Project description:Analysis of organic residues from different typologies of ancient funerary pottery found in graves at two archaeological sites of Campania Region in southern Italy and dating back to the age of the Italic populations during the first millennium BC. Several analytical techniques have been exploited. Proteomics was decisive for the characterization of the proteins and the assignment of the species of origin. Samples were encrustations on two bowls of the 3rd-4th century BC unhearted in Capua and one Phoenician-type amphora with unusual shape, found in a grave at the necropolis of the Greek colony in Cuma (7th century BC). Concretions on bowls were identified with the decisive contribution of proteomics as bovine bone. The amphora contained 2,500 years old bovine milk.
Project description:To identify host signaling pathways triggered by P. omnivora<br>infection, we used microarrays to monitor the expression profiles<br>and the molecular process associated with initial entry at 3 days post-inoculation and colonization at 5 days post-inoculation
Project description:This study examines how histone modification confers salt stress in Arabidopsis. The floral initiator SKB1 is found to mediate the plant’s response to salt stress by altering the methylation status of histone H4R3 and of the small nuclear ribonucleoprotein (snRNP) LSM4, and thereby affecting the expression of stress-responsive genes. Total RNA was isolated with Trizol reagent (Invitrogen) from eleven11-day-old seedlings of the wild type and skb1-1 mutant without or with 200 mM NaCl for 6 hrs. 29k Arabidopsis Genome Array hybridization was carried out by CapitalBio Corporation (Beijing, China).
Project description:Proteins and peptides are minor components of vegetal oils. The presence of these compounds in virgin olive oil was first reported in 2001, but the nature of the olive oil proteome is still a puzzling question for food science researchers. In this project, we have compiled for a first time a comprehensive proteomic dataset of olive fruit and fungal proteins that are present at low but measurable concentrations in a vegetable oil from a crop of great agronomical relevance as olive (Olea europaea L.). Accurate mass nLC-MS data were collected in high definition direct data analysis (HD-DDA) mode using the ion mobility separation step. Protein identification was performed using the Mascot Server v2.2.07 software (Matrix Science) against an ad hoc database made of olive protein entries. Starting from this proteomic record, the impact of these proteins on olive oil stability and quality could be tested. Moreover, the effect of olive oil proteins on human health and their potential use as functional food components could be also evaluated. In addition, this dataset provides a resource for use in further functional comparisons across other vegetable oils, and also expands the proteomic resources to non-model species, thus also allowing further comparative inter-species studies.
Project description:Successful establishment and maintenance of pregnancy can be attained only through optimum conceptus-maternal cross talk. Despite significant progress in our understanding of the temporal changes in the transcriptome of the uterine endometrium, we have only a rudimentary knowledge of the genes and pathways governing growth and development of the bovine conceptus. In particular, very little information exists for the posthatchingembryo and elongating conceptus. This period of development is arguably the most important, as approximately 40% of all embryonic loss occurs between Days 8 and 17 of pregnancy in cattle. Here, we describe the global transcriptome profile of the bovine conceptus at five key stages of its pre- and peri-implantation growth (Days 7, 10, 13, 16, and 19) using state-of-the-art RNA sequencing techniques. More than 287 million reads were generated at the five stages, and more than 22?700 unique transcripts were detected. Analysis of variance followed by self-organizing maps identified differentially regulated (P < 0.05) genes organized in nine gene clusters forming a sequential transcript dynamics across these developmental stages. Of particular interest, genes in clusters 3 (n = 236) and 6 (n = 1409) were significantly up-regulated on Days 16 and 19, suggesting a role in maternal recognition and initiation of implantation. This transcriptome analysis of the bovine conceptus will provide a blueprint of the dynamic changes in gene expression occurring during maternal recognition and implantation and will complement existing knowledge of the temporal changes in the endometrial transcriptome, thus facilitating a better understanding of conceptus-maternal cross talk during the peri-implantation period of pregnancy. mRNA-seq study of bovine conceptuses at 5 stages of development (days 7, 10, 13, 16 and 19) post fertilization.
Project description:Escherichia coli O157:H7 strains have been classified into different genotypes based on the presence of specific shiga toxin-encoding bacteriophage insertion sites. Genotypes that are predominant in clinical isolates are named clinical genotypes and those that are isolated mostly from bovine sources are bovine-biased genotypes. To determine whether inherent differences in gene expression could possibly explain the variation in infectivity of these genotypes, we compared the expression patterns of O157:H7 strains isolated from cattle, which belonged to either clinical genotype 1 or bovine-biased genotype 5. Important virulence factors of O157, including locus of enterocyte effacement, enterohemolysin, and pO157 plasmid encoded genes, showed increased expression in clinical genotype. Genes essential for acid resistance such as gadA, gadB, and gadC and other stress fitness-associated genes were up-regulated in the bovine-biased genotype 5. Overall, these results suggest that clinical genotype 1 strains more commonly cause human illness because of an enhanced ability to express O157 virulence factors known to be important for disease pathogenesis. By contrast, strains of the bovine-biased genotype 5 appear to be more resistant to adverse environmental conditions, which enable them to survive well in bovines without causing disease. The results are based on O157:H7 clinical and bovine-biased genotype cultures grown in DMEM medium to exponential phase. Four strains were selected from each genotype and strains were considered as biological replicates. A double loop microarray design was used for comparing the samples. Differences in transcript levels were determined using a mixed model ANOVA in R/MAANOVA which tested for significant differences due to strain (clinical or bovine-biased) using the following linear model: array+dye+sample (biological replicate)+strain+error. We incorporated the dye-swaps among the biological replicates.
Project description:Polycomb group (PcG) proteins are involved in chromatin modifications for maintaining gene repression that play important roles in the regulation of gene expression, tumorigenesis, chromosome X-inactivation, and genomic imprinting in Drosophila melanogaster, mammals, and even plants. PcG proteins act together in three multimeric complexes, Polycomb repressive complex 1 (PRC1), Polycomb repressive complex 2 (PRC2), and Pleiohomeotic repressive complex (PhoRC), to repress transcription of the target genes. Here, we identified Polycomb target genes in Bombyx mori using genome-wide expression screening based on the knockdown of the BmSCE, BmESC, BmPHO, or BmSCM gene, which represent the distinct complexes. As a result, most genes were up-regulated after knocking down these four PcG genes, which indicated a potential epigenetic mechanism on the regulation of these genes expression by the PcG system. The further analysis of our data will provide some important information for the regulation mediated by PcG proteins in Bombyx mori. Transcription profiling experiments, knockdowns of four Polycomb genes (four samples) in silkworm BmN4-SID1 cells, were analyzed. Dual-channel experiments, with test samples labeled by Cy5 and common reference samples labeled by Cy3. The common reference sample, knockdown of the EGFP gene in BmN4-SID1 cells, was used for data normalization. One biological replicate. No dye-swaps.
Project description:This repository is related to the work” XCP1 cleaves Pathogenesis-related protein 1 into CAPE9 for systemic immunity in Arabidopsis”. In this study, we found that the C-terminal proteolytic processing of a caspase-like substrate motif “CNYD” within Pathogenesis-related protein 1 (PR1) generates an immunomodulatory cytokine (CAPE9) in Arabidopsis. Salicylic acid enhances CNYD-targeted protease activity and the proteolytic release of CAPE9 from PR1 in Arabidopsis. This process involves a protease exhibiting caspase-like enzyme activity, identified as Xylem cysteine peptidase 1 (XCP1). XCP1 exhibits a calcium-modulated pH-activity profile and a comparable activity to human caspases. XCP1 is required to induce systemic immunity triggered by pathogen-associated molecular patterns. This work reveals XCP1 as a key protease for plant immunity, which produces the cytokine CAPE9 from the canonical salicylic acid signaling marker PR1 to activate systemic immunity. The following files are stored here: one MS datasets (include .raw, preprocessed .mgf, and Mascot MS/MS ion search result .dat file) generated in this work, including: “Total identified endogenous peptides observed in SA-treated Arabidopsis leaves on Q Exactive HF (named as supplementaldata2)”
Project description:Insect cuticle plays essential roles in multiple physiological functions. During molting and metamorphosis, tremendous changes occur in silkworm cuticles. Silkworm is a model of Lepidoptera insects; however, little is known about the stage expression profiles of genes in cuticles of silkworm. In the present study, we selected 16 developmental stages, ranging from day 1 of the first instar larvae to day 8 of pupae, to perform microarray-based expression profiles. The data told us that various functions and physiological pathways were activated in the cuticle. Moreover, the expression profiles of cuticular protein genes, as the important components of cuticle, were investigated. The current study provides important insights for the functional study of insect cuticle and the regulation of insect cuticular protein genes. Transcription profiling experiments, 16 developmental stages (samples) were analyzed. Dual-channel experiments, with test samples labeled by Cy5 and common reference samples labeled by Cy3. Common reference sample was used for data normalization. One biological replicate. No dye-swaps.
Project description:Exosomes and microvesicles (i.e., extracellular vesicles; EVs) have been identified within ovarian follicular fluid, and recent evidence suggests that EVs are able to elicit profound effects on ovarian cell function. While existence of miRNA within EVs has been reported, it remains unknown if EV size and concentration as well as their cargos (i.e., proteins and RNA) change during antral follicle growth. Extracellular vesicles isolated from follicular fluid of small, medium and large bovine follicles were similar in size, while concentration of EVs decreased progressively as follicle size increased. Electron microscopy indicated a highly purified population of the lipid bilayer enclosed vesicles that were enriched in exosome biomarkers including CD81 and Alix. Small RNA sequencing identified a large number of known and novel miRNAs that changed in the EVs of different size follicles. Ingenuity Pathway Analysis (IPA) indicated that miRNA abundant in small follicle EV preparations were associated with cell proliferation pathways, while those miRNA abundant in large follicle preparations were related to inflammatory response pathways. These studies are the first to demonstrate that EVs change in their levels and makeup during antral follicle development and point to the potential for a unique vesicle-mediated cell-to-cell communication network within the ovarian follicle. Examination of small RNA population in bovine follicular fluid extracellular vesicles isolated from antral follicles