Genetics and Genomics Commons^™

The Consequences Of Denoising Marker-Based Metagenomic Data, John M. Gaspar, W. K. Thomas

Molecular, Cellular & Biomedical Sciences

No abstract provided.

One Can’T Stand On Its Own: Are Non-Luminescence Traits Necessary For V. Fischeri Colonization Of E. Scolopes?, Feier Liu

Honors Theses and Capstones

Vibrio fischeri and Euprymna scolopes squid establish mutualistic symbiosis and select for each other in the natural environment. V. fischeri provides bioluminescent camouflage for E. scolopes while E. scolopes provides nutrients for V. fischeri. The most intriguing aspect of this relationship is that E. scolopes is highly selective and only allows sustained colonization by luminous, but not dark V. fischeri. Luminescence is the key symbiosis trait; however, other bacterial factors may also allow squid recognition. We hypothesized that there are luminescence linked traits that contribute to colonization. V. fischeri with luminescence variation was isolated and tested for oxidative resistance, …

Sequencing And Analysis Of The Gastrula Transcriptome Of The Brittle Star Ophiocoma Wendtii, Roy Vaughn, Nancy Garnhart, James R. Garey, W. Kelley Thomas, Brian T. Livingston

Hubbard Center for Genome Studies (HCGS)

Background

The gastrula stage represents the point in development at which the three primary germ layers diverge. At this point the gene regulatory networks that specify the germ layers are established and the genes that define the differentiated states of the tissues have begun to be activated. These networks have been well-characterized in sea urchins, but not in other echinoderms. Embryos of the brittle star Ophiocoma wendtii share a number of developmental features with sea urchin embryos, including the ingression of mesenchyme cells that give rise to an embryonic skeleton. Notable differences are that no micromeres are formed during cleavage …

The Effects Of Cytokinin On The Transcriptional Regulation Of Pin Expression In Arabidopsis Thaliana, Elizabeth Burgess

Honors Theses and Capstones

The processes of cell division and differentiation are critical to the development of any multicellular organism. During the formation of plant roots these processes take place at a region of the root tip called the meristem. Cytokinin and auxin are two plant growth hormones that influence this process. Although these two growth hormones are both necessary they also appear in many ways to have an antagonistic relationship. As meristematic root cells undergo differentiation they cease dividing. It has been proposed that the size of the root meristem and thus the overall rate of root growth are determined by the balance …

Dramatic Shifts In Benthic Microbial Eukaryote Communities Following The Deepwater Horizon Oil Spill, Holly M. Bik, Kenneth M. Halanych, Jyotsna Sharma, W. Kelley Thomas

Hubbard Center for Genome Studies (HCGS)

Benthic habitats harbour a significant (yet unexplored) diversity of microscopic eukaryote taxa, including metazoan phyla, protists, algae and fungi. These groups are thought to underpin ecosystem functioning across diverse marine environments. Coastal marine habitats in the Gulf of Mexico experienced visible, heavy impacts following the Deepwater Horizon oil spill in 2010, yet our scant knowledge of prior eukaryotic biodiversity has precluded a thorough assessment of this disturbance. Using a marker gene and morphological approach, we present an intensive evaluation of microbial eukaryote communities prior to and following oiling around heavily impacted shorelines. Our results show significant changes in community structure, …

Replication Protein A (Rpa70c) Negatively Regulates Ribonucleotide Reductase (Rnr) In The Model Plant Arabidopsis Thaliana, Stacy Wong

Honors Theses and Capstones

Replication protein A (RPA) is a heterotrimeric single-stranded DNA-binding protein that plays an important role in cellular responses to DNA damage. For example, RPA can activate the cell-cycle checkpoint protein ATR in the presence of persisting DNA damage. The model plant Arabidopsis thaliana has 5 functional homologous RPA70 genes which may play specific roles in response to DNA damaging agents. One chemical that causes DNA damage in Arabidopsis is Hydroxyurea (HU), which blocks DNA replication by inhibiting activity in Ribonucleotide Reductase (RNR), an enzyme responsible for the production of free deoxyribonucleotides (dNTPs). In studies of Arabidopsis mutants, atr plants, but …

Transformation Of Tobacco With The Ba5 Cement Protein Gene From Balanus Amphitrite, Matt Marquis

Honors Theses and Capstones

Expressing barnacle cement proteins genes such as the BA5 gene in plants may enable individual study and analysis. This technique is effective since barnacle cement is difficult to work with as a whole in the lab setting. The BA5 gene extracted from Balanus amphitrite is transferred to tobacco leaf tissue using Agrobacterium tumefaciens.

Shifting Patterns Of Natural Variation In The Nuclear Genome Of Caenorhabditis Elegans, Eleanne Solorzano, Kazufusa Okamoto, Pushpa Datla, Way Sung, R. D. Bergeron, W. Kelley Thomas

Hubbard Center for Genome Studies (HCGS)

Background: Genome wide analysis of variation within a species can reveal the evolution of fundamental biological processes such as mutation, recombination, and natural selection. We compare genome wide sequence differences between two independent isolates of the nematode Caenorhabditis elegans (CB4856 and CB4858) and the reference genome (N2). Results: The base substitution pattern when comparing N2 against CB4858 reveals a transition over transversion bias (1.32:1) that is not present in CB4856. In CB4856, there is a significant bias in the direction of base substitution. The frequency of A or T bases in N2 that are G or C bases in CB4856 …

Simple Sequence Repeat Variation In The Daphnia Pulex Genome, Way Sung, Abraham Tucker, R. Daniel Bergeron, Michael Lynch, W. Kelley Thomas

Molecular, Cellular & Biomedical Sciences

Background: Simple sequence repeats (SSRs) are highly variable features of all genomes. Their rapid evolution makes them useful for tracing the evolutionary history of populations and investigating patterns of selection and mutation across gnomes. The recently sequenced Daphnia pulex genome provides us with a valuable data set to study the mode and tempo of SSR evolution, without the inherent biases that accompany marker selection. Results: Here we catalogue SSR loci in the Daphnia pulex genome with repeated motif sizes of 1-100 nucleotides with a minimum of 3 perfect repeats. We then used whole genome shotgun reads to determine the average …

Evolutionary Rates And Gene Dispensability Associate With Replication Timing In The Archaeon Sulfolobus Islandicus, Kenneth M. Flynn, Samuel H. Vohr, Philip J. Hatcher, Vaughn S. Cooper

Molecular, Cellular & Biomedical Sciences

In bacterial chromosomes, the position of a gene relative to the single origin of replication generally reflects its replication timing, how often it is expressed, and consequently, its rate of evolution. However, because some archaeal genomes contain multiple origins of replication, bias in gene dosage caused by delayed replication should be minimized and hence the substitution rate of genes should associate less with chromosome position. To test this hypothesis, six archaeal genomes from the genus Sulfolobus containing three origins of replication were selected, conserved orthologs were identified, and the evolutionary rates (dN and dS) of these orthologs were quantified. Ortholog …

Why Genes Evolve Faster On Secondary Chromosomes In Bacteria, Vaughn S. Cooper, Samuel H. Vohr, Sarah C. Wrocklage, Philip J. Hatcher

Molecular, Cellular & Biomedical Sciences

In bacterial genomes composed of more than one chromosome, one replicon is typically larger, harbors more essential genes than the others, and is considered primary. The greater variability of secondary chromosomes among related taxa has led to the theory that they serve as an accessory genome for specific niches or conditions. By this rationale, purifying selection should be weaker on genes on secondary chromosomes because of their reduced necessity or usage. To test this hypothesis we selected bacterial genomes composed of multiple chromosomes from two genera, Burkholderia and Vibrio, and quantified the evolutionary rates (dN and dS) of all orthologs …

From The Fields To The Molecules: An Investigation Of Mitochondrial Dna Inheritance In Strawberries, Monica Quimby

Inquiry Journal 2010

No abstract provided.

Cloned Meat, Voluntary Food Labeling, And Organic Oreos, Donna M. Byrne

The University of New Hampshire Law Review

[Excerpt] “In December 2006, the Food and Drug Administration (FDA) announced that it had reviewed all the available evidence and was poised to approve meat and milk from cloned animals and their progeny. I remember telling one of my colleagues, a patent law professor, who should be as comfortable with technology as anyone, about this development, and his response was, “Yuck. I’m not eating it!” To which of course I replied, “Humph. You won’t know the difference.” Meat or milk from a clone or its descendant is virtually identical to meat or milk from a non-clone, said the FDA, as …

Insertion Sequence Content Reflects Genome Plasticity In Strains Of The Root Nodule Actinobacterium Frankia, Derek M. Bickhart, Johann P. Gogarten, Pascal Lapierre, Louis S. Tisa, Philippe Normand, David R. Benson

Molecular, Cellular & Biomedical Sciences

Background: Genome analysis of three Frankia sp. strains has revealed a high number of transposable elements in two of the strains. Twelve out of the 20 major families of bacterial Insertion Sequence (IS) elements are represented in the 148 annotated transposases of Frankia strain HFPCcI3 (CcI3) comprising 3% of its total coding sequences (CDS). EAN1pec (EAN) has 183 transposase ORFs from 13 IS families comprising 2.2% of its CDS. Strain ACN14a (ACN) differs significantly from the other strains with only 33 transposase ORFs (0.5% of the total CDS) from 9 IS families. Results: Insertion sequences in the Frankia genomes were …

Understanding The Physical Properties That Control Protein Crystallization By Analysis Of Largescale Experimental Data, W. Nicholson Price Ii, Yang Chen, Samuel K. Handelman, Helen Neely, Philip Manor, Richard Karlin, Rajesh Nair, Jinfeng Liu, Michael Baran, John Everett, Saichiu N. Tong, Farhad Forouhar, Swarup S. Swaminathan, Thomas Acton, Rong Xiao, Joseph R. Luft, Angela Lauricella, George T. Detitta, Burkhard Rost, Gaetano T. Montelione, John T. Hunt

Law Faculty Scholarship

Crystallization is the most serious bottleneck in high-throughput protein-structure determination by diffraction methods. We have used data mining of the large-scale experimental results of the Northeast Structural Genomics Consortium and experimental folding studies to characterize the biophysical properties that control protein crystallization. This analysis leads to the conclusion that crystallization propensity depends primarily on the prevalence of well-ordered surface epitopes capable of mediating interprotein interactions and is not strongly influenced by overall thermodynamic stability. We identify specific sequence features that correlate with crystallization propensity and that can be used to estimate the crystallization probability of a given construct. Analyses of …

Comparative Secretome Analysis Suggests Low Plant Cell Wall Degrading Capacity In Frankia Symbionts, Juliana E. Mastronunzio, Louis S. Tisa, Philippe Normand, David R. Benson

Molecular, Cellular & Biomedical Sciences

Background: Frankia sp. strains, the nitrogen-fixing facultative endosymbionts of actinorhizal plants, have long been proposed to secrete hydrolytic enzymes such as cellulases, pectinases, and proteases that may contribute to plant root penetration and formation of symbiotic root nodules. These or other secreted proteins might logically be involved in the as yet unknown Molecular interactions between Frankia and their host plants. We compared the genome-based secretomes of three Frankia strains representing diverse host specificities. Signal peptide detection algorithms were used to predict the individual secretomes of each strain, and the set of secreted proteins shared among the strains, termed the core …

Sampling Daphnia's Expressed Genes: Preservation, Expansion And Invention Of Crustacean Genes With Reference To Insect Genomes, John K. Colbourne, Brian D. Eads, Joseph Shaw, Elizabeth Bohuski, Darren J. Bauer, Justen Andrews

Hubbard Center for Genome Studies (HCGS)

Background

Functional and comparative studies of insect genomes have shed light on the complement of genes, which in part, account for shared morphologies, developmental programs and life-histories. Contrasting the gene inventories of insects to those of the nematodes provides insight into the genomic changes responsible for their diversification. However, nematodes have weak relationships to insects, as each belongs to separate animal phyla. A better outgroup to distinguish lineage specific novelties would include other members of Arthropoda. For example, crustaceans are close allies to the insects (together forming Pancrustacea) and their fascinating aquatic lifestyle provides an important comparison for understanding the …

Bayer Ag V. Housey Pharmaceuticals: Protection For Biotechnological Research Tools Under Section 271(G) Found Wanting, Matthew Barthalow

The University of New Hampshire Law Review

[Excerpt] "Research tools, a subset of biotechnological inventions protected by process patents, are “tools that scientists use in the laboratory, including cell lines, monoclonal antibodies, reagents, animal models, growth factors, combinatorial chemistry and DNA libraries, clones and cloning tools (such as PCR), methods, laboratory equipment and machines.” Many companies base their business models on the ability to find pharmaceutical products using their proprietary drug discovery research tools. Research tools used for drug discovery ‘include bioinformatic methods for identifying the interaction of certain proteins and their association with disease, methods for confirming protein targets, screening assays to identify molecules active against …

A Bac-Based Physical Map Of The Nile Tilapia Genome, Takayuki Katagiri, Celeste Kidd, Elizabeth Tomasino, Jesse T. Davis, Cassandra Wishon, Justin E. Stern, Karen L. Carleton, Aimee E. Howe, Thomas D. Kocher

Hubbard Center for Genome Studies (HCGS)

Background

Cichlid fishes, particularly tilapias, are an important source of animal protein in tropical countries around the world. To support selective breeding of these species we are constructing genetic and physical maps of the tilapia genome. Physical maps linking collections of BAC clones are a critical resource for both positional cloning and assembly of whole genome sequences.

Results

We constructed a genome-wide physical map of the tilapia genome by restriction fingerprinting 35,245 bacterial artificial chromosome (BAC) clones using high-resolution capillary polyacrylamide gel electrophoresis. The map consists of 3,621 contigs and is estimated to span 1.752 Gb in physical length. An …

Federal Court Adjudication Of State Prisoner Claims For Post-Conviction Dna Testing: A Bifurcated Approach, Dylan Ruga

The University of New Hampshire Law Review

[Excerpt] “Undoubtedly, there are innocent people in prison. Moreover, it is probable that the wrongly convicted, if given a chance to conduct DNA testing on evidence used against them at trial, could establish their innocence. […]

Part II of this Comment will examine the reasoning behind recent circuit court decisions concerning prisoners’ rights to post-conviction genetic testing. I will explain that a bifurcated approach is the appropriate paradigm for reviewing these claims and demonstrate why three of the four circuit courts erred in their analyses. This part also will review the Supreme Court decisions cited by the circuit courts and …

Poorer European Countries Are Less Concerned About Biotechnology Than Richer Countries, Michael Siegrist

RISK: Health, Safety & Environment (1990-2002)

The author examines the relationship between GNP, media coverage, and public perceptions of the utility, risk, and acceptability of medical and food-related applications of biotechnology.

Review Of: Alan Mchughen, Pandora's Picnic Basket: The Potential And Hazards Of Genetically Modified Foods, Shimona Pratap Singh

RISK: Health, Safety & Environment (1990-2002)

Review of the book: Alan McHughen, Pandora's Picnic Basket: The Potential and Hazards of Genetically Modified Foods (Oxford University Press 2000).Acknowledgements, introduction, glossary and abbreviations, resources, index. ISBN 0-19-850674-0 [277 pp. $25.00 Cloth, 198 Madison Avenue, New York, NY 10016-4314].

Review Of: The Human Genome Project And Minority Communities - Ethical, Social, And Political Dilemmas (Raymond A. Zilinskas & Peter J. Balint Eds.), Craig Steven Jepson

RISK: Health, Safety & Environment (1990-2002)

Review of the book: The Human Genome Project and Minority Communities -Ethical, Social, and Political Dilemmas (Raymond A. Zilinskas & Peter J. Balint eds., Praeger Publishers 2001). Preface, index, about the contributors. LC 00-032390; ISBN 0-275-96961-4 [160 pp. $54.50.Cloth, 88 Post Road West, Westport, CT 06881].

Genetic Monitoring In The Workplace: A Tool Not A Solution, Lillian Trettin, Catherine Musham, Richard Jablonski

RISK: Health, Safety & Environment (1990-2002)

The authors differentiate between genetic monitoring and screening, and discuss the potential risks and benefits of predictive testing technologies.

Psychosocial Risks Of Storing And Using Human Tissues In Research, Jon F. Merz

RISK: Health, Safety & Environment (1990-2002)

Dr. Merz argues that genetics technology makes it more compelling that researchers plan more carefully for the collection and disposition of information derived from subjects' tissues and blood.

Genome Research And Traditional Intellectual Property Protection -- A Bad Fit?, Kate H. Murashige

RISK: Health, Safety & Environment (1990-2002)

Dr. Murashige addresses the need for a patent system more closely tailored to the needs of biotechnology. For example, the obviousness requirement may interfere with using patents to recoup high costs of work when it could arguably be done by researchers of ordinary skill.

Social Issues Of Genome Innovation And Intellectual Property, Elaine Alma Draper

RISK: Health, Safety & Environment (1990-2002)

Dr. Draper's focus is the use of personal information derived from genome research. She identifies several potential problems, including access to and control of genetic information, employment discrimination and social stratification. She also recommends possible solutions.

Genome-Wide High-Resolution Mapping By Recurrent Intermating Using Arabidopsis Thaliana As A Model, Sin-Chieh Liu, Stanley Kowalski, Tien-Hung Lan, Kenneth A. Feldmann, Andrew H. Patterson

Law Faculty Scholarship

We demonstrate a method for developing populations suitable for genome-wide high-resolution genetic linkage mapping, by recurrent intermating among F2 individuals derived from crosses between homozygous parents. Comparison of intermated progenies to F2 and “recombinant inbred” (RI) populations from the same pedigree corroborate theoretical expectations that progenies intermated for four generations harbor about threefold more information for estimating recombination fraction between closely linked markers than either RI-selfed or F2 individuals (which are, in fact, equivalent in this regard) . Although intermated populations are heterozygous, homozygous “intermated recombinant inbred” (IN) populations can readily be generated, combining additional information afforded by intermating with …

Review Of: The Genetic Frontier: Ethics, Law, And Policy (Mark S. Frankel & Albert Teich Eds., American Association For The Advancement Of Science 1994), Suzanne A. Sprunger

RISK: Health, Safety & Environment (1990-2002)

Review of: The Genetic Frontier: Ethics, Law, and Policy (Mark S. Frankel & Albert Teich eds., American Association for the Advancement of Science 1994). Acknowledgments, appendix, contributors, figures, index, introduction, notes, references, tables. LC 93-37230, ISBN 0-87168-526-4. [260 pp. Paper $22.95. 1333 H St., NW, Washington DC 20005.]

Maximizing The Return From Genome Research: Introduction, Thomas G. Field Jr.

RISK: Health, Safety & Environment (1990-2002)

Professor Field introduces and explains the origins of the symposium.