Genetics and Genomics Commons^™

An Afternoon With Dr. Freeman Dyson, Freeman Dyson

IMSA Great Minds Program ®

Dyson will speak with IMSA students and faculty on a variety of topics including space, origins of the universe, and how science and technology change society. Learn how three burgeoning technologies – solar energy, genetic engineering and the Internet could narrow the gap between rich and poor in this century. Dyson’s visions for the future include forests of genetically enhanced trees oozing high-octane fuel from their roots and laser-launched earthlings colonizing the comets of the Kuiper Belt. Are his visions convincing? You can decide by joining us at IMSA’s website.

The Meowplex: A New Dna Test Using Tetranucleotide Str Markers For The Domestic Cat, John M. Butler, Victor A. David, Stephen J. O'Brien, Marilyn Menotti-Raymond

Biology Faculty Articles

No abstract provided.

Comparing Clustering Algorithms For Use With Genomic And Proteomic Data, Rebecca A. Olson

Theses and Dissertations

The Human Genome Project and related projects have resulted in the development of a number of new experimental and analytic tools for use in genomic and proteomic research. In the area of toxicogenomics, researchers are concerned with how genes react to exposure to certain chemicals. The United States Air Force is interested in the effect of exposure to mission-essential chemicals. Although military personnel may come into contact with chemicals such as hydrazine, risk assessment is usually very limited. On the genomic level, risk assessment is a multi-stop and multi-disciplinary process. The process begins with an experiment that exposes cells to …

Comparative Genomic Hybridization Array Analysis, Annette M. Molinaro, Mark J. Van Der Laan, Dan H. Moore

U.C. Berkeley Division of Biostatistics Working Paper Series

At the present time, there is increasing evidence that cancer may be regulated by the number of copies of genes in tumor cells. Through microarray technology it is now possible to measure the number of copies of thousands of genes and gene segments in samples of chromosomal DNA. Microarray comparative genomic hybridization (array CGH) provides the opportunity to both measure DNA sequence copy number gains and losses and map these aberrations to the genomic sequence. Gains can signify the over-expression of oncogenes, genes which stimulate cell growth and have become hyperactive, while losses can signify under-expression of tumor suppressor genes, …

Production Of A Monoclonal Antibody Against Benzo[Α]Pyrene Diol Epoxide Dna Adducts, Brian Peden Austin

Chemistry & Biochemistry Theses & Dissertations

Benzo[α]pyrene is a ubiquitous pollutant produced from the incomplete combustion of organic material such as fossil fuels. It is found in the workplace, urban air, drinking water, and the food supply. Recently, it has been proposed that benzo[α]pyrene may be the causative agent in the formation of lung adenocarcinomas among some Taiwanese women exposed to cooking oil fumes without adequate ventilation. In this study, calf thymus DNA was modified in vitro with benzo[α]pyrene-diol epoxide (BPDE) to a level consistent with that found in biological samples. This DNA of low modification was used as an immunogen in the production of a …

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 …

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 …

Statistical Inference For Simultaneous Clustering Of Gene Expression Data, Katherine S. Pollard, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

Current methods for analysis of gene expression data are mostly based on clustering and classification of either genes or samples. We offer support for the idea that more complex patterns can be identified in the data if genes and samples are considered simultaneously. We formalize the approach and propose a statistical framework for two-way clustering. A simultaneous clustering parameter is defined as a function of the true data generating distribution, and an estimate is obtained by applying this function to the empirical distribution. We illustrate that a wide range of clustering procedures, including generalized hierarchical methods, can be defined as …

Designing An Intelligent System For Genetic Biology Learning, Seenivasagam S.Gangatharan

Student Works (2000-2009)

With the changing education scenario, an issue which has come strongly on how to create intelligent tutoring system to educate learners in a more intelligent way. So a need has emerged for the development of an intelligent tutoring system. This part or thesis describes the design of a collection of intelligent systems under the name GENETIC BIOLOGY for basic genetic biology tutoring. GENETIC BIOLOGY consist of three intelligent systems which arc designed for cell, DNA and gene learning. GENETIC BIOLOGY systems employ natural language processing and various techniques normally used in the construction of intelligent systems. Production rules and frames …

Application Of Ai In Medicine, Tarmizi Amirul Hisyam

Student Works (2000-2009)

From the beginning of human civilization, mankind have been trying to fins solution on how to make life easier. They create, modify and adapt, as they would please their need. From the smallest things in our life to the biggest part of all technologies, has improved our life tremendously. Computer technology nowadays has an important role in education, communication, medicine, and many more. In the field of medicine, we have seen many support systems had been developed and use to help human in their daily lives. Application of AI in medicine was proposed in this reason in mind, as a …

The Translocation Of Barramundi. A Discussion Paper., Makaira Pty Ltd

Fisheries Management Papers

There is recognisable economic benefit to the translocation of barramundi, but there is also a need to ensure the translocation will not adversely impact upon the genetic diversity, introduce disease or impact on the natural environment and biodiversity. This discussion paper has been prepared to provide information to assist in the assessment of the possible impact of translocation of barramundi into and within Western Australia, for the purposed of recreational stock enhancement, aquaculture development and domestic stocking. In contemplating the translocation any aquatic species, signigicant economic and social benefits must be balanced with biological and environmental risks; that is, the …

Abalone Aquaculture In Western Australia. Discussion Paper And Draft Policy Guidelines., Cameron Westaway, Jeff Norriss

Fisheries Management Papers

The purposes of this discussion paper is to highlight relevant issues associated with abalone aquaculture development and outline a set of draft policy guidelines. The paper is being disseminated to members of the aquaculture industry, commercial and recreational fishing bodies and the broader community to allow comment.

Achievements In Wool 1997, Agriculture Western Australia

Animal production and livestock published reports

The Wool Strategy Group, which I initiated in 1993, and Agriculture Western Australia's Wool Program are strategic partners working together with industry to develop and market this State's wool industry.

Wool is Western Australia's second most important agricultural industry, with a current export value of $643 million. It has the potential to return to a billion dollar industry in the next five years and the industry needs to be strongly focused on producing what the market requires to take advantage of this.

The Wool Strategy Group, led by Chairman Mr Philip Gardiner, and the Wool Program, have established an international …

Metal-Resistance Genetically Engineered Bacteria, Sylvia Daunert, Donna Scott, Sridhar Ramanathan

KWRRI Research Reports

Bacterial-based electrochemical and optical sensing systems that respond in a highly selective and sensitive manner to antimonite and arsenite have been developed. This was accomplished by using genetically engineered bacteria bearing one of two plasmids constructed for our studies. The first plasmid, pBGD23, contains the operator/promoter region (O/P) and the gene of the ArsR protein from the ars operon upstream from the β-galactosidase gene. In the absence of antimonite/arsenite, ArsR binds to the 0/P site and prevents the transcription of the genes for ArsR and β-galactosidase, thus blocking expression of these proteins. When antimonite or arsenite is present in the …

A Study Of Euplotes Crassus Telomere Proteins And Related Genes, John Scott Perez

Department of Chemistry: Dissertations, Theses, and Student Research

A novel PCR technique used to amplify Euplotes crassus macronuclear chromosomes was developed to provide scientific proof that an Euplotes crassus 1.0 kb gene is not genetically related to an Oxytricha nova 1.8 kb β-telomere protein gene. Theories and experimental procedures associated with the development of this PCR technique were the product of research that will have a profound impact on future studies of telomere protein genes and telomeric DNA in a multitude of eukaryotic cells. The hypothesis that a β-telomere protein does not exist in Euplotes crassus was supported by the result of this study.

Expression of the recombinant …

Approximation Methods For Singular Diffusions Arising In Genetics, Nacer E. Abrouk

Mathematical Sciences Technical Reports (MSTR)

Stochastic models in population genetics leading to diffusion equations are considered. When the drift and the square of the diffusion coefficients are polynomials, an infinite system of ordinary differential equations for the moments of the diffusion process can be derived using the Martingale property. An example is provided to show how the classical Fokker-Planck Equation approach may not be appropriate for this derivation. A Gauss-Galerkin method for approximating the laws of the diffusion, originally proposed by Dawson (1980), is examined. In the few special cases for which exact solutions are known, comparison shows that the method is accurate and the …

Sheep And Wool Industries Need To Improve Their Performance, Rob Kelly, Tim Marshall

Journal of the Department of Agriculture, Western Australia, Series 4

Today in Western Australia, sheep are run at slightly higher stocking rates, are achieving greater lambing percentages (up JO per cent) and higher wool cuts per animal ( up 0. 6 kg greasy) than in the 1960s. When all components of production are considered, the productivity of sheep fanns has increased by 2. 7 per cent per year over the past 35 years.

The challenge of the next decade is to achieve substantially greater rates of improvement than for past years if the sheep and wool industries are to maintain their significant place in Western Australian agriculture.

The Australian Lupin Collection - Passport Data For Wild And Semi-Domesticated Accessions Introduced Into Australia To 1990, J. C. Clements, W. A. Cowling

Grain and other field crops published reports

This report contains passport (including collection site) data and Commonwealth Plant Introduction (CPI) numbers for all wild and semi-domesticated Lupinus accessions introduced into Australia to 1990 (a total of 1071 accessions with CPI numbers between 10650 and 122692). Scientists or plant breeders with an interest in the characteristics of wild lupins from certain natural environments, such as high soil pH or low rainfall, will find this information invaluable when they select accessions for their experiments. The majority of the accessions were introduced by Western Australian scientists following collecting missions in the Mediterranean region, and the remainder were donated from institutions …

The Homeo Domain Of A Murine Protein Binds 5' To Its Own Homeo Box., Abraham Fainsod, Leonard D. Bogarad, Tarmo Ruusala, Martin Lubin

Dartmouth Scholarship

Nuclear protein extracts from day 12.5 mouse embryos were used to study protein binding to DNA sequences 5' of the Hox 1.5 homeo box. Embryos of this developmental stage are known to express this gene. DNA binding protein blotting and retardation gel techniques show that murine embryonic nuclear proteins specifically bind a 753-base pair (bp) DNA fragment from the region upstream of the Hox 1.5 homeo box. A fusion protein containing the Hox 1.5 homeo domain constructed in lambda gt11 also binds the same 753-bp DNA fragment. Specific binding of the fusion protein to the upstream DNA fragment shows that …

Sequence Alignment With Matched Sections, Jerrold R. Griggs, Philip J. Hanlon, Michael S. Waterman

Faculty Publications

In molecular biology, two finite sequences are compared by displaying one sequence written over another in an alignment. The number of alignments of two sequences is related to the Stanton-Cowan numbers. This paper gives asymptotics for the number of alignments of two sequences of length n with matching sections of size at least b.

Expression Of Epstein-Barr Virus (Ebv) Dna And Cloned Dna Fragments In Human Lymphocytes Following Sendai Virus Envelope-Mediated Gene Transfer, David J. Volsky, Thomas Gross, Faruk Sinangil, Charles Kuszynski, Ronald Bartzatt, Timothy Dambaugh, Elliott Kieff

Chemistry Faculty Proceedings & Presentations

Purified EBV DNA and cloned DNA fragments were trapped in Sendai virus (SV) envelopes during envelope reconstitution. The DNA-loaded reconstituted envelopes (RSVE/DNA) served as gene-transfer vehicles using the capability of RSVE to fuse with normal and tumor cells. The efficiency of RSVE-mediated EBV DNA transfer into lymphoid tumor cells and fresh human lymphocytes was 5-10% of the enveloped 3H-labeled EcoRI fragment B of EBV DNA. Purified intracellular EBV (B95-8 strain) DNA induced EBV nuclear antigen (EBNA) in 0.2-1% of human lymphocytes, transiently stimulated cellular DNA synthesis, but did not fully transform cells. Cloned Sal I F1 fragment [approximately equal to …

The Systematics And Biology Of The Genus Zapus (Mammalia, Rodentia, Zapodidae), Gwilym S. Jones

All-Inclusive List of Electronic Theses and Dissertations

This study was undertaken to determine specific and intraspecific relationships within the genus Zapus (Mammalia, Rodentia, Zapodidae). Subspecies are based on the biological subspecies concept where the subspecies is an evolutionary step between a population and species. Approximately 20,000 Recent specimens and representatives of fossil taxa were examined. Cranial and postcranial characteristics, colors, and when available bacula, sperms and karyotypes were incorporated into the morphological analyses. In addition, published biological data were summarized and analyzed for evidence of primary and secondary isolating mechanisms. Supplemental data were acquired during collection of 450 specimens in midwestern and western United States, western Canada, …

The Association Of 5.8 S With 28s Ribosomal Rna, Nandita Banerjee

Chemistry & Biochemistry Theses & Dissertations

5.8S rRNA is a low molecular weight ribosomal RNA which is noncovalently bonded to the larger ribosomal subunit 28S rRNA; through its 3' end and through its 5' end. This interaction is an integral part of the ribosome, and plays an important role in the ribosome structure and function.

There is a high degree of homology between the 5.8S rRNA primary structures of rat, turtle and chicken. The base sequence of rat 5.8S rRNA differs only in one position from that of turtle and in three positions fr.om that of cl1.icken. Tl1ere is a single purine substitution at the 5' …

Objective Measurement And The Stud Breeder, B R. Beetson

Journal of the Department of Agriculture, Western Australia, Series 4

The movement towards sale of wool by certificate and sample highlights the significance of objective measurement in the Merino stud breeders' selection of his top rams.

This article suggests how stud breeders should use the Department of Agriculture's Flock Testing Service to gain genetic progress in wool producing ability without loss of visual buyer appeal.

Studs' use of the service will be evaluated in 1974.

Grade Herd Recording : 1962-63, Maurice C. Cullity

Journal of the Department of Agriculture, Western Australia, Series 4

A poor season coupled with a 16 per cent, increase in the number of cows tested during 1962-63 led to a drop in the average yields of cows in the Grade Herd Recording Scheme.

Select On Fleece Weight And Cull The Low Producers, W L. Mcgarry

Journal of the Department of Agriculture, Western Australia, Series 4

EFFICIENT calling of maiden ewes before they join the breeding flock is an essential part of any policy of flock improvement.

Removal of the low wool producers should be one of the first considerations when culling the flock.