Carrie D. Nicora Biological Sciences Division Pacific Northwest National Laboratory Biography Publications Institution JoVE Articles Carrie D. Nicora has not added a biography. If you are Carrie D. Nicora and would like to personalize this page please email our Author Liaison for assistance. Publications Urinary Virome Perturbations in Kidney Transplantation Frontiers in Medicine. 2018 | Pubmed ID: 29725592 Optimization for Peptide Sample Preparation for Urine Peptidomics Methods in Molecular Biology (Clifton, N.J.). Apr, 2018 | Pubmed ID: 29623538 Salmonella-Mediated Inflammation Eliminates Competitors for Fructose-Asparagine in the Gut Infection and Immunity. May, 2018 | Pubmed ID: 29483291 Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction Metabolites. Jan, 2018 | Pubmed ID: 29342073 MERS-CoV and H5N1 Influenza Virus Antagonize Antigen Presentation by Altering the Epigenetic Landscape Proceedings of the National Academy of Sciences of the United States of America. Jan, 2018 | Pubmed ID: 29339515 Multiplexed Targeted Mass Spectrometry Assays for Prostate Cancer-associated Urinary Proteins Oncotarget. Nov, 2017 | Pubmed ID: 29254211 LC-SRM-Based Targeted Quantification of Urinary Protein Biomarkers Methods in Molecular Biology (Clifton, N.J.). Nov, 2017 | Pubmed ID: 29116567 Sulfide Generation by Dominant Microorganisms in Hydraulically Fractured Shales MSphere. Jul-Aug, 2017 | Pubmed ID: 28685163 Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in MBio. 06, 2017 | Pubmed ID: 28634240 Targeted Quantification of Functional Enzyme Dynamics in Environmental Samples for Microbially Mediated Biogeochemical Processes Environmental Microbiology Reports. Oct, 2017 | Pubmed ID: 28618201 Phycobilisome Truncation Causes Widespread Proteome Changes in Synechocystis Sp. PCC 6803 PloS One. 2017 | Pubmed ID: 28253354 Effects of Delayed NSAID Administration After Experimental Eccentric Contraction Injury - A Cellular and Proteomics Study PloS One. 2017 | Pubmed ID: 28245256 MPLEx: a Method for Simultaneous Pathogen Inactivation and Extraction of Samples for Multi-omics Profiling The Analyst. Jan, 2017 | Pubmed ID: 28091625 New Roles in Hemicellulosic Sugar Fermentation for the Uncultivated Bacteroidetes Family BS11 The ISME Journal. 03, 2017 | Pubmed ID: 27959345 An Efficient Method for Native Protein Purification in the Selected Range from Prostate Cancer Tissue Digests Chinese Clinical Oncology. Dec, 2016 | Pubmed ID: 28061542 Proteome Remodeling in Response to Sulfur Limitation in " Pelagibacter Ubique" MSystems. Jul-Aug, 2016 | Pubmed ID: 27822545 Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes MSystems. May-Jun, 2016 | Pubmed ID: 27822530 MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses MSystems. May-Jun, 2016 | Pubmed ID: 27822525 The Fungal Cultivar of Leaf-cutter Ants Produces Specific Enzymes in Response to Different Plant Substrates Molecular Ecology. Nov, 2016 | Pubmed ID: 27696597 The Abundant Marine Bacterium Pelagibacter Simultaneously Catabolizes Dimethylsulfoniopropionate to the Gases Dimethyl Sulfide and Methanethiol Nature Microbiology. 05, 2016 | Pubmed ID: 27573103 Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis MBio. 08, 2016 | Pubmed ID: 27555310 Unambiguous Metabolite Identification in High-throughput Metabolomics by Hybrid 1D H NMR/ESI MS Approach Magnetic Resonance in Chemistry : MRC. Dec, 2016 | Pubmed ID: 27539910 Conservation of Protein Abundance Patterns Reveals the Regulatory Architecture of the EGFR-MAPK Pathway Science Signaling. 07, 2016 | Pubmed ID: 27405981 Mining the Human Urine Proteome for Monitoring Renal Transplant Injury Kidney International. 06, 2016 | Pubmed ID: 27165815 Multi-omics Analysis Reveals Regulators of the Response to Nitrogen Limitation in Yarrowia Lipolytica BMC Genomics. Feb, 2016 | Pubmed ID: 26911370 Integrated Omics Analysis of Pathogenic Host Responses During Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism Cell Host & Microbe. Feb, 2016 | Pubmed ID: 26867183 Multi-Omic Dynamics Associate Oxygenic Photosynthesis with Nitrogenase-Mediated H2 Production in Cyanothece Sp. ATCC 51142 Scientific Reports. Nov, 2015 | Pubmed ID: 26525576 Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus Gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants PloS One. 2015 | Pubmed ID: 26317212 Diacyltransferase Activity and Chain Length Specificity of Mycobacterium Tuberculosis PapA5 in the Synthesis of Alkyl β-Diol Lipids Biochemistry. Sep, 2015 | Pubmed ID: 26271001 Subunit Compositions of Arabidopsis RNA Polymerases I and III Reveal Pol I- and Pol III-specific Forms of the AC40 Subunit and Alternative Forms of the C53 Subunit Nucleic Acids Research. Apr, 2015 | Pubmed ID: 25813043 Sensitive Targeted Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells Without Affinity Enrichment Analytical Chemistry. Jan, 2015 | Pubmed ID: 25517423 Perturbations in the Urinary Exosome in Transplant Rejection Frontiers in Medicine. 2014 | Pubmed ID: 25593928 Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements Molecular & Cellular Proteomics : MCP. Dec, 2014 | Pubmed ID: 25433089 Functional Diversification of Maize RNA Polymerase IV and V Subtypes Via Alternative Catalytic Subunits Cell Reports. Oct, 2014 | Pubmed ID: 25284785 Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements Molecular & Cellular Proteomics : MCP. Aug, 2014 | Pubmed ID: 25129695 Proteomics Informed by Transcriptomics Identifies Novel Secreted Proteins in Dermacentor Andersoni Saliva International Journal for Parasitology. Nov, 2014 | Pubmed ID: 25110293 The Fungus Gardens of Leaf-cutter Ants Undergo a Distinct Physiological Transition During Biomass Degradation Environmental Microbiology Reports. Aug, 2014 | Pubmed ID: 24992538 Proteomic Profiles of Five Strains of Oxygenic Photosynthetic Cyanobacteria of the Genus Cyanothece Journal of Proteome Research. Jul, 2014 | Pubmed ID: 24846609 Metabolic Interdependencies Between Phylogenetically Novel Fermenters and Respiratory Organisms in an Unconfined Aquifer The ISME Journal. Jul, 2014 | Pubmed ID: 24621521 Optimization for Peptide Sample Preparation for Urine Peptidomics Clinical Proteomics. Feb, 2014 | Pubmed ID: 24568099 The Identification of Novel Potential Injury Mechanisms and Candidate Biomarkers in Renal Allograft Rejection by Quantitative Proteomics Molecular & Cellular Proteomics : MCP. Feb, 2014 | Pubmed ID: 24335474 A Highly Sensitive Targeted Mass Spectrometric Assay for Quantification of AGR2 Protein in Human Urine and Serum Journal of Proteome Research. Feb, 2014 | Pubmed ID: 24251762 Proteomic and Transcriptomic Analyses of "Candidatus Pelagibacter Ubique" Describe the First PII-independent Response to Nitrogen Limitation in a Free-living Alphaproteobacterium MBio. Nov, 2013 | Pubmed ID: 24281717 Long-gradient Separations Coupled with Selected Reaction Monitoring for Highly Sensitive, Large Scale Targeted Protein Quantification in a Single Analysis Analytical Chemistry. Oct, 2013 | Pubmed ID: 24004026 Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass PloS One. 2013 | Pubmed ID: 23894306 Amino Acid Treatment Enhances Protein Recovery from Sediment and Soils for Metaproteomic Studies Proteomics. Oct, 2013 | Pubmed ID: 23776032 Development of an Ecophysiological Model for Diplosphaera Colotermitum TAV2, a Termite Hindgut Verrucomicrobium The ISME Journal. Sep, 2013 | Pubmed ID: 23657364 Trauma-associated Human Neutrophil Alterations Revealed by Comparative Proteomics Profiling Proteomics. Clinical Applications. Aug, 2013 | Pubmed ID: 23589343 Leucoagaricus Gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-cutter Ant Fungus Gardens Applied and Environmental Microbiology. Jun, 2013 | Pubmed ID: 23584789 Fluctuations in Species-level Protein Expression Occur During Element and Nutrient Cycling in the Subsurface PloS One. 2013 | Pubmed ID: 23472107 Suite of Activity-based Probes for Cellulose-degrading Enzymes Journal of the American Chemical Society. Dec, 2012 | Pubmed ID: 23176123 In Vitro Transcription Activities of Pol IV, Pol V, and RDR2 Reveal Coupling of Pol IV and RDR2 for DsRNA Synthesis in Plant RNA Silencing Molecular Cell. Dec, 2012 | Pubmed ID: 23142082 A Systematic Analysis of a Deep Mouse Epididymal Sperm Proteome Biology of Reproduction. Jun, 2012 | Pubmed ID: 23115268 Metagenomic and Metaproteomic Insights into Bacterial Communities in Leaf-cutter Ant Fungus Gardens The ISME Journal. Sep, 2012 | Pubmed ID: 22378535 Simple Sodium Dodecyl Sulfate-assisted Sample Preparation Method for LC-MS-based Proteomics Applications Analytical Chemistry. Mar, 2012 | Pubmed ID: 22339560 Dynamic Proteome Analysis of Cyanothece Sp. ATCC 51142 Under Constant Light Journal of Proteome Research. Feb, 2012 | Pubmed ID: 22060561 Time-course Analysis of the Shewanella Amazonensis SB2B Proteome in Response to Sodium Chloride Shock Scientific Reports. 2011 | Pubmed ID: 22355544 Trypsin-catalyzed Oxygen-18 Labeling for Quantitative Proteomics Methods in Molecular Biology (Clifton, N.J.). 2011 | Pubmed ID: 21604114 Diurnal Rhythms Result in Significant Changes in the Cellular Protein Complement in the Cyanobacterium Cyanothece 51142 PloS One. 2011 | Pubmed ID: 21364985 Development of a Biomarker for Geobacter Activity and Strain Composition; Proteogenomic Analysis of the Citrate Synthase Protein During Bioremediation of U(VI) Microbial Biotechnology. Jan, 2011 | Pubmed ID: 21255372 Proteome Insights into the Symbiotic Relationship Between a Captive Colony of Nasutitermes Corniger and Its Hindgut Microbiome The ISME Journal. Jan, 2011 | Pubmed ID: 20613792 Proteome Analysis of Borrelia Burgdorferi Response to Environmental Change PloS One. Nov, 2010 | Pubmed ID: 21072190 Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles Environmental Science & Technology. Dec, 2010 | Pubmed ID: 21058662 Transcriptional and Translational Regulatory Responses to Iron Limitation in the Globally Distributed Marine Bacterium Candidatus Pelagibacter Ubique PloS One. May, 2010 | Pubmed ID: 20463970 Proteomic Detection of Non-annotated Protein-coding Genes in Pseudomonas Fluorescens Pf0-1 PloS One. Dec, 2009 | Pubmed ID: 20041161 Proteogenomic Monitoring of Geobacter Physiology During Stimulated Uranium Bioremediation Applied and Environmental Microbiology. Oct, 2009 | Pubmed ID: 19717633 Subunit Compositions of the RNA-silencing Enzymes Pol IV and Pol V Reveal Their Origins As Specialized Forms of RNA Polymerase II Molecular Cell. Jan, 2009 | Pubmed ID: 19110459 Proteomic Analysis of Stationary Phase in the Marine Bacterium "Candidatus Pelagibacter Ubique" Applied and Environmental Microbiology. Jul, 2008 | Pubmed ID: 18469119 Application of the Accurate Mass and Time Tag Approach to the Proteome Analysis of Sub-cellular Fractions Obtained from Rhodobacter Sphaeroides 2.4.1. Aerobic and Photosynthetic Cell Cultures Journal of Proteome Research. Aug, 2006 | Pubmed ID: 16889416 Comparison of Aerobic and Photosynthetic Rhodobacter Sphaeroides 2.4.1 Proteomes Journal of Microbiological Methods. Dec, 2006 | Pubmed ID: 16828186 Phosphoproteome Profiling of Human Skin Fibroblast Cells in Response to Low- and High-dose Irradiation Journal of Proteome Research. May, 2006 | Pubmed ID: 16674116 The MPLEx Protocol for Multi-omic Analyses of Soil Samples Carrie D. Nicora*1, Kristin E. Burnum-Johnson*1, Ernesto S. Nakayasu1, Cameron P. Casey1, Richard A. White III1, Taniya Roy Chowdhury1, Jennifer E. Kyle1, Young-Mo Kim1, Richard D. Smith1, Thomas O. Metz1, Janet K. Jansson1, Erin S. Baker1 1Biological Sciences Division, Pacific Northwest National Laboratory JoVE 57343 Química
The MPLEx Protocol for Multi-omic Analyses of Soil Samples Carrie D. Nicora*1, Kristin E. Burnum-Johnson*1, Ernesto S. Nakayasu1, Cameron P. Casey1, Richard A. White III1, Taniya Roy Chowdhury1, Jennifer E. Kyle1, Young-Mo Kim1, Richard D. Smith1, Thomas O. Metz1, Janet K. Jansson1, Erin S. Baker1 1Biological Sciences Division, Pacific Northwest National Laboratory JoVE 57343 Química