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https://www.readbyqxmd.com/read/29150517/multi-omics-reveal-the-lifestyle-of-the-acidophilic-mineral-oxidizing-model-species-leptospirillum-ferriphilum-t
#1
Stephan Christel, Malte Herold, Sören Bellenberg, Mohamed El Hajjami, Antoine Buetti-Dinh, Igor V Pivkin, Wolfgang Sand, Paul Wilmes, Ansgar Poetsch, Mark Dopson
Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of this model species' type strain is available, limiting the possibilities to investigate the strategies and adaptations Leptospirillum ferriphilum(T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum(T) DSM 14647 obtained by PacBio SMRT long read sequencing for use as a high quality reference...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29150354/editorial-integration-of-omics-into-mra
#2
Luca Cocolin, Jeanne-Marie Membré, Marcel Zwietering
No abstract text is available yet for this article.
November 13, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29149350/a-data-fusion-pipeline-for-generating-and-enriching-adverse-outcome-pathway-descriptions
#3
Penny Nymark, Linda Rieswijk, Friederike Ehrhart, Nina Jeliazkova, Georgia Tsiliki, Haralambos Sarimveis, Chris T Evelo, Vesa Hongisto, Pekka Kohonen, Egon Willighagen, Roland C Grafström
Increasing amounts of systems toxicology data, including omics results, are becoming publically available and accessible in databases. Data-driven and informatics-tool supported pipeline schemas for fitting such data into Adverse Outcome Pathway (AOP) descriptions could potentially aid the development of non-animal based hazard and risk assessment methods. We devised a six-step workflow that integrated diverse types of toxicology data into a novel AOP scheme for pulmonary fibrosis. Mining of literature references and diverse data sources covering previous pathway descriptions and molecular results were coupled in a stepwise manner with informatics tools applications that enabled gene linkage and pathway identification in molecular interaction maps...
November 15, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29149186/cell-cycle-time-series-gene-expression-data-encoded-as-cyclic-attractors-in-hopfield-systems
#4
Anthony Szedlak, Spencer Sims, Nicholas Smith, Giovanni Paternostro, Carlo Piermarocchi
Modern time series gene expression and other omics data sets have enabled unprecedented resolution of the dynamics of cellular processes such as cell cycle and response to pharmaceutical compounds. In anticipation of the proliferation of time series data sets in the near future, we use the Hopfield model, a recurrent neural network based on spin glasses, to model the dynamics of cell cycle in HeLa (human cervical cancer) and S. cerevisiae cells. We study some of the rich dynamical properties of these cyclic Hopfield systems, including the ability of populations of simulated cells to recreate experimental expression data and the effects of noise on the dynamics...
November 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29148757/cross-linked-artificial-enzyme-crystals-as-heterogeneous-catalysts-for-oxidation-reactions
#5
Sarah Lopez, Laurianne Rondot, Chloé Leprêtre, Caroline Marchi-Delapierre, Stéphane Ménage, Christine Cavazza
Designing systems that merge the advantages of heterogeneous catalysis, enzymology and molecular catalysis represents the next major goal for sustainable chemistry. Cross-linked enzyme crystals display most of these essential assets (well-designed mesoporous support, protein selectivity, molecular recognition of substrates). Nevertheless, a lack of reaction diversity, particularly in the field of oxidation, remains a constraint for their increased use in the field. Here, thanks to the design of cross-linked artificial non-heme iron oxygenase crystals, we filled this gap by developing bio-based heterogeneous catalysts capable of oxidizing carbon-carbon double bonds...
November 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29146431/database-taxonomics-as-key-to-modern-plant-biology
#6
Marcus A Koch, Dmitry A German, Markus Kiefer, Andreas Franzke
The advent of omic technologies opened new and multiple avenues to access higher levels of complexity. Taxonomy - discovering and naming biodiversity - has also entered a taxonomics epoch and serves as a tool not only to name biological diversity, but also to fully explore biological knowledge and to build bridges between disciplines.
November 13, 2017: Trends in Plant Science
https://www.readbyqxmd.com/read/29143719/microbial-protein-targets-towards-understanding-and-intervention
#7
Paul W Denny
The rise of antimicrobial resistance, coupled with a lack of industrial focus on antimicrobial discovery over preceding decades, has brought the world to a crisis point. With both human and animal health set to decline due to increased disease burdens caused by near untreatable microbial pathogens, there is an urgent need to identify new antimicrobials. Central to this is the elucidation of new, robustly validated, drug targets. Informed by industrial practice and concerns, the use of both biological and chemical tools in validation is key...
November 16, 2017: Parasitology
https://www.readbyqxmd.com/read/29143176/the-treatment-landscape-and-new-opportunities-of-molecular-targeted-therapies-in-gastroenteropancreatic-neuroendocrine-tumors
#8
REVIEW
Fabiola Amair-Pinedo, Ignacio Matos, Tamara Saurí, Jorge Hernando, Jaume Capdevila
Neuroendocrine neoplasms (NENs) are a heterogeneous group of neoplasms that originate from neuroendocrine stem cells and express both neural and endocrine markers. They are found in almost every organ, and while NENs are mostly associated with slow growth, complications due to the uncontrolled secretion of active peptides, and metastatic disease, may significantly impair the quality of life and can ultimately lead to the death of affected individuals. Expanding knowledge of the genetic, epigenetic, and proteomic landscapes of NENs has led to a better understanding of their molecular pathology and consequently increased treatment options for patients...
November 15, 2017: Targeted Oncology
https://www.readbyqxmd.com/read/29142286/discovery-of-bladder-cancer-related-genes-using-integrative-heterogeneous-network-modeling-of-multi-omics-data
#9
Chen Peng, Ao Li, Minghui Wang
In human health, a fundamental challenge is the identification of disease-related genes. Bladder cancer (BC) is a worldwide malignant tumor, which has resulted in 170,000 deaths in 2010 up from 114,000 in 1990. Moreover, with the emergence of multi-omics data, more comprehensive analysis of human diseases become possible. In this study, we propose a multi-step approach for the identification of BC-related genes by using integrative Heterogeneous Network Modeling of Multi-Omics data (iHNMMO). The heterogeneous network model properly and comprehensively reflects the multiple kinds of relationships between genes in the multi-omics data of BC, including general relationships, unique relationships under BC condition, correlational relationships within each omics and regulatory relationships between different omics...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29141195/determination-of-the-effect-of-pinellia-ternata-thunb-breit-on-nervous-system-development-by-proteomics
#10
Jian-Ya Xu, Chen Dai, Jin-Jun Shan, Tong Xie, Hui-Hui Xie, Ming-Ming Wang, Guang Yang
ETHNOPHARMACOLOGICAL RELEVANCE: Banxia (BX) is the dried tuber of Pinellia ternata (Thunb.) Breit., a commonly prescribed Chinese medicinal herb for the treatment of cough, phlegm, and vomiting in pregnant women. However, raw BX has been demonstrated to exert toxic effects on reproduction and the precise and comprehensive mechanisms remain elusive. AIM OF THE STUDY: We applied an iTRAQ (isobaric tags for relative and absolute quantitation, iTRAQ)-based proteomic method to explore the mechanisms of raw BX-induced fetal toxicity in mice...
November 12, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/29140768/public-health-burden-of-hearing-impairment-and-the-promise-of-genomics-and-environmental-research-a-case-study-in-ghana-africa
#11
Samuel Mawuli Adadey, Gordon Awandare, Goffrey Kwabla Amedofu, Ambroise Wonkam
Hearing impairment (HI) is one of the most disabling conditions of major global health burden that contributes adversely to the social and economic development of a country, if not managed properly. A proper assessment of the nationwide burden and etiology of HI is instrumental in the prevention, treatment, and management of the condition. This article sought to perform an expert review of HI in Ghana to determine the present knowledge of its burden and possible causes of the condition. A literature search was conducted in PubMed using the following keywords: "hearing loss" OR "hearing impairment" OR "deafness" AND "Ghana...
November 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29140597/improving-omics-based-research-and-precision-health-in-minority-populations-recommendations-for-nurse-scientists
#12
Jacquelyn Y Taylor, Veronica Barcelona de Mendoza
PURPOSE: The purpose of this article is to provide an overview of the role of nurse scientists in -omics-based research and to promote discussion around the conduct of -omics-based nursing research in minority communities. Nurses are advocates, educators, practitioners, scientists, and researchers, and are crucial to the design and successful implementation of -omics studies, particularly including minority communities. The contribution of nursing in this area of research is crucial to reducing health disparities...
November 15, 2017: Journal of Nursing Scholarship
https://www.readbyqxmd.com/read/29140259/ramanomics-new-omics-disciplines-using-micro-raman-spectrometry-with-biomolecular-component-analysis-for-molecular-profiling-of-biological-structures
#13
REVIEW
Andrey N Kuzmin, Artem Pliss, Paras N Prasad
Modern instrumentation for Raman microspectroscopy and current techniques in analysis of spectral data provide new opportunities to study molecular interactions and dynamics at subcellular levels in biological systems. Implementation of biomolecular component analysis (BCA) to microRaman spectrometry provides basis for the emergence of Ramanomics, a new biosensing discipline with unprecedented capabilities to measure concentrations of distinct biomolecular groups in live cells and organelles. Here we review the combined use of microRaman-BCA techniques to probe absolute concentrations of proteins, DNA, RNA and lipids in single organelles of live cells...
November 15, 2017: Biosensors
https://www.readbyqxmd.com/read/29138457/functional-annotation-of-structural-ncrnas-within-enhancer-rnas-in-the-human-genome-implications-for-human-disease
#14
Chao Ren, Feng Liu, Zhangyi Ouyang, Gaole An, Chenghui Zhao, Jun Shuai, Shuhong Cai, Xiaochen Bo, Wenjie Shu
Enhancer RNAs (eRNAs) are a novel class of non-coding RNA (ncRNA) molecules transcribed from the DNA sequences of enhancer regions. Despite extensive efforts devoted to revealing the potential functions and underlying mechanisms of eRNAs, it remains an open question whether eRNAs are mere transcriptional noise or relevant biologically functional species. Here, we identified a catalogue of eRNAs in a broad range of human cell/tissue types and extended our understanding of eRNAs by demonstrating their multi-omic signatures...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29138271/addressing-the-perfect-storm-biomarkers-in-obesity-and-pathophysiology-of-cardiometabolic-risk
#15
REVIEW
Krasimira Aleksandrova, Dariush Mozaffarian, Tobias Pischon
BACKGROUND: The worldwide rise of obesity has provoked intensified research to better understand its pathophysiology as a means for disease prevention. Several biomarkers that may reflect various pathophysiological pathways that link obesity and cardiometabolic diseases have been identified over the past decades. CONTENT: We summarize research evidence regarding the role of established and novel obesity-related biomarkers, focusing on recent epidemiological evidence for detrimental associations with cardiometabolic diseases including obesity-related cancer...
November 14, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/29138111/recent-advances-in-melanoma-research-via-omics-platforms
#16
REVIEW
Carmen Rodríguez-Cerdeira, Alberto Molares-Vila, Miguel Carnero-Gregorio, Alberte Corbalán-Rivas
Melanoma has a high mortality rate and metastatic melanoma is highly resistant to conventional therapies. "Omics" fields such as proteomics and microRNA and exosome studies have provided new knowledge to complement the information generated by genomic studies. This work aimed to review the current status of biomarker discovery for melanoma through multi-"omics" platforms. A few sets of novel microRNAs and proteins are described, some of them with important implications in suppressing melanoma at different stages...
November 11, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29137180/metabolomic-modularity-analysis-mma-to-quantify-human-liver-perfusion-dynamics
#17
Gautham Vivek Sridharan, Bote Bruinsma, Shyam Sundhar Bale, Anandh Swaminathan, Nima Saeidi, Martin L Yarmush, Korkut Uygun
Large-scale -omics data are now ubiquitously utilized to capture and interpret global responses to perturbations in biological systems, such as the impact of disease states on cells, tissues, and whole organs. Metabolomics data, in particular, are difficult to interpret for providing physiological insight because predefined biochemical pathways used for analysis are inherently biased and fail to capture more complex network interactions that span multiple canonical pathways. In this study, we introduce a nov-el approach coined Metabolomic Modularity Analysis (MMA) as a graph-based algorithm to systematically identify metabolic modules of reactions enriched with metabolites flagged to be statistically significant...
November 13, 2017: Metabolites
https://www.readbyqxmd.com/read/29136656/genetic-diversity-linkage-disequilibrium-and-association-mapping-analyses-of-gossypium-barbadense-l-germplasm
#18
Alisher A Abdullaev, Ilkhom B Salakhutdinov, Sharof S Egamberdiev, Ernest E Khurshut, Sofiya M Rizaeva, Mauricio Ulloa, Ibrokhim Y Abdurakhmonov
Limited polymorphism and narrow genetic base, due to genetic bottleneck through historic domestication, highlight a need for comprehensive characterization and utilization of existing genetic diversity in cotton germplasm collections. In this study, 288 worldwide Gossypium barbadense L. cotton germplasm accessions were evaluated in two diverse environments (Uzbekistan and USA). These accessions were assessed for genetic diversity, population structure, linkage disequilibrium (LD), and LD-based association mapping (AM) of fiber quality traits using 108 genome-wide simple sequence repeat (SSR) markers...
2017: PloS One
https://www.readbyqxmd.com/read/29136241/wikipathways-a-multifaceted-pathway-database-bridging-metabolomics-to-other-omics-research
#19
Denise N Slenter, Martina Kutmon, Kristina Hanspers, Anders Riutta, Jacob Windsor, Nuno Nunes, Jonathan Mélius, Elisa Cirillo, Susan L Coort, Daniela Digles, Friederike Ehrhart, Pieter Giesbertz, Marianthi Kalafati, Marvin Martens, Ryan Miller, Kozo Nishida, Linda Rieswijk, Andra Waagmeester, Lars M T Eijssen, Chris T Evelo, Alexander R Pico, Egon L Willighagen
WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. WikiPathways and other pathway databases are used to analyze experimental data by research groups in many fields. Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway database. Previously, however, the focus was primarily on genes and proteins, leaving many metabolites with only limited annotation...
November 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29136207/linkedomics-analyzing-multi-omics-data-within-and-across-32-cancer-types
#20
Suhas V Vasaikar, Peter Straub, Jing Wang, Bing Zhang
The LinkedOmics database contains multi-omics data and clinical data for 32 cancer types and a total of 11 158 patients from The Cancer Genome Atlas (TCGA) project. It is also the first multi-omics database that integrates mass spectrometry (MS)-based global proteomics data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) on selected TCGA tumor samples. In total, LinkedOmics has more than a billion data points. To allow comprehensive analysis of these data, we developed three analysis modules in the LinkedOmics web application...
November 9, 2017: Nucleic Acids Research
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