Genetics Commons^™

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 …

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 …

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, …

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 …

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 …

Genetic Variability Studies In A Selected Population Of Azadirachta Excelsa (Sentang) With Aflp Marker Technology, Chiew Foan Chin

Student Works (2000-2009)

A maternal half-s/b population of Azadirachta excelsa was established from seeds in a randomised complete block design with three replicates. 100 to 200 seeds were collected from each of the 13 selected mother trees. The mother trees were categorised into three groups i.e. large, medium and small according to their girth sizes. 50 progeny seedlings from each scedlot per replicate were planted in the experimental field. Genetic studies on phenotypic measurements and molecular marker analysis were carried out on the established A. excelsa population. Measurements of quantitative traits including diameter breast height (Dbh) and total height were made. Mean Dbh …

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 …

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 …

Identification Of Regulatory Elements Using A Feature Selection Method, Sunduz Keles, Mark J. Van Der Laan, Michael B. Eisen

U.C. Berkeley Division of Biostatistics Working Paper Series

Many methods have been described to identify regulatory motifs in the transcription control regions of genes that exhibit similar patterns of gene expression across a variety of experimental conditions. Here we focus on a single experimental condition, and utilize gene expression data to identify sequence motifs associated with genes that are activated under this experimental condition. We use a linear model with two way interactions to model gene expression as a function of sequence features (words) present in presumptive transcription control regions. The most relevant features are selected by a feature selection method called stepwise selection with monte carlo cross …

The Wings Of Bombyx Mori Develop From Larval Discs Exhibiting An Early Differentiated State: A Preliminary Report, Madhuri Kango-Singh, Amit Singh, K. P. Gopinathan

Biology Faculty Publications

Lepidopteran insects present a complex organization of appendages which develop by various mechanisms. In the mulberry silkworm, Bombyx mori, a pair of meso- and meta-thoracic discs located on either side in the larvae gives rise to the corresponding fore- and hind-wings of the adult. These discs do not experience massive cell rearrangements during metamorphosis and display the adult wing vein pattern. We have analysed wing development in B. mori by two approaches, viz., expression of patterning genes in larval wing discs, and regulatory capacities of larval discs following explantation or perturbation. Expression of Nubbin is seen all over the presumptive …

Salivary Acinar Cells From Aquaporin 5-Deficient Mice Have Decreased Membrane Water Permeability And Altered Cell Volume Regulation, Carissa M. Krane, James E. Melvin, Ha-Van Nguyen, Linda Richardson, Jennifer E. Towne, Thomas Doetschman, Anil G. Menon

Biology Faculty Publications

Aquaporins (AQPs) are channel proteins that regulate the movement of water through the plasma membrane of secretory and absorptive cells in response to osmotic gradients. In the salivary gland, AQP5 is the major aquaporin expressed on the apical membrane of acinar cells. Previous studies have shown that the volume of saliva secreted by AQP5-deficient mice is decreased, indicating a role for AQP5 in saliva secretion; however, the mechanism by which AQP5 regulates water transport in salivary acinar cells remains to be determined. Here we show that the decreased salivary flow rate and increased tonicity of the saliva secreted byAqp5 …

A "Frozen Exception" For The Frozen Embryo: The Davis "Reasonable Alternatives Exception", Jennifer L. Medenwald

Indiana Law Journal

No abstract provided.

Consent To The Use Of Stored Dna For Genetics Research: A Survey Of Attitudes In The Jewish Population, Marc D. Schwartz, Karen H. Rothenberg, Linda Joseph, Judith Benkendorf, Caryn Lerman

Faculty Scholarship

No abstract provided.

Detection Of Aneuploidy For Chromosomes 7 And 8 Using Fluorescence In Situ Hybridization In Patients With Aplastic Anemia And Sequencing Of The Mitotic Checkpoint Gene Hbub1, Laura Jane Aridgides

Theses and Dissertations in Biomedical Sciences

Aplastic anemia (AA) is characterized by complete bone marrow failure. Progression to myelodysplastic syndromes (MDS) and acute nonlymphocytic leukemia (ANLL) occurs frequently. At the time of transformation, cytogenetic abnormalities are common. Detection of cytogenetic abnormalities prior to leukemic transformation may indicate future disease progression. Karyotype analysis is the current method of choice to evaluate chromosome aberrations. However, fluorescence in situ hybridization (FISH) is more sensitive in detecting these abnormalities.

hBUB1, a mitotic spindle checkpoint gene, was shown to be mutated in two colorectal cancer cell lines with high levels of aneuploidy (Cahill, et al., 1998). Although theoretically possible, conclusive …

Review Of "Illuminating Life: Selected Papers From Cold Spring Harbor (1903-1969). Volume 1" By J. Witkowski, John B. Jenkins

Biology Faculty Works

No abstract provided.

Genomic Diversity Of Pseudomonas Aeruginosa In Cystic Fibrosis, Nathaniel Edwards Head

Theses, Dissertations and Capstones

Pseudomonas aeruginosa is a common environmental microorganism. However, it has the genetic capacity to cause diseases in patients with compromised host defense systems. Cystic fibrosis (CF) is one of the major hereditary diseases among Caucasian populations. CF patients are born with a defective chloride channel that is responsible for maintaining fluid and electrolyte balance across the lumen of the lung. This imbalance leads to the production of an abnormal dehydrated viscous mucous, prohibiting the patient from normally clearing the respiratory airway. Chronic pulmonary infections with P. aeruginosa are the major causes of high morbidity and mortality in CF. Two of …

Origin And Conservation Genetics Of Threatened Ute Ladies’-Tresses, Spiranthes Diluvialis (Orchidaceae), Allen L. Szalanski, Gerry Steinauer, Richard Bischof, Jessica Lynn Petersen

Department of Animal Science: Faculty Publications

The Ute ladies’-tresses, Spiranthes diluvialis, is listed as a threatened orchid in west-central United States by the Federal government. Information on its origin and patterns of genetic variation is needed to develop effective conservation strategies for this species. DNA sequencing and polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) was used to evaluate genetic variation and structure of 23 populations of S. diluvialis. In addition, four congeneric species were analyzed to determine possible origins of the putative allotetraploid S. diluvialis. DNA sequencing and PCR-RFLP analysis of the nuclear ribosomal internal transcribed spacer (ITS) and mitochondrial and chloroplast DNA …

Aquaporin 5-Deficient Mouse Lungs Are Hyperresponsive To Cholinergic Stimulation, Carissa M. Krane, Christopher N. Fortner, Arthur R. Hand, Dennis W. Mcgraw, John N. Lorenz, Susan E. Wert, Jennifer E. Towne, Richard J. Paul, Jeffrey A. Whitsett, Anil G. Menon

Biology Faculty Publications

Although aquaporin 5 (AQP5) is the major water channel expressed in alveolar type I cells in the lung, its actual role in the lung is a matter of considerable speculation. By using immunohistochemical staining, we show that AQP5 expression in mouse lung is not restricted to type I cells, but is also detected in alveolar type II cells, and in tracheal and bronchial epithelium. Aqp5 knockout (Aqp5−/−) mice were used to analyze AQP5 function in pulmonary physiology. Compared with Aqp5+/+ mice, Aqp5−/− mice show a significantly increased concentration-dependent bronchoconstriction to intravenously administered Ach, as shown by …

Hawaiian Freshwater Polychaeta: A Potentially Substantial Trophic Component Of Stream Depositional Habitats, M. Eric Benbow, Albert J. Burky, Carl M. Way

Biology Faculty Publications

In this paper we report the widespread occurrence of large annelids (Polychaeta: Nereididae) in Hawaiian stream depositional habitats, drawing attention to the lack of knowledge of Hawaiian stream energetics. Specimens of Namalycastis sp. were collected from five Hawaiian Islands from May–July 1995 and from the island of Maui from July–December 1999 and April–July 2000. Most specimens collected were N. hawaiiensis, while two specimens of N. abiuma were collected from a single site on the island of Molokai. Specimens were collected from elevations ranging from 3–240 m; several collections were from sites above at least one major (> 15 m …

Hard Cases For Autonomy, Respect, And Professionalism In Medical Genetics, Roger B. Dworkin

Articles by Maurer Faculty

No abstract provided.

Genetic Diversity In The Bo'an, Salar, And Dongxiang : Co-Resident Muslim Populations In Gansu Province, P.R. China, Thomas Baric

Theses : Honours

Patterns s of genetic diversity within and between three co-resident Muslim populations from Gansu Provence in the Peoples Republic of China were examined and the results contrasted with historical information. This study of members of the Bo'an, Salar and Dongxiang communities will contribute to a clearer understanding of the origins and migratory patterns of Muslims in PR China, and more generally the effect of population subdivision on gene pool structure and composition. Ten autosomal and live Y-chromosome microsatellite loci were genotyped to determine allele distribution patterns. Subsequently, the D-loop region of mitochondrial DNA was sequenced to complement the autosomal and …

An Assessment Of Prothrombotic Tendency In Humans Using Functional And Genomic Determinants In The South Eastern Irish Population, Carmel Cullen

Theses

Venous thrombosis occurs in about 1 per 1,000 individuals per year. It is a serious disorder and accounts for a significant number of hospital admissions and deaths annually. Thrombophilia describes the familial or acquired disorders of the haemostatic mechanism that predispose to thrombosis. Inherited thrombophilia can be defined as a genetically determined tendency to venous thromboembolism Mutations in genes that code for proteins involved directly (or indirectly) In blood coagulation have been associated with prothrombotic status. Laboratory investigations for thrombophilia include screening for deficiencies of antithrombin, protein C or protein S and testing for activated protein C resistance. Together these …

Female Sensitivity To Diet And Irradiation Treatments Underlies Sex-Mortality Differentials In The Mediterranean Fruit Fly, James R. Carey, Pablo Liedo, Hans-Georg Müller, Jane-Ling Wang, Brad Love, Lawrence G. Harshman, Linda Partridge

Lawrence G. Harshman Publications

Large-scale experiments on medflies that were subjected to sterilizing doses of ionizing radiation (plus intact controls) and maintained on either sugar-only or full, protein-enriched diets revealed that, whereas the mortality trajectories of both intact and irradiated male cohorts maintained on both diets are similar, the mortality patterns of females are highly variable. Mean mortality rates at 35 days in male cohorts ranged from 0.2 to 0.3 but in female cohorts ranged from 0.09 to 0.35, depending on treatment. The study reports three main influences: (a) qualitative differences exist in the sex–mortality response of medflies subjected to dietary manipulations and irradiation, …

Characterization Of Natural Variants Of Local Wild Bananas & Seed Progeny Of Musa Acuminata, Muhammad Asif Javed

Student Works (2000-2009)

The purpose of this study was to characterize the variation pattern that exists in the wild Musa acuminata (AA) populations. widely distributed in Malaysia. Fourteen populations of Musa acuminata, which included subspecies malaccensis, siamea and truncata were collected from different locations including Selangor, Pahang, Perak, Kelantan, Kedah and Terengganu for studies on variation within and between populations, based on morphological characters, biochemical, ploidy and genomic DNA content. Techniques of numerical taxonomy were employed to determine the variation pattern and these included use of the clustering method and principal component analysis. Ploidy level and genomic DNA content were determined by flow …

The Occurrence Of The Freshwater Clams, Musculium Partumeium (Say) And Pisidium Casertanum (Poli) (Bivalvia: Sphaeriidae), In The Hawaiian Islands, Albert J. Burky, Carl M. Way, Skippy Hau, M. Eric Benbow

Biology Faculty Publications

Sphaeriid clams were collected from an ancient, continuously cultivated taro pond complex at Ke‘anae Peninsula, Maui. Both species are known for adaptations for temporary pond habitats and could have been initially introduced by the earliest Hawaiian settlers transported with moist taro root stock from other areas of Oceania.

Electrically Mediated Plasmid Dna Delivery To Hepatocellular Carcinomas In Vivo, L. Heller, M. J. Jaroszeski, D. Coppola, C. Pottinger, R. Gilbert, Richard Heller

Bioelectrics Publications

Gene therapy by direct delivery of plasmid DNA has several advantages over viral gene transfer, but plasmid delivery is less efficient. In vivo electroporation has been used to enhance delivery of chemotherapeutic agents to tumors in both animal and human studies. Recently, this delivery technique has been extended to large molecules such as plasmid DNA. Here, the successful delivery of plasmids encoding reporter genes to rat hepatocellular carcinomas by in vivo electroporation is demonstrated.

"An Evolutionary No Man’S Land" And "Reply From L. G. Harshman And A. A. Hoffmann", Margarida Matos, André Levy, Henrique Teotónio, Michael R. Rose, Lawrence G. Harshman, Ary A. Hoffmann

Lawrence G. Harshman Publications

The gap between evolutionary studies in laboratory versus natural populations is a persistent problem.

Test Of Intron Predictions Reveals Novel Splice Sites, Alternatively Spliced Mrnas And New Introns In Meiotically Regulated Genes Of Yeast, Carrie Davis, Leslie Grate, Marc Spingola, Manuel Ares

Biology Department Faculty Works

Correct identification of all introns is necessary to discern the protein-coding potential of a eukaryotic genome. The existence of most of the spliceosomal introns predicted in the genome of Saccharomyces cerevisiae remains unsupported by molecular evidence. We tested the intron predictions for 87 introns predicted to be present in non-ribosomal protein genes, more than a third of all known or suspected introns in the yeast genome. Evidence supporting 61 of these predictions was obtained, 20 predicted intron sequences were not spliced and six predictions identified an intron-containing region but failed to specify the correct splice sites, yielding a successful prediction …

Whole Genome Sequencing Of L.Monocytogenes And L.Innocua : A Basis For Comparative Genomics Of The Genus Listeria, Rachel Purcell

Theses

Listeria monocytogenes is a gram-positive, food-borne human and animal pathogen. L.innocua is a non-pathogenic species the most closely related to L. monocytogenes. Comparative genomics between a pathogenic and a closely related non-pathogenic species is a powerful approach for identifying genes or regions on the chromosome, which might be involved in virulence. Therefore whole genome sequencing of these two organisms was undertaken. The strategy used was based on a random approach combined with end-sequencing of a medium insert library for the finishing phase. Based on the available sequence data for these two species an in silico analysis for the presence of …

Analysis Of Genetic Factors Affecting High Density Lipoprotein Levels And Apoall Levels In C57 B1/6j And Fvb/N Wildtype Mice Using A Qtl Mapping Approach, Judith Barrios

Seton Hall University Dissertations and Theses (ETDs)

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