7 results on '"David C. Ream"'
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2. Biases in the Experimental Annotations of Protein Function and their Effect on Our Understanding of Protein Function Space
- Author
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Alexandra M. Schnoes, David C. Ream, Alexander W. Thorman, Patricia C. Babbitt, and Iddo Friedberg
- Published
- 2013
Catalog
3. Comparative analysis of error-prone replication mononucleotide repeats across baculovirus genomes
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Chun Liang, David C. Ream, Iddo Friedberg, Guo-Hua Huang, Samuel T. Murakami, Emily Schmidt, and Xiao-Wen Cheng
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Genetics ,fp25k acquisition ,Cancer Research ,biology ,DNA polymerase ,viruses ,Strain (biology) ,Genetic Variation ,DNA-Directed DNA Polymerase ,Genome, Viral ,Virus Replication ,Genome ,Viral genome evolution ,Infectious Diseases ,Replication slippage ,Virology ,Replication (statistics) ,biology.protein ,Viral genome replication ,Baculoviridae ,Gene ,Repetitive Sequences, Nucleic Acid - Abstract
Genome replication by the baculovirus DNA polymerase often generates errors in mononucleotide repeat (MNR) sequences due to replication slippage. This results in the inactivation of genes that affects different stages of the cell infection cycle. Here we mapped these MNRs in the 59 baculovirus genomes. We found that the MNR frequencies of baculovirus genomes are different and not correlated with the genome sizes. Although the average A/T content of baculoviruses is 58.67%, the A/T MNR frequency is significantly higher than that of the G/C MNRs. Furthermore, the A7/T7 MNRs are the most frequent of those we studied. Finally, MNR frequencies in different classes of baculovirus genes, such as immediate early genes, show differences between baculovirus genomes, suggesting that the distribution and frequency of different MNRs are unique to each baculovirus species or strain. Therefore, the results of this study can help select appropriate baculoviruses for the development of biological insecticides. more...
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- 2013
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4. Diversity and Expression of RubisCO Genes in a Perennially Ice-Covered Antarctic Lake during the Polar Night Transition
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David C. Ream, Weidong Kong, Rachael M. Morgan-Kiss, and John C. Priscu
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DNA, Bacterial ,Cyanobacteria ,Ribulose-Bisphosphate Carboxylase ,Molecular Sequence Data ,Antarctic Regions ,Real-Time Polymerase Chain Reaction ,Photosynthesis ,Applied Microbiology and Biotechnology ,Haptophyte ,Chlorophyta ,Phytoplankton ,Botany ,Environmental Microbiology ,DNA, Fungal ,Autotrophic Processes ,Ecology ,biology ,Polar night ,fungi ,RuBisCO ,Carbon fixation ,Genetic Variation ,Sequence Analysis, DNA ,biology.organism_classification ,biology.protein ,Seasons ,Water Microbiology ,Polar desert ,Food Science ,Biotechnology - Abstract
The autotrophic communities in the lakes of the McMurdo Dry Valleys, Antarctica, have generated interest since the early 1960s owing to low light transmission through the permanent ice covers, a strongly bimodal seasonal light cycle, constant cold water temperatures, and geographical isolation. Previous work has shown that autotrophic carbon fixation in these lakes provides an important source of organic matter to this polar desert. Lake Bonney has two lobes separated by a shallow sill and is one of several chemically stratified lakes in the dry valleys that support year-round biological activity. As part of an International Polar Year initiative, we monitored the diversity and abundance of major isoforms of RubisCO in Lake Bonney by using a combined sequencing and quantitative PCR approach during the transition from summer to polar winter. Form ID RubisCO genes related to a stramenopile, a haptophyte, and a cryptophyte were identified, while primers specific for form IA/B RubisCO detected a diverse autotrophic community of chlorophytes, cyanobacteria, and chemoautotrophic proteobacteria. Form ID RubisCO dominated phytoplankton communities in both lobes of the lake and closely matched depth profiles for photosynthesis and chlorophyll. Our results indicate a coupling between light availability, photosynthesis, and rbcL mRNA levels in deep phytoplankton populations. Regulatory control of rbcL in phytoplankton living in nutrient-deprived shallow depths does not appear to be solely light dependent. The distinct water chemistries of the east and west lobes have resulted in depth- and lobe-dependent variability in RubisCO diversity, which plays a role in transcriptional activity of the key gene responsible for carbon fixation. more...
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- 2012
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5. Draft Genome of the Multidrug-Resistant Acinetobacter baumannii Strain A155 Clinical Isolate
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Steven E. Fiester, David C. Ream, Brock A. Arivett, Maria Soledad Ramirez, Luis A. Actis, Marcelo E. Tolmasky, and Daniela Centrón
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Contig ,Strain (biology) ,Otras Ciencias Biológicas ,COMPARTIVE GENOMICS ,Biology ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,bacterial infections and mycoses ,Genome ,Microbiology ,Acinetobacter baumannii ,purl.org/becyt/ford/1 [https] ,Ciencias Biológicas ,Human health ,Genetics ,ANTIBIOTIC RESISTANCE ,Prokaryotes ,ACINETOBACTER BAUMANNII ,Multidrug resistant Acinetobacter baumannii ,purl.org/becyt/ford/1.6 [https] ,Molecular Biology ,Pathogen ,DRAFT GENOME ,CIENCIAS NATURALES Y EXACTAS - Abstract
Acinetobacter baumannii is a bacterial pathogen with serious implications for human health, due to increasing reports of multidrug-resistant strains isolated from patients. Total DNA from the multidrug-resistant A. baumannii strain A155 clinical isolate was sequenced to greater than 65x coverage, providing high-quality contig assemblies. Fil: Arivett, Brock A.. Miami University; Estados Unidos Fil: Fiester, Steven E.. Miami University; Estados Unidos Fil: Ream, David C.. Miami University; Estados Unidos Fil: Centron, Daniela. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; Argentina Fil: Ramirez, Maria Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; Argentina Fil: Tolmasky, Marcelo. Fullerton University; Estados Unidos Fil: Actis, Luis A.. Miami University; Estados Unidos more...
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- 2015
6. Draft Genome Sequences of Klebsiella pneumoniae Clinical Type Strain ATCC 13883 and Three Multidrug-Resistant Clinical Isolates
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Amanda L. Roth, Steven E. Fiester, Daniel V. Zurawski, Shrinidhi Kanduru, Amy Summers, Brock A. Arivett, Mitchell G. Thompson, David C. Ream, Luis A. Actis, Clinton K. Murray, and Katrin Mende
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Strain atcc ,Klebsiella pneumoniae ,Human pathogen ,Biology ,Clinical type ,biology.organism_classification ,Genome ,Microbiology ,Multiple drug resistance ,Human health ,chemistry.chemical_compound ,chemistry ,Genetics ,Prokaryotes ,Molecular Biology ,DNA - Abstract
Klebsiella pneumoniae is a Gram-negative human pathogen capable of causing hospital-acquired infections with an increasing risk to human health. The total DNA from four clinically relevant strains was sequenced to >100× coverage, providing high-quality genome assemblies for K. pneumoniae strains ATCC 13883, KP4640, 101488, and 101712. more...
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- 2015
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- View/download PDF
7. Biases in the Experimental Annotations of Protein Function and their Effect on Our Understanding of Protein Function Space
- Author
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Iddo Friedberg, Patricia C. Babbitt, David C. Ream, Alexandra M. Schnoes, and A. Thorman
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FOS: Computer and information sciences ,Protein structure database ,QH301-705.5 ,Sequence analysis ,media_common.quotation_subject ,Computer Science - Information Theory ,0206 medical engineering ,02 engineering and technology ,Computational biology ,Biology ,computer.software_genre ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Annotation ,Protein sequencing ,Genetics ,Animals ,Humans ,Digital Libraries (cs.DL) ,Quantitative Biology - Genomics ,Biology (General) ,Databases, Protein ,Function (engineering) ,Molecular Biology ,Throughput (business) ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,media_common ,Genomics (q-bio.GN) ,0303 health sciences ,Ecology ,Information Theory (cs.IT) ,Small number ,Computational Biology ,Proteins ,Molecular Sequence Annotation ,Computer Science - Digital Libraries ,High-Throughput Screening Assays ,Computational Theory and Mathematics ,FOS: Biological sciences ,Modeling and Simulation ,Data mining ,computer ,020602 bioinformatics ,Research Article - Abstract
The ongoing functional annotation of proteins relies upon the work of curators to capture experimental findings from scientific literature and apply them to protein sequence and structure data. However, with the increasing use of high-throughput experimental assays, a small number of experimental studies dominate the functional protein annotations collected in databases. Here we investigate just how prevalent is the "few articles -- many proteins" phenomenon. We examine the experimentally validated annotation of proteins provided by several groups in the GO Consortium, and show that the distribution of proteins per published study is exponential, with 0.14% of articles providing the source of annotations for 25% of the proteins in the UniProt-GOA compilation. Since each of the dominant articles describes the use of an assay that can find only one function or a small group of functions, this leads to substantial biases in what we know about the function of many proteins. Mass-spectrometry, microscopy and RNAi experiments dominate high throughput experiments. Consequently, the functional information derived from these experiments is mostly of the subcellular location of proteins, and of the participation of proteins in embryonic developmental pathways. For some organisms, the information provided by different studies overlap by a large amount. We also show that the information provided by high throughput experiments is less specific than those provided by low throughput experiments. Given the experimental techniques available, certain biases in protein function annotation due to high-throughput experiments are unavoidable. Knowing that these biases exist and understanding their characteristics and extent is important for database curators, developers of function annotation programs, and anyone who uses protein function annotation data to plan experiments., Accepted to PLoS Computational Biology. Press embargo applies. v4: text corrected for style and supplementary material inserted more...
- Published
- 2013
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