Project description:The aim of this study was to identify umbilical cord microRNA (miRNA) associated with catch-up growth in SGA infants. miRCURY LNA™ Universal RT microRNA PCR Human Panel I+II (Exiqon) were used to study the miRNA profile in umbilical cord tissue of 5 SGA infants with catch-up (SGA-CU), 5 SGA infants without catch-up (SGA-nonCU) and 5 control infants (appropriate-for-gestational-age, AGA). Catch-up differentially expressed miRNA were studied and validated in a larger cohort.

2019-03-22 | GSE128694 | GEO

Cuatro Cienegas Basin, Archaean Domes

Project description:Cuatro Cienegas Basin, Archean Domes Metagenomes

| PRJNA847603 | ENA

Considered Absent: A first inventory of prehistoric human remains from the Scheldt basin, Belgium

Project description:Throughout prehistory, human groups inhabited the Scheldt basin in northern Belgium, though few prehistoric human remains have been found there compared to the Meuse basin, where many caves contain human remains from various prehistoric phases. The limited preservation in the Scheldt basin is due to the region's high soil acidity, decalcification, and dryness, which degrade bones. The oldest known human bone is a clavicle dated to around 5790 years ago. Until recently, little effort had been made to identify human remains in the Scheldt basin. However, a recent survey identified four additional sites with prehistoric human remains. The paper aims to document these findings and explore their radiocarbon dates to better understand the region’s occupation history. The scarcity of remains before the Neolithic is attributed to taphonomic factors, and the lack of Late Neolithic remains might indicate a population decline, though flint mines and Meuse basin burials suggest otherwise. Another possibility is a shift in burial practices, with collective burials in megaliths or caves becoming common in western Europe during this time, unsuitable for the wet floodplains of the Scheldt basin. Most of the human bones discovered in the Scheldt basin were found in secondary contexts, likely displaced by fluvial activity. The bones were retrieved from former river channels and gullies, complicating interpretations of whether they originated from primary graves or were part of secondary burial practices. The absence of defleshing marks suggests the bones were not part of secondary burial rites, pointing instead to the erosion of primary graves from earlier settlements. The presence of settlement debris, including pottery and stone tools, supports this theory

2026-04-07 | PXD056419 | Pride

Capture of Associated Targets on Chromatin (CATCH) Links Long-Distance Chromatin Looping to Transcriptional Coordination

Project description:We describe here a sensitive and novel method of identifying endogenous DNA-DNA interactions. Capture of Associated Targets on CHromatin (CATCH) uses efficient capture and enrichment of specific genomic loci of interest through hybridization and subsequent purification via complementary biotinylated oligonucleotide. The CATCH assay requires no enzymatic digestion or ligation, requires little starting material, provides high quality data, has excellent reproducibility and is completed in less than 24 hours. Efficacy is demonstrated through capture of three disparate loci, which demonstrate unique subsets of long-distance chromatin interactions enriched for both enhancer marks and estrogen receptor binding sites. In each experiment, CATCH-seq peaks representing long-distance chromatin interactions were centered near the TSS of genes, and critically, the genes identified as physically interacting are shown to be transcriptionally co-expressed. These interactions could potentially create transcriptional hubs for the regulation of gene expression programs.

2016-09-22 | GSE85762 | GEO

Overcoming T cell tolerance to tumor self-antigens through catch-bond engineering

Project description:T cells are often weakly responsive to tumor self-antigens because of central tolerance, which constrains their ability to eliminate tumors. Affinity-matured T cell receptors can exhibit enhanced tumor killing properties but in therapeutic settings have been accompanied by off-target cross-reactivity and toxicity, because high-affinity TCRs antigen specificity is altered compared to naturally selected TCRs. Here, we exploited the physiological biophysical mechanism of TCR activation through mechanical force, by engineering to a weakly reactive TCR specific for a non-mutated human prostate tumor associated antigen (TAA), Prostatic Acid Phosphatase (PAP). We isolated a catch bonding “hotspot” whose mutation enhanced T cell activity by increasing TCR-pMHC bond lifetime, whilst maintaining physiological affinities and antigen fine-specificities. T cells expressing these engineered TCRs showed vastly superior expansion and tumor killing properties in vitro and in vivo, as well as enhanced effector phenotypes and proliferation in the tumor, as measured by single-cell RNA-seq. High resolution structures and molecular dynamics simulations of the TCR-pMHC complexes reveal the structural hotspot in TCR CDR1 is primed for peptide interaction in the catch bond engineered TCR. These studies establish catch bond engineering as a viable biophysically-based strategy to convert tolerized anti-tumor T cells into potent TCR-T killers.

2026-03-25 | GSE307528 | GEO

CATCH-IT method for measuring nucleosome turnover

Project description:Direct measurement of nucleosome turnover dynamics by using co-translational incorporation of the methionine (Met) surrogate azidohomoalaine (Aha) into proteins and subsequent ligation of biotin to Aha-containing proteins through the [3+2] cycloaddition reaction between the azide group of Aha and an alkyne linked to biotin. To measure turnover rates, we treat cells briefly with Aha, couple biotin to nucleosomes containing newly incorporated histones, affinity purify with strepavidin, wash stringently to remove non-histone proteins and H2A/H2B dimers, and analyze the affinity-purified DNA using tiling microarrays. We call this strategy 'CATCH-IT' for Covalent Attachment of Tags to Capture Histones and Identify Turnover. Keywords: Chromatin affinity-purification on microarray All experiments were done using strepavidin pulldown DNA cohybridized with total input DNA to the same array. Two channels per array, Cy5 and Cy3, were used in each experiment.

2010-05-27 | E-GEOD-19788 | biostudies-arrayexpress

metagenomes

Project description:Metagenomes

| PRJNA377521 | ENA