Genome-Wide Expression Analysis In Down Syndrome: Insight Into Immunodeficiency,
2012
Philadelphia College of Osteopathic Medicine
Genome-Wide Expression Analysis In Down Syndrome: Insight Into Immunodeficiency, Chong Li, Lei Jin, Yun Bai, Qimin Chen, Lijun Fu, Minjun Yang, Huasheng Xiao, Guoping Zhao, Shengyue Wang
PCOM Scholarly Works
Down syndrome (DS) is caused by triplication of Human chromosome 21 (Hsa21) and associated with an array of deleterious phenotypes, including mental retardation, heart defects and immunodeficiency. Genome-wide expression patterns of uncultured peripheral blood cells are useful to understanding of DS-associated immune dysfunction. We used a Human Exon microarray to characterize gene expression in uncultured peripheral blood cells derived from DS individuals and age-matched controls from two age groups: neonate (N) and child (C). A total of 174 transcript clusters (gene-level) with eight located on Hsa21 in N group and 383 transcript clusters including 56 on Hsa21 in C group …
Comparative Developmental Transcriptomics Of Echinoderms,
2012
University of South Florida
Comparative Developmental Transcriptomics Of Echinoderms, Roy Vaughn
USF Tampa Graduate Theses and Dissertations
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 …
Lineage-Specific Differences Between Human And Simian
Immunodeficiency Virus Regulation Of Gp120 Trimer Association And
Cd4 Binding,
2012
Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute
Lineage-Specific Differences Between Human And Simian Immunodeficiency Virus Regulation Of Gp120 Trimer Association And Cd4 Binding, Andrés Finzi, Beatriz Pacheco, Shi-Hua Xiang, Marie Pancera, Alon Herschhorn, Liping Wang, Xing Zeng, Anik Desormeaux, Peter D. Kwong, Joseph Sodroski
Nebraska Center for Virology: Faculty Publications
Metastable conformations of the gp120 and gp41 envelope glycoproteins of human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) must be maintained in the unliganded state of the envelope glycoprotein trimer. Binding of gp120 to the primary receptor, CD4, triggers the transition to an open conformation of the trimer, promoting interaction with the CCR5 chemokine receptor and ultimately leading to gp41-mediated virus-cell membrane fusion and entry. Topological layers in the gp120 inner domain contribute to gp120-trimer association in the unliganded state and to CD4 binding. Here we describe similarities and differences between HIV-1 and SIVmac gp120. In both …
Subunit Organization Of The Membrane-Bound Hiv-1 Envelope Glycoprotein Trimer,
2012
Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School
Subunit Organization Of The Membrane-Bound Hiv-1 Envelope Glycoprotein Trimer, Youdong Mao, Liping Wang, Christopher Gu, Alon Herschhorn, Shi-Hua Xiang, Hillel Haim, Xinzhen Yang, Joseph Sodroski
Nebraska Center for Virology: Faculty Publications
The trimeric human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) spike is a molecular machine that mediates virus entry into host cells and is the sole target for virus-neutralizing antibodies. The mature Env spike results from cleavage of a trimeric gp160 precursor into three gp120 and three gp41 subunits. Here we describe an ~11-Å cryo-EM structure of the trimeric HIV-1 Env precursor in its unliganded state. The three gp120 and three gp41 subunits form a cage-like structure with an interior void surrounding the trimer axis. Interprotomer contacts are limited to the gp41 transmembrane region, the torus-like gp41 ectodomain, and …
Comparative Analysis Of The Fusion Efficiency
Elicited By The Envelope Glycoprotein V1–V5
Regions Derived From Human
Immunodeficiency Virus Type 1 Transmitted
Perinatally,
2012
Nankai University
Comparative Analysis Of The Fusion Efficiency Elicited By The Envelope Glycoprotein V1–V5 Regions Derived From Human Immunodeficiency Virus Type 1 Transmitted Perinatally, Hongyan Guo, Levon Abrahamyan, Chang Liu, Mackenzie Waltke, Yunqi Geng, Qimin Chen, Charles Wood, Xiaohong Kong
Nebraska Center for Virology: Faculty Publications
Understanding the properties of viruses preferentially establishing infection during perinatal transmission of human immunodeficiency virus type 1 (HIV-1) is critical for the development of effective measures to prevent transmission. A previous study demonstrated that the newly transmitted viruses (in infants) of chronically infected mother–infant pairs (MIPs) were fitter in terms of growth, which was imparted by their envelope (Env) glycoprotein V1–V5 regions, than those in the corresponding chronically infected mothers. In order to investigate whether the higher fitness of transmitted viruses was conferred by their higher entry efficiency directed by the V1–V5 regions during perinatal transmission, the fusogenicity of Env …
Development And Application Of Methods Used To Source Prehistoric Southwestern Maize: A Review,
2012
U.S. Geological Survey
Development And Application Of Methods Used To Source Prehistoric Southwestern Maize: A Review, Larry Benson
United States Geological Survey: Staff Publications
Archaeological cobs free of mineral contaminants should be used to source the soils in which they were grown. Mineral contaminants often contain much higher concentrations of metals than vegetal materials and can alter a cob’s apparent metal and heavy-isotope content. Cleaning a cob via immersion in an acid solution for more than a few minutes will result in the incongruent and sometimes complete leaching of metals, including strontium (Sr), from the cob. When using 87Sr/86Sr to determine the location of potential agriculture fields, it is best to either integrate several depth-integrated soil samples or to integrate several …
Antibody Responses To Lytic And Latent Human Herpesvirus 8
Antigens Among Hiv-Infected Patients In Central China,
2012
Fudan University
Antibody Responses To Lytic And Latent Human Herpesvirus 8 Antigens Among Hiv-Infected Patients In Central China, Tiejun Zhang, Na He, Yingying Ding, Qingwu Jiang, Charles Wood
Nebraska Center for Virology: Faculty Publications
Human herpesvirus 8 (HHV8) is an important opportunistic infection of HIV/AIDS. However, very little is known about antibody seropositivities to HHV8 lytic and latent antigens among HIVinfected patients in China. Therefore, a cross-sectional study was conducted to explore HHV8 serostatus among 316 HIV-infected patients in a rural area of central China. The antibody seropositivity to HHV8 ORF65 (lytic) and LANA (latent) antigens was 12.7% and 10.4%, respectively. Patients who were naïve to antiretroviral therapy (ART) were more likely to be seropositive for antibodies to ORF65 (OR: 3.79; 95% CI: 1.71–8.42) and LANA (OR: 3.77; 95% CI: 1.55–9.14) than patients receiving …
Heme Oxygenase-1 Regulates The Immune Response To Influenza Virus Infection And Vaccination In Aged Mice,
2012
Mayo Clinic, Rochester
Heme Oxygenase-1 Regulates The Immune Response To Influenza Virus Infection And Vaccination In Aged Mice, Nathan W. Cummins, Eric A. Weaver, Shannon M. May, Anthony J. Croatt, Oded Foreman, Richard B. Kennedy, Gregory A. Polan, Michael A. Barry, Karl A. Nath, Andrew D. Badley
Nebraska Center for Virology: Faculty Publications
Underlying mechanisms of individual variation in severity of influenza infection and response to vaccination are poorly understood. We investigated the effect of reduced heme oxygenase-1 (HO-1) expression on vaccine response and outcome of influenza infection. HO-1-deficient and wild-type (WT) mice (kingdom, Animalia; phylum, Chordata; genus/species, Mus musculus) were infected with influenza virus A/PR/8/34 with or without prior vaccination with an adenoviral-based influenza vaccine. A genome-wide association study evaluated the expression of single-nucleotide polymorphisms (SNPs) in the HO-1 gene and the response to influenza vaccination in healthy humans. HO-1-deficient mice had decreased survival after influenza infection compared to WT mice (median …
Chloroviruses: Not Your Everyday Plant Virus,
2012
University of Nebraska-Lincoln
Chloroviruses: Not Your Everyday Plant Virus, James L. Van Etten, David D. Dunigan
Nebraska Center for Virology: Faculty Publications
Viruses infecting higher plants are among the smallest viruses known and typically have four to ten protein-encoding genes. By contrast, many viruses that infect algae (classified in the virus family Phycodnaviridae) are among the largest viruses found to date and have up to 600 protein- encoding genes. This brief review focuses on one group of plaque-forming phycodnaviruses that infect unicellular chlorella-like green algae. The prototype chlorovirus PBCV-1 has more than 400 protein-encoding genes and 11 tRNA genes. About 40% of the PBCV-1 encoded proteins resemble proteins of known function including many that are completely unexpected for a virus. In many …
Molecular Genetic And Biochemical Characterization Of The Vaccinia
Virus I3 Protein, The Replicative Single-Stranded Dna Binding
Protein,
2012
Department of Microbiology and Molecular Genetics, Medical College of Wisconsin
Molecular Genetic And Biochemical Characterization Of The Vaccinia Virus I3 Protein, The Replicative Single-Stranded Dna Binding Protein, Matthew D. Greseth, Kathleen A. Boyle, Matthew S. Bluma, Bethany Unger, Matthew S. Wiebe, Jamaria A. Soares-Martins, Nadi T. Wickramasekera, James Wahlberg, Paula Traktman
Nebraska Center for Virology: Faculty Publications
Vaccinia virus, the prototypic poxvirus, efficiently and faithfully replicates its approximately 200-kb DNA genome within the cytoplasm of infected cells. This intracellular localization dictates that vaccinia virus encodes most, if not all, of its own DNA replication machinery. Included in the repertoire of viral replication proteins is the I3 protein, which binds to single-stranded DNA (ssDNA) with great specificity and stability and has been presumed to be the replicative ssDNA binding protein (SSB). We substantiate here that I3 colocalizes with bromodeoxyuridine (BrdU)-labeled nascent viral genomes and that these genomes accumulate in cytoplasmic factories that are delimited by membranes derived from …
Distribution Of Genes And Repetitive Elements In The Diabrotica Virgifera Virgifera Genome Estimated Using Bac Sequencing,
2012
USDA-ARS, Ames, Iowa and Iowa State University
Distribution Of Genes And Repetitive Elements In The Diabrotica Virgifera Virgifera Genome Estimated Using Bac Sequencing, Brad S. Coates, Analiza P. Alves, Haichuan Wang, Kimberly K. O. Walden, B. Wade French, Nicholas J. Miller, Craig A. Abel, Hugh M. Robertson, Thomas W. Sappington, Blair D. Siegfried
Department of Entomology: Faculty Publications
Feeding damage caused by the western corn rootworm, Diabrotica virgifera virgifera, is destructive to corn plants in North America and Europe where control remains challenging due to evolution of resistance to chemical and transgenic toxins. A BAC library, DvvBAC1, containing 109,486 clones with 104 ± 34.5 kb inserts was created, which has an ~4.56X genome coverage based upon a 2.58 Gb (2.80 pg) flow cytometry-estimated haploid genome size. Paired end sequencing of 1037 BAC inserts produced 1.17Mb of data (~0.05% genome coverage) and indicated ~9.4 and 16.0% of reads encode, respectively, endogenous genes and transposable elements (TEs). …
High-Resolution Mapping Of Open Chromatin In The Rice Genome,
2012
University of Wisconsin - Madison
High-Resolution Mapping Of Open Chromatin In The Rice Genome, Wenli Zhang, Yufeng Wu, James C. Schnable, Zixian Zeng, Michael Freeling, Gregory E. Crawford, Jiming Jiang
Department of Agronomy and Horticulture: Faculty Publications
Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We generated genome-wide high-resolution maps of DNase I hypersensitive (DH) sites from both seedling and callus tissues of rice (Oryza sativa). Approximately 25% of the DH sites from both tissues were found in putative promoters, indicating that the vast majority of the gene regulatory elements in rice are not located in promoter regions. We found 58% more DH sites in …
Cryptic Distant Relatives Are Common In Both Isolated And Cosmopolitan Genetic Samples,
2012
23andMe
Cryptic Distant Relatives Are Common In Both Isolated And Cosmopolitan Genetic Samples, Brenna M. Henn, Lawrence S. Hon, J. Michael Macpherson, Nicholas Eriksson, Serge Saxonov, Itsik Pe'er, Joanna Mountain
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Although a few hundred single nucleotide polymorphisms (SNPs) suffice to infer close familial relationships, high density genome-wide SNP data make possible the inference of more distant relationships such as 2nd to 9th cousinships. In order to characterize the relationship between genetic similarity and degree of kinship given a timeframe of 100–300 years, we analyzed the sharing of DNA inferred to be identical by descent (IBD) in a subset of individuals from the 23andMe customer database (n = 22,757) and from the Human Genome Diversity Panel (HGDP-CEPH, n = 952). With data from 121 populations, we show that the average amount …
Causes And Consequences Of Mitochondrial Variation In Caenorhabditid Nematodes,
2012
Portland State University
Causes And Consequences Of Mitochondrial Variation In Caenorhabditid Nematodes, Kiley Ann Hicks
Dissertations and Theses
Mitochondria are dynamic organelles that harbor their own stream-lined genome and generate much of the ATP necessary to sustain eukaryotic life via an electron transport chain (ETC). Because of the central role for mitochondria in organismal physiology, mitochondrial genetic and phenotypic variation can alter organismal fitness and affect population genetic and evolutionary outcomes. Despite the far-reaching relevance of mitochondria to evolutionary processes and human health, we lack a basic understanding of the causes and consequences of mitochondrial genetic and phenotypic variation. In this thesis, I quantified mitochondrial reactive oxygen species (ROS), membrane potential (δΨM), and mitochondrial morphological traits within Caenorhabditis …
A Shared Gene Expression Signature In Mouse Models Of Ebv-Associated And Non-Ebv-Associated Burkitt Lymphoma,
2011
Northwestern University
A Shared Gene Expression Signature In Mouse Models Of Ebv-Associated And Non-Ebv-Associated Burkitt Lymphoma, Kathryn T. Bieging, Kamonwan Fish, Subbarao Bondada, Richard Longnecker
Microbiology, Immunology, and Molecular Genetics Faculty Publications
The link between EBV infection and Burkitt lymphoma (BL) is strong, but the mechanism underlying that link has been elusive. We have developed a mouse model for EBV-associated BL in which LMP2A, an EBV latency protein, and MYC are expressed in B cells. Our model has demonstrated the ability of LMP2A to accelerate tumor onset, increase spleen size, and bypass p53 inactivation. Here we describe the results of total gene expression analysis of tumor and pretumor B cells from our transgenic mouse model. Although we see many phenotypic differences and changes in gene expression in pretumor B cells, the transcriptional …
High Connectivity In The Deepwater Snapper Pristipomoides Filamentosus (Lutjanidae) Across The Indo-Pacific With Isolation Of The Hawaiian Archipelago,
2011
University of Hawaii, at Manoa, Kaneohe, USA
High Connectivity In The Deepwater Snapper Pristipomoides Filamentosus (Lutjanidae) Across The Indo-Pacific With Isolation Of The Hawaiian Archipelago, Michelle R. Gaither, Shelley A. Jones, Christopher Kelley, Stephen J. Newman, Laurie Sorenson, Brian W. Bowen
Fisheries Research Articles
In the tropical Indo-Pacific, most phylogeographic studies have focused on the shallow-water taxa that inhabit reefs to approximately 30 m depth. Little is known about the large predatory fishes, primarily snappers (subfamily Etelinae) and groupers (subfamily Epinephelinae) that occur at 100–400 m. These long-lived, slow-growing species support fisheries across the Indo-Pacific, yet no comprehensive genetic surveys within this group have been conducted. Here we contribute the first range-wide survey of a deepwater Indo-Pacific snapper, Pristipomoides filamentosus, with special focus on Hawai'i. We applied mtDNA cytochrome b and 11 microsatellite loci to 26 samples (N = 1,222) collected across …
Reverse Protection Assay: A Tool To Analyze Transcriptional Rates From Individual Promoters,
2011
Dartmouth College
Reverse Protection Assay: A Tool To Analyze Transcriptional Rates From Individual Promoters, Yan O. Zubo, Victor V. Kusnetsov, Thomas Börner, Karsten Liere
Dartmouth Scholarship
Transcriptional activity of entire genes in chloroplasts is usually assayed by run-on analyses. To determine not only the overall intensity of transcription of a gene, but also the rate of transcription from a particular promoter, we created the Reverse RNase Protection Assay (RePro): in-organello run-on transcription coupled to RNase protection to define distinct transcript ends during transcription. We demonstrate successful application of RePro in plastid promoter analysis and transcript 3' end processing.
The Murine Caecal Microrna Signature Depends On The Presence Of The Endogenous Microbiota,
2011
University of Toronto
The Murine Caecal Microrna Signature Depends On The Presence Of The Endogenous Microbiota, Natasha Singh, Elize A. Shirdel, Levi Waldron, Regan-Heng Zhang, Igor Jurisica, Elena M. Comelli
Publications and Research
The intestinal messenger RNA expression signature is affected by the presence and compo-sition of the endogenous microbiota, with effects on host physiology. The intestine is also characterized by a distinctive micronome. However, it is not known if microbes also impact intestinal gene expression epigenetically. We investigated if the murine caecal microRNA expression signature depends on the presence of the microbiota, and the potential implica-tions of this interaction on intestinal barrier function. Three hundred and thirty four mi-croRNAs were detectable in the caecum of germ-free and conventional male mice and 16 were differentially expressed, with samples from the two groups clustering …
Fine Roots Of Aspen Clones In High Salt And Petroleum Hydrocarbon Pollution,
2011
University of Helsinki
Fine Roots Of Aspen Clones In High Salt And Petroleum Hydrocarbon Pollution, Kim Yrjälä, Ivika Ostonen, Shinjini Mukherjee, Timo Sipila, Lu-Min Vaario, Pertti Pulkkinen
Aspen Bibliography
The quality of polluted soil can much be improved and the environmental risks reduced by use of phytoremediation. Harmful hydrocarbon compounds can be degraded through the activity of plant and its associated microbes. We previously showed that PAHs increase aromatic ring-cleavage gene diversity in rhizosphere of birch (Sipilä et al. 2008, Yrjälä et al. 2010a) and the rhizosphere of aspen harbors Burkholderia bacteria able to degrade aromatics (Yrjälä et al. 2010b). The results are promising for successful remediation of polluted soils with woody plants. The aim of our studies is to elucidate the response of the plant and the associated …
Modeling Protein Expression And Protein Signaling Pathways,
2011
UCLA
Modeling Protein Expression And Protein Signaling Pathways, Donatello Telesca, Peter Muller, Steven Kornblau, Marc Suchard, Yuan Ji
COBRA Preprint Series
High-throughput functional proteomic technologies provide a way to quantify the expression of proteins of interest. Statistical inference centers on identifying the activation state of proteins and their patterns of molecular interaction formalized as dependence structure. Inference on dependence structure is particularly important when proteins are selected because they are part of a common molecular pathway. In that case inference on dependence structure reveals properties of the underlying pathway. We propose a probability model that represents molecular interactions at the level of hidden binary latent variables that can be interpreted as indicators for active versus inactive states of the proteins. The …
