| Structural Rearrangements in DNA Repair Genes in Breast Cancer |
Oct 2011 |
9 pages |
| Authors:
Adrian Lee; PITTSBURGH UNIV PA
|
 | The genetic basis of cancer has been firmly established in the last few decades. Genomic instability is a hallmark feature of virtually all breast cancer cells, and is caused either by inherited mutations in genes that control genomic fidelity and stability (particularly in DNA repair pathways), or somatic mutations that are acquired during breast cancer progression. We hypothesized that structural genomic alterations in the genes that are actually themselves involved ... |
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| Genetic Analysis of a Novel Human Adenovirus With a Serologically Unique Hexon and a Recombinant Fiber Gene |
07 Sep 2011 |
12 pages |
| Authors:
Elizabeth B Liu; Leonardo Ferreyra; Stephen L Fischer; Jorge V Pavan; Silvia V Nates; Nolan R Hudson; Damaris Tirado; David W Dyer; James Chodosh; Donald Seto; Morris S Jones; NAVAL HOSPITAL CAMP PENDLETON CA
|
| In February of 1996 a human adenovirus (formerly known as Ad-Cor-96-487) was isolated from the stool of an AIDS patient who presented with severe chronic diarrhea. To characterize this apparently novel pathogen of potential public health significance, the complete genome of this adenovirus was sequenced to elucidate its origin. Bioinformatic and phylogenetic analyses of this genome demonstrate that this virus, heretofore referred to as HAdV-D58, contains a novel hexon gene ... |
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| Structure and Function of the Splice Variants of TMPRSS2-ERG, a Prevalent Genomic Alteration in Prostate Cancer |
Sep 2011 |
|
| Authors:
Shiv Srivastava; HENRY M JACKSON FOUNDATION ROCKVILLE MD
|
| The most common early genetic defect in prostate cancer (CaP) is the TMPRSS2-ERG gene fusion that results in the expression of the ERG protooncogene. In the context of rearranged genome ERG is transcribed under the control of the androgen inducible TMPRSS2 promoter producing cancer-associated splice variants of ERG. Although, much has been learned in recent years about gene fusions in prostate cancer, the function of TMPRSS2-ERG splice variants is not ... |
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| Investigating the Role of Cyclin D1 in the Promotion of Genomic Instability and Breast Cancer |
Sep 2011 |
60 pages |
| Authors:
Laura L Pontano; J A Diehl; PENNSYLVANIA UNIV PHILADELPHIA
|
| Cyclin D1 deregulation is implicated in the genesis of breast cancer, and elevated cyclin D1 protein expression occurs in the absence of gene amplification, suggesting that post-translational regulation is disrupted during the neoplastic process. Cyclin D1 protein is tightly regulated following the G1/S transition via threonine-286 (T286) phosphorylation and cytoplasmic degradation directed by the SCFFbx4 E3 ubiquitin ligase. Disruption of this regulation is deleterious to cell homeostasis, as nuclear cyclin ... |
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| Interfering Breast Cancer Metastasis by Blocking NGAL Function |
Sep 2011 |
11 pages |
| Authors:
Ralph B Arlinghaus; M D ANDERSON CANCER CENTER HOUSTON TX
|
| NGAL project was initiated based on the genome-wide transcript analysis using RNA samples of 318 breast cancer patients diagnosed in MD Anderson Cancer Center. We found that the transcript of NGAL from the tumor mass correlates with advanced tumor stage, metastatic status and other poor clinical indexes. NGAL (neutrophil gelatinase associated lipocalin) is a glycosylated secreted protein and it also can be detected at high concentration in the plasma of ... |
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| Genome-Wide Association Mapping for Intelligence in Military Working Dogs: Canine Cohort, Canine Intelligence Assessment Regimen, Genome-Wide Single Nucleotide Polymorphism (SNP) Typing, and Unsupervised Classification Algorithm for Genome-Wide Associatio |
Sep 2011 |
39 pages |
| Authors:
Victor T Chan; Camilla A Mauzy; Armando Soto; Jessica A Wagner; Amy D Walters; Jeanette S Frey; Tiffany M Hill; Karen L Overall; Soraya Juarbe-Diaz; Donna Dyer; AIR FORCE RESEARCH LAB WRIGHT-PATTERSON AFB OH HUMAN PERFORMANCE WING (711TH) BIOSCIENCES AND PERFORMANCE DIV/APPLIED BIOTECHNOLOGY BRANCH
|
| This seedling project aimed to genetically map intelligence in the military working dog (MWD) population. A total of 199 canine subjects were recruited from United States working dog contractors. Of the recruited subjects, 153 were tested using the Canine Intelligence Testing Protocol (CITP), developed by Dr. Karen Overall (UPENN) to specifically analyze canine intelligence. CITP allows quantitative assessment of intelligence in individual dogs using a scoring system based on the ... |
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| Identification of Estrogen Receptor Beta Binding Sites in the Human Genomes |
Aug 2011 |
16 pages |
| Authors:
Thien Le; CHICAGO UNIV IL
|
| ER knock-out mice developed prostatic hyperplasia at late age, suggesting an important role of ER in the development of the prostate as well as prostate cancer. Here we describe a study that thoroughly investigates the genomic function of ER . A FLAG-tagged ER was stably expressed in MCF7 C4-12 cells, which allowed ER transcriptional activity to be studied in an ER -independent background. Interestingly, in our chromatin immunoprecipitation followed by ... |
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| Using Computer Models to Identify Common Therapeutic Targets in Host Adapted Bacterial Threat Agents |
Aug 2011 |
56 pages |
| Authors:
Simon Daefler; MOUNT SINAI SCHOOL OF MEDICINE NEW YORK
|
| This proposal seeks to develop computer algorithms for the evaluation of metabolic pathways in bacterial biothreat agents that can be exploited as therapeutic targets. We have completed genome-scale metabolic models for Francisella Schu4 (type A strain, Francisella LVS (type B), Burkholderia mallei, and Burkholderia pseudomallei. Some models were validated by metabolic assays, growth experiments in defined media, and transcriptomic data. Algorithms were developed and implemented for genome scale in silico ... |
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| Francisella tularensis Molecular Typing Using Differential Insertion Sequence Amplification |
Aug 2011 |
13 pages |
| Authors:
Marilynn A Larson; Paul D Fey; Amanda M Bartling; Peter C Iwen; Michael P Dempsey; Stephen C Francesconi; Steven H Hinrichs; NAVAL MEDICAL RESEARCH CENTER SILVER SPRING MD
|
| Tularemia is a potentially fatal disease that is caused by the highly infectious and zoonotic pathogen Francisella tularensis. Despite the monomorphic nature of sequenced F. tularensis genomes, there is a significant degree of plasticity in the organization of genetic elements. The observed variability in these genomes is due primarily to the transposition of direct repeats and insertion sequence (IS) elements. Since current methods used to genotype F. tularensis are time-consuming ... |
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| Systematic Search for Gene-Gene Interaction Effect on Prostate Cancer Risk |
Jul 2011 |
155 pages |
| Authors:
Jielin Sun; WAKE FOREST UNIV WINSTON-SALEM NC
|
| Prostate cancer (PCa) is the most common cancer and the second leading cause of cancer death among men in the United States. Considering that PCa development requires the coordination of many genes, it is expected that simultaneous evaluation of multiple genetic variants can improve the statistical power to detect additional PCa risk variants. Recent improvements in analytical methods and computation make it feasible to search for gene-gene interaction of SNPs ... |
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| Discovery of Metastatic Breast Cancer Suppressor Genes Using Functional Genome Analysis |
Jul 2011 |
17 pages |
| Authors:
Xiaoxing Wang; DANA-FARBER CANCER INST BOSTON MA
|
| I hypothesize that metastasis is governed by specific genetic alterations and that identifying this genetic program will provide candidates for new therapeutic targets. My aim is to discover potential metastasis suppressor genes (MSGs) in murine model of breast cancer metastasis through genome scale loss-of-function studies. As a first step to establish a system for prescreening candidate MSGs among the vast number of gene candidates, I calibrated two in vitro tumor ... |
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| A Genome-Wide Investigation of Autozygosity and Breast Cancer Risk |
Jul 2011 |
33 pages |
| Authors:
Brandon L Pierce; CHICAGO UNIV IL
|
| Longs segments ( 1 megabase) of homozygous DNA are common in the genomes of outbred human populations. Several lines of research indicate that elevated genome-wide homozygosity and runs of homozygosity (RoH) at specific loci may increase breast cancer risk. In this project, we determine if genome-wide RoH content and individual RoHs are more common in breast cancer cases than in controls, using logistic regression methods. Using genome-wide SNP data (525,000 ... |
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| Endoplasmic Reticulum-Associated Degradation Factor ERLIN2: Oncogenic Roles and Molecular Targeting of Breast Cancer |
01 JUN 2011 |
9 pages |
| Authors:
Kezhong Zhang; WAYNE STATE UNIV DETROIT MI
|
| Amplification of the chromosome 8p11-12 region has been found in approximately 15% of human breast cancer and is associated with poor prognosis. Previous genomic analysis has led us to identify an endoplasmic reticulum (ER) lipid raft-associated 2 (ERLIN2) gene as one of candidate oncogenes within the 8p11-12 amplicon in human breast cancer. ERLIN2 is an ER membrane protein that was recently identified as a novel mediator of ER-associated degradation. In ... |
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| Integrative Functional Genomics and Proteomics to Uncover Mechanisms of Resistance to Chemotherapy in Ovarian Cancer |
01 JUN 2011 |
8 pages |
| Authors:
Jeremy Chien; MAYO CLINIC ROCHESTER MN
|
| Ovarian cancer affects approximately 22,000 women and kills approximately 16,000 women each year in the United States. Resistance to chemotherapy is the major contributing factor in ovarian cancer-related death. The primary objective of this study is to gain mechanistic insights into the development of chemotherapy resistance in ovarian cancer. We expect that advances in this study will contribute to our understanding of chemotherapy resistance in ovarian cancer and will facilitate ... |
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| Histone Code Modulation by Oncogenic PWWP-Domain Protein in Breast Cancers |
JUN 2011 |
12 pages |
| Authors:
Zeng-Quan Yang; WAYNE STATE UNIV DETROIT MI
|
| Amplification of 8p11-12 occurs in approximately 15% of human breast cancer (HBC), and this region of amplification is significantly associated with disease-specific survival and distant recurrence in breast cancer patients. Earlier, we used genomic analysis of copy number and gene expression to perform a detailed analysis of the 8p11-12 amplicon for identifying candidate oncogenes in breast cancer. We identified Wolf-Hirschhorn syndrome candidate 1-like 1 (WHSC1L1) as a candidate oncogene based ... |
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| Endoplasmic Reticulum-Associated Degradation Factor ERLIN2: Oncogenic Roles and Molecular Targeting of Breast Cancer |
JUN 2011 |
9 pages |
| Authors:
Zeng-Quan Yang; WAYNE STATE UNIV DETROIT MI
|
| Amplification of the chromosome 8p11-12 region has been found in approximately 15% of human breast cancer and is associated with poor prognosis. Previous genomic analysis has led us to identify an endoplasmic reticulum (ER) lipid raft-associated 2 (ERLIN2) gene as one of candidate oncogenes within the 8p11-12 amplicon in human breast cancer. ERLIN2 is an ER membrane protein that was recently identified as a novel mediator of ER-associated degradation. In ... |
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| Defining Genomic Changes in Triple Negative Breast Cancer in Women of African Descent |
JUN 2011 |
11 pages |
| Authors:
Lisa Baumbach; MIAMI UNIV FL
|
| Breast cancer (BC) is the second leading cause of cancer death among African-American (AA) women, with mortality 20% greater than that in Caucasians (Cauc). However, the basis for such disparity remains an enigma. Recent observations from our laboratory suggest the involvement of unidentified genes contributing to AA BC risk. Matched tumor and normal FFPE samples from Cauc and AA patients were obtained from the UM /Sylvester Breast Tissue Bank (UM/S ... |
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| Defining Genomic Changes in Triple Negative Breast Cancer in Women of African Descent |
JUN 2011 |
11 pages |
| Authors:
Mark Pegram; MIAMI UNIV FL
|
| Breast cancer (BC) is the second leading cause of cancer death among African-American (AA) women, with mortality 20% greater than that in Caucasians (Cauc). However, the basis for such disparity remains an enigma. Recent observations from our laboratory suggest the involvement of unidentified genes contributing to AA BC risk. Matched tumor and normal FFPE samples from Cauc and AA patients were obtained from the UM /Sylvester Breast Tissue Bank (UM/S ... |
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| Function of ZFAND3 in the DNA Damage Response |
Jun 2011 |
21 pages |
| Authors:
Bianca M Sirbu; VANDERBILT UNIV NASHVILLE TN
|
| The DNA-damage response (DDR) functions to maintain genomic integrity and prevent tumorigenesis. Cells in human precancerous lesions contain high levels of DNA damage, potentially resulting from unresolved problems accrued during DNA replication. Such replication stress can arise from stalling of replication forks at DNA lesions. The dynamic coordination of mechanisms that detect and repair these damaged replication forks is the subject of this research. Several mechanisms to repair a damaged ... |
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| A Genome-Wide Breast Cancer Scan in African Americans |
Jun 2011 |
22 pages |
| Authors:
Christopher Haiman; UNIVERSITY OF SOUTHERN CALIFORNIA LOS ANGELES
|
| Genome-wide association studies (GWAS) of breast cancer have been completed among populations of European ancestry, and several regions have been identified that appear to contribute susceptibility to this cancer. However, recent data suggest that not all risk alleles for common cancers will be revealed by studies limited to Whites of European ancestry, and that similar efforts in other racial and ethnic populations will be needed to identify the full spectrum ... |
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| Genomic Instability and Breast Cancer |
Jun 2011 |
43 pages |
| Authors:
Junjie Chen; M D ANDERSON CANCER CENTER HOUSTON TX
|
| Our breast cancer research program initially focused on tumor suppressor BRCA1. In the past few years, we elucidated how BRCA1 is regulated and participates in the maintenance of genomic stability. Our studies demonstrated that loss of BRCA1 function leads to cell cycle checkpoint and repair defects and thus contributes to the development of familial breast cancer. Recently, we expanded our research program beyond BRCA1 and DNA damage responsive pathways. We ... |
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| Androgenic Regulation of White Adipose Tissue-Prostate Cancer Interactions |
MAY 2011 |
17 pages |
| Authors:
Timothy Thompson; M D ANDERSON CANCER CENTER HOUSTON TX
|
| During this year, we generated Glipr1 WT (wild-type) and KO (knockout) male mice, surgically castrated them, and collected the VP and epididymal WAT on days 3, 14, and 35 after castration, as outlined in the Statement of Work ([SOW], Aim 1, Tasks 1-3). We isolated RNA and performed microarray analysis to characterize genes affected by castration in WAT obtained 14 days after castration from both mouse genotypes. Analyses of all ... |
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| The Path of the Blind Watchmaker: A Model of Evolution |
06 APR 2011 |
152 pages |
| Authors:
Andrew A. Poggio; CALIFORNIA UNIV BERKELEY DEPT OF ELECTRICAL ENGINEERING AND COMPUTER SCIENCE
|
| Evolution has been described by Dawkins as a blind watchmaker due to its being unconscious and random but selective and able to produce complex forms. Evolution from an early, primitive organism (the Last Universal Common Ancestor of all life, LUCA) to Homo sapiens is the most dramatic biological process that has taken place on Earth and knowledge of it is important to understanding many aspects of biology including disease prevention ... |
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| Genome-Wide Association Mapping for Intelligence in Military Working Dogs: Development of Advanced Classification Algorithm for Genome-Wide Single Nucleotide Polymorphism (SNP) Data Analysis |
APR 2011 |
21 pages |
| Authors:
Victor T. Chan; Camila A. Mauzy; Armando Soto; Jessica A. Wagner; Amy D. Walters; Jeanette S. Frey; Tiffany M. Hill; Karen L. Overall; Richard M. Wolfe; Lonnie R. Welch; HENRY M JACKSON FOUNDATION FOR THE ADVANCEMENT OF MILITARY MEDICINE WRIGHT-PATTERSON AFB OH
|
| This project collected data to genetically map superior intelligence in the military working dog. A behavioral testing regimen was developed by canine cognitive expert Dr Karen Overall (UPENN) which enabled quantitative intelligence testing of individual dogs and blood samples were taken, and genome-wide SNP typing completed by means of the Affymetrix Canine SNP (single nucleotide polymorphism) Array v2. In order to identify SNP markers for mapping of small-effect-sized genes that ... |
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| Toward Personalized Ovarian Cancer Therapy through the Cancer Genome Atlas |
Apr 2011 |
7 pages |
| Authors:
Douglas Levine; SLOAN-KETTERING INST FOR CANCER RESEARCH NEW YORK
|
| There is a growing recognition that the molecular biology of ovarian cancers is complex and that the disease is correspondingly heterogeneous. There is a need for platforms that can translate molecular findings into useful diagnostic tests for patient stratification, therapeutic decision making, and clinical trial design. The Cancer Genome Atlas (TCGA) pilot project is comprehensively cataloguing the genomic aberrations of advanced serous ovarian carcinoma. The project objective is to identify ... |
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| Chemical Agonists of the PML/Daxx Pathway for Prostate Cancer Therapy |
Apr 2011 |
26 pages |
| Authors:
John Reed; BURNHAM INST LA JOLLA CA
|
| Metastatic, hormone refractory prostate cancer is currently an incurable disease. Consequently, novel therapeutic agents are needed that promote killing of malignant prostate cancer cells in a more efficient, less toxic manner. The goal of this project was to identify chemicals that activate an endogenous anti-cancer mechanism that induces tumor cell suicide and auto-destruction. To achieve this goal, we focused on an intrinsic tumor suppressor system involving the proteins PML and ... |
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| Genomic Signatures of Strain Selection and Enhancement in Bacillus atrophaeus var. globigii, a Historical Biowarfare Simulant |
25 MAR 2011 |
19 pages |
| Authors:
Henry S. Gibbons; Stacey M. Broomall; Lauren A. McNew; Hajnalka Daligault; Carol Chapman; David Bruce; Mark Karavis; Michael Krepps; Paul A. McGregor; Charles Hong; EDGEWOOD CHEMICAL BIOLOGICAL CENTER ABERDEEN PROVING GROUND MD
|
| Background: Despite the decades-long use of Bacillus atrophaeus var. globigii (BG) as a simulant for biological warfare (BW) agents, knowledge of its genome composition is limited. Furthermore, the ability to differentiate signatures of deliberate adaptation and selection from natural variation is lacking for most bacterial agents. We characterized a lineage of BG with a long history of use as a simulant for BW operations, focusing on classical bacteriological markers, metabolic ... |
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| Identification, Characterization and Clinical Development of the New Generation of Breast Cancer Susceptibility Alleles |
MAR 2011 |
68 pages |
| Authors:
Nazneen Rahman; INSTITUTE OF CANCER RESEARCH LONDON (UNITED KINGDOM)
|
| Enter a brief (approximately 200 words) unclassified summary of the most significant finding during the research period. There is considerable evidence that genetic factors play an important role in causing breast cancer, but the genes involved in the majority of breast cancers are currently unknown. Our aim was to identify genetic factors that increase the risk of breast cancer occurring by performing analyses in our unparalleled series familial breast cancer ... |
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| Bureaucracy vs. Bioterrorism: Countering a Globalized Threat |
16 Feb 2011 |
28 pages |
| Authors:
Stephen G Hoffman; AIR WAR COLL MAXWELL AFB AL
|
| Two things are certain: death and taxes! Or maybe just taxes. Scientists are attempting to cheat death with rapidly progressing technologies capable of constructing and manipulating life synthetically from basic chemical elements. While the advancing rates of capability in computing speed, genomics, synthetic biology and nanotechnology have the potential to improve and lengthen life for all humans, they also enable biological weapons that can destroy wide swaths of humanity or ... |
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| Identification of Genes Required for the Survival of BRCA 1-/- Cells |
Feb 2011 |
9 pages |
| Authors:
Stephen Elledge; BRIGHAM AND WOMENS HOSPITAL BOSTON MA
|
| A major obstacle for breast cancer drug discovery is target identification. Despite the wealth of information on copy number alterations and mutations recently available from sequencing efforts such as The Cancer Genome Atlas, identifying new targets for breast cancer therapeutics has proved challenging because causative perturbations cannot be determined from benign changes without functional studies. Genetic shRNA screens are powerful tools for identifying loss-of-function phenotypes in mammalian cells and can ... |
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| Genomic Instability and Breast Cancer |
JAN 2011 |
32 pages |
| Authors:
Junjie Chen; M D ANDERSON CANCER CENTER HOUSTON TX
|
| We are continuing our investigation of mechanisms underlying the maintenance of genomic stability and breast cancer development. Our analyses on BRCA1 and DNA damage response have resulted in the identification of several new components involved in DNA damage signaling pathways and revealed how these pathways act together to ensure genomic stability in response to DNA damage. In addition, we have performed a series of studies focusing on replication checkpoint control, ... |
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| SNIT: SNP Identification for Strain Typing |
Jan 2011 |
6 pages |
| Authors:
Ravi V Satya; Nela Zavaljevski; Jaques Reifman; ARMY MEDICAL RESEARCH AND MATERIEL COMMAND FORT DETRICK MD TELEMEDICINE AND ADVANCED TECH RESEARCH CENTER
|
| With ever-increasing numbers of microbial genomes being sequenced, efficient tools are needed to perform strainlevel identification of any newly sequenced genome. Here, we present the SNP identification for strain typing (SNIT) pipeline, a fast and accurate software system that compares a newly sequenced bacterial genome with other genomes of the same species to identify single nucleotide polymorphisms (SNPs) and small insertions/ deletions (indels). Based on this information, the pipeline analyzes ... |
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| QuartetS: A Fast and Accurate Algorithm for Large-Scale Orthology Detection |
2011 |
12 pages |
| Authors:
Chenggang Yu; Nela Zavaljevski; Valmik Desai; Jaques Reifman; ARMY MEDICAL RESEARCH AND MATERIEL COMMAND FORT DETRICK MD TELEMEDICINE AND ADVANCED TECH RESEARCH CENTER
|
| The unparalleled growth in the availability of genomic data offers both a challenge to develop orthology detection methods that are simultaneously accurate and high throughput and an opportunity to improve orthology detection by leveraging evolutionary evidence in the accumulated sequenced genomes. Here, we report a novel orthology detection method, termed QuartetS, that exploits evolutionary evidence in a computationally efficient manner. Based on the well-established evolutionary concept that gene duplication events ... |
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| High-Redundancy Draft Sequencing of 15 Clinical and Environmental Burkholderia Strains |
Dec 2010 |
3 pages |
| Authors:
Sanghamitra Mukhopadhyay; Maureen K Thomason; Shannon Lentz; Nichole Nolan; Kristin Willner; Jay E Gee; Mindy B Glass; Timothy J Inglis; Adam Merritt; Avram Levy; NAVAL MEDICAL RESEARCH CENTER SILVER SPRING MD BIOLOGICAL DEFENSE RESEARCH DIRECTORATE
|
| The Gram-negative Burkholderia genus includes several species or intracellular bacterial pathogens that pose substantial risk to humans. Jn this study, we have generated draft genome sequences of 15 strains of B. okklhomensis, B. pseudomaUei, B. thaiklndensis, and B. ubonensis to an average sequence read coverage of 25 to 40-fold. |
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| A Commensal Gone Bad: Complete Genome Sequence of the Prototypical Enterotoxigenic Escherichia coli Strain H10407 |
Nov 2010 |
11 pages |
| Authors:
Lisa C Crossman; Roy R Chaudhuri; Scott A Beatson; Timothy J Wells; Mickael Desvaux; Adam F Cunningham; Nicola K Petty; Vivienne Mahon; Carl Brinkley; Jon L Hobman; NAVAL MEDICAL RESEARCH CENTER SILVER SPRING MD ENTERIC DISEASES DEPT
|
| In most cases, Escherichia coli exists as a harmless commensal organism, but it may on occasion cause intestinal and/or extraintestinal disease. Enterotoxigenic E. coli (ETEC) is the predominant cause of E. coli-mediated diarrhea in the developing world and is responsible for a significant portion of pediatric deaths. In this study, we determined the complete genomic sequence of E. coli 810407, a prototypical strain of enterotoxigenic E. coli, which reproducibly elicits ... |
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| Hormonal Involvement in Breast Cancer Gene Amplification |
OCT 2010 |
40 pages |
| Authors:
Susan A. Gerbi; Alexander Brodsky; Ben Raphael; BROWN UNIV PROVIDENCE RI
|
| Our specific aims were to map origins of replication in the breast cancer genome and compare these sites with genomic positions that bind the estrogen receptor (ER) and genomic regions of DNA amplification. Correlations would support our hypothesis that ER adjacent to replication origins may interact with the replication machinery to drive DNA amplification, hallmark of many cancers. We began our experiments with the well-studied breast cancer cell line MCF7. ... |
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| Allelochemical Control of Non-Indigenous Invasive Plant Species Affecting Military Testing and Training Activities |
OCT 2010 |
114 pages |
| Authors:
Jorge M. Vivanco; Mark W. Paschke; Ragan Callaway; COLORADO STATE UNIV FORT COLLINS
|
| Allelopathy is a relatively controversial concept in the ecological literature as it is hard to quantify in the field. Interest in allelopathy has increased in recent years with reports of invasive plants using allelopathy as an invasion mechanism. The present project aimed to understand this process under a variety of conditions including natural habitats and to utilize this basic knowledge in strategies to control invasive plant species affecting military testing ... |
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| Effectiveness of Three Decontamination Treatments Against Influenza Virus Applied to Filtering Facepiece Respirators |
Oct 2010 |
12 pages |
| Authors:
Michael B Lore; TeAnne L Brown; Steven H Hinrichs; Brian K Heimbuch; Joseph D Wander; NEBRASKA UNIV MEDICAL CENTER OMAHA
|
| Single-use filtering facepiece respirators (FFRs) are effective precautions against airborne pathogenic microorganisms; however, during pandemics the demand for FFRs may far exceed availability. Reuse of FFRs following decontamination has been suggested but few studies to date have addressed the feasibility. Concerns regarding biocidal efficacy, filter performance post decontamination and cost of decontamination may affect the adoption of reuse measures. This study examined the effectiveness of three energetic decontamination methods (ultraviolet ... |
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| Discovery of Genomic Breakpoints Affecting Breast Cancer Progression and Prognosis |
Oct 2010 |
34 pages |
| Authors:
Petra den Hollander; BAYLOR COLL OF MEDICINE HOUSTON TX
|
| 157 genomic breakpoints could be confirmed as likely somatic mutations. We focused on breakpoints predicted to lead to fusion transcripts. By RT-PCR we determined that 4 showed a fusion mRNA. In the case of the ARFGEF2/SULF2, a non-functional Sulfatase 2 might be created. To give insight, SULF2 mRNA was knocked down using siRNA. Cells treated with SULF2 siRNA, exhibited a growth advantage enhanced survival, and an advantage in anchorage-independent growth ... |
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| Determination of Metastatic Potential in Breast Tumors by Global Molecular Characterization Using Multiple Modalities |
Oct 2010 |
33 pages |
| Authors:
Richard J Mural; WINDBER RESEARCH INST PA
|
| Breast cancer is the most frequently diagnosed non-skin cancer in women and the second leading cause of cancer related deaths in women today. Early detection has been instrumental in improving outcomes for women with breast cancer. Primary tumors are rarely, if ever, the cause of cancer mortality, rather cancer deaths are the consequence of metastasis. The ability of a tumor to metastasize is a fundamental property which determines the severity ... |
|
| Technology Convergence and National Security |
25 AUG 2010 |
34 pages |
| Authors:
James J. Valdes; NATIONAL DEFENSE UNIV WASHINGTON DC
|
| Many traditional R&D programs have been commodity or capability driven, and based on a perceived threat rather than science and technology * Creates artificial technology stovepipes and incremental advances * Results in never ending game of catch-up to emerging threats * In corporate world, tends to preserve status quo and miss disruptive technologies * We need a transdisciplinary revolution: an integrated and comprehensive science and technology approach that transcends traditional ... |
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| Coordination of BRCA1/BARD1- and MRE11/RAD50/NBS1-Dependent DNA Transactions in Breast Tumor Suppression |
JUL 2010 |
11 pages |
| Authors:
Jean Gautier; Eric Greene; COLUMBIA UNIV NEW YORK MEDICAL CENTER
|
| BRCA1/BARD1 and MRE11/RAD50/NBS1 (MRN) play critical roles in preventing the onset of breast tumorigenesis. This is underscored by the fact that mutations in BRCA1 are associated with the most frequent form of hereditary breast cancer (1) and women who inherit mutations in the BRCA1 gene have an estimated lifetime risk of breast and/or ovarian carcinoma as high as 85% (2). In addition, mutations in NBS1, RAD50 and Mre11 are associated ... |
|
| Histone Code Modulation by Oncogenic PWWP-Domain Protein in Breast Cancers |
JUN 2010 |
35 pages |
| Authors:
Zeng-Quan Yang; WAYNE STATE UNIV DETROIT MI
|
| Earlier, we used genomic analysis of copy number and gene expression to perform a detailed analysis of the 8p11-12 amplicon to identify candidate oncogenes in breast cancer. We identified 21 candidate genes and provided evidence that three genes; LSM-1, TC-1 and BAG4 have transforming properties when over expressed. Recently, we systematically investigated the transforming properties of thirteen newly identified 8p11-12 candidate oncogenes in vitro. We found that WHSC1L1, DDHD2 and ... |
|
| Large-Scale Orthology Predictions for Inferring Gene Functions Across Multiple Species |
Jun 2010 |
6 pages |
| Authors:
Chenggang Yu; Valmik Desai; Nela Zavaljevski; Jaques Reifman; ARMY MEDICAL RESEARCH AND MATERIEL COMMAND FORT DETRICK MD
|
| An effective approach to infer the functions of genes is to use the concept of gene orthology. Because orthologous genes are likely to share similar functions the functions of genes in an unstudied species can be inferred through the functions of their orthologs in a studied model species. To infer gene functions for a multitude of species, we developed a high-throughput orthology prediction method, termed PhyloTrace. PhyloTrace is both highly ... |
|
| Rapid Multi-Locus Sequence Typing Using Microfluidic Biochips |
12 May 2010 |
8 pages |
| Authors:
Timothy D Read; Rosemary S Turingan; Christopher Cook; Heidi Giese; Ulrich H Thomann; Catherine C Hogan; Eugen Tan; Richard F Selden; NAVAL MEDICAL RESEARCH CENTER ROCKVILLE MD BIOLOGICAL DEFENSE RESEARCH DIRECTORATE (BDRD ANNEX)
|
| Multiple locus sequence typing (MLST) has become a central genotyping strategy for analysis of bacterial populations. The scheme involves de novo sequencing of 6-8 housekeeping loci to assign unique sequence types. In this work we adapted MLST to a rapid microfluidics platform in order to enhance speed and reduce laboratory labor time. Methodology/Principal Findings: Using two integrated microfluidic devices, DNA was purified from 100 Bacillus cereus soil isolates, used as ... |
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| Effect of Stromal Adipokines on Breast Cancer Development |
APR 2010 |
24 pages |
| Authors:
Richard A. Woo; SOUTHERN ILLINOIS UNIV SPRINGFIELD
|
| Obesity increases the risk of breast cancer in post-menopausal women. The degree of risk increases proportionally with an increase in adiposity. There is mounting evidence that stromal cells in the tumor microenvironment make pivotal contributions to tumor progression. Adipocytes have been shown to exert their influence on breast cancer cells via two secreted adipocytokines, leptin and adiponectin. Leptin stimulates proliferation and invasiveness of breast cancer cell lines. Conversely, adiponectin is ... |
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| Large Direct Repeats Flank Genomic Rearrangements between a New Clinical Isolate of Francisella tularensis subsp. tularensis A1 and Schu S4 |
03 Feb 2010 |
9 pages |
| Authors:
Ufuk Nalbantoglu; Khalid Sayood; Michael P Dempsey; Peter C Iwen; Stephen C Francesconi; Ravi D Barabote; Gary Xie; Thomas S Brettin; Steven H Hinrichs; Paul D Fey; NAVAL MEDICAL RESEARCH CENTER SILVER SPRING MD
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| Francisella tularensis subspecies tularensis consists of two separate populations A1 and A2. This report describes the complete genome sequence of NE061598, an F. tularensis subspecies tularensis A1 isolated in 1998 from a human with clinical disease in Nebraska, United States of America. The genome sequence was compared to Schu S4, an F. tularensis subspecies tularensis A1a strain originally isolated in Ohio in 1941. It was determined that there were 25 ... |
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| Engineering Complex Microbial Phenotypes with Continuous Genetic Integration and Plasmid Based Multi-Gene Library |
Jan 2010 |
14 pages |
| Authors:
Eleftherios Papoutsakis; DELAWARE UNIV NEWARK DEPT OF CHEMICAL ENGINEERING
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| Scientific and Technical Objectives: To develop tools & strategies to facilitate the development of complex phenotypes in microbial cells by combining DNA from different organisms in order to develop desirable complex traits, such as tolerance for chemicals, such as ethanol (EtOH) and 1,2,4-butanetriol (BT), which are used as testbeds for the proof of the proposed concept. BT is a chemical of interest to Navy for possible production by a biological ... |
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| Finishing Genomes with Limited Resources: Lessons from an Ensemble of Microbial Genomes |
Jan 2010 |
11 pages |
| Authors:
Niranjan Nagarajan; Christopher Cook; MariaPia Di Bonaventura; Hong Ge; Allen Richards; Kimberly A Bishop-Lilly; Robert DeSalle; Timothy D Read; Mihai Pop; NAVAL MEDICAL RESEARCH CENTER SILVER SPRING MD
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| While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still remained elusive. Due to shorter read lengths and limitations in library construction protocols, shotgun sequencing and assembly based on these technologies often results in fragmented assemblies. Correspondingly, while draft assemblies can be obtained in days, finishing can take ... |
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| Molecular Epidemiology of Emerging Adenovirus 14 Associated Respiratory Disease in the United States |
Jan 2010 |
13 pages |
| Authors:
Adriana E Kajon; Xiaoyan Lu; Dean D Erdman; Janice Louie; David Schnurr; Kirsten St George; Marion P Koopmans; Taslim Allibhai; David Metzgar; NAVAL HEALTH RESEARCH CENTER SAN DIEGO CA
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| First isolated in the Netherlands in 1955 during an outbreak of acute respiratory disease (ARD) among military recruits, human adenovirus 14 (HAdV-14) has historically been considered a rare respiratory HAdV. With no precedent of circulation in North America, HAdV-14 has been isolated in the United States since 2003 from military and civilian cases of ARD of variable severity. Genomic analysis of isolates representing different locations and circulation dates showed all ... |
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GENOME
