Accessing Cryptosporidium Omic and Isolate Data via CryptoDB.org.
Abstract Cryptosporidium has historically been a difficult organism to work with, and molecular genomic data for this important pathogen have typically lagged behind other prominent protist pathogens. CryptoDB ( http://cryptodb.org/ ) was launched in 2004 following the appearance of draft genome sequences for both C. parvum and C. hominis. CryptoDB merged with the EuPathDB Bioinformatics Resource Center family of databases ( https://eupathdb.org ) and has been maintained and updated regularly since its establishment. These resources are freely available, are web-based, and permit users to analyze their own sequenc...
Source: Genomics Proteomics ... - August 30, 2019 Category: Genetics & Stem Cells Authors: Warrenfeltz S, Kissinger JC, EuPathDB Team Tags: Methods Mol Biol Source Type: research

C3: Consensus Cancer Driver Gene Caller.
Abstract Next-generation sequencing has allowed identification of millions of somatic mutations in human cancer cells. A key challenge in interpreting cancer genomes is to distinguish drivers of cancer development among available genetic mutations. To address this issue, we present the first web-based application, consensus cancer driver gene caller (C3), to identify the consensus driver genes using six different complementary strategies, i.e., frequency-based, machine learning-based, functional bias-based, clustering-based, statistics model-based, and network-based strategies. This application allows users to spe...
Source: Genomics Proteomics ... - August 26, 2019 Category: Genetics & Stem Cells Authors: Zhu CY, Zhou C, Chen YQ, Shen AZ, Guo ZM, Yang ZY, Ye XY, Qu S, Wei J, Liu Q Tags: Genomics Proteomics Bioinformatics Source Type: research

Trait Loci Mapping and CSF Proteome.
Abstract Recent advance in high-throughput proteome analysis has enabled genome-wide and proteome-wide analyses of associations between single nucleotide polymorphisms and protein expression levels. Protein quantitative trait locus (pQTL) studies using cerebrospinal fluid (CSF) and DNA samples may provide valuable insights into the genetic basis and molecular mechanisms regulating protein expression in the central nervous system. In this chapter, we describe a step-by-step procedures of CSF collection and pQTL analysis, by using PLINK and R software. PMID: 31432426 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - August 23, 2019 Category: Genetics & Stem Cells Authors: Sasayama D, Hattori K, Kunugi H Tags: Methods Mol Biol Source Type: research

gFACs: Gene Filtering, Analysis, and Conversion to Unify Genome Annotations Across Alignment and Gene Prediction Frameworks.
Abstract Published genomes frequently contain erroneous gene models that represent issues associated with identification of open reading frames, start sites, splice sites, and related structural features. The source of these inconsistencies is often traced back to integration across text file formats designed to describe long read alignments and predicted gene structures. In addition, the majority of gene prediction frameworks do not provide robust downstream filtering to remove problematic gene annotations, nor do they represent these annotations in a format consistent with current file standards. These framework...
Source: Genomics Proteomics ... - August 19, 2019 Category: Genetics & Stem Cells Authors: Caballero M, Wegrzyn J Tags: Genomics Proteomics Bioinformatics Source Type: research

ITRAQ-based proteomic analysis reveals possible target-related proteins in human adrenocortical adenomas.
CONCLUSIONS: This study is the first proteomic research to investigate alterations in protein levels and affected pathways in ACA using the iTRAQ technique. Thus, this study not only provides a comprehensive dataset on overall protein changes but also sheds light on its potential molecular mechanism in human ACAs. PMID: 31419939 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - August 16, 2019 Category: Genetics & Stem Cells Authors: Ma H, Li R, Di X, Jin X, Wang Y, Lai B, Shi C, Ji M, Zhu X, Wang K Tags: BMC Genomics Source Type: research

ERBB3 and IGF1R signaling are required for Nrf2-dependent growth in KEAP1-mutant lung cancer.
Abstract Mutations in KEAP1 and NFE2L2 (encoding the protein Nrf2) are prevalent in both adenocarcinoma and squamous subtypes of non-small cell lung cancer. The consequence of these mutations is stabilized Nrf2 and chronic induction of several Nrf2 target genes. Here, downregulation of Nrf2 resulted in modest growth inhibition of cells growing in 2D; this was more pronounced in cell lines expressing mutant KEAP1. In contrast, downregulation of Nrf2 caused almost complete regression of established KEAP1-mutant tumors in mice, with little effect on wildtype (WT) KEAP1 tumors. The strong dependency on Nrf2 could be r...
Source: Genomics Proteomics ... - August 15, 2019 Category: Genetics & Stem Cells Authors: Vartanian S, Lee J, Klijn C, Gnad F, Bagniewska M, Schaefer G, Zhang D, Tan J, Watson SA, Liu L, Chen H, Liang Y, Watanabe C, Cuellar T, Kan D, Hartmaier RJ, Lau T, Costa MR, Martin SE, Merchant M, Haley B, Stokoe D Tags: Cancer Res Source Type: research

HENA, heterogeneous network-based data set for Alzheimer's disease.
In this study we describe a heterogeneous network-based data set for Alzheimer's disease (HENA). Additionally, we demonstrate the application of state-of-the-art graph convolutional networks, i.e. deep learning methods for the analysis of such large heterogeneous biological data sets. We expect HENA to allow scientists to explore and analyze their own results in the broader context of Alzheimer's disease research. PMID: 31413325 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - August 14, 2019 Category: Genetics & Stem Cells Authors: Sügis E, Dauvillier J, Leontjeva A, Adler P, Hindie V, Moncion T, Collura V, Daudin R, Loe-Mie Y, Herault Y, Lambert JC, Hermjakob H, Pupko T, Rain JC, Xenarios I, Vilo J, Simonneau M, Peterson H Tags: Sci Data Source Type: research

Current status of clinical proteogenomics in lung cancer.
Furuya N, Saji H Abstract Introduction: Lung cancer is the leading cause of cancer death worldwide. Proteogenomics, a way to integrate genomics, transcriptomics, and proteomics, have emerged as a way to understand molecular causes in cancer tumorigenesis. This understanding will help identify therapeutic targets that are urgently needed to improve individual patient outcomes. Areas covered: To explore underlying molecular mechanisms of lung cancer subtypes, several efforts have used proteogenomic approaches that integrate next generation sequencing (NGS) and mass spectrometry (MS)-based technologies. Expert Opini...
Source: Genomics Proteomics ... - August 11, 2019 Category: Genetics & Stem Cells Authors: Nishimura T, Nakamura H, Végvári Á, Marko-Varga G, Furuya N, Saji H Tags: Expert Rev Proteomics Source Type: research

Proteogenomic landscape of squamous cell lung cancer.
omen JM, Eschrich SA, Haura EB Abstract How genomic and transcriptomic alterations affect the functional proteome in lung cancer is not fully understood. Here, we integrate DNA copy number, somatic mutations, RNA-sequencing, and expression proteomics in a cohort of 108 squamous cell lung cancer (SCC) patients. We identify three proteomic subtypes, two of which (Inflamed, Redox) comprise 87% of tumors. The Inflamed subtype is enriched with neutrophils, B-cells, and monocytes and expresses more PD-1. Redox tumours are enriched for oxidation-reduction and glutathione pathways and harbor more NFE2L2/KEAP1 alterations ...
Source: Genomics Proteomics ... - August 8, 2019 Category: Genetics & Stem Cells Authors: Stewart PA, Welsh EA, Slebos RJC, Fang B, Izumi V, Chambers M, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Fellows KM, Francis JM, Saller JJ, Mesa T, Zhang C, Yoder S, DeNicola GM, Beg AA, Boyle TA, Teer JK, Ann Chen Y, K Tags: Nat Commun Source Type: research

The Oncogenic Action of NRF2 Depends on De-glycation by Fructosamine-3-Kinase.
Abstract The NRF2 transcription factor controls a cell stress program that is implicated in cancer and there is great interest in targeting NRF2 for therapy. We show that NRF2 activity depends on Fructosamine-3-kinase (FN3K)-a kinase that triggers protein de-glycation. In its absence, NRF2 is extensively glycated, unstable, and defective at binding to small MAF proteins and transcriptional activation. Moreover, the development of hepatocellular carcinoma triggered by MYC and Keap1 inactivation depends on FN3K in vivo. N-acetyl cysteine treatment partially rescues the effects of FN3K loss on NRF2 driven tumor ...
Source: Genomics Proteomics ... - August 8, 2019 Category: Genetics & Stem Cells Authors: Sanghvi VR, Leibold J, Mina M, Mohan P, Berishaj M, Li Z, Miele MM, Lailler N, Zhao C, de Stanchina E, Viale A, Akkari L, Lowe SW, Ciriello G, Hendrickson RC, Wendel HG Tags: Cell Source Type: research

Quantifying the impact of public omics data.
kob H Abstract The amount of omics data in the public domain is increasing every year. Modern science has become a data-intensive discipline. Innovative solutions for data management, data sharing, and for discovering novel datasets are therefore increasingly required. In 2016, we released the first version of the Omics Discovery Index (OmicsDI) as a light-weight system to aggregate datasets across multiple public omics data resources. OmicsDI aggregates genomics, transcriptomics, proteomics, metabolomics and multiomics datasets, as well as computational models of biological processes. Here, we propose a set of no...
Source: Genomics Proteomics ... - August 5, 2019 Category: Genetics & Stem Cells Authors: Perez-Riverol Y, Zorin A, Dass G, Vu MT, Xu P, Glont M, Vizcaíno JA, Jarnuczak AF, Petryszak R, Ping P, Hermjakob H Tags: Nat Commun Source Type: research

Flexible Implementation of the BASIL CURE.
Abstract Course-based Undergraduate Research Experiences (CUREs) can be a very effective means to introduce a large number of students to research. CUREs are often an extension of the instructor's research, which may make them difficult to replicate in other settings because of differences in expertise or facilities. The BASIL (Biochemistry Authentic Scientific Inquiry Lab) CURE has evolved over the past 4 years as faculty members with different backgrounds, facilities, and campus cultures have all contributed to a robust curriculum focusing on enzyme function prediction that is suitable for implementation in a wi...
Source: Genomics Proteomics ... - August 5, 2019 Category: Genetics & Stem Cells Authors: Roberts R, Hall B, Daubner C, Goodman A, Pikaart M, Sikora A, Craig P Tags: Biochem Mol Biol Educ Source Type: research

Global Investigation of Immune Repertoire Suggests Kawasaki Disease Has Infectious Cause.
CONCLUSIONS: The results of D50 value, VDJ usage and CDR3 peptide length analyses suggested the characteristics of infectious disease for KD. PMID: 31378745 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - August 3, 2019 Category: Genetics & Stem Cells Authors: Kuo HC, Pan CT, Huang YH, Huang FC, Lin YS, Li SC, Huang LH Tags: Circ J Source Type: research

ACTINN: Automated Identification of Cell Types in Single Cell RNA Sequencing.
Abstract MOTIVATION: Cell type identification is one of the major goals in single cell RNA sequencing (scRNA-seq). Current methods for assigning cell types typically involve the use of unsupervised clustering, the identification of signature genes in each cluster, followed by a manual lookup of these genes in the literature and databases to assign cell types. However, there are several limitations associated with these approaches, such as unwanted sources of variation that influence clustering and a lack of canonical markers for certain cell types. Here, we present ACTINN (Automated Cell Type Identification using ...
Source: Genomics Proteomics ... - July 29, 2019 Category: Genetics & Stem Cells Authors: Ma F, Pellegrini M Tags: Bioinformatics Source Type: research

Novel Candidates for Vaccine Development Against Mycoplasma Capricolum Subspecies Capripneumoniae (Mccp)-Current Knowledge and Future Prospects.
Abstract Exploration of novel candidates for vaccine development against Mycoplasma capricolum subspecies capripneumoniae (Mccp), the causative agent of contagious caprine pleuropneumonia (CCPP), has recently gained immense importance due to both the increased number of outbreaks and the alarming risk of transboundary spread of disease. Treatment by antibiotics as the only therapeutic strategy is not a viable option due to pathogen persistence, economic issues, and concerns of antibiotic resistance. Therefore, prophylactics or vaccines are becoming important under the current scenario. For quite some time inactiva...
Source: Genomics Proteomics ... - July 23, 2019 Category: Genetics & Stem Cells Authors: Yatoo MI, Parray OR, Muheet, Bhat RA, Nazir QU, Haq AU, Malik HU, Fazilli MUR, Gopalakrishnan A, Bashir ST, Tiwari R, Khurana SK, Chaicumpa W, Dhama K Tags: Vaccines (Basel) Source Type: research

That's A Scientist Should Do - A Dialog with Tomas Lindahl.
PMID: 31323385 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - July 16, 2019 Category: Genetics & Stem Cells Authors: Xie S, Jiao Y Tags: Genomics Proteomics Bioinformatics Source Type: research

Systematic analysis of the lysine succinylome in the model medicinal mushroom Ganoderma lucidum.
CONCLUSIONS: These findings indicate that lysine succinylation is related to many metabolic pathways, especially pharmacologically bioactive compounds metabolism. This study provides the first global investigation of lysine succinylation in G. lucidum and the succinylome dataset provided in this study serves as a resource to further explore the physiological roles of these modifications in secondary metabolism. PMID: 31311503 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - July 16, 2019 Category: Genetics & Stem Cells Authors: Wang G, Xu L, Yu H, Gao J, Guo L Tags: BMC Genomics Source Type: research

Delineating the Plausible Molecular Vaccine Candidates and Drug Targets of Multidrug-Resistant Acinetobacter baumannii.
Abstract Nosocomial infections have become alarming with the increase of multidrug-resistant bacterial strains of Acinetobacter baumannii. Being the causative agent in ~80% of the cases, these pathogenic gram-negative species could be deadly for hospitalized patients, especially in intensive care units utilizing ventilators, urinary catheters, and nasogastric tubes. Primarily infecting an immuno-compromised system, they are resistant to most antibiotics and are the root cause of various types of opportunistic infections including but not limited to septicemia, endocarditis, meningitis, pneumonia, skin, and wound s...
Source: Genomics Proteomics ... - July 12, 2019 Category: Genetics & Stem Cells Authors: Mujawar S, Mishra R, Pawar S, Gatherer D, Lahiri C Tags: Front Cell Infect Microbiol Source Type: research

Developing a pan-cancer research autopsy programme.
CONCLUSIONS: Large-scale rapid procurement and biobanking of cancer tissues from a rapid autopsy programme is feasible. Multidisciplinary integration between health and administrative staff from medical oncology, palliative care, pathology and biospecimen sciences is critical for the success of this challenging endeavour. PMID: 31262953 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - July 1, 2019 Category: Genetics & Stem Cells Authors: Bavi P, Siva M, Abi-Saab T, Chadwick D, Dhani N, Butany J, Joshua AM, Roehrl MH Tags: J Clin Pathol Source Type: research

Contribution of Matrix Metalloproteinase-2 Promoter Genotypes to Nasopharyngeal Cancer Susceptibility and Metastasis in Taiwan.
CONCLUSION: CT and TT genotypes at MMP2 C-1306T were associated with a significantly decreased risk of NPC metastasis. PMID: 31243109 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - June 29, 2019 Category: Genetics & Stem Cells Authors: Hsu SW, Gong CL, Hsu HM, Chao CC, Wang YC, Chang WS, Tsai YT, Shih LC, Tsai CW, Bau DT Tags: Cancer Genomics Proteomics Source Type: research

Serum Proteome Alterations in Human Cystathionine β-Synthase Deficiency and Ischemic Stroke Subtypes.
Serum Proteome Alterations in Human Cystathionine β-Synthase Deficiency and Ischemic Stroke Subtypes. Int J Mol Sci. 2019 Jun 25;20(12): Authors: Sikora M, Lewandowska I, Kupc M, Kubalska J, Graban A, Marczak Ł, Kaźmierski R, Jakubowski H Abstract Ischemic stroke induces brain injury via thrombotic or embolic mechanisms involving large or small vessels. Cystathionine β-synthase deficiency (CBS), an inborn error of metabolism, is associated with vascular thromboembolism, the major cause of morbidity and mortality in affected patients. Because thromboembolism involves the brain vasculature i...
Source: Genomics Proteomics ... - June 25, 2019 Category: Genetics & Stem Cells Authors: Sikora M, Lewandowska I, Kupc M, Kubalska J, Graban A, Marczak Ł, Kaźmierski R, Jakubowski H Tags: Int J Mol Sci Source Type: research

Isobaric tag for relative and absolute quantitation based quantitative proteomics reveals unique urinary protein profiles in patients with preeclampsia.
Abstract Preeclampsia (PE) is one of the most significant pregnancy-related hypertensive disorders. Currently, there are no useful markers to predict the onset of the condition in pregnant women. To provide further insights into the pathogenesis of PE and identify biomarkers of the condition, we used isobaric tags for relative and absolute quantitation (iTRAQ) proteomics coupled with 2-D LC-MS/MS, to analyze urinary protein profiles from 7 PE patients and 7 normotensive pregnant women. A total of 294 proteins were abnormally expressed in PE patients. Of these, 233 were significantly down-regulated and 61 proteins ...
Source: Genomics Proteomics ... - June 24, 2019 Category: Genetics & Stem Cells Authors: Ding W, Qiu B, Cram DS, Chen X, Li S, Zhou X, Liu J, Wu Z, Song Y Tags: J Cell Mol Med Source Type: research

Chronic Food Antigen-specific IgG-mediated Hypersensitivity Reaction as A Risk Factor for Adolescent Depressive Disorder.
Abstract Major depressive disorder (MDD) is the most common nonfatal disease burden worldwide. Systemic chronic low-grade inflammation has been reported to be associated with MDD progression by affecting monoaminergic and glutamatergic neurotransmission. However, whether various proinflammatory cytokines are abnormally elevated before the first episode of depression is still largely unclear. Here, we evaluated 184 adolescent patients who were experiencing their first episode of depressive disorder, and the same number of healthy individuals were included as controls. We tested the serum levels of high-sensitivity ...
Source: Genomics Proteomics ... - June 21, 2019 Category: Genetics & Stem Cells Authors: Tao R, Fu Z, Xiao L Tags: Genomics Proteomics Bioinformatics Source Type: research

Single-cell Analysis of CAR-T Cell Activation Reveals A Mixed TH1/TH2 Response Independent of Differentiation.
We present the first comprehensive portrait of single-cell level transcriptional and cytokine signatures of anti-CD19/4-1BB/CD28/CD3ζ CAR-T cells upon antigen-specific stimulation. Both CD4+helper T (TH) cells and CD8+cytotoxic CAR-T cells are equally effective in directly killing target tumor cells and their cytotoxic activity is associated with the elevation of a range of TH1 and TH2 signature cytokines, e.g., interferon γ, tumor necrotic factor α, interleukin 5 (IL5), and IL13, as confirmed by the expression of master transcription factor genes TBX21 and GATA3. However, rather than conforming to stringe...
Source: Genomics Proteomics ... - June 20, 2019 Category: Genetics & Stem Cells Authors: Xhangolli I, Dura B, Lee G, Kim D, Xiao Y, Fan R Tags: Genomics Proteomics Bioinformatics Source Type: research

Mapping spatiotemporal microproteomics landscape in experimental model of traumatic brain injury unveils a link to Parkinson's disease.
Abstract Traumatic brain injury (TBI) represents a major health concerns with no clinically-approved FDA drug available for therapeutic intervention. Several genomics and neuroproteomics studies have been employed to decipher the underlying pathological mechanisms involved that can serve as potential neurotherapeutic targets and unveil a possible underlying relation of TBI to other secondary neurological disorders. In this work, we present a novel high throughput systems biology approach using a spatially-resolved microproteomics platform conducted on different brain regions in an experimental rat model of moderat...
Source: Genomics Proteomics ... - June 16, 2019 Category: Genetics & Stem Cells Authors: Mallah K, Quanico J, Raffo-Romero A, Cardon T, Aboulouard S, Devos D, Kobeissy F, Zibara K, Salzet M, Fournier I Tags: Mol Cell Proteomics Source Type: research

Transcriptome and Regulatory Network Analyses of CD19-CAR-T Immunotherapy for B-ALL.
In this study, we reported the transcriptome profiles of bone marrow cells in four B-cell acute lymphoblastic leukemia (B-ALL) patients before and after CD19-specific CAR-T therapy. CD19-CAR-T therapy remarkably reduced the number of leukemia cells, and three patients achieved bone marrow remission (minimal residual disease negative). The efficacy of CD19-CAR-T therapy on B-ALL was positively correlated with the abundance of CAR and immune cell subpopulations, e.g., CD8+ T cells and natural killer (NK) cells, in the bone marrow. Additionally, CD19-CAR-T therapy mainly influenced the expression of genes linked to cell cycle...
Source: Genomics Proteomics ... - June 12, 2019 Category: Genetics & Stem Cells Authors: Zhang Q, Hu H, Chen SY, Liu CJ, Hu FF, Yu J, Wu Y, Guo AY Tags: Genomics Proteomics Bioinformatics Source Type: research

Global Quantitative Mapping of Enhancers in Rice by STARR-seq.
Abstract Enhancers activate transcription in a distance-, orientation-, and position-independent manner, which makes them difficult to be identified. Self-transcribing active regulatory region sequencing (STARR-seq) measures the enhancer activity of millions of DNA fragments in parallel. Here we used STARR-seq to generate a quantitative global map of rice enhancers. Most enhancers were mapped within genes, especially at the 5' untranslated regions (5'UTR) and in coding sequences. Enhancers were also frequently mapped proximal to silent and lowly-expressed genes in transposable element (TE)-rich regions. Analysis o...
Source: Genomics Proteomics ... - June 12, 2019 Category: Genetics & Stem Cells Authors: Sun J, He N, Niu L, Huang Y, Shen W, Zhang Y, Li L, Hou C Tags: Genomics Proteomics Bioinformatics Source Type: research

SSCC: A Novel Computational Framework for Rapid and Accurate Clustering Large-scale Single Cell RNA-seq Data.
Abstract Clustering is a prevalent analytical means to analyze single cell RNA sequencing (scRNA-seq) data but the rapidly expanding data volume can make this process computationally challenging. New methods for both accurate and efficient clustering are of pressing needs. Here we proposed Spearman subsampling-clustering-classification (SSCC), a new clustering framework based on random projection and feature construction, for large-scale scRNA-seq data. SSCC greatly improves clustering accuracy, robustness, and computational efficacy for various state-of-the-art algorithms benchmarked on multiple real datasets. On...
Source: Genomics Proteomics ... - June 12, 2019 Category: Genetics & Stem Cells Authors: Ren X, Zheng L, Zhang Z Tags: Genomics Proteomics Bioinformatics Source Type: research

H3K27me3 Signal in the Cis Regulatory Elements Reveals the Differentiation Potential of Progenitors During Drosophila Neuroglial Development.
Abstract Drosophila neural development undergoes extensive chromatin remodeling and precise epigenetic regulation. However, the roles of chromatin remodeling in establishment and maintenance of cell identity during cell fate transition remain enigmatic. Here, we compared the changes in gene expression, as well as the dynamics of nucleosome positioning and key histone modifications between the four major neural cell types during Drosophila neural development. We find that the neural progenitors can be separated from the terminally differentiated cells based on their gene expression profiles, whereas nucleosome dist...
Source: Genomics Proteomics ... - June 10, 2019 Category: Genetics & Stem Cells Authors: Chen X, Ye Y, Gu L, Sun J, Du Y, Liu WJ, Li W, Zhang X, Jiang C Tags: Genomics Proteomics Bioinformatics Source Type: research

Proteomes of exosomes from HPV(+) or HPV(-) head and neck cancer cells: differential enrichment in immunoregulatory proteins.
Abstract Human papillomavirus (HPV) is an etiologic factor in head and neck squamous cell carcinoma (HNSCC). HPV(+) cancers respond favorably to therapy potentially due to more robust anti-tumor immune responses. We hypothesized that tumor-derived exosomes (TEX) produced by HPV(+) or HPV(-) HNSCCs differentially modulate anti-tumor immune responses. Proteomes of exosomes from HPV(+) and HPV(-) HNSCC cell lines were compared in search for proteins putatively involved in the communication with immune system. TEX were isolated from supernatants of HPV(+) (SCC-2, SCC-47, and SCC-90) or HPV(-) (PCI-13 and PCI-30) cells...
Source: Genomics Proteomics ... - June 2, 2019 Category: Genetics & Stem Cells Authors: Ludwig S, Marczak L, Sharma P, Abramowicz A, Gawin M, Widlak P, Whiteside TL, Pietrowska M Tags: Oncoimmunology Source Type: research

Proteomics analysis of Trichoplusia ni midgut epithelial cell brush border membrane vesicles.
This study reports the identification of proteins from BBM vesicles (BBMVs) using single dimension polyacrylamide gel electrophoresis coupled with multi-dimensional protein identification technology. More than 3000 proteins were associated with the BBMV, of which 697 were predicted to possess either a signal peptide, at least one transmembrane domain or a GPI-anchor signal. Of these, bioinformatics analysis and manual curation predicted that 185 may be associated with the BBMV or epithelial cell plasma membrane. These are discussed with respect to their predicted functions, namely digestion, nutrient uptake, cell signaling...
Source: Genomics Proteomics ... - March 29, 2019 Category: Genetics & Stem Cells Authors: Javed MA, Coutu C, Theilmann DA, Erlandson MA, Hegedus DD Tags: Insect Sci Source Type: research

Metabolomic responses triggered by arbuscular mycorrhiza enhance tolerance to water stress in wheat cultivars.
This study proposes new insights on the modulation of the tripartite interaction plant-AMF-environmental stress. PMID: 30802803 [PubMed - indexed for MEDLINE] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - March 9, 2019 Category: Genetics & Stem Cells Authors: Bernardo L, Carletti P, Badeck FW, Rizza F, Morcia C, Ghizzoni R, Rouphael Y, Colla G, Terzi V, Lucini L Tags: Plant Physiol Biochem Source Type: research

Seasonal variation in equine follicular fluid proteome.
CONCLUSIONS: The balance between the FF contents in prothrombin, plasminogen, and coagulation factor XII proteins favoring FF fluidity may be crucial at the peak of the ovulatory season (SUM) and may explain the reported lower incidence of hemorrhagic anovulatory follicles during the SUM season. PMID: 30841911 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - March 6, 2019 Category: Genetics & Stem Cells Authors: Dutra GA, Ishak GM, Pechanova O, Pechan T, Peterson DG, Jacob JCF, Willard ST, Ryan PL, Gastal EL, Feugang JM Tags: Reprod Biol Endocrinol Source Type: research

Publisher Correction: Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.
ras P Abstract In the original HTML version of this Article, the order of authors within the author list was incorrect. The IMEx Consortium contributing authors were incorrectly listed as the last author and should have been listed as the first author. This error has been corrected in the HTML version of the Article; the PDF version was correct at the time of publication. PMID: 30833551 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - March 4, 2019 Category: Genetics & Stem Cells Authors: IMEx Consortium contributing authors, Del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras P Tags: Nat Commun Source Type: research

The genese of predictive-personified medicine and the problems of its implementation in Ukraine.
Abstract The concepts, content and significance of predictive-personified medicine that are able to improve the quality of treatment, using genetic information when choosing the medical procedures that are necessary for a particular person are considered. Characteristic of the principles of predictive-personified medicine and its fundamental foundations are carried out: genomics; proteomics; metabolism; bioinformatics The history of the formation and development of predictive-personified medicine in the world is investigated, the relevant legal documents are analyzed. The main advantages of predictive-personified ...
Source: Genomics Proteomics ... - February 25, 2019 Category: Genetics & Stem Cells Authors: Terzi OO Tags: Wiad Lek Source Type: research

Study of Cathepsin B inhibition in VEGFR TKI treated human renal cell carcinoma xenografts.
Abstract Several therapeutic options are available for metastatic RCC, but responses are almost never complete, and resistance to therapy develops in the vast majority of patients. Consequently, novel treatments are needed to combat resistance to current therapies and to improve patient outcomes. We have applied integrated transcriptome and proteome analyses to identify cathepsin B (CTSB), a cysteine proteinase of the papain family, as one of the most highly upregulated gene products in established human RCC xenograft models of resistance to vascular endothelial growth factor receptor (VEGFR) tyrosine kinase inhib...
Source: Genomics Proteomics ... - February 22, 2019 Category: Genetics & Stem Cells Authors: Chen CH, Bhasin S, Khanna P, Joshi M, Joslin PM, Saxena R, Amin S, Liu S, Sindhu S, Walker SR, Catalano P, Frank DA, Alper SL, Bhasin M, Bhatt RS Tags: Oncogenesis Source Type: research

Dihydroartemisinin inhibits prostate cancer via JARID2/miR-7/miR-34a-dependent downregulation of Axl.
Abstract Axl expression is deregulated in several cancer types, predicts poor overall patient survival and is linked to resistance to drug therapy. Here, we evaluated a library of natural compounds for inhibitors of Axl and identified dihydroartemisinin, the active principle of the anti-malarial drug artemisinin, as an Axl-inhibitor in prostate cancer. Dihydroartemisinin blocks Axl expression leading to apoptosis, decrease in cell proliferation, migration, and tumor development of prostate cancer cells. Dihydroartemisinin treatment synergizes with docetaxel, a standard of care in metastatic prostate cancer increas...
Source: Genomics Proteomics ... - February 19, 2019 Category: Genetics & Stem Cells Authors: Paccez JD, Duncan K, Sekar D, Correa RG, Wang Y, Gu X, Bashin M, Chibale K, Libermann TA, Zerbini LF Tags: Oncogenesis Source Type: research

Translating transcription: proteomics in chronic rhinosinusitis with nasal polyps reveals significant discordance with messenger RNA expression.
Abstract BACKGROUND: Much of the literature examining chronic rhinosinusitis with nasal polyps (CRSwNP) immunopathology has been predicated on messenger RNA (mRNA) analysis with the assumption that transcriptional changes would reflect end-effector protein expression. The purpose of this study was to test this hypothesis using matched transcriptomic and proteomic data sets. METHODS: Matched tissue proteomic and transcriptomic arrays were quantified in CRSwNP polyp tissue and control inferior turbinate tissue (n = 10/group). Mucus samples were additionally collected in 6 subjects from each group. Proteins were...
Source: Genomics Proteomics ... - February 18, 2019 Category: Genetics & Stem Cells Authors: Workman AD, Nocera AL, Mueller SK, Otu HH, Libermann TA, Bleier BS Tags: Int Forum Allergy Rhinol Source Type: research

Delirium and Alzheimer's Disease: A Proposed Model for Shared Pathophysiology.
PMID: 30773695 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - February 17, 2019 Category: Genetics & Stem Cells Authors: Fong TG, Vasunilashorn SM, Libermann T, Marcantonio ER, Inouye SK Tags: Int J Geriatr Psychiatry Source Type: research

Quantitative label-free mass spectrometry using contralateral and adjacent breast tissues reveal differentially expressed proteins and their predicted impacts on pathways and cellular functions in breast cancer.
In this study, the mass spectrometry-based label-free quantification followed by functional annotation was performed to investigate the most significant deregulated proteins among tissues of primary breast tumor (PT) and axillary metastatic lymph node (LN) and corresponding non-tumor tissues contralateral (NCT) and adjacent (ANT) from patients diagnosed with invasive ductal carcinoma. A total of 462 proteins was observed as differentially expressed (DEPs) among the groups analyzed. A high level of similarity was observed in the proteome profile of both non-tumor breast tissues and DEPs (n = 12) were mainly predicted in...
Source: Genomics Proteomics ... - February 14, 2019 Category: Genetics & Stem Cells Authors: Gomig THB, Cavalli IJ, de Souza RLR, Vieira E, Lucena ACR, Batista M, Machado KC, Marchini FK, Marchi FA, Lima RS, de Andrade Urban C, Cavalli LR, de Souza Fonseca Ribeiro EM Tags: J Proteomics Source Type: research

Rice Genomics: Over the Past Two Decades and Into the Future.
Abstract Domestic rice (Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct field applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we briefly review its achievements over the past two decades and present the potential for its bright future. PMID: 30771506 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - February 13, 2019 Category: Genetics & Stem Cells Authors: Song S, Tian D, Zhang Z, Hu S, Yu J Tags: Genomics Proteomics Bioinformatics Source Type: research

Biomolecular Reaction & Interaction Dynamics Global Environment (BRIDGE).
We present the foundations of BRIDGE developed on the Galaxy platform that makes possible fundamental molecular dynamics of proteins through workflows and pipelines via commonly used packages such as NAMD, GROMACS and CHARMM. BRIDGE can be used to set up and simulate biological macromolecules, perform conformational analysis from trajectory data and conduct data analytics of large scale protein motions using statistical rigor. We illustrate the basic BRIDGE simulation and analytics capabilities on a previously reported CBH1 protein simulation. Availability: Publicly available at https://github.com/scientificomputing/B...
Source: Genomics Proteomics ... - February 13, 2019 Category: Genetics & Stem Cells Authors: Senapathi T, Bray S, Barnett CB, Grüning B, Naidoo KJ Tags: Bioinformatics Source Type: research

Enhanced Growth of Pilin-Deficient Geobacter sulfurreducens Mutants in Carbon Poor and Electron Donor Limiting Conditions.
Abstract Geobacter sulfurreducens pili enable extracellular electron transfer and play a role in secretion of c-type cytochromes such as OmcZ. PilA-deficient mutants of G. sulfurreducens have previously been shown to accumulate cytochromes within their membranes. This cytochrome retaining phenotype allowed for enhanced growth of PilA-deficient mutants in electron donor and carbon-limited conditions where formate and fumarate are provided as the sole electron donor and acceptor with no supplementary carbon source. Conversely, wild-type G. sulfurreducens, which has normal secretion of cytochromes, has comparative li...
Source: Genomics Proteomics ... - February 13, 2019 Category: Genetics & Stem Cells Authors: Semenec L, Vergara IA, Laloo AE, Mathews ER, Bond PL, Franks AE Tags: Microb Ecol Source Type: research

An immunoproteomic approach to characterize the CAR interactome and signalosome.
B, Abate-Daga D Abstract Adoptive transfer of T cells that express a chimeric antigen receptor (CAR) is an approved immunotherapy that may be curative for some hematological cancers. To better understand the therapeutic mechanism of action, we systematically analyzed CAR signaling in human primary T cells by mass spectrometry. When we compared the interactomes and the signaling pathways activated by distinct CAR-T cells that shared the same antigen-binding domain but differed in their intracellular domains and their in vivo antitumor efficacy, we found that only second-generation CARs induced the expression of a c...
Source: Genomics Proteomics ... - February 12, 2019 Category: Genetics & Stem Cells Authors: Ramello MC, Benzaïd I, Kuenzi BM, Lienlaf-Moreno M, Kandell WM, Santiago DN, Pabón-Saldaña M, Darville L, Fang B, Rix U, Yoder S, Berglund A, Koomen JM, Haura EB, Abate-Daga D Tags: Sci Signal Source Type: research

Metformin Treatment Suppresses Melanoma Cell Growth and Motility Through Modulation of microRNA Expression.
Abstract Melanoma is a highly aggressive cancer with high mortality in advanced stages.Metformin is an oral biguanide drug used for diabetes and has demonstrated positive effects oncancer prevention and treatment. Herein, we found that metformin significantly suppressedmelanoma cancer cell motility and growth through inducing cell cycle arrest at the G2/M phase andpromoting cell apoptosis. Using the next-generation sequencing approach, we identified threeupregulated microRNAs (miRNA; miR-192-5p, miR-584-3p, and miR-1246) in melanoma cellstreated with metformin. Among these, we examined the roles of miR-192-5p and ...
Source: Genomics Proteomics ... - February 11, 2019 Category: Genetics & Stem Cells Authors: Tseng HW, Li SC, Tsai KW Tags: Cancers (Basel) Source Type: research

A Time for Celebration: 40th Anniversary of GSC and 15th Anniversary of BIG, CAS.
PMID: 30743051 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - February 8, 2019 Category: Genetics & Stem Cells Authors: Yu J Tags: Genomics Proteomics Bioinformatics Source Type: research

An Exome-seq Based Tool for Mapping and Selection of Candidate Genes in Maize Deletion Mutants.
This study demonstrates the efficiency and cost-effectiveness of BSEx-seq for causal mutation mapping and candidate gene selection, providing a new option in mapping-by-sequencing for maize functional genomics studies. PMID: 30743052 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - February 8, 2019 Category: Genetics & Stem Cells Authors: Jia S, Morton K, Zhang C, Holding D Tags: Genomics Proteomics Bioinformatics Source Type: research

The application of omics techniques to understand the role of the gut microbiota in inflammatory bowel disease.
Abstract The aetiopathogenesis of inflammatory bowel diseases (IBD) involves the complex interaction between a patient's genetic predisposition, environment, gut microbiota and immune system. Currently, however, it is not known if the distinctive perturbations of the gut microbiota that appear to accompany both Crohn's disease and ulcerative colitis are the cause of, or the result of, the intestinal inflammation that characterizes IBD. With the utilization of novel systems biology technologies, we can now begin to understand not only details about compositional changes in the gut microbiota in IBD, but increasingl...
Source: Genomics Proteomics ... - February 6, 2019 Category: Genetics & Stem Cells Authors: Segal JP, Mullish BH, Quraishi MN, Acharjee A, Williams HRT, Iqbal T, Hart AL, Marchesi JR Tags: Therap Adv Gastroenterol Source Type: research

Progress and Challenges for Live-cell Imaging of Genomic Loci Using CRISPR-based Platforms.
Abstract Chromatin conformation, localization, and dynamics are crucial regulators of cellular behaviors. Although fluorescence in situ hybridization-based techniques have been widely utilized for investigating chromatin architectures in healthy and diseased states, the requirement for cell fixation precludes the comprehensive dynamic analysis necessary to fully understand chromatin activities. This has spurred the development and application of a variety of imaging methodologies for visualizing single chromosomal loci in the native cellular context. In this review, we describe currently-available approaches for i...
Source: Genomics Proteomics ... - January 30, 2019 Category: Genetics & Stem Cells Authors: Wu X, Mao S, Ying Y, Krueger CJ, Chen AK Tags: Genomics Proteomics Bioinformatics Source Type: research

Proteome-wide onco-proteogenomic somatic variant identification in ER-positive breast cancer.
CONCLUSIONS: While proteomics fails to identify the vast majority of exome DNA variants in the resulting proteome, its ability to detect a small subset of SAAVs could prove valuable for precision medicine applications. PMID: 30684468 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - January 23, 2019 Category: Genetics & Stem Cells Authors: Dimitrakopoulos L, Prassas I, Sieuwerts AM, Diamandis EP, Martens JWM, Charames GS Tags: Clin Biochem Source Type: research