Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic profiling of archeological human bone

ABSTRACT: We performed shotgun proteomics of human remains using rib bones from the Hitotsubashi site (1657–1683 AD) in Tokyo, called Edo in ancient times. Two infants and six adults, including four elderly adults, were obtained from the skeletal collection of the Hitotsubashi site in Tokyo, Japan. The individuals buried in this graveyard are townspeople, known from the fact that the largest proportion of graves consisted of the wooden coffins typically used for the lower social classes. The sex and age at death of the adult skeletons were estimated using the diagnostic standards of Nagaoka and Hirata (Nagaoka et al., 2007). Sex was determined by the sexual dimorphism of the pelvis (e.g., Bruzek, 2002). This study estimated age at death for each individual by the observation of the auricular surface of the ilium using the method of Buckberry and Chamberlain. Each obtained stage of the auricular surface of the ilium is then transformed into an average age at death with standard deviation shown in the data of Buckberry and Chamberlain. The age at death of sub-adults was estimated by the degree of formation and eruption of teeth.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Bone, Bone Marrow

SUBMITTER: Rikai Sawafuji

LAB HEAD: Shintaroh Ueda

PROVIDER: PXD006256 | Pride | 2017-06-08

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20140612_QE5_UPLC8_RJC_COLLAB_EE_293_01.raw	Raw
	20140612_QE5_UPLC8_RJC_COLLAB_EE_294_01.raw	Raw
	20140612_QE5_UPLC8_RJC_COLLAB_EE_295_01.raw	Raw
	20140612_QE5_UPLC8_RJC_COLLAB_EE_318_01.raw	Raw
	20140612_QE5_UPLC8_RJC_COLLAB_EE_319_01.raw	Raw

Items per page:

1 - 5 of 10

Similar Datasets

Identification of new proteins related with cisplatin resistance in S. cerevisiae

Project description:The aim of this study is to select a cisplatin resistant Saccharomyces cerevisiae strain as a model organism to look for new molecular markers of cisplatin resistance and the identification of mechanisms/interactions involved. A cisplatin resistant S. cerevisiae strain was obtained after continuous exposure to the drug during 80 days. Then, total protein extraction, purification and identification were carried out, in wild type (wt) and resistant strains, by tandem mass spectrometry using a "nano HPLC-ESI-MS/MS" ion trap system. The increase in emPAI (resistant vs wt strains) was calculated to study the increase in protein expression. "Genemania" software (http://www.Genemania.org/) was used to compare the effects, functions and interactions of proteins. The selected cisplatin resistant strain showed 2.5 times more resistance than the wt strain (for the ID50 value) and 2.78 times more resistant for the ID90 value. The long-term exposure to cisplatin induced resistance in S. cerevisiae, obtaining an increased expression of QCR2, QCR1, ALDH4, ATPB, ATPA, SCW10, HSP26, ATPG, and PCKA proteins. The overexpression of the above-mentioned proteins suggests that they could be involved in cisplatin resistance. The resistance acquisition process is complex and involves the activation of multiple mechanisms that interact together.

2021-02-25 | PXD020665 | Pride

Ribosome profiling upon glucose starvation in S. cerevisiae

Project description:A universal feature of the response to stress and nutrient limitation is transcriptional upregulation of genes encoding proteins important for survival. Interestingly, under many of these conditions overall protein synthesis levels are reduced, thereby dampening the stress response at the level of protein expression. For example, during glucose starvation in yeast, translation is rapidly and reversibly repressed, yet transcription of many stress- and glucose-repressed genes is increased. Using ribosome profiling and microscopy, we found that this transcriptionally upregulated gene set consists of two classes: (1) one producing mRNAs that are preferentially translated during glucose limitation and are diffusely localized in the cytoplasm – this class includes many heat shock protein mRNAs; and (2) another producing mRNAs that are poorly translated during glucose limitation, have high rates of translation initiation, and are concentrated in foci that co-localize with P bodies and stress granules – this class is enriched for glucose metabolism mRNAs. Remarkably, the information specifying differential localization and translation of these two classes of mRNAs is encoded in the promoter sequence – promoter responsiveness to heat shock factor (Hsf1) specifies diffuse cytoplasmic localization and preferential translation upon glucose starvation, whereas different promoter elements upstream of genes encoding poorly translated glucose metabolism mRNAs direct these mRNAs to RNA granules under glucose starvation. Thus, promoter sequences and transcription factor binding can influence not only mRNA levels, but also subcellular localization of mRNAs and the efficiency with which they are translated, enabling cells to tailor protein production to environmental conditions. Examination of mRNA translation in S. cerevisiae upon glucose starvation.

2014-07-28 | E-GEOD-56622 | biostudies-arrayexpress

Proteome Analysis of stromal cells embedded in nanocomposite hydrogels stimulated with ultrasound

Project description:The regeneration of cartilage is a crucial aspect in the treatment of osteoarthritis. In recent years, cartilage regeneration has been pursued through several bioengineering strategies and using different stem cell types, such as adipose tissue-derived mesenchymal stromal cells (ASCs), however with a rather inefficient expression of key chondrogenic markers. Here, we analyzed the proteome of ASCs embedded in a nanocomposite hydrogel stimulated with ultrasound waves, focusing on pathways related to cartilage regeneration.

2024-05-24 | PXD038147 | Pride

Protein turnover rate along the gastrointestinal tract is coordinated by the spatial location and the microbiota

Project description:The gastrointestinal tract is covered by a single layer of epithelial cells that, together with the mucus layers, protect the underlying tissue from bacterial invasion. The epithelium has one of the highest turnover rates in the body, renewing every 4-5 days. Using stable isotope labelling, high-resolution mass spectrometry and computational analysis, we report here a comprehensive dataset of the turnover rate of 3041 and the expression of 5012 intestinal epithelial cell proteins, analyzed under conventional and germ-free conditions across five different segments in mouse intestine. The median protein half-life was shorter in small intestine compared to colon, ranging from 3.5 to 4.2 days. Differences in protein turnover rates along the intestinal tract can be explained by distinct physiological functions and site-specific immune responses between the small and large intestine. Absence of microflora resulted in increased protein half-life by approximately one day.

2020-01-24 | PXD011457 | Pride

A repurposed, non-canonical cytochrome c, chaperones calcium binding by PilY1 for type IVa pili formation - Dataset 1/2

Project description:Type IVa pili (T4aP) are versatile bacterial cell surface structures that undergo extension/adhesion/retraction cycles powered by the cell envelope-spanning T4aP machine. In this machine, a complex composed of four minor pilins and PilY1 primes T4aP extension and is also present at the pilus tip mediating adhesion. Similar to many other bacteria, Myxococcus xanthus contains multiple minor pilins/PilY1 sets, the function of which remains unknown.Here, we report that minor pilins and PilY1 of cluster_1 (PilY1.1) form calcium-responsive priming and tip complexes contingent on a non-canonical cytochrome c (TfcP) with an unusual His/Cys heme ligation. We provide evidence that TfcP is unlikely to participate in electron transport and has been repurposed to promote calcium binding by PilY1.1 at low calcium concentrations, thereby stabilising PilY1.1 and enabling its function in a broader range of calcium concentrations. These results identify a novel function of cytochromes c and illustrate how incorporating an accessory factor expands the environmental range under which the T4aP system functions.

2022-01-30 | PXD031263 | Pride

Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides

Project description:Rhodotorula toruloides is a non-conventional, oleaginous yeast able to naturally accumulate high amounts of microbial lipids. Constraint-based modeling of R. toruloides has been mainly focused on the comparison of experimentally measured and model predicted growth rates, while the analysis of intracellular flux patterns has been superficial. Hence, the intrinsic metabolic properties of R. toruloides that make lipid synthesis possible are not thoroughly understood. At the same time, the lack of diverse physiological data sets has often been the bottleneck to predict accurate fluxes. In this study, we collected detailed physiology data sets of R. toruloides while growing on glucose, xylose and acetate as the sole carbon source in mineral medium. Regardless of the carbon source, the growth was divided into two phases from which proteomic and lipidomic data were collected. Complemental physiological parameters were collected in these two phases and altogether implemented into metabolic models. Simulated intracellular flux patterns acknowledged the role of phosphoketolase in the generation of acetyl-CoA, one of the main precursors during lipid biosynthesis, while the role of ATP citrate lyase was not confirmed. Metabolic modeling on xylose as a carbon substrate was greatly improved by the detection of chirality of D-arabinitol, which together with D-ribulose were involved in an alternative xylose assimilation pathway. Further, flux patterns pointed to a metabolic trade-offs associated with NADPH allocation between nitrogen assimilation and lipid biosynthetic pathways, which was linked to large-scale differences in protein and lipid content. This work includes the first extensive multi-condition analysis of R. toruloides using enzyme-constrained models and quantitative proteomics. Further, more precise kcat values should extend the application of the newly developed enzyme-constrained models that are publicly available for future studies.

2023-03-13 | PXD037281 | Pride

Transcriptome profiles derived from parallel venipuncture, dried blood spot (DBS), and saliva samples

Project description:Comparison of transcript abundance estimates derived from DBS vs saliva vs gold standard peripheral blood mononuclear cell (PBMC) samples. Gene expression profiling was conducted using parallel collection and assay of venipuncture blood samples (PBMC), DBS samples, and saliva. Data come from 58 community dwelling adults recruited from the Los Angeles metropolitan area. Analyzed data include basic demographic characteristics (age, sex, race/ethnicity) and body mass index (BMI) as well as RNA indicators of major leukocyte subset prevalence (i.e., estimated abundance of mRNA for CD3, CD4, CD8, CD19, FCGR3A/CD16, NCAM1/CD56, and CD14; all provided here as log2-transformed values of normalized gene expression data). Categorial variables were coded 0=no/absent and 1=yes/present.

2016-07-27 | E-GEOD-79269 | biostudies-arrayexpress

Surveillance Colonoscopy in Older Adults: The SurvOlderAdults Study

Project description:Colorectal cancer is a leading cause of cancer death. Detection and removal of polyps can reduce risk for developing colorectal cancer. After finding and removing precancerous polyps, repeat colonoscopy is routinely recommended. However, it is unclear whether repeat additional colonoscopy further reduces risk for colorectal cancer. For older adults age 75 and older, the lack of this information is especially important, given that the risks of colonoscopy go up with age. This research will evaluate whether older adults with a prior history of precancerous polyps have higher colorectal cancer risks compared to older adults who had a prior normal colonoscopy, and whether, among those with prior precancerous polyps, repeating a colonoscopy after age 75 is associated with reduced cancer risk. The investigators will synthesize these data and gather perspectives from Veterans and clinical stakeholders to make recommendations on whether older adults with a prior history of polyps should continue or defer colonoscopy after age 75.

| 70659 | ecrin-mdr-crc

Differences in the transcriptomic response of human adult, neonatal, and older adult monocytes to Listeria monocytogenes infection

Project description:Listeria monocytogenes (Lm) kills up to 60% of infected newborns and adults >60 years of age but is asymptomic is most young adults. Monocytes are central to effective host defense against Lm. We hypothesize that age-dependent, pathway-specific differences in the ability of the monocyte to respond to Lm explain the increased risk of the newborn and older adult to severely suffer or die from Lm infection. To delineate age-dependent differences in innate responses that lead to differential infectious outcome, monocytes were isolated from cord blood (newborn) and peripheral blood (young and older adults) and infected with Lm. RNA was collected to determine age-dependent transcriptomic changes upon infection.

2015-09-01 | GSE67983 | GEO

Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in Saccharomyces cerevisiae

Project description:Computing absolute protein abundances using mass spectrometry (MS) is a widely used technique in quantitative biology. An important and often overlooked aspect in this methodology is to assess technical reproducibility, i.e. how precise are predictions of abundance when we use the instrument on repeated occasions to measure the same sample. Here, we present a proteomics dataset of Saccharomyces cerevisiae with both biological and inter-run technical triplicates, which we use to analyze both accuracy and precision of the MS instrument. We also investigate how we can improve the quality of predictions by using 4 alternative methods for estimating absolute protein abundance starting from MS intensities. We show that using a simple normalization and rescaling approach performs equally accurate, but much more precise, than methods that rely on external standards. Furthermore, we show that technical reproducibility is significantly lower than biological reproducibility for all the evaluated methods. The results presented here serve as a benchmark for assessing the best way of interpreting MS results to compute protein abundances, and as a consideration of the limitations of the technique when interpreting results.

2020-04-09 | PXD011725 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data