http://lod.bco-dmo.org/id/dataset/471914 eng; USA utf8 dataset Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 2013-11-21 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Predicted regulon of the regulatory RNA ryhB in Vibrio fischeri (Iron regulation in Vibrio project) 2013-11-21 publication 2013-11-21 revision BCO-DMO Linked Data URI 2013-11-21 creation http://lod.bco-dmo.org/id/dataset/471914 Dr Elizabeth Mann Skidaway Institute of Oceanography principalInvestigator Dr Eric Stabb University of Georgia principalInvestigator Dr Eberhard Voit Georgia Institute of Technology principalInvestigator Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. publisher Cite this dataset as: Mann, E., Stabb, E., Voit, E. (2013) Predicted regulon of the regulatory RNA ryhB in Vibrio fischeri (Iron regulation in Vibrio project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2013-11-21 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/471914 [access date] Predicted regulon of the regulatory RNA ryhB in Vibrio fischeri Dataset Description: &lt;p&gt;An RNA-Seq experiment was performed in order to define the regulon of the small, regulatory RNA RyhB in Vibrio fischeri ES114. This was done by comparing the global gene expression in wildtype and ryhB mutant strains of V. fischeri. Since RyhB is de-repressed only under iron limiting conditions, this comparison must be performed when the level of intracellular iron is low.&lt;/p&gt; Methods and Sampling: &lt;p&gt;&amp;nbsp;Wildtype and mutant ryhB strains of ES114 were grown in Aquil media with glucose and NH4 as carbon and nitrogen sources, respectively. Parallel cultures of each strain were resuspended in media containing low iron and followed until the growth rates decreased. At this point, samples for RNA were collected by filtration, stored in RNAlater and later extracted using standard methods. rRNA depleted cDNA libraries were submitted to UGA’s Georgia Genomics Center for sequencing on an Illumina MiSeq instrument.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0929203 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0929203 completed Dr Elizabeth Mann Skidaway Institute of Oceanography 912-655-9782 34 Old Marlboro Road Maynard MA 01754 mann.elizabeth8@gmail.com pointOfContact Dr Eric Stabb University of Georgia 706-542-2414 Department of Microbiology 258B Biological Sciences Building Athens GA 30602 estabb@uga.edu pointOfContact Dr Eberhard Voit Georgia Institute of Technology Wallace H. Coulter Dept. of Biomedical Engineering BME - 4103 Atlanta GA 30332-0535 eberhard.voit@bme.gatech.edu pointOfContact asNeeded Unknown gene_function gene_name gene_identifier predict_bind FPKM_RyhB FPKM_WT FPKM_RyhB_WT Log2_FPKM_RyhB_WT p_value Automated Sequencer theme None, User defined No BCO-DMO term featureType BCO-DMO Standard Parameters Automated DNA Sequencer instrument BCO-DMO Standard Instruments otherRestrictions otherRestrictions Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use. Iron limitation, carbon metabolism and siderophore production in marine bacteria - a systems biology approach https://osprey.bco-dmo.org/project/471905 Iron limitation, carbon metabolism and siderophore production in marine bacteria - a systems biology approach <p>This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).</p> <p>Iron limitation of heterotrophic bacteria has substantial biogeochemical implications, including lower assimilation efficiencies and reduced incorporation of CO2 into biomass. Marine bacterioplankton also have a large impact on iron speciation in seawater through their production of siderophores, ligands with a high affinity for iron. Over 99.9% of the dissolved iron in seawater is strongly bound to organic ligands, which are likely to include siderophores since they have functional groups and conditional stability constants for iron that are similar to chelators detected in situ. Iron limitation and siderophore synthesis are linked since these ligands are produced specifically in response to low intracellular iron concentrations. Neither process is completely understood in marine bacteria. For instance, the production of iron binding ligands in seawater unexpectedly increases, not decreases when iron is added to HNLC regions. One possible explanation is the role of carbon, which complicates studies of both iron limitation and siderophore synthesis. The extent to which low iron concentrations reduce bacterioplankton growth efficiencies or productivity in situ is not well-quantified because of the rapid stimulation of primary production that occurs after iron limitation of phytoplankton is relieved. The resulting increase in available carbon makes it is difficult to distinguish between direct and indirect iron (i.e. carbon) limitation of marine bacteria. Carbon source and availability may also play a secondary but important role in regulating siderophore production, which can be either stimulated or repressed by the addition of glucose.</p> <p>The objective of this project is to model the interacting gene regulatory networks that control iron acquisition and carbon metabolism in gamma -proteobacteria, specifically Vibrio fischeri. Iron and carbon regulatory pathways are tightly linked in a complex web of relationships mediated by global transcriptional regulators (Fur and CRP) and the small RNA RyhB. In order to construct a gene regulatory network model, the PIs will use an integrated systems biology approach that combines computational, bioinformatics based research and laboratory experimentation. Predictions of gene expression, siderophore production and the flux of iron with changing environmental conditions will be validated by quantifying gene expression using qRT-PCR and global transcriptome analyses, as well as determining iron quotas and iron uptake rates.</p> <p>Intellectual Merit: This study will contribute to the general understanding of iron speciation in the upper ocean by elucidating the interactions between iron and carbon limitation, carbon source and siderophore production. The gene regulatory network model will be capable of identifying environmental variables critical to siderophore production and evaluating potential biomarkers for iron limitation. This project will facilitate the discovery of new genes and control mechanisms involved in iron metabolism and shed light on other processes such as virulence and luminescence, which utilize the same or similar interactions and transcription factors. Finally, this approach also provides a framework for synthesizing information on the genetic level and using it to make predictions about processes such as siderophore production that are ecologically important.</p> <p>Broader Impacts: This project will enhance infrastructure for scientific research and education by mentoring young scientists and supporting both outreach programs and course development at several educational levels. Support is requested for graduate students to participate in the proposed research and all three PIs will recruit undergraduates for summer internships, often targeting underrepresented groups. Research Experiences for Teachers supplements are requested to allow two high school science educators to participate in our research at the Skidaway Institute of Oceanography and design a laboratory exercise that will illustrate how microbes respond to nutrient limitation. The aim is to provide a research experience that will strengthen collaborations among educators at both the local and national levels.</p> Iron regulation in Vibrio largerWorkCitation project eng; USA oceans 2013-11-21 0 BCO-DMO catalogue of parameters from Predicted regulon of the regulatory RNA ryhB in Vibrio fischeri (Iron regulation in Vibrio project) Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact http://lod.bco-dmo.org/id/dataset-parameter/471968.rdf Name: gene_function Units: unitless Description: <p>gene function: specific category</p> http://lod.bco-dmo.org/id/dataset-parameter/471969.rdf Name: gene_name Units: unitless Description: <p>gene name</p> http://lod.bco-dmo.org/id/dataset-parameter/471970.rdf Name: gene_identifier Units: unitless Description: <p>The VF_#### code includes a code for the particular organism (VF=Vibrio fischeri) and the gene's location (e.g. VF_0619 and VF_0620 will be adjacent genes)</p> http://lod.bco-dmo.org/id/dataset-parameter/471971.rdf Name: predict_bind Units: unitless Description: <p>Genes marked with a &quot;P&quot; have a predicted RyhB binding site identified by the programs sTarPicker or TargetRNA</p> http://lod.bco-dmo.org/id/dataset-parameter/471972.rdf Name: FPKM_RyhB Units: fragments/kilobase/million fragments mapped Description: <p>RyhB mutant fragments per kilobase of gene per million fragments mapped</p> http://lod.bco-dmo.org/id/dataset-parameter/471973.rdf Name: FPKM_WT Units: fragments/kilobase/million fragments mapped Description: <p>wild type mutant fragments per kilobase of gene per million fragments mapped</p> http://lod.bco-dmo.org/id/dataset-parameter/471974.rdf Name: FPKM_RyhB_WT Units: unitless Description: <p>ratio of RyhB to wild type</p> http://lod.bco-dmo.org/id/dataset-parameter/471975.rdf Name: Log2_FPKM_RyhB_WT Units: unitless Description: <p>log base 2 of ratio</p> http://lod.bco-dmo.org/id/dataset-parameter/471976.rdf Name: p_value Units: unitless Description: <p>probability of significance</p> GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 23759 https://datadocs.bco-dmo.org/file/6YYMwPqiPPlKGW/Vibrio_RNASeq5.csv Vibrio_RNASeq5.csv Primary data file for dataset ID 471914 download https://osprey.bco-dmo.org/dataset/471914/data/download download onLine dataset &lt;p&gt;&amp;nbsp;Wildtype and mutant ryhB strains of ES114 were grown in Aquil media with glucose and NH4 as carbon and nitrogen sources, respectively. Parallel cultures of each strain were resuspended in media containing low iron and followed until the growth rates decreased. At this point, samples for RNA were collected by filtration, stored in RNAlater and later extracted using standard methods. rRNA depleted cDNA libraries were submitted to UGA’s Georgia Genomics Center for sequencing on an Illumina MiSeq instrument.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;Base quality and trimming of reads was assessed using the FastX-Toolkit v0.0.13.2, only reads above a Q30 value were retained. Reads were mapped back to the Vibrio fischeri reference genome using TopHat v1.2.0. Expressed genes and transcripts were assembled for each replicate culture separately using Cufflinks v2.1.1. Cuffmerge v.2.1.1 was then utilized to merge all assemblies from the wildtype and ryhB mutant cultures, respectively. Finally, differentially expressed genes were identified using Cuffdiff v2.1.1.&lt;/p&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; Specified by the Principal Investigator(s) asNeeded 7.x-1.1 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact Automated Sequencer Automated Sequencer PI Supplied Instrument Name: Automated Sequencer PI Supplied Instrument Description:Illumina MiSeq Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.