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https://www.readbyqxmd.com/read/28319609/developmental-alterations-in-huntington-s-disease-neural-cells-and-pharmacological-rescue-in-cells-and-mice
#1
(no author information available yet)
Neural cultures derived from Huntington's disease (HD) patient-derived induced pluripotent stem cells were used for 'omics' analyses to identify mechanisms underlying neurodegeneration. RNA-seq analysis identified genes in glutamate and GABA signaling, axonal guidance and calcium influx whose expression was decreased in HD cultures. One-third of gene changes were in pathways regulating neuronal development and maturation. When mapped to stages of mouse striatal development, the profiles aligned with earlier embryonic stages of neuronal differentiation...
March 20, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28317029/listeriomics-an-interactive-web-platform-for-systems-biology-of-listeria
#2
Christophe Bécavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede, Hélène Chiapello, Christine Gaspin, Pascale Cossart
As for many model organisms, the amount of Listeria omics data produced has recently increased exponentially. There are now >80 published complete Listeria genomes, around 350 different transcriptomic data sets, and 25 proteomic data sets available. The analysis of these data sets through a systems biology approach and the generation of tools for biologists to browse these various data are a challenge for bioinformaticians. We have developed a web-based platform, named Listeriomics, that integrates different tools for omics data analyses, i...
March 2017: MSystems
https://www.readbyqxmd.com/read/28316117/how-consistent-are-we-interlaboratory-comparison-study-in-fathead-minnows-using-the-model-estrogen-17%C3%AE-ethinylestradiol-to-develop-recommendations-for-environmental-transcriptomics
#3
April Feswick, Meghan Isaacs, Adam Biales, Robert W Flick, David C Bencic, Rong-Lin Wang, Chris Vulpe, Marianna Brown-Augustine, Alex Loguinov, Francesco Falciani, Philipp Antczak, John Herbert, Lorraine Brown, Nancy D Denslow, Kevin J Kroll, Candice Lavelle, Viet Dang, Lynn Escalon, Natàlia Garcia-Reyero, Christopher J Martyniuk, Kelly R Munkittrick
Fundamental questions remain about the application of omics in environmental risk assessments, such as the consistency of data across laboratories. The objective of this study was to determine the congruence of transcript data across six independent laboratories. Male fathead minnows (FHM) were exposed to a measured concentration of 15.8 ng /L EE2 for 96 h. Livers were divided equally and sent to the participating laboratories for transcriptomic analysis using the same FHM microarray. Each laboratory was free to apply bioinformatics pipelines of their choice...
March 18, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28315793/highlighting-the-effects-of-coumarin-on-adult-plants-of-arabidopsis-thaliana-l-heynh-by-an-integrated-omic-approach
#4
Fabrizio Araniti, Monica Scognamiglio, Angela Chambery, Rosita Russo, Assunta Esposito, Brigida D'Abrosca, Antonio Fiorentino, Antonio Lupini, Francesco Sunseri, Maria Rosa Abenavoli
In this study, the effects of the allelochemical coumarin through a metabolomic, proteomic and morpho-physiological approach in Arabidopsis adult plants (25days old) were investigated. Metabolomic analysis evidenced an increment of amino acids and a high accumulation of soluble sugars, after 6days of coumarin treatment. This effect was accompanied by a strong decrease on plant fresh and dry weights, as well as on total protein content. On the contrary, coumarin did not affect leaf number but caused a reduction in leaf area...
March 1, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28314298/multi-omics-profiling-of-patients-with-melanoma-treated-with-nivolumab-in-project-hope
#5
Shusuke Yoshikawa, Yoshio Kiyohara, Masaki Otsuka, Ryota Kondou, Chizu Nonomura, Haruo Miyata, Akira Iizuka, Keiichi Ohshima, Kenichi Urakami, Takeshi Nagashima, Masatoshi Kusuhara, Takashi Sugino, Tohru Mochizuki, Ken Yamaguchi, Yasuto Akiyama
BACKGROUND: Project HOPE (High-tech Omics-based Patient Evaluation) has been in progress since 2014 and uses whole-exome sequencing (WES) and gene expression profiling (GEP). Among a total of 1,685 patients with cancer, 13 with melanoma were registered and characterized using multi-omics analyses to investigate specific biomarkers in responders to programmed cell death-1 (PD-1) blockade. MATERIALS AND METHODS: The patients with melanoma comprised of six males and seven females, and their mean age was 68 years...
March 2017: Anticancer Research
https://www.readbyqxmd.com/read/28302330/precision-surgery-for-colorectal-liver-metastases-opportunities-and-challenges-of-omics-based-decision-making
#6
REVIEW
R P Jones, K W Brudvik, J M Franklin, G J Poston
Precision surgery involves improving patient selection to ensure that surgical intervention that is proven to benefit on a population level is the optimal treatment for each individual patient. For patients with colorectal liver metastases (CRLM), existing prognostic scoring systems rely on well-recognised histopathological features such as size and number of lesions. Advances in preoperative imaging algorithms mean that increasingly low volume disease can be detected, improving assessment of these factors...
March 6, 2017: European Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28300637/integrated-mass-spectrometry-imaging-and-omics-workflows-on-the-same-tissue-section-using-grid-aided-parafilm-assisted-microdissection
#7
Jusal Quanico, Julien Franck, Maxence Wisztorski, Michel Salzet, Isabelle Fournier
BACKGROUND: In spite of the number of applications describing the use of MALDI MSI, one of its major drawbacks is the limited capability of identifying multiple compound classes directly on the same tissue section. METHODS: We demonstrate the use of grid-aided, parafilm-assisted microdissection to perform MALDI MS imaging and shotgun proteomics and metabolomics in a combined workflow and using only a single tissue section. The grid is generated by microspotting acid dye 25 using a piezoelectric microspotter, and this grid was used as a guide to locate regions of interest and as an aid during manual microdissection...
March 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28296247/comprehensive-proteome-analysis-of-human-skeletal-muscle-in-cachexia-and-sarcopenia-a-pilot-study
#8
H Alexander Ebhardt, Simone Degen, Valentina Tadini, Alain Schilb, Neil Johns, Carolyn A Greig, Kenneth C H Fearon, Ruedi Aebersold, Carsten Jacobi
BACKGROUND: Cancer cachexia (cancer-induced muscle wasting) is found in a subgroup of cancer patients leaving the patients with a poor prognosis for survival due to a lower tolerance of the chemotherapeutic drug. The cause of the muscle wasting in these patients is not fully understood, and no predictive biomarker exists to identify these patients early on. Skeletal muscle loss is an inevitable consequence of advancing age. As cancer frequently occurs in old age, identifying and differentiating the molecular mechanisms mediating muscle wasting in cancer cachexia vs...
March 15, 2017: Journal of Cachexia, Sarcopenia and Muscle
https://www.readbyqxmd.com/read/28287094/enlightening-discriminative-network-functional-modules-behind-principal-component-analysis-separation-in-differential-omic-science-studies
#9
Sara Ciucci, Yan Ge, Claudio Durán, Alessandra Palladini, Víctor Jiménez-Jiménez, Luisa María Martínez-Sánchez, Yuting Wang, Susanne Sales, Andrej Shevchenko, Steven W Poser, Maik Herbig, Oliver Otto, Andreas Androutsellis-Theotokis, Jochen Guck, Mathias J Gerl, Carlo Vittorio Cannistraci
Omic science is rapidly growing and one of the most employed techniques to explore differential patterns in omic datasets is principal component analysis (PCA). However, a method to enlighten the network of omic features that mostly contribute to the sample separation obtained by PCA is missing. An alternative is to build correlation networks between univariately-selected significant omic features, but this neglects the multivariate unsupervised feature compression responsible for the PCA sample segregation...
March 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28285833/integrative-proteomics-and-phosphoproteomics-profiling-reveals-dynamic-signaling-networks-and-bioenergetics-pathways-underlying-t-cell-activation
#10
Haiyan Tan, Kai Yang, Yuxin Li, Timothy I Shaw, Yanyan Wang, Daniel Bastardo Blanco, Xusheng Wang, Ji-Hoon Cho, Hong Wang, Sherri Rankin, Cliff Guy, Junmin Peng, Hongbo Chi
The molecular circuits by which antigens activate quiescent T cells remain poorly understood. We combined temporal profiling of the whole proteome and phosphoproteome via multiplexed isobaric labeling proteomics technology, computational pipelines for integrating multi-omics datasets, and functional perturbation to systemically reconstruct regulatory networks underlying T cell activation. T cell receptors activated the T cell proteome and phosphoproteome with discrete kinetics, marked by early dynamics of phosphorylation and delayed ribosome biogenesis and mitochondrial activation...
March 3, 2017: Immunity
https://www.readbyqxmd.com/read/28284040/comparison-and-visualisation-of-agreement-for-paired-lists-of-rankings
#11
Margaret R Donald, Susan R Wilson
Output from analysis of a high-throughput 'omics' experiment very often is a ranked list. One commonly encountered example is a ranked list of differentially expressed genes from a gene expression experiment, with a length of many hundreds of genes. There are numerous situations where interest is in the comparison of outputs following, say, two (or more) different experiments, or of different approaches to the analysis that produce different ranked lists. Rather than considering exact agreement between the rankings, following others, we consider two ranked lists to be in agreement if the rankings differ by some fixed distance...
March 1, 2017: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28273855/integration-of-traditional-and-metabolomics-biomarkers-identifies-prognostic-metabolites-for-predicting-responsiveness-to-nutritional-intervention-against-oxidative-stress-and-inflammation
#12
You Jin Kim, Iksoo Huh, Ji Yeon Kim, Saejong Park, Sung Ha Ryu, Kyu-Bong Kim, Suhkmann Kim, Taesung Park, Oran Kwon
Various statistical approaches can be applied to integrate traditional and omics biomarkers, allowing the discovery of prognostic markers to classify subjects into poor and good prognosis groups in terms of responses to nutritional interventions. Here, we performed a prototype study to identify metabolites that predict responses to an intervention against oxidative stress and inflammation, using a data set from a randomized controlled trial evaluating Korean black raspberry (KBR) in sedentary overweight/obese subjects...
March 4, 2017: Nutrients
https://www.readbyqxmd.com/read/28272536/prediction-of-years-of-life-after-diagnosis-of-breast-cancer-using-omics-and-omic-by-treatment-interactions
#13
Agustín González-Reymúndez, Gustavo de Los Campos, Lucía Gutiérrez, Sophia Y Lunt, Ana I Vazquez
Breast cancer (BC) is the second most common type of cancer and a major cause of death for women. Commonly, BC patients are assigned to risk groups based on the combination of prognostic and prediction factors (eg, patient age, tumor size, tumor grade, hormone receptor status, etc). Although this approach is able to identify risk groups with different prognosis, patients are highly heterogeneous in their response to treatments. To improve the prediction of BC patients, we extended clinical models (including prognostic and prediction factors with whole-omic data) to integrate omics profiles for gene expression and copy number variants (CNVs)...
March 8, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28271980/mosquito-borne-diseases-and-omics-salivary-gland-proteome-of-the-female-aedes-aegypti-mosquito
#14
Rakhi Dhawan, Manish Kumar, Ajeet Kumar Mohanty, Gourav Dey, Jayshree Advani, T S Keshava Prasad, Ashwani Kumar
The female Aedes aegypti mosquito is an important vector for several tropical and subtropical diseases such as dengue, chikungunya, and Zika and yellow fever. The disease viruses infect the mosquito and subsequently spread to the salivary glands after which the viruses can be transmitted to humans with probing or feeding by the mosquito. Omics systems sciences offer the opportunity to characterize vectors and can inform disease surveillance, vector control and development of innovative diagnostics, personalized medicines, vaccines, and insecticide targets...
January 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28269041/multi-omic-approaches-for-characterization-of-hepatocellular-carcinoma
#15
Habtom W Ressom, Cristina Di Poto, Alessia Ferrarini, Yunli Hu, Mohammad R Nezami Ranjbar, Ehwang Song, Rency S Varghese, Minkun Wang, Shiyue Zhou, Rui Zhu, Yiming Zuo, Mahlet G Tadesse, Yehia Mechref
Multi-omic approaches offer the opportunity to characterize complex diseases such as cancer at various molecular levels. In this paper, we present transcriptomic, proteomic/glycoproteomic, glycomic, and metabolomic (TPGM) data we acquired by analysis of liver tissues from hepatocellular carcinoma (HCC) cases and patients with liver cirrhosis. We evaluated changes in the levels of transcripts, proteins, glycans, and metabolites between tumor and cirrhotic tissues by statistical methods. We demonstrated the potential of multi-omic approaches and network analysis to investigate the interactions among these biomolecules in the progression of liver cirrhosis to HCC...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28266329/enhanced-understanding-of-the-host-pathogen-interaction-in-sepsis-new-opportunities-for-omic-approaches
#16
REVIEW
Cyndi Goh, Julian C Knight
Progress in sepsis research has been severely hampered by a heterogeneous disease phenotype, limiting the interpretation of clinical trials and the development of effective therapeutic interventions. Application of omics-based methodologies is advancing understanding of the dysregulated host immune response to infection in sepsis. However, the frequently elusive nature of the infecting organism in sepsis has limited efforts to understand the effect of disease heterogeneity involving the pathogen. Recent advances in nucleic acid sequencing-based pathogen analysis provide the opportunity for more accurate and comprehensive microbiological diagnosis...
March 2017: Lancet Respiratory Medicine
https://www.readbyqxmd.com/read/28265997/a-systems-biology-methodology-combining-transcriptome-and-interactome-datasets-to-assess-the-implications-of-cytokinin-signaling-for-plant-immune-networks
#17
Meik Kunz, Thomas Dandekar, Muhammad Naseem
Cytokinins (CKs) play an important role in plant growth and development. Also, several studies highlight the modulatory implications of CKs for plant-pathogen interaction. However, the underlying mechanisms of CK mediating immune networks in plants are still not fully understood. A detailed analysis of high-throughput transcriptome (RNA-Seq and microarrays) datasets under modulated conditions of plant CKs and its mergence with cellular interactome (large-scale protein-protein interaction data) has the potential to unlock the contribution of CKs to plant defense...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28263888/combined-venomics-antivenomics-and-venom-gland-transcriptome-analysis-of-the-monocoled-cobra-naja-kaouthia-from-china
#18
Ning Xu, Hong-Yan Zhao, Yin Yin, Shan-Shan Shen, Lin-Lin Shan, Chuan-Xi Chen, Yan-Xia Zhang, Jian-Fang Gao, Xiang Ji
We conducted an omics-analysis of the venom of Naja kaouthia from China. Proteomics analysis revealed six protein families [three-finger toxins (3-FTx), phospholipase A2 (PLA2), nerve growth factor, snake venom metalloproteinase (SVMP), cysteine-rich secretory protein and ohanin], and venom-gland transcriptomics analysis revealed 28 protein families from 79 unigenes. 3-FTx (56.5% in proteome/82.0% in transcriptome) and PLA2 (26.9%/13.6%) were identified as the most abundant families in venom proteome and venom-gland transcriptome...
March 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28263171/omics-markers-of-the-red-cell-storage-lesion-and-metabolic-linkage
#19
REVIEW
Angelo D'alessandro, Travis Nemkov, Julie Reisz, Monika Dzieciatkowska, Matthew J Wither, Kirk C Hansen
The introduction of omics technologies in the field of Transfusion Medicine has significantly advanced our understanding of the red cell storage lesion. While the clinical relevance of such a lesion is still a matter of debate, quantitative and redox proteomics approaches, as well quantitative metabolic flux analysis and metabolic tracing experiments promise to revolutionise our understanding of the role of blood processing strategies, inform the design and testing of novel additives or technologies (such as pathogen reduction), and evaluate the clinical relevance of donor and recipient biological variability with respect to red cell storability and transfusion outcomes...
March 2017: Blood Transfusion, Trasfusione del Sangue
https://www.readbyqxmd.com/read/28261716/virulence-factor-activity-relationships-vfars-a-bioinformatics-perspective
#20
REVIEW
Hassan Waseem, Maggie R Williams, Tiffany Stedtfeld, Benli Chai, Robert D Stedtfeld, James R Cole, James M Tiedje, Syed A Hashsham
Virulence factor activity relationships (VFARs) - a concept loosely based on quantitative structure-activity relationships (QSARs) for chemicals was proposed as a predictive tool for ranking risks due to microorganisms relevant to water safety. A rapid increase in sequencing capabilities and bioinformatics tools has significantly increased the potential for VFAR-based analyses. This review summarizes more than 20 bioinformatics databases and tools, developed over the last decade, along with their virulence and antimicrobial resistance prediction capabilities...
March 6, 2017: Environmental Science. Processes & Impacts
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