Iridovirus and Microsporidian Linked to Honey Bee Colony Decline
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ
SUBMITTER: Cramer, Robert A.
PROVIDER: MSV000078942 | Massive | Wed Nov 19 10:07:00 GMT 2014
SECONDARY ACCESSION(S): PXD001517
REPOSITORIES: MassIVE
Publications
Iridovirus and microsporidian linked to honey bee colony decline.
Bromenshenk Jerry J JJ Henderson Colin B CB Wick Charles H CH Stanford Michael F MF Zulich Alan W AW Jabbour Rabih E RE Deshpande Samir V SV McCubbin Patrick E PE Seccomb Robert A RA Welch Phillip M PM Williams Trevor T Firth David R DR Skowronski Evan E Lehmann Margaret M MM Bilimoria Shan L SL Gress Joanna J Wanner Kevin W KW Cramer Robert A RA
PloS one 20101006 10
In 2010 Colony Collapse Disorder (CCD), again devastated honey bee colonies in the USA, indicating that the problem is neither diminishing nor has it been resolved. Many CCD investigations, using sensitive genome-based methods, have found small RNA bee viruses and the microsporidia, Nosema apis and N. ceranae in healthy and collapsing colonies alike with no single pathogen firmly linked to honey bee losses.We used Mass spectrometry-based proteomics (MSP) to identify and quantify thousands of pro ...[more]
Similar Datasets
Project description:Acclimatization to high altitude over 21 days, and upon re-ascent 7 and 21 days post-descent. See Subudhi et al. (2014) PLoS One 9(3):e92191, PMCID PMC3962396, PMID 24658407 for experiment details. Overall design: 98 total samples representing 21 subjects at 6 time points (not all subjects represented at all time points) were taken. Significance was determined by change vs. baseline (sea level).
| GSE106527 | GEO
Project description:Acclimatization to high altitude over 21 days, and upon re-ascent 7 and 21 days post-descent. See Subudhi et al. (2014) PLoS One 9(3):e92191, PMCID PMC3962396, PMID 24658407 for experiment details. Overall design: 112 total samples representing 21 subjects at 7 time points (not all subjects represented at all time points) were taken. Significance was determined by change vs. baseline (sea level). Genes represented by probesets showing significant change vs. baseline (Benjamini-Hochberg FDR q-value less than or equal to 0.01) at any time point were subject to WGCNA clustering.
| GSE103927 | GEO
Project description:HLA-DR molecules are highly expressed in synovial tissue (ST), the target of the immune response in chronic inflammatory arthritides, including in rheumatoid arthritis (RA) and Lyme arthritis (LA). In the current study, we identified HLA-DR-presented self-peptides (T cell epitopes) in ST, synovial fluid mononuclear cells (SF), and peripheral blood mononuclear cells (PB) from five patients with RA and eight with LA. Altogether, from 22 samples, 1,532 non-redundant HLA-DR-presented peptides were identified that were derived from 778 source proteins. Moreover, as the study progressed, application of newer, high sensitivity LC-MS instruments resulted in the identification of larger numbers of HLA-DR-presented peptides. Surprisingly, the source proteins for HLA-DR-presented peptides were as likely to have intracellular as extracellular locations. Although the number of peptides identified was greater in ST than in SF or PB, 68% of the peptides identified in SF were found in ST, and 55% of the peptides in PB were found in ST. Two RA patients had the same HLA-DR genotype (DRB1*0401 and 0101), and 44% of the peptides identified in these two patients were the same. In contrast, among the patients with RA or LA who had no shared HLA-DR alleles, only 6% of the peptides were the same. In the RA patients, HLA-DR-presented peptides were identified from source proteins that are thought to serve as potential autoantigens: collagen, enolase, fibrinogen, fibronectin, immunoglobulin and vimentin. Interestingly, peptides from these same source proteins were also commonly found in LA patients. However, citrullinated T cell epitopes were not identified in any patient. Thus, LC-MS/MS techniques are now sensitive enough to identify large numbers of T cell epitopes from tissue or fluids in individual patients. Importantly, analysis of SF or PB allowed us to identify a broader range of HLA-DR-presented self-peptides from individual patients and from patients seen earlier in the disease.
2016-10-13 | PXD003051 | Pride
Project description:Growth hormone (GH)-regulated transcription factors, notably STAT5 and BCL6, play a major role in regulating genes showing sex differences in expression in mouse liver, primarily through their effects in male liver, where male-biased genes are up regulated and many female-biased genes are actively repressed. Here we investigate whether complementary mechanisms, involving up regulation of female-biased genes and down regulation of male-biased genes occur in female liver. To address this question, we identified genes regulated by Cux2, a highly female-specific transcription factor that is repressed in male liver and is induced by the female plasma GH pattern in female liver. ChIP-seq analysis identified Cux2 binding sites in female liver only, where they are enriched at sites of male-biased DNase hypersensitivity and at genomic regions showing male-enriched STAT5 binding. Cux2 binding sites were enriched at genes repressed by adenoviral-Cux2, but not at genes induced by adenoviral-Cux2 (see GSE35897), indicating a direct binding mechanism in Cux2 repression but not in Cux2-dependent gene induction. (Published in: TL Conforto et al 2012, Mol Cell Biol. 2012, 32:4611-4627. PubMed PMID: 22966202; PMCID: PMC3486175) Overall design: Mouse livers were excised from individual male and female. Sonicated, cross-linked liver nuclear chromatin was then used to identify Cux2 binding sites by ChIP-Seq using antibody specific to Cux2, amino acids 356 to 415
| GSE35985 | GEO
Project description:Growth hormone (GH)-regulated transcription factors, notably STAT5 and BCL6, play a major role in regulating genes showing sex differences in expression in mouse liver, primarily through their effects in male liver, where male-biased genes are up regulated and many female-biased genes are actively repressed. Here we investigate whether complementary mechanisms, involving up regulation of female-biased genes and down regulation of male-biased genes occur in female liver. To address this question, we identified genes regulated by Cux2, a highly female-specific transcription factor that is repressed in male liver and is induced by the female plasma GH pattern in female liver. ChIP-seq analysis identified Cux2 binding sites in female liver only, where they are enriched at sites of male-biased DNase hypersensitivity and at genomic regions showing male-enriched STAT5 binding. Cux2 binding sites were enriched at genes repressed by adenoviral-Cux2, but not at genes induced by adenoviral-Cux2 (see GSE35897), indicating a direct binding mechanism in Cux2 repression but not in Cux2-dependent gene induction. (Published in: TL Conforto et al 2012, Mol Cell Biol. 2012, 32:4611-4627. PubMed PMID: 22966202; PMCID: PMC3486175) Mouse livers were excised from individual male and female. Sonicated, cross-linked liver nuclear chromatin was then used to identify Cux2 binding sites by ChIP-Seq using antibody specific to Cux2, amino acids 356 to 415
2012-09-10 | E-GEOD-35985 | ArrayExpress
Project description:The putative transcription factor, activity-dependent neuroprotective protein (ADNP) is a zinc finger and homeodomain - like profile containing protein. ADNP knockout mice die at day 9 of gestation. To reveal ADNP-associated pathways, a 22,690- Affymetrix probe array was used on ADNP knockout and control embryos. References:; Complete sequence of a novel protein containing a femtomolar-activity-dependent neuroprotective peptide. J Neurochem. 1999 Mar;72(3):1283-93. PMID: 10037502 [PubMed - indexed for MEDLINE]; Cloning and characterization of the human activity-dependent neuroprotective protein. J Biol Chem. 2001 Jan 5;276(1):708-14. PMID: 11013255 [PubMed - indexed for MEDLINE]; Activity-dependent neuroprotective protein: a novel gene essential for brain formation. Brain Res Dev Brain Res. 2003 Aug 12;144(1):83-90. PMID: 12888219 [PubMed - indexed for MEDLINE] Experiment Overall Design: To identify downstream target genes of ADNP, we examined global gene expression profiles of whole E9 knockout embryos (KO - ADNP -l-), their wild-type (WT - ADNP +l+ ) and their heterozygous (H - ADNP –l+ ) littermates, using the Affymetrix Murine Genome 430A oligonucleotide microarrays. Gestation day 9 was chosen as it is the period at which embryos lacking ADNP exhibit distinct morphological and developmental changes prior to degeneration and in uterus absorption. Total RNA was extracted from four ADNP knockout embryos, four normal embryos and six heterozygous embryos. A pool of two genotype identical littermates was used on seven different arrays (pooling of two embryos was necessary to obtain enough RNA on each of the gene microarrays).
2008-06-12 | E-GEOD-4068 | ArrayExpress
Project description:This is the model described in the article:
Reconstruction of the action potential of ventricular myocardial fibres.
Beeler GW, Reuter H. J Physiol.
1977 Jun;268(1):177-210. Pubmed ID: 874889
, full text
at PubMed central (PMCID:PMC1283659).
Abstract:
1. A mathematical model of membrane action potentials of mammalian ventricular myocardial fibres is described. The reconstruction model is based as closely as possible on ionic currents which have been measured by the voltage-clamp method.
2. Four individual components of ionic current were formulated mathematically in terms of Hodgkin-Huxley type equations. The model incorporates two voltage- and time-dependent inward currents, the excitatory inward sodium current, i(Na), and a secondary or slow inward current, i(s), primarily carried by calcium ions. A time-independent outward potassium current, i(K1), exhibiting inward-going rectification, and a voltage- and time-dependent outward current, i(x1), primarily carried by potassium ions, are further elements of the model.
3. The i(Na) is primarily responsible for the rapid upstroke of the action potential, while the other current components determine the configuration of the plateau of the action potential and the re-polarization phase. The relative importance of inactivation of i(s) and of activation of i(x1) for termination of the plateau is evaluated by the model.
4. Experimental phenomena like slow recovery of the sodium system from inactivation, frequency dependence of the action potential duration, all-or-nothing re-polarization, membrane oscillations are adequately described by the model.
5. Possible inadequacies and shortcomings of the model are discussed.
This model was taken from the CellML repository
and automatically converted to SBML.
The original model was:
Beeler, Reuter, 1977 version 8
The original CellML model was created and curated by:
Catherine May Lloyd
c.lloyd(at)auckland.ac.nz
University of Auckland,
Auckland Bioengineering Institute
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2005-01-01 | MODEL7889395724 | BioModels
Project description:To prevent activation of plant innate immunity the oomycete pathogen Hyaloperonospora arabidopsidis translocates effector proteins into infected cells of its host Arabidopsis thaliana. We noticed that some H. arabidopsidis effectors, when over-expressed in A. thaliana, render the plant more susceptible to infection by biotrophic pathogens (Fabro et al., 2011, PubMed PMID: 22072967). Here we performed transcriptome profiling of a representative transgenic line constitutively expressing H. arabidopsidis effector HaRxL106. We compared the transcriptomes of A. thaliana wild-type (Col-0) plants and an isogenic line expressing HaRxL106 before pathogen challenge and 24 h after infection with the compatible bacterial pathogen Pseudomonas syringae pv. tomato strain DC3000. HaRxL106 interacts with several Arabidopsis proteins (Mukhtar et al., 2011, PubMed PMID: 21798943; Wirthmueller et al., 2015, PubMed PMID: 25284001). To test whether the HaRxL106-interacting A. thaliana proteins MODIFIER OF SNC1, 6 (MOS6), 6B-INTERACTING PROTEIN 1-LIKE 1 (ASIL1) or RADICAL-INDUCED CELL DEATH1 (RCD1) are altered in their transcriptional response to a biotrophic pathogen we performed transcriptome profiling of mos6-1, asil1-1 and rcd1-1 mutants before and 24 h after infection with P. syringae pv. tomato DC3000. Overall design: Five weeks old Arabidopsis plants (Col-0, HaRxL106-overexpressing Col-0 plants, mos6-1, asil1-1 and rcd1-1 mutants) were either left untreated (untreated), infiltrated with P. syringae pv. tomato DC3000 (DC3000) or infiltrated with 10 mM MgCl2 buffer (Mock) at 12:00 (4h after lights on). All samples were harvested 24 hours later for total RNA extraction. mRNA profiles were generated by deep sequencing on Illumina GAIIx using EXPRSS tag-seq protocol. Each biological replicate set of samples were sequenced as one batch (biorep1, biorep2 and biorep3 in filenames).
| GSE89402 | GEO
Project description:In Hymenoptera, sex is determined by a single-locus complementary sex determining system (sl-CSD). Males are normally haploid (hemizygous at the sl-CSD locus) but if the genotype of the sl-CSD locus is homozygous, they develop into diploid males. Here, we study the effects of ploidy and the sl-CSD-locus genotype by comparing gene expression differences between haploid males, diploid males and virgin queens at three developmental stages, pupae, 1 day and 11 days after eclosion. Keywords: diploid males, sl-CSD, ploidy-spcific gene, sex-specific gene, doublesex, sex-biased gene Six-condition experiment: haploid male pupae, diploid male pupae, queen pupae, 1-day-old haploid male adults, 1-day-old diploid male adults, 1-day-old queen adults (accession number GSM1031732 - GSM1031734, GSM1031737 - GSM1031738, GSM1031740 - GSM1031742, GSM1031745 - GSM1031746; reprocessed for this study), 11-day-old haploid male adults, 11-day-old diploid male adults, 11-day-old queen adults (accession number GSM1031748 - GSM1031750, GSM1031753 - GSM1031754, GSM1031756 - GSM1031758, GSM1031761 - GSM1031762; reprocessed for this study). Biological replicates: 5 colonies (x 2 genotypes for each colony). Samples were labeled with Cy3 and were compared to the same common reference RNA labeled with Cy5.
2012-12-06 | E-GEOD-42779 | ArrayExpress
Project description:In Hymenoptera, sex is determined by a single-locus complementary sex determining system (sl-CSD). Males are normally haploid (hemizygous at the sl-CSD locus) but if the genotype of the sl-CSD locus is homozygous, they develop into diploid males. Here, we study the effects of ploidy and the sl-CSD-locus genotype by comparing gene expression differences between haploid males, diploid males and virgin queens at three developmental stages, pupae, 1 day and 11 days after eclosion. Keywords: diploid males, sl-CSD, ploidy-spcific gene, sex-specific gene, doublesex, sex-biased gene Six-condition experiment: haploid male pupae, diploid male pupae, queen pupae, 1-day-old haploid male adults, 1-day-old diploid male adults, 1-day-old queen adults (accession number GSM1031732 - GSM1031734, GSM1031737 - GSM1031738, GSM1031740 - GSM1031742, GSM1031745 - GSM1031746; reprocessed for this study), 11-day-old haploid male adults, 11-day-old diploid male adults, 11-day-old queen adults (accession number GSM1031748 - GSM1031750, GSM1031753 - GSM1031754, GSM1031756 - GSM1031758, GSM1031761 - GSM1031762; reprocessed for this study). Biological replicates: 5 colonies (x 2 genotypes for each colony). Samples were labeled with Cy3 and were compared to the same common reference RNA labeled with Cy5.
2012-12-06 | E-GEOD-42494 | ArrayExpress