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https://www.readbyqxmd.com/read/29231872/a-deeper-examination-of-thorellius-atrox-scorpion-venom-components-with-omic-techonologies
#1
Teresa Romero-Gutierrez, Esteban Peguero-Sanchez, Miguel A Cevallos, Cesar V F Batista, Ernesto Ortiz, Lourival D Possani
This communication reports a further examination of venom gland transcripts and venom composition of the Mexican scorpion Thorellius atrox using RNA-seq and tandem mass spectrometry. The RNA-seq, which was performed with the Illumina protocol, yielded more than 20,000 assembled transcripts. Following a database search and annotation strategy, 160 transcripts were identified, potentially coding for venom components. A novel sequence was identified that potentially codes for a peptide with similarity to spider ω-agatoxins, which act on voltage-gated calcium channels, not known before to exist in scorpion venoms...
December 12, 2017: Toxins
https://www.readbyqxmd.com/read/29231702/stacked-injections-of-biphasic-extractions-for-improved-metabolomic-coverage-and-sample-throughput
#2
Corey David Broeckling, Jessica E Prenni
Omics technologies attempt to provide comprehensive coverage of their target analytes. Comprehensive coverage of metabolites - the aim of non-targeted metabolomics applications - is hindered by the extreme diversity in physiochemical properties of the metabolome. One approach to deal with this challenge is the use of biphasic extractions. These methods generate two largely complementary extracts from a single sample, with an organic lipid-rich fraction and an aqueous fraction containing largely primary and secondary metabolites...
December 12, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29227475/an-alox12-12-hete-gpr31-signaling-axis-is-a-key-mediator-of-hepatic-ischemia-reperfusion-injury
#3
Xiao-Jing Zhang, Xu Cheng, Zhen-Zhen Yan, Jing Fang, Xiaozhan Wang, Weijun Wang, Zhen-Yu Liu, Li-Jun Shen, Peng Zhang, Pi-Xiao Wang, Rufang Liao, Yan-Xiao Ji, Jun-Yong Wang, Song Tian, Xue-Yong Zhu, Yan Zhang, Rui-Feng Tian, Lin Wang, Xin-Liang Ma, Zan Huang, Zhi-Gang She, Hongliang Li
Hepatic ischemia-reperfusion (IR) injury is a common clinical issue lacking effective therapy and validated pharmacological targets. Here, using integrative 'omics' analysis, we identified an arachidonate 12-lipoxygenase (ALOX12)-12-hydroxyeicosatetraenoic acid (12-HETE)-G-protein-coupled receptor 31 (GPR31) signaling axis as a key determinant of the hepatic IR process. We found that ALOX12 was markedly upregulated in hepatocytes during ischemia to promote 12-HETE accumulation and that 12-HETE then directly binds to GPR31, triggering an inflammatory response that exacerbates liver damage...
December 11, 2017: Nature Medicine
https://www.readbyqxmd.com/read/29227469/integrative-single-cell-analysis-of-transcriptional-and-epigenetic-states-in-the-human-adult-brain
#4
Blue B Lake, Song Chen, Brandon C Sos, Jean Fan, Gwendolyn E Kaeser, Yun C Yung, Thu E Duong, Derek Gao, Jerold Chun, Peter V Kharchenko, Kun Zhang
Detailed characterization of the cell types in the human brain requires scalable experimental approaches to examine multiple aspects of the molecular state of individual cells, as well as computational integration of the data to produce unified cell-state annotations. Here we report improved high-throughput methods for single-nucleus droplet-based sequencing (snDrop-seq) and single-cell transposome hypersensitive site sequencing (scTHS-seq). We used each method to acquire nuclear transcriptomic and DNA accessibility maps for >60,000 single cells from human adult visual cortex, frontal cortex, and cerebellum...
December 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29224359/a-reduced-transcriptome-approach-to-assess-environmental-toxicants-using-zebrafish-embryo-test
#5
Pingping Wang, Pu Xia, Jianghua Yang, Zhihao Wang, Ying Peng, Wei Shi, Daniel L Villeneuve, Hongxia Yu, Xiaowei Zhang
Omics approaches can monitor responses and alterations of biological pathways at genome-scale, which are useful to predict potential adverse effects by environmental toxicants. However, high throughput application of transcriptomics in chemical assessment is limited due to the high cost and lack of "standardized" toxicogenomic methods. Here, a reduced zebrafish transcriptome (RZT) approach was developed to represent the whole transcriptome and to profile bioactivity of chemical and environmental mixtures in zebrafish embryo...
December 11, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/29223976/zinc-detoxification-a-functional-genomics-and-transcriptomics-analysis-in-drosophila-melanogaster-cultured-cells
#6
Stephanie E Mohr, Kirstin Rudd, Yanhui Hu, Wei R Song, Quentin Gilly, Michael Buckner, Benjamin E Housden, Colleen Kelley, Jonathan Zirin, Rong Tao, Gabriel Amador, Katarzyna Sierzputowska, Aram Comjean, Norbert Perrimon
Cells require some metals, such as zinc and manganese, but excess levels of these metals can be toxic. As a result, cells have evolved complex mechanisms for maintaining metal homeostasis and surviving metal intoxication. Here, we present the results of a large-scale functional genomic screen in Drosophila cultured cells for modifiers of zinc chloride toxicity, together with transcriptomics data for wildtype or genetically zinc-sensitized cells challenged with mild zinc chloride supplementation. Altogether, we identified 47 genes for which knockdown conferred sensitivity or resistance to toxic zinc or manganese chloride treatment, and more than 1800 putative zinc-responsive genes...
December 9, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29222756/metabolic-model-reconstruction-and-analysis-of-an-artificial-microbial-ecosystem
#7
Chao Ye, Nan Xu, Xiulai Chen, Liming Liu
Microbial communities are widespread in the environment, and to isolate and identify species or to determine relations among microorganisms, some 'omics methods like metagenomics, proteomics, and metabolomics have been used. When combined with various 'omics data, models known as artificial microbial ecosystems (AME) are powerful methods that can make functional predictions about microbial communities. Reconstruction of an AME model is the first step for model analysis. Many techniques have been applied to the construction of AME models, e...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222021/identification-and-validation-of-salivary-proteomic-signatures-for-non-invasive-detection-of-ovarian-cancer
#8
Md Tajmul, Farhat Parween, Lata Singh, Sandeep R Mathur, J B Sharma, Sunesh Kumar, D N Sharma, Savita Yadav
Ovarian cancer (OC) is one of the most lethal cancers among all gynecological malignancies. An effective and non-invasive screening approach is needed urgently to reduce high mortality rate. The purpose of this study was to identify the salivary protein signatures (SPS) for non-invasive detection of ovarian cancer. Differentially expressed SPS were identified by fluorescence-based 2D-DIGE coupled with MALDI/TOF-MS. The expression levels of three differential proteins (Lipocalin-2, indoleamine-2, 3-dioxygenase1 (IDO1) and S100A8) were validated using western blotting and ELISA...
December 5, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29218899/precision-medicine-from-diplotypes-to-disparities-towards-improved-health-and-therapies
#9
Dana C Crawford, Alexander A Morgan, Joshua C Denny, Bruce J Aronow, Steven E Brenner
Precision medicine research efforts both in basic science discovery and clinical implementation are well underway and promise to provide individualized preventions and treatments, improving overall health care delivery. To achieve these goals, advances in data capture and analysis are needed spanning different types of 'omic and clinical data. The efforts to enhance precise treatments for all may accentuate healthcare disparities unless specific challenges are identified and addressed. This session of the 2018 Pacific Symposium on Biocomputing presents the latest developments in this transdisciplinary research space of genomics, medicine, and population health...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218873/session-introduction-challenges-of-pattern-recognition-in-biomedical-data
#10
Shefali Setia Verma, Anurag Verma, Anna Okula Basile, Marta-Byrska Bishop, Christian Darabos
The analysis of large biomedical data often presents with various challenges related to not just the size of the data, but also to data quality issues such as heterogeneity, multidimensionality, noisiness, and incompleteness of the data. The data-intensive nature of computational genomics problems in biomedical informatics warrants the development and use of massive computer infrastructure and advanced software tools and platforms, including but not limited to the use of cloud computing. Our session aims to address these challenges in handling big data for designing a study, performing analysis, and interpreting outcomes of these analyses...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29208510/differential-impacts-of-individual-and-combined-exposures-of-deoxynivalenol-and-zearalenone-on-the-heparg-human-hepatocyte-proteome
#11
Marie-Caroline Smith, Emma Timmins-Schiffman, Monika Coton, Emmanuel Coton, Nolwenn Hymery, Brook L Nunn, Stéphanie Madec
Numerous surveys have highlighted the natural co-occurrence of deoxynivalenol (DON) and zearalenone (ZEA) mycotoxins in food and feed. Nevertheless, data regarding cellular mechanisms involved in response to their individual and simultaneous exposures are lacking. In this study, in order to analyze how low mycotoxin doses could impact cellular physiology and homeostasis, proteomic profiles of proliferating human hepatocytes (HepaRG) exposed for 1h and 24h to low DON and ZEA cytotoxicity levels (0.2 and 20μM respectively), alone or in combination, were analyzed by LC-MS/MS...
December 2, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29201151/complete-genome-sequences-of-clostridium-perfringens-del1-strain-isolated-from-chickens-affected-by-necrotic-enteritis
#12
Charles Li, Xianghe Yan, Hyun S Lillehoj
Background: Clostridium perfringens is ubiquitous in nature. It is a normal inhabitant in the intestinal tract of animals and humans. As the primary etiological agent of gas gangrene, necrosis and bacteremia, C. perfringens causes food poisoning, necrotic enteritis (NE), and even death. Epidemiology research has indicated that the increasing incidence of NE in poultry is associated with the withdrawal of in-feed antibiotic growth promoters in poultry production in response to government regulations...
2017: Gut Pathogens
https://www.readbyqxmd.com/read/29199021/an-integrated-systems-genetics-and-omics-toolkit-to-probe-gene-function
#13
Hao Li, Xu Wang, Daria Rukina, Qingyao Huang, Tao Lin, Vincenzo Sorrentino, Hongbo Zhang, Maroun Bou Sleiman, Danny Arends, Aaron McDaid, Peiling Luan, Naveed Ziari, Laura A Velázquez-Villegas, Karim Gariani, Zoltan Kutalik, Kristina Schoonjans, Richard A Radcliffe, Pjotr Prins, Stephan Morgenthaler, Robert W Williams, Johan Auwerx
Identifying genetic and environmental factors that impact complex traits and common diseases is a high biomedical priority. Here, we developed, validated, and implemented a series of multi-layered systems approaches, including (expression-based) phenome-wide association, transcriptome-/proteome-wide association, and (reverse-) mediation analysis, in an open-access web server (systems-genetics.org) to expedite the systems dissection of gene function. We applied these approaches to multi-omics datasets from the BXD mouse genetic reference population, and identified and validated associations between genes and clinical and molecular phenotypes, including previously unreported links between Rpl26 and body weight, and Cpt1a and lipid metabolism...
November 30, 2017: Cell Systems
https://www.readbyqxmd.com/read/29197663/prediction-of-potential-drivers-connecting-different-dysfunctional-levels-in-lung-adenocarcinoma-via-a-protein-protein-interaction-network
#14
Fei Yuan, WenCong Lu
Lung cancer is a serious disease that threatens an affected individual's life. Its pathogenesis has not yet to be fully described, thereby impeding the development of effective treatments and preventive measures. "Cancer driver" theory considers that tumor initiation can be associated with a number of specific mutations in genes called cancer driver genes. Four omics levels, namely, (1) methylation, (2) microRNA, (3) mutation, and (4) mRNA levels, are utilized to cluster cancer driver genes. In this study, the known dysfunctional genes of these four levels were used to identify novel driver genes of lung adenocarcinoma, a subtype of lung cancer...
November 29, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29197583/evaluation-of-ion-mobility-for-the-separation-of-glycoconjugate-isomers-due-to-different-types-of-sialic-acid-linkage-at-the-intact-glycoprotein-glycopeptide-and-glycan-level
#15
Albert Barroso, Estela Giménez, Albert Konijnenberg, Jaime Sancho, Victoria Sanz-Nebot, Frank Sobott
The study of protein glycosylation can be regarded as an intricate but very important task, making glycomics one of the most challenging and interesting, albeit under-researched, type of "omics" science. Complexity escalates remarkably when considering that carbohydrates can form severely branched structures with many different constituents, which often leads to the formation of multiple isomers. In this regard, ion mobility (IM) spectrometry has recently demonstrated its power for the separation of isomeric compounds...
November 29, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29194470/idingo-integrative-differential-network-analysis-in-genomics-with-shiny-application
#16
Caleb A Class, Min Jin Ha, Veerabhadran Baladandayuthapani, Kim-Anh Do
Motivation: Differential network analysis is an important way to understand network rewiring involved in disease progression and development. Building differential networks from multiple `omics data provides insight into the holistic differences of the interactive system under different patient-specific groups. DINGO was developed to infer group-specific dependencies and build differential networks. However, DINGO and other existing tools are limited to analyze data arising from a single platform, and modeling each of the multiple 'omics data independently does not account for the hierarchical structure of the data...
November 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29193773/post-genomic-behavioral-genetics-from-revolution-to-routine
#17
REVIEW
David G Ashbrook, Megan K Mulligan, Robert W Williams
What was once expensive and revolutionary-full genome sequence-is now affordable and routine. Costs will continue to drop, opening up new frontiers in behavioral genetics. This shift in costs from the genome to the phenome is most notable in large clinical studies of behavior and associated diseases in cohorts that exceed hundreds of thousands of subjects. Examples include the Women's Health Initiative (www.whi.org), the Million Veterans Program (www. RESEARCH: va.gov/MVP), the 100,000 Genomes Project (genomicsengland...
November 28, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/29193384/concurrent-isotope-assisted-metabolic-flux-analysis-and-transcriptome-profiling-reveal-responses-of-poplar-cells-to-altered-nitrogen-and-carbon-supply
#18
Xiaofeng Zhang, Ashish Misra, Shilpa Nargund, Gary D Coleman, Ganesh Sriram
Reduced nitrogen is indispensable to plants. However, its limited availability in soil combined with the energetic and environmental impacts of nitrogen fertilizers motivates research into molecular mechanisms toward improving plant nitrogen use efficiency (NUE). We performed a systems-level investigation of this problem by employing multiple 'omics methodologies on cell suspensions of hybrid poplar (Populus tremula x Populus alba). Acclimation and growth of the cell suspensions in four nutrient regimes ranging from abundant to deficient supplies of carbon and nitrogen revealed that cell growth under low-nitrogen levels was associated with substantially higher NUE...
November 29, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29190951/multi-omics-analysis-reveals-that-ornithine-decarboxylase-contributes-to-erlotinib-resistance-in-pancreatic-cancer-cells
#19
Won-Jun Jang, Boyeon Choi, Sang-Hoon Song, Naeun Lee, Dong-Joon Kim, Sooyeun Lee, Chul-Ho Jeong
Molecular and metabolic alterations in cancer cells are one of the leading causes of acquired resistance to chemotherapeutics. In this study, we explored an experimental strategy to identify which of these alterations can induce erlotinib resistance in human pancreatic cancer. Using genetically matched erlotinib-sensitive (BxPC-3) and erlotinib-resistant (BxPC-3ER) pancreatic cancer cells, we conducted a multi-omics analysis of metabolomes and transcriptomes in these cells. Untargeted and targeted metabolomic analyses revealed significant changes in metabolic pathways involved in the regulation of polyamines, amino acids, and fatty acids...
November 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/29190747/characterizing-the-heterogeneity-of-tumor-tissues-from-spatially-resolved-molecular-measures
#20
John F Graf, Maria I Zavodszky
BACKGROUND: Tumor heterogeneity can manifest itself by sub-populations of cells having distinct phenotypic profiles expressed as diverse molecular, morphological and spatial distributions. This inherent heterogeneity poses challenges in terms of diagnosis, prognosis and efficient treatment. Consequently, tools and techniques are being developed to properly characterize and quantify tumor heterogeneity. Multiplexed immunofluorescence (MxIF) is one such technology that offers molecular insight into both inter-individual and intratumor heterogeneity...
2017: PloS One
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