Identification, Biosynthesis, and Decapping of NAD-Capped RNAs in B.  subtilis.
Identification, Biosynthesis, and Decapping of NAD-Capped RNAs in B. subtilis. Cell Rep. 2018 Aug 14;24(7):1890-1901.e8 Authors: Frindert J, Zhang Y, Nübel G, Kahloon M, Kolmar L, Hotz-Wagenblatt A, Burhenne J, Haefeli WE, Jäschke A Abstract The ubiquitous coenzyme nicotinamide adenine dinucleotide (NAD) decorates various RNAs in different organisms. In the proteobacterium Escherichia coli, the NAD-cap confers stability against RNA degradation. To date, NAD-RNAs have not been identified in any other bacterial microorganism. Here, we report the identification of NAD-RNA in the firmicute ...
Source: Genomics Proteomics ... - August 14, 2018 Category: Genetics & Stem Cells Authors: Frindert J, Zhang Y, Nübel G, Kahloon M, Kolmar L, Hotz-Wagenblatt A, Burhenne J, Haefeli WE, Jäschke A Tags: Cell Rep Source Type: research

Highly multiplexed proteomic analysis reveals significant tissue and exosomal coagulation pathway derangement in chronic rhinosinusitis with nasal polyps.
Abstract BACKGROUND: The coagulation pathway has been previously implicated in the etiopathogenesis of chronic rhinosinusitis with nasal polyps (CRSwNP) through analysis of individual proteins within the cascade. The purpose of this study was to: (1) apply a large-scale proteomic approach to confirm these previous findings; and (2) correlate the protein aberrations between tissue and exosomes to establish exosomal proteomics as a method to probe the pathophysiology of CRSwNP. METHODS: This investigation was an internal review board-approved study in which matched tissue and mucus exosomal proteomes were compa...
Source: Genomics Proteomics ... - August 9, 2018 Category: Genetics & Stem Cells Authors: Mueller SK, Nocera AL, Dillon ST, Wu D, Libermann TA, Bleier BS Tags: Int Forum Allergy Rhinol Source Type: research

The Cancer Omics Atlas: an integrative resource for cancer omics annotations.
CONCLUSIONS: TCOA is a useful tool that supplies a number of unique and new functions complementary to the existing tools to facilitate exploration of the TCGA resource. PMID: 30089500 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - August 8, 2018 Category: Genetics & Stem Cells Authors: Sun Q, Li M, Wang X Tags: BMC Med Genomics Source Type: research

Prolonged restraint stressor exposure in outbred CD-1 mice impacts microbiota, colonic inflammation, and short chain fatty acids.
Abstract Stressor-exposure has been shown to exacerbate inflammation and change the composition of the gastrointestinal microbiota; however stressor-induced effects on microbiota-derived metabolites and their receptors are unknown. Thus, bacterial-produced short chain fatty acids (SCFAs), as well as microbial community composition, were assessed in the colons of mice exposed to stress during infection with Citrobacter rodentium. Mice were exposed to overnight restraint on 7 consecutive nights, or left undisturbed as a control. After the first exposure of restraint, mice were orally challenged with C. rodentium or ...
Source: Genomics Proteomics ... - August 5, 2018 Category: Genetics & Stem Cells Authors: Maltz RM, Keirsey J, Kim SC, Mackos AR, Gharaibeh RZ, Moore CC, Xu J, Bakthavatchalu V, Somogyi A, Bailey MT Tags: PLoS One Source Type: research

Mitochondrial genomics in the cancer cell line encyclopedia and a scoring method to effectively pair cell lines for cytoplasmic hybridization.
Abstract Mitochondrial sequence variants have been associated with many human diseases, including cancer. A well-established experimental strategy to assess the impact of mitochondrial sequence variants is to generate cytoplasmic hybrids (cybrids). Cybridization facilitates the study of mitochondrial DNA (mtDNA) mutations under a controlled nuclear genetic background. However, in generating cybrids, it is important to select most suitable mtDNA donor and recipient cells so that any change in recipient's cellular phenotype may be attributed to the introduction, through the donor, of mutations in the gene of interes...
Source: Genomics Proteomics ... - July 31, 2018 Category: Genetics & Stem Cells Authors: Grandhi S, Gould L, Wang J, Grandhi A, LaFramboise T Tags: Mitochondrion Source Type: research

Whole genome SNP analysis suggests unique virulence factor differences of the Beijing and Manila families of Mycobacterium tuberculosis found in Hawaii.
This study further identified an ancient clade that shared some virulence factor mutations with the Manila family, and investigated the relationship of those and other "Manila-like" spoligotypes to the Manila family with this SNP dataset. This work identified a set of virulence genes that are worth pursuing to determine potential differences in transmission or virulence displayed by these two Mtb families. PMID: 30036392 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - July 25, 2018 Category: Genetics & Stem Cells Authors: Koster K, Largen A, Foster JT, Drees KP, Qian L, Desmond EP, Wan X, Hou S, Douglas JT Tags: PLoS One Source Type: research

Maternal auxin supply contributes to early embryo patterning in Arabidopsis.
haus T, Friml J, Laux T Abstract The angiosperm seed is composed of three genetically distinct tissues: the diploid embryo that originates from the fertilized egg cell, the triploid endosperm that is produced from the fertilized central cell, and the maternal sporophytic integuments that develop into the seed coat1. At the onset of embryo development in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small apical embryonic cell and a larger basal cell that connects the embryo to the maternal tissue2. The coordinated and synchronous development of the embryo and the surrounding integuments, and...
Source: Genomics Proteomics ... - July 16, 2018 Category: Genetics & Stem Cells Authors: Robert HS, Park C, Gutièrrez CL, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald W, Dresselhaus T, Friml J, Laux T Tags: Nat Plants Source Type: research

iSEE: Interactive SummarizedExperiment Explorer.
Abstract Data exploration is critical to the comprehension of large biological data sets generated by high-throughput assays such as sequencing. However, most existing tools for interactive visualisation are limited to specific assays or analyses. Here, we present the iSEE (Interactive SummarizedExperiment Explorer) software package, which provides a general visual interface for exploring data in a SummarizedExperiment object. iSEE is directly compatible with many existing R/Bioconductor packages for analysing high-throughput biological data, and provides useful features such as simultaneous examination of (meta)d...
Source: Genomics Proteomics ... - July 15, 2018 Category: Genetics & Stem Cells Authors: Rue-Albrecht K, Marini F, Soneson C, Lun ATL Tags: F1000Res Source Type: research

Genetic variation of SORBS1 gene is associated with glucose homeostasis and age at onset of diabetes: A SAPPHIRe Cohort Study.
Abstract The SORBS1 gene plays an important role in insulin signaling. We aimed to examine whether common single-nucleotide polymorphisms (SNPs) of SORBS1 are associated with prevalence and incidence of diabetes, age at onset of diabetes, and the related traits of glucose homeostasis. A total of 1135 siblings from 492 ethnic Chinese families were recruited at baseline, and 630 were followed up for 5.19 ± 0.96 years. Nine SNPs including rs7081076, rs2281939, rs3818540, rs2274490, rs61739184, rs726176, rs2296966, rs17849148, and rs3193970 were genotyped and examined. To deal with correlated data...
Source: Genomics Proteomics ... - July 12, 2018 Category: Genetics & Stem Cells Authors: Chang TJ, Wang WC, Hsiung CA, He CT, Lin MW, Sheu WH, Chang YC, Quertermous T, Chen YI, Rotter JI, Chuang LM, SAPPHIRe Study Group Tags: Sci Rep Source Type: research

CD44 glycoprotein in cancer: a molecular conundrum hampering clinical applications.
Abstract CD44 is a heavily glycosylated membrane receptor playing a key role in cell adhesion, signal transduction and cytoskeleton remodelling. It is also one of the most studied glycoproteins in cancer, frequently explored for stem cell identification, and associated with chemoresistance and metastasis. However, CD44 is a general designation for a large family of splicing variants exhibiting different degrees of glycosylation and, potentially, functionally distinct roles. Moreover, structural diversity associated with ambiguous nomenclature has delayed clinical developments. Herein, we attempt to comprehensively...
Source: Genomics Proteomics ... - July 10, 2018 Category: Genetics & Stem Cells Authors: Azevedo R, Gaiteiro C, Peixoto A, Relvas-Santos M, Lima L, Santos LL, Ferreira JA Tags: Clin Proteomics Source Type: research

Genome-wide MicroRNA Expression Profiles in COPD: Early Predictors for Cancer Development.
oup Abstract Chronic obstructive pulmonary disease (COPD) significantly increases the risk for developing cancer. Biomarker studies frequently follow a case-control set-up in which patients diagnosed with a disease are compared to controls. Longitudinal cohort studies such as the COPD-centered German COPD and SYstemic consequences-COmorbidities NETwork (COSYCONET) study provide the patient and biomaterial base for discovering predictive molecular markers. We asked whether microRNA (miRNA) profiles in blood collected from COPD patients prior to a tumor diagnosis could support an early diagnosis of tumor development...
Source: Genomics Proteomics ... - July 5, 2018 Category: Genetics & Stem Cells Authors: Keller A, Fehlmann T, Ludwig N, Kahraman M, Laufer T, Backes C, Vogelmeier C, Diener C, Biertz F, Herr C, Jörres RA, Lenhof HP, Meese E, Bals R, COSYCONET Study Group Tags: Genomics Proteomics Bioinformatics Source Type: research

Proteomic biomarkers of cognitive impairment in obstructive sleep apnea syndrome.
CONCLUSIONS: Proteomic biomarkers in participants with cognitive impairment suggest roles for insulin, and vascular signaling pathways, some of which are similar to findings in Alzheimer's disease. A better understanding of the pathogenic mechanisms of CI in OSAS will help focus clinical trials needed in this patient population. PMID: 29968150 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - July 2, 2018 Category: Genetics & Stem Cells Authors: Lal C, Hardiman G, Kumbhare S, Strange C Tags: Sleep Breath Source Type: research

Community-Driven Data Analysis Training for Biology.
, Le Corguillé G, Manke T, Mareuil F, Ramírez F, Ryan D, Sigloch FC, Soranzo N, Wolff J, Videm P, Wolfien M, Wubuli A, Yusuf D, Galaxy Training Network, Taylor J, Backofen R, Nekrutenko A, Grüning B Abstract The primary problem with the explosion of biomedical datasets is not the data, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, inte...
Source: Genomics Proteomics ... - June 27, 2018 Category: Genetics & Stem Cells Authors: Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Brillet-Guéguen L, Čech M, Chilton J, Clements D, Doppelt-Azeroual O, Erxleben A, Freeberg MA, Gladman S, Hoogstrate Y, Hotz HR, Houwaart T, Jagtap P, Larivière D, Le Corgui Tags: Cell Syst Source Type: research

Decreased mitochondrial respiration in aneurysmal aortas of Fibulin-4 mutant mice is linked to PGC1A regulation.
Conclusion: Our data indicate altered mitochondrial function and metabolic dysregulation, leading to increased ROS levels and altered energy production, as a novel mechanism, which may contribute to thoracic aortic aneurysm formation. PMID: 29931197 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - June 21, 2018 Category: Genetics & Stem Cells Authors: van der Pluijm I, Burger J, van Heijningen PM, IJpma A, van Vliet N, Milanese C, Schoonderwoerd K, Sluiter W, Ringuette LJ, Dekkers DHW, Que I, Kaijzel EL, Te Riet L, MacFarlane E, Das D, van der Linden R, Vermeij M, Demmers JA, Mastroberardino PG, Davis Tags: Cardiovasc Res Source Type: research

Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center.
SC Abstract The NIH-funded LINCS Consortium is creating an extensive reference library of cell-based perturbation response signatures and sophisticated informatics tools incorporating a large number of perturbagens, model systems, and assays. To date, more than 350 datasets have been generated including transcriptomics, proteomics, epigenomics, cell phenotype and competitive binding profiling assays. The large volume and variety of data necessitate rigorous data standards and effective data management including modular data processing pipelines and end-user interfaces to facilitate accurate and reliable data exch...
Source: Genomics Proteomics ... - June 19, 2018 Category: Genetics & Stem Cells Authors: Stathias V, Koleti A, Vidović D, Cooper DJ, Jagodnik KM, Terryn R, Forlin M, Chung C, Torre D, Ayad N, Medvedovic M, Ma'ayan A, Pillai A, Schürer SC Tags: Sci Data Source Type: research

Salivary Exosomes: Emerging Roles in Systemic Disease.
Abstract Saliva, which contains biological information, is considered a valuable diagnostic tool for local and systemic diseases and conditions because, similar to blood, it contains important molecules like DNA, RNA, and proteins. Exosomes are cell-derived vesicles 30-100 nm in diameter with substantial biological functions, including intracellular communication and signalling. These vesicles, which are present in bodily fluids, including saliva, are released upon fusion of multivesicular bodies (MVBs) with the cellular plasma membrane. Salivary diagnosis has notable advantages, which include noninvasiveness, eas...
Source: Genomics Proteomics ... - June 16, 2018 Category: Genetics & Stem Cells Authors: Han Y, Jia L, Zheng Y, Li W Tags: Int J Biol Sci Source Type: research

Author Correction: The landscape of genomic alterations across childhood cancers.
S, Waszak S, Blattmann C, Borkhardt A, Kuhlen M, Eggert A, Fulda S, Gessler M, Wegert J, Kappler R, Baumhoer D, Burdach S, Kirschner-Schwabe R, Kontny U, Kulozik AE, Lohmann D, Hettmer S, Eckert C, Bielack S, Nathrath M, Niemeyer C, Richter GH, Schulte J, Siebert R, Westermann F, Molenaar JJ, Vassal G, Witt H, Burkhardt B, Kratz CP, Witt O, van Tilburg CM, Kramm CM, Fleischhack G, Dirksen U, Rutkowski S, Frühwald M, von Hoff K, Wolf S, Klingebiel T, Koscielniak E, Landgraf P, Koster J, Resnick AC, Zhang J, Liu Y, Zhou X, Waanders AJ, Zwijnenburg DA, Raman P, Brors B, Weber UD, Northcott PA, Pajtler KW, Kool M, Piro RM...
Source: Genomics Proteomics ... - June 6, 2018 Category: Genetics & Stem Cells Authors: Gröbner SN, Worst BC, Weischenfeldt J, Buchhalter I, Kleinheinz K, Rudneva VA, Johann PD, Balasubramanian GP, Segura-Wang M, Brabetz S, Bender S, Hutter B, Sturm D, Pfaff E, Hübschmann D, Zipprich G, Heinold M, Eils J, Lawerenz C, Erkek S, Lambo S, Wasz Tags: Nature Source Type: research

Stability and reproducibility of proteomic profiles measured with an aptamer-based platform.
Abstract The feasibility of SOMAscan, a multiplex, high sensitivity proteomics platform, for use in studies using archived plasma samples has not yet been assessed. We quantified 1,305 proteins from plasma samples donated by 16 Nurses' Health Study (NHS) participants, 40 NHSII participants, and 12 local volunteers. We assessed assay reproducibility using coefficients of variation (CV) from duplicate samples and intra-class correlation coefficients (ICC) and Spearman correlation coefficients (r) of samples processed (i.e., centrifuged and aliquoted into separate components) immediately, 24, and 48 hours afte...
Source: Genomics Proteomics ... - May 30, 2018 Category: Genetics & Stem Cells Authors: Kim CH, Tworoger SS, Stampfer MJ, Dillon ST, Gu X, Sawyer SJ, Chan AT, Libermann TA, Eliassen AH Tags: Sci Rep Source Type: research

Cerebrospinal Fluid Protein Changes in Preeclampsia.
Abstract The molecular mechanisms underlying seizure susceptibility in preeclampsia are unknown. We hypothesized that altered expression of distinct proteins in the cerebrospinal fluid (CSF) may reflect pathophysiological changes in the central nervous system that contribute to the neurological manifestations of severe preeclampsia. We obtained CSF samples from 13 patients with preeclampsia and 14 control patients during spinal anesthesia before delivery and analyzed them by SOMAscan, an aptamer-based proteomics platform for alterations in 1310 protein levels. Ingenuity Pathway Analysis was conducted to highlight ...
Source: Genomics Proteomics ... - May 29, 2018 Category: Genetics & Stem Cells Authors: Ciampa E, Li Y, Dillon S, Lecarpentier E, Sorabella L, Libermann TA, Karumanchi SA, Hess PE Tags: Hypertension Source Type: research

SHMT2 and the BRCC36/BRISC deubiquitinase regulate HIV-1 Tat K63-ubiquitylation and destruction by autophagy.
Abstract HIV-1 Tat is a key regulator of viral transcription, however little is known about the mechanisms that control its turnover in T cells. Here we use a novel proteomics technique, called DiffPOP, to identify the molecular target of JIB-04, a small molecule compound that potently and selectively blocks HIV-1 Tat expression, transactivation, and virus replication in T cell lines. Mass-spectrometry analysis of whole-cell extracts from 2D10 Jurkat T cells revealed that JIB-04 targets Serine Hydroxymethyltransferase 2 (SHMT2), a regulator of glycine biosynthesis and an adaptor for the BRCC36 K63Ub-specific deubi...
Source: Genomics Proteomics ... - May 23, 2018 Category: Genetics & Stem Cells Authors: Xu M, Moresco JJ, Chang M, Mukim A, Smith D, Diedrich JK, Yates JR, Jones KA Tags: PLoS Pathog Source Type: research

EuPathDB: The Eukaryotic Pathogen Genomics Database Resource.
Abstract Fighting infections and developing novel drugs and vaccines requires advanced knowledge of pathogen's biology. Readily accessible genomic, functional genomic, and population data aids biological and translational discovery. The Eukaryotic Pathogen Database Resources ( http://eupathdb.org ) are data mining resources that support hypothesis driven research by facilitating the discovery of meaningful biological relationships from large volumes of data. The resource encompasses 13 sites that support over 170 species including pathogenic protists, oomycetes, and fungi as well as evolutionarily related nonpatho...
Source: Genomics Proteomics ... - May 17, 2018 Category: Genetics & Stem Cells Authors: Warrenfeltz S, Basenko EY, Crouch K, Harb OS, Kissinger JC, Roos DS, Shanmugasundram A, Silva-Franco F Tags: Methods Mol Biol Source Type: research

Author Correction: Kanglaite sensitizes colorectal cancer cells to Taxol via NF- κΒ inhibition and connexin 43 upregulation.
Author Correction: Kanglaite sensitizes colorectal cancer cells to Taxol via NF-κΒ inhibition and connexin 43 upregulation. Sci Rep. 2018 Apr 12;8(1):6141 Authors: Wang Y, Zhang C, Zhang S, Zhao Z, Wang J, Song J, Wang Y, Liu J, Hou S Abstract A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper. PMID: 29643394 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - April 12, 2018 Category: Genetics & Stem Cells Authors: Wang Y, Zhang C, Zhang S, Zhao Z, Wang J, Song J, Wang Y, Liu J, Hou S Tags: Sci Rep Source Type: research

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.
CONCLUSIONS: PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download. PMID: 29642841 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - April 11, 2018 Category: Genetics & Stem Cells Authors: Sivade Dumousseau M, Alonso-López D, Ammari M, Bradley G, Campbell NH, Ceol A, Cesareni G, Combe C, De Las Rivas J, Del-Toro N, Heimbach J, Hermjakob H, Jurisica I, Koch M, Licata L, Lovering RC, Lynn DJ, Meldal BHM, Micklem G, Panni S, Porras P, Ricard- Tags: BMC Bioinformatics Source Type: research

VSClust: Feature-based variance-sensitive clustering of omics data.
We present VSClust that accounts for feature-specific variance. Based on an algorithm derived from fuzzy clustering, VSClust unifies statistical testing with pattern recognition to cluster the data into feature groups that more accurately reflect the underlying molecular and functional behavior. We apply VSClust to artificial and experimental data sets comprising hundreds to more than 80,000 features across 6-20 different conditions including genomics, transcriptomics, proteomics and metabolomics experiments. VSClust avoids arbitrary averaging methods, outperforms standard fuzzy c-means clustering and simplifies the data a...
Source: Genomics Proteomics ... - April 9, 2018 Category: Genetics & Stem Cells Authors: Schwämmle V, Jensen ON Tags: Bioinformatics Source Type: research

Specific Transcriptome Changes Associated with Blood Pressure Reduction in Hypertensive Patients After Relaxation Response Training.
CONCLUSIONS: These findings provide the first insights into the molecular mechanisms that are associated with the beneficial effects of the RR on HTN. PMID: 29616846 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - April 4, 2018 Category: Genetics & Stem Cells Authors: Bhasin MK, Denninger JW, Huffman JC, Joseph MG, Niles H, Chad-Friedman E, Goldman R, Buczynski-Kelley B, Mahoney BA, Fricchione GL, Dusek JA, Benson H, Zusman RM, Libermann TA Tags: J Altern Complement Med Source Type: research

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas.
eghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK, Cancer Genome Atlas Research Network, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C Abstract This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV)...
Source: Genomics Proteomics ... - April 3, 2018 Category: Genetics & Stem Cells Authors: Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sa Tags: Cell Rep Source Type: research

The influence of transcript assembly on the proteogenomics discovery of microproteins.
Abstract Proteogenomics methods have identified many non-annotated protein-coding genes in the human genome. Many of the newly discovered protein-coding genes encode peptides and small proteins, referred to collectively as microproteins. Microproteins are produced through ribosome translation of small open reading frames (smORFs). The discovery of many smORFs reveals a blind spot in traditional gene-finding algorithms for these genes. Biological studies have found roles for microproteins in cell biology and physiology, and the potential that there exists additional bioactive microproteins drives the interest in de...
Source: Genomics Proteomics ... - March 28, 2018 Category: Genetics & Stem Cells Authors: Ma J, Saghatelian A, Shokhirev MN Tags: PLoS One Source Type: research

Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli.
Abstract Members of the Mycobacterium tuberculosis complex (MTBC) are the causative agents of tuberculosis in a range of mammals, including humans. A key feature of MTBC pathogens is their high degree of genetic identity yet distinct host tropism. Notably, while Mycobacterium bovis is highly virulent and pathogenic for cattle, the human pathogen M. tuberculosis is attenuated in cattle. Previous research also suggests that host preference amongst MTBC members has a basis in host innate immune responses. To explore MTBC host tropism, we present in-depth profiling of the MTBC reference strains M. bovis AF2122/97 and ...
Source: Genomics Proteomics ... - March 20, 2018 Category: Genetics & Stem Cells Authors: Malone KM, Rue-Albrecht K, Magee DA, Conlon K, Schubert OT, Nalpas NC, Browne JA, Smyth A, Gormley E, Aebersold R, MacHugh DE, Gordon SV Tags: Microb Genom Source Type: research

Acute Heat Stress Changes Protein Expression in the Testes of a Broiler-Type Strain of Taiwan Country Chickens.
In conclusion, acute heat stress causes a change in protein expression in the testes of broiler-type B strain TCCs and may thus impair cell morphology, spermatogenesis, and apoptosis. The expression of heat shock proteins increased to attenuate the testicular injury induced by acute heat stress. PMID: 29553885 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - March 19, 2018 Category: Genetics & Stem Cells Authors: Wang SH, Cheng CY, Chen CJ, Chan HL, Chen HH, Tang PC, Chen CF, Lee YP, Huang SY Tags: Anim Biotechnol Source Type: research

Systematic Functional Annotation of Somatic Mutations in Cancer.
rchin R, Ding L, Lu Y, Cheung LWT, Chen K, Shaw KR, Meric-Bernstam F, Scott KL, Yi S, Sahni N, Liang H, Mills GB Abstract The functional impact of the vast majority of cancer somatic mutations remains unknown, representing a critical knowledge gap for implementing precision oncology. Here, we report the development of a moderate-throughput functional genomic platform consisting of efficient mutant generation, sensitive viability assays using two growth factor-dependent cell models, and functional proteomic profiling of signaling effects for select aberrations. We apply the platform to annotate>1,000 genomic abe...
Source: Genomics Proteomics ... - March 12, 2018 Category: Genetics & Stem Cells Authors: Ng PK, Li J, Jeong KJ, Shao S, Chen H, Tsang YH, Sengupta S, Wang Z, Bhavana VH, Tran R, Soewito S, Minussi DC, Moreno D, Kong K, Dogruluk T, Lu H, Gao J, Tokheim C, Zhou DC, Johnson AM, Zeng J, Ip CKM, Ju Z, Wester M, Yu S, Li Y, Vellano CP, Schultz N, K Tags: Cancer Cell Source Type: research

Exosomal αvβ6 integrin is required for monocyte M2 polarization in prostate cancer.
We describe a novel αvβ6-mediated signaling pathway that has profound effects on the microenvironment. We show that αvβ6 is transferred from cancer cells to monocytes, including β6-/- monocytes, by exosomes and that monocytes from prostate cancer patients, but not from healthy volunteers, express αvβ6. Cancer cell exosomes, purified via density gradients, promote M2 polarization, whereas αvβ6 down-regulation in exosomes inhibits M2 polarization in recipient monocytes. Also, as evaluated by our proteomic analysis, αvβ6 down-regulation causes a significant increase ...
Source: Genomics Proteomics ... - March 9, 2018 Category: Genetics & Stem Cells Authors: Lu H, Bowler N, Harshyne LA, Craig Hooper D, Krishn SR, Kurtoglu S, Fedele C, Liu Q, Tang HY, Kossenkov AV, Kelly WK, Wang K, Kean RB, Weinreb PH, Yu L, Dutta A, Fortina P, Ertel A, Stanczak M, Forsberg F, Gabrilovich DI, Speicher DW, Altieri DC, Languino Tags: Matrix Biol Source Type: research

Deep Learning and its Applications in Biomedicine.
Abstract Advances in biological and medical technologies have been providing us explosive volumes of biological and physiological data, such as medical images, electroencephalography, genomic and protein sequences. Learning from these data facilitates the understanding of human health and disease. Developed from artificial neural networks, deep learning-based algorithms show great promise in extracting features and learning patterns from complex data. The aim of this paper is to provide an overview of deep learning techniques and some of the state-of-the-art applications in the biomedical field. We first introduce...
Source: Genomics Proteomics ... - March 6, 2018 Category: Genetics & Stem Cells Authors: Cao C, Liu F, Tan H, Song D, Shu W, Li W, Zhou Y, Bo X, Xie Z Tags: Genomics Proteomics Bioinformatics Source Type: research

The Immunome of Colon Cancer: Functional In Silico Analysis of Antigenic Proteins Deduced from IgG Microarray Profiling.
ml;usel A Abstract Characterization of the colon cancer immunome and its autoantibody signature from differentially-reactive antigens (DIRAGs) could provide insights into aberrant cellular mechanisms or enriched networks associated with diseases. The purpose of this study was to characterize the antibody profile of plasma samples from 32 colorectal cancer (CRC) patients and 32 controls using proteins isolated from 15,417 human cDNA expression clones on microarrays. 671 unique DIRAGs were identified and 632 were more highly reactive in CRC samples. Bioinformatics analyses reveal that compared to control samples, th...
Source: Genomics Proteomics ... - March 2, 2018 Category: Genetics & Stem Cells Authors: Luna Coronell JA, Sergelen K, Hofer P, Gyurján I, Brezina S, Hettegger P, Leeb G, Mach K, Gsur A, Weinhäusel A Tags: Genomics Proteomics Bioinformatics Source Type: research

The Druggable Pocketome of Corynebacterium diphtheriae: A New Approach for in silico Putative Druggable Targets.
VAC Abstract Diphtheria is an acute and highly infectious disease, previously regarded as endemic in nature but vaccine-preventable, is caused by Corynebacterium diphtheriae (Cd). In this work, we used an in silico approach along the 13 complete genome sequences of C. diphtheriae followed by a computational assessment of structural information of the binding sites to characterize the "pocketome druggability." To this end, we first computed the "modelome" (3D structures of a complete genome) of a randomly selected reference strain Cd NCTC13129; that had 13,763 open reading frames (ORFs) and resu...
Source: Genomics Proteomics ... - March 1, 2018 Category: Genetics & Stem Cells Authors: Hassan SS, Jamal SB, Radusky LG, Tiwari S, Ullah A, Ali J, Behramand, de Carvalho PVSD, Shams R, Khan S, Figueiredo HCP, Barh D, Ghosh P, Silva A, Baumbach J, Röttger R, Turjanski AG, Azevedo VAC Tags: Front Genet Source Type: research

Quantitative Peptidomics with Isotopic and Isobaric Tags.
Abstract In differential peptidomics, peptide profiles are compared between biological samples and the resulting expression levels are correlated to a phenotype of interest. This, in turn, allows us insight into how peptides may affect the phenotype of interest. In quantitative differential peptidomics, both label-based and label-free techniques are often employed. Label-based techniques have several advantages over label-free methods, primarily that labels allow for various samples to be pooled prior to liquid chromatography-mass spectrometry (LC-MS) analysis, reducing between-run variation. Here, we detail a met...
Source: Genomics Proteomics ... - February 28, 2018 Category: Genetics & Stem Cells Authors: Boonen K, De Haes W, Van Houtven J, Verdonck R, Baggerman G, Valkenborg D, Schoofs L Tags: Methods Mol Biol Source Type: research

Genome Writing: Current Progress and Related Applications.
Abstract The ultimate goal of synthetic biology is to build customized cells or organisms to meet specific industrial or medical needs. The most important part of the customized cell is a synthetic genome. Advanced genomic writing technologies are required to build such an artificial genome. Recently, the partially-completed synthetic yeast genome project represents a milestone in this field. In this mini review, we briefly introduce the techniques for de novo genome synthesis and genome editing. Furthermore, we summarize recent research progresses and highlight several applications in the synthetic genome field. ...
Source: Genomics Proteomics ... - February 20, 2018 Category: Genetics & Stem Cells Authors: Wang Y, Shen Y, Gu Y, Zhu S, Yin Y Tags: Genomics Proteomics Bioinformatics Source Type: research

Preprocessing of 2-Dimensional Gel Electrophoresis Images Applied to Proteomic Analysis: A Review.
-Trejos E Abstract Various methods and specialized software programs are available for processing two-dimensional gel electrophoresis (2-DGE) images. However, due to the anomalies present in these images, a reliable, automated, and highly reproducible system for 2-DGE image analysis has still not been achieved. The most common anomalies found in 2-DGE images include vertical and horizontal streaking, fuzzy spots, and background noise, which greatly complicate computational analysis. In this paper, we review the preprocessing techniques applied to 2-DGE images for noise reduction, intensity normalization, and backg...
Source: Genomics Proteomics ... - February 20, 2018 Category: Genetics & Stem Cells Authors: Mauricio Goez M, Constanza Torres-Madroñero M, Röthlisberger S, Delgado-Trejos E Tags: Genomics Proteomics Bioinformatics Source Type: research

Human Gut Microbiota and Gastrointestinal Cancer.
Abstract Human gut microbiota play an essential role in both healthy and diseased states of humans. In the past decade, the interactions between microorganisms and tumors have attracted much attention in the efforts understanding various features of the complex microbial communities, as well as the possible mechanisms through which the microbiota are involved in cancer prevention, carcinogenesis, and anti-cancer therapy. A large number of studies have indicated that microbial dysbiosis contributes to cancer susceptibility via multiple pathways. Further studies have suggested that the microbiota and their associate...
Source: Genomics Proteomics ... - February 20, 2018 Category: Genetics & Stem Cells Authors: Meng C, Bai C, Brown TD, Hood L, Tian Q Tags: Genomics Proteomics Bioinformatics Source Type: research

Microvesicles as Emerging Biomarkers and Therapeutic Targets in Cardiometabolic Diseases.
Abstract Microvesicles (MVs, also known as microparticles) are small vesicles that originate from plasma membrane of almost all eukaryotic cells during apoptosis or activation. MVs can serve as extracellular vehicles to transport bioactive molecules from their parental cells to recipient target cells, thereby serving as novel mediators for intercellular communication. Importantly, more and more evidence indicates that MVs could play important roles in early pathogenesis and subsequent progression of cardiovascular and metabolic diseases. Elevated plasma concentrations of MVs, originating from red blood cells, leuk...
Source: Genomics Proteomics ... - February 17, 2018 Category: Genetics & Stem Cells Authors: Chen Y, Li G, Liu ML Tags: Genomics Proteomics Bioinformatics Source Type: research

Genome-wide gene expression analysis of 45  days pregnant fetal cotyledons vis-a-vis non-pregnant caruncles in buffalo (Bubalus bubalis).
Genome-wide gene expression analysis of 45 days pregnant fetal cotyledons vis-a-vis non-pregnant caruncles in buffalo (Bubalus bubalis). Gene. 2018 Feb 14;: Authors: Lotfan M, Ali SA, Yadav M, Chuadhary S, Jena MK, Kumar S, Mohanty AK Abstract The crosstalk between fetus and mother starts with the onset of placental attachment to the uterus. The cotyledons and caruncles are the two anatomically distinct structures that play a crucial role in this physiological communication. Using Agilent Gene Chip Genome microarray, we measured the expression profile of pregnancy cotyledons in comparison to caruncu...
Source: Genomics Proteomics ... - February 14, 2018 Category: Genetics & Stem Cells Authors: Lotfan M, Ali SA, Yadav M, Chuadhary S, Jena MK, Kumar S, Mohanty AK Tags: Gene Source Type: research

PClass: Protein Quaternary Structure Classification by Using Bootstrapping Strategy as Model Selection.
Abstract Protein quaternary structure complex is also known as a multimer, which plays an important role in a cell. The dimer structure of transcription factors is involved in gene regulation, but the trimer structure of virus-infection-associated glycoproteins is related to the human immunodeficiency virus. The classification of the protein quaternary structure complex for the post-genome era of proteomics research will be of great help. Classification systems among protein quaternary structures have not been widely developed. Therefore, we designed the architecture of a two-layer machine learning technique in th...
Source: Genomics Proteomics ... - February 14, 2018 Category: Genetics & Stem Cells Authors: Huang CC, Chang CC, Chen CW, Ho SY, Chang HP, Chu YW Tags: Genes (Basel) Source Type: research

Effect of Seasonal Change on Testicular Protein Expression in White Roman Geese.
Abstract The purpose of this study was to investigate the change in protein expression in the testes of ganders at various breeding stages. A total of nine 3-year-old male White Roman ganders were used. The blood and testis samples were collected at the nonbreeding, sexual reactivation, and breeding stages for sex hormone analysis and proteomic analysis, respectively. The testicular weight and serum testosterone observed for ganders at the breeding stage were higher than those for ganders at nonbreeding and sexual reactivation stages (P 
Source: Genomics Proteomics ... - February 9, 2018 Category: Genetics & Stem Cells Authors: Zhuang ZX, Chang SC, Chen CJ, Chan HL, Lin MJ, Liao HY, Cheng CY, Lin TY, Jea YS, Huang SY Tags: Anim Biotechnol Source Type: research

Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure.
Abstract In recent years, electron capture (ECD) and electron transfer dissociation (ETD) have emerged as two of the most useful methods in mass spectrometry-based protein analysis, evidenced by a considerable and growing body of literature. In large part, the interest in these methods is due to their ability to induce backbone fragmentation with very little disruption of noncovalent interactions which allows inference of information regarding higher order structure from the observed fragmentation behavior. Here, we review the evolution of electron-based dissociation methods, and pay particular attention to their ...
Source: Genomics Proteomics ... - February 9, 2018 Category: Genetics & Stem Cells Authors: Lermyte F, Valkenborg D, Loo JA, Sobott F Tags: Mass Spectrom Rev Source Type: research

Comparison of genomes and proteomes of four whole genome-sequenced Campylobacter jejuni from different phylogenetic backgrounds.
In this study we compare the closed, finished genome sequences of these isolates to the total proteome. Genomes of the four isolates differ in phage content and location, plasmid content, capsular polysaccharide biosynthesis loci, a type VI secretion system, orientation of the ~92 kb invertible element, and allelic differences. Proteins with 99% sequence identity can be differentiated using isobaric tags for relative and absolute quantification (iTRAQ) comparative proteomic methods. GO enrichment analysis and the type of artefacts produced in comparative proteomic analysis depend on whether proteins are encoded in only one...
Source: Genomics Proteomics ... - February 6, 2018 Category: Genetics & Stem Cells Authors: Clark CG, Chen CY, Berry C, Walker M, McCorrister SJ, Chong PM, Westmacott GR Tags: PLoS One Source Type: research

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.
ute;no JA Abstract On behalf of The Human Proteome Organization (HUPO) Proteomics Standards Initiative, we introduce here two novel standard data formats, proBAM and proBed, that have been developed to address the current challenges of integrating mass spectrometry-based proteomics data with genomics and transcriptomics information in proteogenomics studies. proBAM and proBed are adaptations of the well-defined, widely used file formats SAM/BAM and BED, respectively, and both have been extended to meet the specific requirements entailed by proteomics data. Therefore, existing popular genomics tools such as SAMtool...
Source: Genomics Proteomics ... - January 31, 2018 Category: Genetics & Stem Cells Authors: Menschaert G, Wang X, Jones AR, Ghali F, Fenyö D, Olexiouk V, Zhang B, Deutsch EW, Ternent T, Vizcaíno JA Tags: Genome Biol Source Type: research

Omics technologies for microalgae-based fuels and chemicals; challenges and opportunities.
Abstract Microalgae have been appeared as promising feedstocks of significant biotechnological interest due to their enormous potential for the sustainable production of industrially valuable compounds such as lipids/fatty acids, proteins, metabolites, pigments, and biofuels. However, exploitation of algal biomass for commercial purposes is still in infancy due to the dearth of the knowledge regarding state-of-the-art sophisticated technologies. Inarguably, over the past several years, biological sciences have witnessed an explosion of innovative strategies enabling scientific community and research-based organiza...
Source: Genomics Proteomics ... - January 21, 2018 Category: Genetics & Stem Cells Authors: Khan AZ, Shahid A, Cheng H, Mahboob S, Al-Ghanim KA, Bilal M, Nawaz MZ Tags: Protein Pept Lett Source Type: research

Multiple target autoantigens on endothelial cells identified in juvenile dermatomyositis using proteomics.
Conclusion: Children with JDM express antibodies to autoantigens in endothelial cells. The clinical and pathological significance of such autoantibodies require further investigation. PMID: 29361142 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - January 18, 2018 Category: Genetics & Stem Cells Authors: Karasawa R, Tamaki M, Sato T, Tanaka M, Nawa M, Yudoh K, Jarvis JN Tags: Rheumatology (Oxford) Source Type: research

Integrative Personal Omics Profiles during Periods of Weight Gain and Loss.
bbott C, Gerstein M, Mardinoglu A, Smith U, Rubin DL, Pitteri S, Sodergren E, McLaughlin TL, Weinstock GM, Snyder MP Abstract Advances in omics technologies now allow an unprecedented level of phenotyping for human diseases, including obesity, in which individual responses to excess weight are heterogeneous and unpredictable. To aid the development of better understanding of these phenotypes, we performed a controlled longitudinal weight perturbation study combining multiple omics strategies (genomics, transcriptomics, multiple proteomics assays, metabolomics, and microbiomics) during periods of weight gain and lo...
Source: Genomics Proteomics ... - January 16, 2018 Category: Genetics & Stem Cells Authors: Piening BD, Zhou W, Contrepois K, Röst H, Gu Urban GJ, Mishra T, Hanson BM, Bautista EJ, Leopold S, Yeh CY, Spakowicz D, Banerjee I, Chen C, Kukurba K, Perelman D, Craig C, Colbert E, Salins D, Rego S, Lee S, Zhang C, Wheeler J, Sailani MR, Liang L, Abbo Tags: Cell Syst Source Type: research

Bioinformatics and genomic databases.
Abstract High-throughput, low-cost sequencing technologies have begun to yield new insights into biology and medicine. New data enable the interrogation of the molecular biology of disease from DNA to RNA to protein, charting the central dogma. This chapter reviews some of the key advances and resources in the application of bioinformatics to understanding, and ultimately diagnosing and treating, diseases of the nervous system. Array genotyping, exome sequencing, and whole-genome sequencing, in both disease and healthy populations, have enabled the interpretation of new genetic data. Profiling of epigenetic marker...
Source: Genomics Proteomics ... - January 13, 2018 Category: Genetics & Stem Cells Authors: Chen J, Coppola G Tags: Handb Clin Neurol Source Type: research

Integrative genomic and transcriptomic analysis of leiomyosarcoma.
Eils R, Stenzinger A, Weichert W, Glimm H, Gröschel S, Kopp HG, Omlor G, Lehner B, Bauer S, Schimmack S, Ulrich A, Mechtersheimer G, Rippe K, Brors B, Hutter B, Renner M, Hohenberger P, Scholl C, Fröhling S Abstract Leiomyosarcoma (LMS) is an aggressive mesenchymal malignancy with few therapeutic options. The mechanisms underlying LMS development, including clinically actionable genetic vulnerabilities, are largely unknown. Here we show, using whole-exome and transcriptome sequencing, that LMS tumors are characterized by substantial mutational heterogeneity, near-universal inactivation of TP53 and RB1, ...
Source: Genomics Proteomics ... - January 10, 2018 Category: Genetics & Stem Cells Authors: Chudasama P, Mughal SS, Sanders MA, Hübschmann D, Chung I, Deeg KI, Wong SH, Rabe S, Hlevnjak M, Zapatka M, Ernst A, Kleinheinz K, Schlesner M, Sieverling L, Klink B, Schröck E, Hoogenboezem RM, Kasper B, Heilig CE, Egerer G, Wolf S, von Kalle C, Eils R Tags: Nat Commun Source Type: research