Several publications have described biological roles for human patatin-like phospholipases (PNPLAs) in the regulation of adipocyte differentiation. Here, we report on characterization and expression profiling 10 PNPLAs. A variety bioinformatics approaches were used to identify characterize all PNPLAs encoded by genome. The genes represent a divergent family, most with highly conserved ortholog several mammalian species. In silico predicts that two function as integral membrane proteins are...

Remarkable progress has been made recently in identifying a new gene family related to the capsaicin (vanilloid) receptor, VR1. Using combination of silico analysis expressed sequence tag (EST) databases and conventional molecular cloning, we have isolated novel vanilloid-like which call VRL-2, from human kidney. The translated shares 46% 43% identity with VR1 VRL-1, respectively, maps chromosome 12q23–24.1, locus associated bipolar affective disorder. VRL-2 mRNA was most strongly trachea,...

Sarcopenia is the loss of muscle size and function during ageing. The aim this study was to test whether serum concentrations myostatin interacting proteins (GASP-1, FLRG, follistatin) differed between young elderly sarcopenic men. Isometric knee extensor maximal voluntary contraction quadriceps cross-sectional area (magnetic resonance imaging measurement) were significantly higher in (22 ± 2 years; 266 54 N/m; 8,686 1,154 mm2) than mildly (69 3 183 17 6,621±718 severely men (76 6 127 23...

Abstract Motivation: Phosphoproteomics measurements are widely applied in cellular biology to detect changes signalling dynamics. However, due the inherent complexity of phosphorylation patterns and lack knowledge on how phosphorylations related functions, it is often not possible directly deduce protein activities from those measurements. Here, we present a heuristic machine learning algorithm that infers kinases data using kinase–target information PhosphoSitePlus database. By comparing...

For almost two decades, 1H-NMR spectroscopy has been used as an 'open' system to study the temporal changes in biochemical composition of biofluids, including urine, response adverse toxic events. Many these vivo studies have reported individual metabolites and patterns that correlated with toxicological changes. However, many proposed novel biomarkers are common a number different types toxicity. These may therefore reflect non-specific effects toxicity, such weight loss, rather than...

Recent research adds to a growing body of literature on the essential role ceramides in glucose homeostasis and insulin signaling, while mechanistic interplay between various components ceramide metabolism remains be quantified. We present an extended model C16:0 production through both de novo synthesis salvage pathways. verify our with combination published models independent experimental data. In silico experiments behavior related bioactive lipids accordance observed transcriptomic...

Proton nuclear magnetic resonance (1H NMR) spectroscopic analysis of mixtures has been used extensively for a variety applications ranging from the plant extracts, wine, and food to evaluation toxicity in animals. For example, NMR urine samples biomarker discovery and, more simply, construction classification models toxicity, disease, biochemical phenotype. However, spectra complex typically show unwanted local peak shifts caused by matrix instrument variability, which must be compensated...

This paper introduces the genome annotating proteomic pipeline (GAPP), a totally automated publicly available software for identification of peptides and proteins from human tandem mass spectrometry data. The takes as its input series MS/MS peak lists given experimental sample produces database entries corresponding to observed within sample, along with related confidence scores. is capable finding any expected, including those that cross intron−exon boundaries, due single nucleotide...

In general, the computational analysis of label-free proteomics dataset consists two major steps: feature detection and alignment.Feature is to extract peptide induced signals from ion

CPF1 is an abundant basic-helix-loop-helix-ZIP protein that binds to the CDEI motif in Saccharomyces cerevisiae centromeres and promoters of numerous genes, including those encoding enzymes methionine biosynthetic pathway. Strains lacking are auxotrophs, it has been proposed might positively influence transcription at MET25 MET16 genes by modulating promoter chromatin structure. We test this hypothesis show regions surrounding motifs maintained a nucleosome-free state requires entire...

Perhaps the greatest difficulty in interpreting large sets of protein identifications derived from mass spectrometric methods is whether or not to trust results. For such experiments, level confidence each identification made needs be far greater than often used 95% significance threshold avoid many false-positives. To provide higher results, we have developed an innovative scoring strategy coupling recently published Average Peptide Score (APS) method with pre-filtering peptide...

Non-negative matrix factorization is a useful tool for reducing the dimension of large datasets. This work considers simultaneous non-negative multiple sources data. In particular, we perform first study that involves more than two We discuss algorithmic issues required to convert approach into practical computational and apply technique new gene expression data quantifying molecular changes in four tissue types due different dosages an experimental panPPAR agonist mouse. interest toxicology...

Genome-wide association studies (GWAs) for type 2 diabetes (T2D) have been successful in identifying many loci with robust signals. Nevertheless, there is a clear need post-GWAs strategies to understand mechanism of action and clinical relevance these variants. The several comorbidities T2D suggests common etiology phenotypes complicates the management disease. In this study, we focused on genetics underlying relationships, using systems genomics identify genetic variation associated 12...

DING proteins have been described as animal and plant with potential biomineralisation, receptor or signalling roles that characterised by an N-terminal DINGGG-sequence. However, these sequences only ever identified either peptides partial cDNA sequences, yet to be detected in any of the many genomic genomes now available. Microbial relatives described, which appear periplasmic phosphate-binding proteins. Recently, full-length Pseudomonas aeruginosa UCBPP-PA14 Hypericum perforatum genes...

Abstract Most biomedical knowledge is published as text, making it challenging to analyse using traditional statistical methods. In contrast, machine-interpretable data primarily comes from structured property databases, which represent only a fraction of the present in literature. Crucial insights and inferences can be drawn these publications by scientific community. We trained language models on literature different time periods evaluate their ranking prospective gene-disease associations...

Biomarker identification, using network methods, depends on finding regular co-expression patterns; the overall connectivity is of greater importance than any single relationship. A second requirement a simple algorithm for ranking patients how relevant gene-set is. For both these requirements discretized data helps to first identify gene cliques, and then stratify patients. We explore biologically intuitive discretization technique which codes genes as up- or down-regulated, with values...

Abstract Background Laboratory Information Management Systems (LIMS) are an increasingly important part of modern laboratory infrastructure. As typically very sophisticated software products, LIMS often require considerable resources to select, deploy and maintain. Larger organisations may have access specialist IT support assist with requirements elicitation customisation, however smaller groups will limited perform the kind iterative development that can resolve difficulties biologists...

CPF1 is an abundant basic-helix-loop-helix-ZIP protein that binds to the CDEI motif in Saccharomyces cerevisiae centromeres and promoters of numerous genes, including those encoding enzymes methionine biosynthetic pathway. Strains lacking are auxotrophs, it has been proposed might positively influence transcription at MET25 MET16 genes by modulating promoter chromatin structure. We test this hypothesis show regions surrounding motifs maintained a nucleosome-free state requires entire...

Abstract Target identification and prioritisation are prominent first steps in modern drug discovery. Traditionally, individual scientists have used their expertise to manually interpret scientific literature prioritise opportunities. However, increasing publication rates the wider routine coverage of human genes by omic-scale research make it difficult maintain meaningful overviews from which identify promising new trends. Here we propose an automated yet flexible pipeline that identifies...

Abstract Background The use of selective reaction monitoring (SRM) based LC-MS/MS analysis for the quantification phosphorylation stoichiometry has been rapidly increasing. At same time, number sites that can be monitored in a single experiment is also manual processes associated with running these experiments have highlighted need computational assistance to quickly design MRM/SRM candidates. Results PChopper developed predict peptides produced via enzymatic protein digest; this includes...

Background Technical advances in the collection of clinical material, such as laser capture microdissection and cell sorting, provide advantage yielding more refined homogenous populations cells. However, these attractive advantages are counter balanced by significant difficultly obtaining adequate nucleic acid yields to allow transcriptomic analyses. Established technologies available carry out global transcriptomics using nanograms input RNA, however, many samples low content would be...

Target selection is crucial in pharmaceutical drug discovery, directly influencing clinical trial success. Despite its importance, development remains resource-intensive, often taking over a decade with significant financial costs. High failure rates highlight the need for better early-stage target selection. We present GATher, graph attention network designed to predict therapeutic gene-disease links by integrating data from diverse biomedical sources into 4.4 million edges. GATher...

We demonstrate a new approach to the determination of amino acid composition from tandem mass spectrometrically fragmented peptides using both experimental and simulated data. The has been developed be used as search-space filter in protein identification pipeline with aim increased performance above that which could attained by immonium ion information. Three automated methods have tested: one based upon simple peak traversal, all intense peaks are treated being either b- or y-ion wide...