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Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages

Description: This article describes the isolation and genomic characterization of 46 phages from environmental samples at various geographic locations in the U.S. infecting a single Arthrobacter sp. strain.
Date: July 17, 2017
Creator: Klyczek, Karen; Bonilla, J. Alfred; Jacobs-Sera, Deborah; Adair, Tamarah; Afram, Patricia; Allen, Katherine G. et al.
Partner: UNT College of Arts and Sciences

Genomic analysis of the symbiotic marine crenarchaeon, Cenarchaeumsymbiosum

Description: Crenarchaea are ubiquitous and abundant microbial constituents of soils, sediments, lakes and ocean waters, yet relatively little is known about their fundamental evolutionary, ecological, and physiological properties. To better describe the ubiquitous nonthermophilic Crenarchaea, we analyzed the genome sequence of one representative, the uncultivated sponge symbiont, Cenarchaeum symbiosum. C. symbiosum genotypes coinhabiting the same host partitioned into two dominant populations, corresponding to previously described a- and b-type ribosomal RNA variants. Although synthetic, overlapping a- and b-type ribotypes harbored significant genetic variability. A single tiling path comprising the dominant a-type genotype was assembled, and used to explore the biological properties of C. symbiosum and its planktonic relatives. Out of a total of 2,066 predicted open reading frames, 36% were more highly conserved with other Archaea. The remainder partitioned between bacteria (18%), eukaryotes (1.5%) and viruses (0.1%). A total of 525 open reading frames were more highly conserved with sequences derived from marine environmental genomic surveys, most probably representing orthologous genes found in free-living planktonic Crenarchaea. The remaining genes partitioned between functional RNAs (2.4%), and hypotheticals (42%) with limited homology to known functional genes. The latter category likely contains genes specifically involved in mediated archaeal-sponge symbiosis. Phylogenetic analyses placed C. symbiosum as a basal crenarchaeon, sharing specific genomic features in common with either Crenarchaea, Euryarchaea, or both. The genome sequence of C. symbiosum reflect a unique and unusual evolutionary, physiological, and ecological history, one remarkably distinct from that of any other previously known microbial lineage.
Date: June 24, 2006
Creator: Hallam, Steven J.; Konstantinidis, Konstantinos T.; Brochier,Celine; Putnam, Nik; Schleper, Christa; Watanabe, Yoh-ichi et al.
Partner: UNT Libraries Government Documents Department

Measurement of background translocation frequencies in individuals with clones

Description: In the leukemia case the unseparated B and T lymphocytes had a high translocation frequency even after 0.0014, respectively. After purging all clones from the data, the translocation frequencies for Bio 8 and Bio 23 were 0.00750.0014 and 0.0073 metaphases were scored for chromosomal aberrations,, specifically reciprocal translocations, using fluorescence in situ hybridization (FISH). Metaphase spreads were used from two healthy, unexposed individuals (not exposed to radiation, chemotherapy or radiotherapy) and one early B- precursor acute lymphocytic leukemia (ALL) patient (metaphase spreads from both separated T lymphocytes and unseparated B and T lymphocytes were scored). All three individuals had an abnormally high translocation frequency. The high translocation frequencies resulted from clonal expansion of specific translocated chromosomes. I show in this thesis that by purging (discounting or removing) clones from the data of unexposed individuals, one can obtain true background translocation frequencies. In two cases, Bio 8 and Bio 23, the measured translocation frequency for chromosomes 1, 2 and 4 was 0.0124 purging all of the clones from the data. This high translocation frequency may be due to a low frequency of some clones and may not be recognized. The separated T lymphocytes had a higher translocation frequency than expected.
Date: August 1, 1996
Creator: Wade, M.J.
Partner: UNT Libraries Government Documents Department

The Human Genome Diversity (HGD) Project. Summary document

Description: In 1991 a group of human geneticists and molecular biologists proposed to the scientific community that a world wide survey be undertaken of variation in the human genome. To aid their considerations, the committee therefore decided to hold a small series of international workshops to explore the major scientific issues involved. The intention was to define a framework for the project which could provide a basis for much wider and more detailed discussion and planning--it was recognized that the successful implementation of the proposed project, which has come to be known as the Human Genome Diversity (HGD) Project, would not only involve scientists but also various national and international non-scientific groups all of which should contribute to the project`s development. The international HGD workshop held in Sardinia in September 1993 was the last in the initial series of planning workshops. As such it not only explored new ground but also pulled together into a more coherent form much of the formal and informal discussion that had taken place in the preceding two years. This report presents the deliberations of the Sardinia workshop within a consideration of the overall development of the HGD Project to date.
Date: December 31, 1993
Partner: UNT Libraries Government Documents Department

Report of the second Human Genome Diversity workshop

Description: The Second Human Genome Diversity Workshop was successfully held at Penn State University from October 29--31, 1992. The Workshop was essentially organized around 7 groups, each comprising approximately 10 participants, representing the sampling issues in different regions of the world. These groups worked independently, using a common format provided by the organizers; this was adjusted as needed by the individual groups. The Workshop began with a presentation of the mandate to the participants, and of the procedures to be followed during the workshop. Dr. Feldman presented a summary of the results from the First Workshop. He and the other organizers also presented brief comments giving their perspective on the objectives of the Second Workshop. Dr. Julia Bodmer discussed the study of European genetic diversity, especially in the context of the HLA experience there, and of plans to extend such studies in the coming years. She also discussed surveys of world HLA laboratories in regard to resources related to Human Genome Diversity. Dr. Mark Weiss discussed the relevance of nonhuman primate studies for understanding how demographic processes, such as mate exchange between local groups, affected the local dispersion of genetic variation. Primate population geneticists have some relevant experience in interpreting variation at this local level, in particular, with various DNA fingerprinting methods. This experience may be relevant to the Human Genome Diversity Project, in terms of practical and statistical issues.
Date: December 31, 1992
Partner: UNT Libraries Government Documents Department

Biochemical basis of drought tolerance in hybrid Populus grown under field production conditions. CRADA final report

Description: The purpose of this cooperative effort was to assess the use of osmotically active compounds as molecular selection criteria for drought tolerance in Populus in a large-scale field trial. It is known that some plant species, and individuals within a plant species, can tolerate increasing stress associated with reduced moisture availability by accumulating solutes. The biochemical matrix of such metabolites varies among species and among individuals. The ability of Populus clones to tolerate drought has equal value to other fiber producers, i.e., the wood products industry, where irrigation is used in combination with other cultural treatments to obtain high dry weight yields. The research initially involved an assessment of drought stress under field conditions and characterization of changes in osmotic constitution among the seven clones across the six moisture levels. The near-term goal was to provide a mechanistic basis for clonal differences in productivity under various irrigation treatments over time.
Date: April 1, 1997
Creator: Tschaplinski, T.J.; Tuskan, G.A. & Wierman, C.
Partner: UNT Libraries Government Documents Department

Effects of seed origin and irrigation on survival and growth of transplanted shrubs

Description: Revegetation is difficult in the Mojave Desert due to limited, erratic precipitation and extreme temperatures. Establishing plant cover by transplanting native shrubs is known to be a promising technique, but many questions still remain regarding its use on a large operational scale. A study was initiated on the US Department of Energy Nevada Test Site (NTS) to determine the effects of seed origin and irrigation on survival and growth of transplanted shrubs. Plants of three species (Larrea tridentata, Ambrosia dumosa, and Atriplex canescens) were grown in a greenhouse and hardened outdoors. Plants of all three species were produced from two seed sources: (1) seed collected from the NTS (Mojave Desert), and (2) commercially available seed collected from outside the NTS. One-year-old containerized plants (180 of each species) were transplanted to a site on the NTS and irrigated with two liters of water at one of the following frequencies: (1) at time of planting only, (2) at time of planting and monthly during the first growing season, and (3) at time of planting and twice monthly during the first growing season. After 16 months, survival of all species was generally greater than 80% and was unaffected by irrigation treatments. Survival of fourwing saltbush was significantly greater from local versus non-local seed. Survival of bursage and creosotebush was generally unaffected by seed origin. Shrub volumes regardless of species or seed origin increased during the first growing season, and then decreased during the second growing season. Shrub volumes for fourwing saltbush were significantly greater for shrubs from local versus non-local seed.
Date: October 1, 1995
Creator: Winkel, V.K.
Partner: UNT Libraries Government Documents Department

Salmonid Gamete Preservation in the Snake River Basin, Annual Report 2002.

Description: In spite of an intensive management effort, chinook salmon (Oncorhynchus tshawytscha) and steelhead (Oncorhynchus mykiss) populations in the Northwest have not recovered and are currently listed as threatened species under the Endangered Species Act. In addition to the loss of diversity from stocks that have already gone extinct, decreased genetic diversity resulting from genetic drift and inbreeding is a major concern. Reduced population and genetic variability diminishes the environmental adaptability of individual species and entire ecological communities. The Nez Perce Tribe (NPT), in cooperation with Washington State University and the University of Idaho, established a germplasm repository in 1992 in order to preserve the remaining salmonid diversity in the region. The germplasm repository provides long-term storage for cryopreserved gametes. Although only male gametes can be cryopreserved, conserving the male component of genetic diversity will maintain future management options for species recovery. NPT efforts have focused on preserving salmon and steelhead gametes from the major river subbasins in the Snake River basin. However, the repository is available for all management agencies to contribute gamete samples from other regions and species. In 2002 a total of 570 viable semen samples were added to the germplasm repository. This included the gametes of 287 chinook salmon from the Lostine River, Catherine Creek, upper Grande Ronde River, Imnaha River (Lookingglass Hatchery), Lake Creek, South Fork Salmon River, Johnson Creek, Big Creek, Capehorn Creek, Marsh Creek, Pahsimeroi River (Pahsimeroi Hatchery), and upper Salmon River (Sawtooth Hatchery) and the gametes of 280 steelhead from the North Fork Clearwater River (Dworshak Hatchery), Fish Creek, Little Sheep Creek, Pahsimeroi River (Pahsimeroi Hatchery) and Snake River (Oxbow Hatchery). In addition, gametes from 60 Yakima River spring chinook and 34 Wenatchee River coho salmon were added to the repository by Washington Department of Fish and Wildlife and Columbia River Intertribal Fish ...
Date: July 1, 2003
Creator: Young, William & Kucera, Paul
Partner: UNT Libraries Government Documents Department

Mice, myths, and men

Description: The author discusses some examples of how different experimental animal systems have helped to answer questions about the effects of radiation, in particular, carcinogenesis, and to indicate how the new experimental model systems promise an even more exciting future. Entwined in these themes will be observations about susceptibility and extrapolation across species. The hope of developing acceptable methods of extrapolation of estimates of the risk of radiogenic cancer increases as molecular biology reveals the trail of remarkable similarities in the genetic control of many functions common to many species. A major concern about even attempting to extrapolate estimates of risks of radiation-induced cancer across species has been that the mechanisms of carcinogenesis were so different among different species that it would negate the validity of extrapolation. The more that has become known about the genes involved in cancer, especially those related to the initial events in carcinogenesis, the more have the reasons for considering methods of extrapolation across species increased.
Date: December 31, 1994
Creator: Fry, R.J.M.
Partner: UNT Libraries Government Documents Department

A theoretical analysis of population genetics of plants on restored habitats

Description: Seed and propagules used for habitat restoration are not likely to be closely adapted to local site conditions. Rapid changes of genotypes frequencies on local microsites and/or microevolution would allow plants to become better adapted to a site. These same factors would help to maintain genetic diversity and ensure the survival of small endangered populations. The authors used population genetics models to examine the selection of genotypes during establishment on restored sites. Vegetative spread was shown to affect selection and significantly reduce genetic diversity. To study general microevolution, the authors linked a model of resource usage with a genetics model and analyzed competition between genotypes. A complex suite of feasible ecogenetic states was shown to result. The state actually resulting would depend strongly on initial conditions. This analysis indicated that genetic structure can vary locally and can produce overall genetic variability that is not simply the result of microsite adaptations. For restoration activities, the implication is that small differences in seed source could lead to large differences in local genetic structure after selection.
Date: July 1, 1997
Creator: Bogoliubov, A.G. & Loehle, C.
Partner: UNT Libraries Government Documents Department

Effect of nutrient limitation on genomic rearrangements in prokaryotes. Final report

Description: During the total agreement period, more than 200 unique heterotrophic aerobic bacteria were isolated from samples of deep subsurface sediments retrieved from depths of 149.2 and 178.9 m of a vertical bore hole at Cerro Negro (CNV1). All the isolates were characterized phylogenetically and deposited to SMCC. Several clones belonging to a family currently believed to be of strictly marine origin (Microscilla) were found among the isolates. The bacteria might be the descendants of those present in marine environment at the time of deposition. This is an important conclusion for the entire deep subsurface Microbial Origins project. The authors determined diversity of populations of prokaryotic genomes of independent bacterial clones isolated from both surface soil, and subsurface sediments. The degree of diversity for deep subsurface isolates was exceedingly high, much higher than that observed for surface soil isolates. The authors have found that the genomes of some subsurface isolates are significantly more plastic than those for strains isolated from surface environments. The most intriguing discovery was isolation and cultivation of populations of nonplateable novel ultra small bacteria, which are phylogenetically more close to chloroplasts of higher plants, than any other existing bacteria including Cyanobacteria.
Date: March 1, 1998
Creator: Zlatkin, I.V. & Forney, L.J.
Partner: UNT Libraries Government Documents Department

Human Genome Diversity workshop 1

Description: The Human Genome Diversity Project (HGD) is an international interdisciplinary program whose goal is to reveal as much as possible about the current state of genetic diversity among humans and the processes that were responsible for that diversity. Classical premolecular techniques have already proved that a significant component of human genetic variability lies within populations rather than among them. New molecular techniques will permit a dramatic increase in the resolving power of genetic analysis at the population level. Recent social changes in many parts of the world threaten the identity of a number of populations that may be extremely important for understanding human evolutionary history. It is therefore urgent to conduct research on human variation in these areas, while there is still time. The plan is to identify the most representative descendants of ancestral human populations worldwide and then to preserve genetic records of these populations. This is a report of the Population Genetics Workshop (Workshop 1), the first of three to be held to plan HGD, which was focused on sampling strategies and analytic methods from population genetics. The topics discussed were sampling and population structure; analysis of populations; drift versus natural selection; modeling migration and population subdivision; and population structure and subdivision.
Date: December 31, 1992
Partner: UNT Libraries Government Documents Department

Pathways to genetic screening: Patient knowledges, patient practices. Annual report

Description: This study is design to assess the impacts of the integration of genetic knowledge in to the life of high-risk family members. The social and cultural barriers and bridges that incorporation of genetic information will have on these families as well as how they use this genetic information to increase reproductive options and improve the quality of family life are a major focus of this work.
Date: December 31, 1994
Partner: UNT Libraries Government Documents Department

Cycle pattern of a R allelic variation. Progress report, 1 November 1978-31 January 1980

Description: Two R alleles vary in cycle fashion. The original, intensely pigmenting forms change to weakly acting ones which revert in turn to the original. Neither direction of change is correlated with recombination of flanking markers. The reversion frequencies do not differ from the respective frequencies of change in the forward direction. The changes are restricted in the life cycle to about the time of meiosis. Modifying tthe incidence of crossing over in the R region altered the frequency of reversion proportionately. These features of instability could result from switching by intrachromosomal recombination between alternative arrangements of an R segment associated with an inverted duplication.
Date: January 1, 1980
Creator: Kermicle, J.L.
Partner: UNT Libraries Government Documents Department

HIV-1 sequence variation between isolates from mother-infant transmission pairs

Description: To examine the sequence diversity of human immunodeficiency virus type 1 (HIV-1) between known transmission sets, sequences from the V3 and V4-V5 region of the env gene from 4 mother-infant pairs were analyzed. The mean interpatient sequence variation between isolates from linked mother-infant pairs was comparable to the sequence diversity found between isolates from other close contacts. The mean intrapatient variation was significantly less in the infants` isolates then the isolates from both their mothers and other characterized intrapatient sequence sets. In addition, a distinct and characteristic difference in the glycosylation pattern preceding the V3 loop was found between each linked transmission pair. These findings indicate that selection of specific genotypic variants, which may play a role in some direct transmission sets, and the duration of infection are important factors in the degree of diversity seen between the sequence sets.
Date: December 31, 1991
Creator: Wike, C. M.; Daniels, M. R.; Furtado, M.; Wolinsky, M.; Korber, B.; Hutto, C. et al.
Partner: UNT Libraries Government Documents Department

Yakima/Klickitat Fisheries Project - Klickitat Monitoring and Evaluation, 2007 Annual Report.

Description: This report describes the results of monitoring and evaluation (M&E) activities for salmonid fish populations and habitat in the Klickitat River subbasin in south-central Washington. The M&E activities described here were conducted as a part of the Bonneville Power Administration (BPA)-funded Yakima/Klickitat Fisheries Project (YKFP) and were designed by consensus of the scientists with the Yakama Nation (YN) Fisheries Program. YKFP is a joint project between YN and Washington Department of Fish and Wildlife (WDFW). Overall YKFP goals are to increase natural production of and opportunity to harvest salmon and steelhead in the Yakima and Klickitat subbasins using hatchery supplementation, harvest augmentation and habitat improvements. Klickitat subbasin M&E activities have been subjected to scientific and technical review by members of the YKFP Science/Technical Advisory Committee (STAC) as part of the YKFP's overall M&E proposal. Yakama Nation YKFP biologists have transformed the conceptual design into the tasks described. YKFP biologists have also been involved with the Collaborative Systemwide Monitoring and Evaluation Project (CSMEP - a project aimed at improving the quality, consistency, and focus of fish population and habitat data to answer key M&E questions relevant to major decisions in the Columbia Basin) and are working towards keeping Klickitat M&E activities consistent with CSMEP recommendations. This report summarizes progress and results for the following major categories of YN-managed tasks under this contract: (1) Monitoring and Evaluation - to gather baseline information in order to characterize habitat and salmonid populations pre- and post-habitat restoration and pre-supplementation. (2) Ecological Interactions - to determine presence of pathogens in wild and naturally produced salmonids in the Klickitat Basin and develop supplementation strategies using this information. (3) Genetics - to develop YKFP supplementation broodstock collection protocols for the preservation of genetic variability, by refining methods of detecting within-stock genetic variability and between-stock genetic variability.
Date: April 2, 2006
Creator: Zendt, Joe & Babcock, Mike
Partner: UNT Libraries Government Documents Department

Salmonid Gamete Preservation in the Snake River Basin, 2001 Annual Report.

Description: Steelhead (Oncorhynchus mykiss) and chinook salmon (Oncorhynchus tshawytscha) populations in the Northwest are decreasing. Genetic diversity is being lost at an alarming rate. Along with reduced population and genetic variability, the loss of biodiversity means a diminished environmental adaptability. The Nez Perce Tribe (Tribe) strives to ensure availability of genetic samples of the existing male salmonid population by establishing and maintaining a germplasm repository. The sampling strategy, initiated in 1992, has been to collect and preserve male salmon and steelhead genetic diversity across the geographic landscape by sampling within the major river subbasins in the Snake River basin, assuming a metapopulation structure existed historically. Gamete cryopreservation conserves genetic diversity in a germplasm repository, but is not a recovery action for listed fish species. The Tribe was funded in 2001 by the Bonneville Power Administration (BPA) and the U.S. Fish and Wildlife Service Lower Snake River Compensation Plan (LSRCP) to coordinate gene banking of male gametes from Endangered Species Act (ESA) listed steelhead and spring and summer chinook salmon in the Snake River basin. In 2001, a total of 398 viable chinook salmon semen samples from the Lostine River, Catherine Creek, upper Grande Ronde River, Lookingglass Hatchery (Imnaha River stock), Lake Creek, the South Fork Salmon River weir, Johnson Creek, Big Creek, Capehorn Creek, Marsh Creek, Pahsimeroi Hatchery, and Sawtooth Hatchery (upper Salmon River stock) were cryopreserved. Also, 295 samples of male steelhead gametes from Dworshak Hatchery, Fish Creek, Grande Ronde River, Little Sheep Creek, Pahsimeroi Hatchery and Oxbow Hatchery were also cryopreserved. The Grande Ronde chinook salmon captive broodstock program stores 680 cryopreserved samples at the University of Idaho as a long-term archive, half of the total samples. A total of 3,206 cryopreserved samples from Snake River basin steelhead and spring and summer chinook salmon, from 1992 through 2001, are ...
Date: June 1, 2002
Creator: Armstrong, Robyn & Kucera, Paul
Partner: UNT Libraries Government Documents Department

Mutations that Cause Human Disease: A Computational/Experimental Approach

Description: International genome sequencing projects have produced billions of nucleotides (letters) of DNA sequence data, including the complete genome sequences of 74 organisms. These genome sequences have created many new scientific opportunities, including the ability to identify sequence variations among individuals within a species. These genetic differences, which are known as single nucleotide polymorphisms (SNPs), are particularly important in understanding the genetic basis for disease susceptibility. Since the report of the complete human genome sequence, over two million human SNPs have been identified, including a large-scale comparison of an entire chromosome from twenty individuals. Of the protein coding SNPs (cSNPs), approximately half leads to a single amino acid change in the encoded protein (non-synonymous coding SNPs). Most of these changes are functionally silent, while the remainder negatively impact the protein and sometimes cause human disease. To date, over 550 SNPs have been found to cause single locus (monogenic) diseases and many others have been associated with polygenic diseases. SNPs have been linked to specific human diseases, including late-onset Parkinson disease, autism, rheumatoid arthritis and cancer. The ability to predict accurately the effects of these SNPs on protein function would represent a major advance toward understanding these diseases. To date several attempts have been made toward predicting the effects of such mutations. The most successful of these is a computational approach called ''Sorting Intolerant From Tolerant'' (SIFT). This method uses sequence conservation among many similar proteins to predict which residues in a protein are functionally important. However, this method suffers from several limitations. First, a query sequence must have a sufficient number of relatives to infer sequence conservation. Second, this method does not make use of or provide any information on protein structure, which can be used to understand how an amino acid change affects the protein. The experimental methods that provide ...
Date: January 11, 2006
Creator: Beernink, P; Barsky, D & Pesavento, B
Partner: UNT Libraries Government Documents Department