Dataset Information

Bbubalis - Milk, NSAF (Pisanuetal,scirep2019)

ABSTRACT: abundance based on NSAF, Interaction consistency score: 4.3, Coverage: 1

ORGANISM(S): 89462

SUBMITTER: Christian von Mering

PROVIDER: 1439943622 | PAXDB | 2019

REPOSITORIES: PAXDB

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	bioprojects-abundance-files-v4.0.zip	Other

Items per page:

1 - 1 of 1

Publications

Proteomic changes in the milk of water buffaloes (Bubalus bubalis) with subclinical mastitis due to intramammary infection by Staphylococcus aureus and by non-aureus staphylococci.

Pisanu Salvatore S Cacciotto Carla C Pagnozzi Daniela D Puggioni Giulia Maria Grazia GMG Uzzau Sergio S Ciaramella Paolo P Guccione Jacopo J Penati Martina M Pollera Claudia C Moroni Paolo P Bronzo Valerio V Addis Maria Filippa MF

Scientific reports 20191101 1

Subclinical mastitis by Staphylococcus aureus (SAU) and by non-aureus staphylococci (NAS) is a major issue in the water buffalo. To understand its impact on milk, 6 quarter samples with >3,000,000 cells/mL (3 SAU-positive and 3 NAS-positive) and 6 culture-negative quarter samples with <50,000 cells/mL were investigated by shotgun proteomics and label-free quantitation. A total of 1530 proteins were identified, of which 152 were significantly changed. SAU was more impacting, with 162 vs 127 diffe ...[more]

PMID: 31676851

Similar Datasets

Project description:Here, we examined the ramifications of between-species diversity by documenting the transcriptional response of three marine diatoms - Thalassiosira pseudonana, Fragilariopsis cylindrus, and Pseudo-nitzschia multiseries - to the onset of nitrate limitation of growth, a common limiting nutrient in the ocean. Less than 5% of orthologous genes, shared across the three diatoms, displayed the same transcriptional responses across species when growth was limited by nitrate availability. Orthologs, such as those involved in nitrogen uptake and assimilation, as well as carbon metabolism, were differently expressed across the three species. The two pennate diatoms, F. cylindrus and P. multiseries, shared 3,839 clusters without orthologs in the genome of the centric diatom T. pseudonana. A majority of these pennate-clustered genes, as well as the non-orthologous genes in each species, had minimal annotation information, but were often significantly differentially expressed under nitrate limitation, indicating their potential importance in the response to nitrogen availability. Despite these variations in the specific transcriptional response of each diatom, overall transcriptional patterns suggested that all three diatoms displayed a common physiological response to nitrate limitation that consisted of a general reduction in carbon fixation and carbohydrate and fatty acid metabolism and an increase in nitrogen recycling. Transcriptomes were collected for diatom cultures harvested at the onset of stationary phase in low nitrate media (55 M-NM-<M NaNO3, 212 M-NM-<M Na2SiO3, 72.4 M-NM-<M NaH2PO4) or during mid-exponential growth in nutrient-replete media (882 M-NM-<M NaNO3, 106 M-NM-<M Na2SiO3, 36.2 M-NM-<M NaH2PO4) in artificial seawater, maintaining three biological replicates per condition and per diatom (N=18). The SOLiD sequencer (version 4) was used to generate the transcriptomes and the SEAStAR software package was used to process the SOLiD reads and to calculate gene counts. Pooled counts for the nitrate-limited treatment were normalized to pooled counts for the nutrient-replete M-bM-^@M-^\controlM-bM-^@M-^] treatment to generate log fold changes in gene transcription using the R software package edgeR from Bioconductor.

Project description:MicroRNAs are important regulatory molecules in most eukaryotes and the identification of their mRNA targets is essential for their functional analysis. From inflorescence tissue of Arabidopsis, >28,000,000 signatures were sequenced from 5’ ends of polyadenylated products of mRNA decay. Within the set of ~27,000 transcripts included in the 3,500,000 non-redundant signatures, several previously predicted but non-validated miRNA targets were found. Like validated targets, most showed a single abundant signature at the miRNA cleavage site, particularly in libraries from a mutant deficient in the 5’ to 3’ exonuclease AtXRN4. Among the most unexpected miRNA targets discovered were miRNA precursor transcripts that are self-targeted by their own mature miRNA. Although the miRNAs of Arabidopsis have been extensively investigated, working in reverse from the cleaved targets, additional novel miRNAs were identified and validated. This deep and versatile approach will impact the study of other aspects of RNA processing beyond miRNA-target RNA pair analyses. Keywords: miRNA-target RNA pairs, Palallel analysis of RNA ends, PARE, SBS RNA from inflorescence tissue from wildtype Arabidopsis and xrn4 mutants was extracted. Following polyA RNA extraction, libraries for PARE were constructed. RNA from inflorescence tissue from wildtype Arabidopsis (Col-0), and rdr2 and dcl2,3,4 mutants was extracted. The material was submitted to Illumina and libraries were constructed for small RNAs. Individual small RNA libraries from inflorescences of Arabidopsis wildtype, rdr2, and dcl2/dcl3/dcl4 were sequenced with SBS at Illumina, Inc. The distribution of small RNA sizes in each library is in agreement with that published previously for the wild type or the respective mutants sequenced with MPSS or 454; however, the presence and abundances of some small RNAs may differ. This may be attributed to the use of different sequencing technologies with different depths, biological differences in the tissue used, or other unknown reasons. raw data requested but not provided for GSM280226 and GSM280227

Project description:Our group is interested in epithelial-to-mesenchymal transition (EMT), in particular, TGF-beta induced EMT. TGF-beta signalling has been shown to be an important factor in the induction of EMT and it has been demonstrated that adding TGF-beta to epithelial cells in culture is a convenient way to study the process of EMT. âIn response to TGF-beta, Smad2 and 3 are activated, and form complexes with Smad4, which then regulate transcription of target genes through interactions with other DNA binding transcription factors. In the induction of EMT, the activated Smads mediate transcriptional regulation through three families of transcription factors, resulting in repression of epithelial marker gene expression and activation of mesenchymal gene expressionâ (Xu J, et al. 2009) Also investigated in this study is the role of H2A.Z in EMT. H2A.Z is an evolutionary conserved and a metazoan essential histone variant of the H2A class. Mice deficient in H2A.Z die during early development but the reason for this is unknown (Faast et al. 2001). Previously, our laboratory showed that the loss of H2A.Z in Xenpous laevis impaired cell movement required for the formation of the mesoderm and neural crest (Ridgway et al. 2004). Given that mesoderm formation is critically dependent upon EMT, we therefore wondered whether H2A.Z might be a chromatin regulator of EMT. We transfected MDCK cells with a lentiviral vector to express a construct encoding an shRNA targeting canine H2A.Z as we wanted to test the hypothesis that H2A.Z is involved in the maintenance of cellular identity and that its loss might trigger de-differentiation. In order to investigate changes in gene expression associated with TGF-beta induced epithelial-to-mesenchymal transition (EMT) we performed paired end RNA-Seq of poly-A selected mRNA in untreated and TGFb-treated MDCK cells. The MDCK cell line has been extensively used as a model system for EMT because they convert fully from the epithelial to the mesenchymal state in response to TGF-beta. Gene expression profiles were also generated from MDCK cells in which H2A.Z was knocked down using shRNA. Please note that ChIP-seq data generated in conjunction to this RNA-seq data set were also deposited at ArrayExpress under accession number E-MTAB-5637 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5637 ).