomis Marginatus), Nancy A. Schable

Masters Theses

Dollar sunfish (Lepomis marginatus) at the Savannah River Site were sampled from two radiocesium contaminated ponds with a history of thermal elevation and from reference ponds with no history of radioactive or thermal contamination. Fluorescent sequencing of a portion of the mitochondrial control region showed no genetic variation within or between populations. Centrarchidae microsatellite loci Lma 120 (6 alleles, N=124 from 5 populations), Lma 20 (10 alleles, N=37 from 3 populations) and Rb 7 (14 alleles. N=17 from 2 populations) were variable for dollar sunfish. An additional 9 microsatellite primer pairs were designed for dollar sunfish. Testing of the designed …

Genetic Diversity Of Balbiani Ring L Gene In Two Species Of Chironomus, Lola-Mae Palmer

Seton Hall University Dissertations and Theses (ETDs)

Differences in genetic composition have been predicted among aquatic midge fly larva called chironomids. Although several genes including microsatellites and ribosomal protein genes have been explored in our lab, the gene that has so far been studied the most is the Balbiani Ring (BR) 1 gene. There are several genes in this family, including Balbiani Ring 2.1, 2.2 and 6. These BR genes are known to contain long arrays of tandemly repeated units with a ranked repeat organization (Paulsson et al.1992). This secretory protein gene forms a large puff located on polytene chromosome IV (Bentivegna et al., 1993). The gene …

Phylogeography And Genetic Diversity Of The Seal Salamander (Desmognathus Monticola), Erin D. Casey

Masters Theses

Phylogeography is defined as the spatial distribution of taxa with respect to geologic and geographic events. It is well documented that the distributions of many taxa have been affected by glacial events during the Pleistocene Era. The patterns generated can be very complex and result from shifts in climate and/or vegetation.

The Seal salamander, (Desmognathus monticola), is one species that still has questions pertaining to its phylogeography. The range of this species extends from southwestern Pennsylvania to northern Alabama and Georgia, with a highly disjunct, state-endangered population in the Red Hills of Alabama. The main goal of this study …