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https://www.readbyqxmd.com/read/27922122/identification-of-critical-paralog-groups-with-indispensable-roles-in-the-regulation-of-signaling-flow
#1
Dezso Modos, Johanne Brooks, David Fazekas, Eszter Ari, Tibor Vellai, Peter Csermely, Tamas Korcsmaros, Katalin Lenti
Extensive cross-talk between signaling pathways is required to integrate the myriad of extracellular signal combinations at the cellular level. Gene duplication events may lead to the emergence of novel functions, leaving groups of similar genes - termed paralogs - in the genome. To distinguish critical paralog groups (CPGs) from other paralogs in human signaling networks, we developed a signaling network-based method using cross-talk annotation and tissue-specific signaling flow analysis. 75 CPGs were found with higher degree, betweenness centrality, closeness, and 'bowtieness' when compared to other paralogs or other proteins in the signaling network...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922074/resistance-gene-identification-from-larimichthys-crocea-with-machine-learning-techniques
#2
Yinyin Cai, Zhijun Liao, Ying Ju, Juan Liu, Yong Mao, Xiangrong Liu
The research on resistance genes (R-gene) plays a vital role in bioinformatics as it has the capability of coping with adverse changes in the external environment, which can form the corresponding resistance protein by transcription and translation. It is meaningful to identify and predict R-gene of Larimichthys crocea (L.Crocea). It is friendly for breeding and the marine environment as well. Large amounts of L.Crocea's immune mechanisms have been explored by biological methods. However, much about them is still unclear...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922044/from-tumour-heterogeneity-to-advances-in-precision-treatment-of-colorectal-cancer
#3
REVIEW
Cornelis J A Punt, Miriam Koopman, Louis Vermeulen
In recent years, the high heterogeneity of colorectal cancer (CRC) has become evident. Hence, biomarkers need to be developed that enable the stratification of patients with CRC into different prognostic subgroups and in relation to response to therapies, according to the distinctive tumour biology. Currently, only RAS-mutation status is used routinely as a negative predictive marker to avoid treatment with anti-EGFR agents in patients with metastatic CRC, and mismatch-repair status can guide the use of adjuvant chemotherapy in patients with early stage colon cancer...
December 6, 2016: Nature Reviews. Clinical Oncology
https://www.readbyqxmd.com/read/27920818/exposition-of-hepatitis-b-surface-antigen-hbsag-on-the-surface-of-hek293t-cell-and-evaluation-of-its-expression
#4
Mina Mirian, Razieh Taghizadeh, Hossein Khanahmad, Mansour Salehi, Ali Jahanian-Najafabadi, Hojjat Sadeghi-Aliabadi, Shirin Kouhpayeh
Hepatitis B virus (HBV) is considered as a global health concern and hepatitis B surface antigen (HBsAg) is the most immunogenic protein of HBV. The purpose of this study was to evaluate the expression of HBsAg on the cell surface of human embryonic kidney cell line (HEK293T). After transformation of expression vector pcDNA/HBsAg to E.coli TOP10F', plasmid was extracted and digested with BglII. Afterwards, the linearized vector was transfected to cells and treated with hygromycin B for 5 weeks to expand the resulted clonies...
October 2016: Research in Pharmaceutical Sciences
https://www.readbyqxmd.com/read/27920767/ecophysiology-and-comparative-genomics-of-nitrosomonas-mobilis-ms1-isolated-from-autotrophic-nitrifying-granules-of-wastewater-treatment-bioreactor
#5
Soe Myat Thandar, Norisuke Ushiki, Hirotsugu Fujitani, Yuji Sekiguchi, Satoshi Tsuneda
Ammonia-oxidizing bacteria (AOB), which oxidize ammonia to nitrite in the first step of nitrification, play an important role in biological wastewater treatment systems. Nitrosomonas mobilis is an important and dominant AOB in various wastewater treatment systems. However, the detailed physiological and genomic properties of N. mobilis have not been thoroughly investigated because of limited success isolating pure cultures. This study investigated the key physiological characteristics of N. mobilis Ms1, which was previously isolated into pure culture from the nitrifying granules of wastewater treatment bioreactor...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27920554/next-generation-sequence-detects-arap3-as-a-novel-oncogene-in-papillary-thyroid-carcinoma
#6
Qing-Xuan Wang, En-Dong Chen, Ye-Feng Cai, Yi-Li Zhou, Zhou-Ci Zheng, Ying-Hao Wang, Yi-Xiang Jin, Wen-Xu Jin, Xiao-Hua Zhang, Ou-Chen Wang
PURPOSE: Thyroid cancer is the most frequent malignancies of the endocrine system, and it has became the fastest growing type of cancer worldwide. Much still remains unknown about the molecular mechanisms of thyroid cancer. Studies have found that some certain relationship between ARAP3 and human cancer. However, the role of ARAP3 in thyroid cancer has not been well explained. This study aimed to investigate the role of ARAP3 gene in papillary thyroid carcinoma. METHODS: Whole exon sequence and whole genome sequence of primary papillary thyroid carcinoma (PTC) samples and matched adjacent normal thyroid tissue samples were performed and then bioinformatics analysis was carried out...
2016: OncoTargets and Therapy
https://www.readbyqxmd.com/read/27920208/genetic-modification-of-er-hoxb8-osteoclast-precursors-using-crispr-cas9-as-a-novel-way-to-allow-studies-on-osteoclast-biology
#7
Irene Di Ceglie, Guus G H van den Akker, Giuliana Ascone, Bas Ten Harkel, Hans Häcker, Fons A J van de Loo, Marije I Koenders, Peter M van der Kraan, Teun J de Vries, Thomas Vogl, Johannes Roth, Peter L E M van Lent
Osteoclasts are cells specialized in bone resorption. Currently, studies on murine osteoclasts are primarily performed on bone marrow-derived cells with the use of many animals and limited cells available. ER-Hoxb8 cells are conditionally immortalized monocyte/macrophage murine progenitor cells, recently described to be able to differentiate toward functional osteoclasts. Here, we produced an ER-Hoxb8 clonal cell line from C57BL/6 bone marrow cells that strongly resembles phenotype and function of the conventional bone marrow-derived osteoclasts...
December 5, 2016: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/27920057/acropora-digitifera-encodes-the-largest-known-family-of-fluorescent-proteins-that-has-persisted-during-the-evolution-of-acropora-species
#8
Shiho Takahashi-Kariyazono, Jun Gojobori, Yoko Satta, Kazuhiko Sakai, Yohey Terai
Fluorescent proteins (FPs) are well known and broadly used as bio-imaging markers in molecular biology research. Many FP genes were cloned from anthozoan species and it was suggested that multi-copies of these genes are present in their genomes. However, the full complement of FP genes in any single coral species remained unidentified. In this study, we analyzed the FP genes in two stony coral species. FP cDNA sequences from Acropora digitifera and Acropora tenuis revealed the presence of a multi-gene family with an unexpectedly large number of genes, separated into short-/middle-wavelength emission (S/MWE), middle-/long-wavelength emission (M/LWE), and chromoprotein (CP) clades...
December 5, 2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27919805/uplc-ms-for-metabolomics-a-giant-step-forward-in-support-of-pharmaceutical-research
#9
REVIEW
Ala F Nassar, Terence Wu, Samuel F Nassar, Adam V Wisnewski
Metabolomics is a relatively new and rapidly growing area of post-genomic biological research. As use of metabolomics technology grows throughout the spectrum of drug discovery and development, and its applications broaden, its impact is expanding dramatically. This review seeks to provide the reader with a brief history of the development of metabolomics, its significance and strategies for conducting metabolomics studies. The most widely used analytical tools for metabolomics: NMR, LC-MS and GC-MS, are discussed along with considerations for their use...
December 2, 2016: Drug Discovery Today
https://www.readbyqxmd.com/read/27919705/the-complete-mitochondrial-genome-of-thitarodes-sejilaensis-lepidoptera-hepialidae-a-host-insect-of-ophiocordyceps-sinensis-and-its-implication-in-taxonomic-revision-of-hepialusadopted-in-china
#10
Zhiwen Zou, Qiang Min, Shiyu Cheng, Tianrong Xin, Bin Xia
The mitochondrial genome is widely used for phylogenetic analyses and evolutionary biology. The complete mitochondrial genome of Thitarodes sejilaensis (Lepidoptera: Hepialidae) was sequenced and analyzed in this study. This mitogenome is a typical circular molecule of 15,290bp, with the gene content, orientation and order identical to other insects in the family Hepialidae. The genome nucleotide composition is heavily biased towards As and Ts, accounting for 80.87% of total nucleotide content. The major strand shows a positive AT-skew and negative GC-skew...
December 2, 2016: Gene
https://www.readbyqxmd.com/read/27919067/genome-wide-changes-in-lncrna-splicing-and-regional-gene-expression-patterns-in-autism
#11
Neelroop N Parikshak, Vivek Swarup, T Grant Belgard, Manuel Irimia, Gokul Ramaswami, Michael J Gandal, Christopher Hartl, Virpi Leppa, Luis de la Torre Ubieta, Jerry Huang, Jennifer K Lowe, Benjamin J Blencowe, Steve Horvath, Daniel H Geschwind
Autism spectrum disorder (ASD) involves substantial genetic contributions. These contributions are profoundly heterogeneous but may converge on common pathways that are not yet well understood. Here, through post-mortem genome-wide transcriptome analysis of the largest cohort of samples analysed so far, to our knowledge, we interrogate the noncoding transcriptome, alternative splicing, and upstream molecular regulators to broaden our understanding of molecular convergence in ASD. Our analysis reveals ASD-associated dysregulation of primate-specific long noncoding RNAs (lncRNAs), downregulation of the alternative splicing of activity-dependent neuron-specific exons, and attenuation of normal differences in gene expression between the frontal and temporal lobes...
December 5, 2016: Nature
https://www.readbyqxmd.com/read/27918597/seqplots-interactive-software-for-exploratory-data-analyses-pattern-discovery-and-visualization-in-genomics
#12
Przemyslaw Stempor, Julie Ahringer
Experiments involving high-throughput sequencing are widely used for analyses of chromatin function and gene expression. Common examples are the use of chromatin immunoprecipitation for the analysis of chromatin modifications or factor binding, enzymatic digestions for chromatin structure assays, and RNA sequencing to assess gene expression changes after biological perturbations. To investigate the pattern and abundance of coverage signals across regions of interest, data are often visualized as profile plots of average signal or stacked rows of signal in the form of heatmaps...
2016: Wellcome Open Res
https://www.readbyqxmd.com/read/27918534/multiethnic-genome-wide-meta-analysis-of-ectopic-fat-depots-identifies-loci-associated-with-adipocyte-development-and-differentiation
#13
Audrey Y Chu, Xuan Deng, Virginia A Fisher, Alexander Drong, Yang Zhang, Mary F Feitosa, Ching-Ti Liu, Olivia Weeks, Audrey C Choh, Qing Duan, Thomas D Dyer, John D Eicher, Xiuqing Guo, Nancy L Heard-Costa, Tim Kacprowski, Jack W Kent, Leslie A Lange, Xinggang Liu, Kurt Lohman, Lingyi Lu, Anubha Mahajan, Jeffrey R O'Connell, Ankita Parihar, Juan M Peralta, Albert V Smith, Yi Zhang, Georg Homuth, Ahmed H Kissebah, Joel Kullberg, René Laqua, Lenore J Launer, Matthias Nauck, Michael Olivier, Patricia A Peyser, James G Terry, Mary K Wojczynski, Jie Yao, Lawrence F Bielak, John Blangero, Ingrid B Borecki, Donald W Bowden, John Jeffrey Carr, Stefan A Czerwinski, Jingzhong Ding, Nele Friedrich, Vilmunder Gudnason, Tamara B Harris, Erik Ingelsson, Andrew D Johnson, Sharon L R Kardia, Carl D Langefeld, Lars Lind, Yongmei Liu, Braxton D Mitchell, Andrew P Morris, Thomas H Mosley, Jerome I Rotter, Alan R Shuldiner, Bradford Towne, Henry Völzke, Henri Wallaschofski, James G Wilson, Matthew Allison, Cecilia M Lindgren, Wolfram Goessling, L Adrienne Cupples, Matthew L Steinhauser, Caroline S Fox
Variation in body fat distribution contributes to the metabolic sequelae of obesity. The genetic determinants of body fat distribution are poorly understood. The goal of this study was to gain new insights into the underlying genetics of body fat distribution by conducting sample-size-weighted fixed-effects genome-wide association meta-analyses in up to 9,594 women and 8,738 men of European, African, Hispanic and Chinese ancestry, with and without sex stratification, for six traits associated with ectopic fat (hereinafter referred to as ectopic-fat traits)...
December 5, 2016: Nature Genetics
https://www.readbyqxmd.com/read/27917953/the-core-subunit-of-a-chromatin-remodeling-complex-zmchb101-plays-essential-roles-in-maize-growth-and-development
#14
Xiaoming Yu, Lili Jiang, Rui Wu, Xinchao Meng, Ai Zhang, Ning Li, Qiong Xia, Xin Qi, Jinsong Pang, Zheng-Yi Xu, Bao Liu
ATP-dependent chromatin remodeling complexes play essential roles in the regulation of diverse biological processes by formulating a DNA template that is accessible to the general transcription apparatus. Although the function of chromatin remodelers in plant development has been studied in A. thaliana, how it affects growth and development of major crops (e.g., maize) remains uninvestigated. Combining genetic, genomic and bioinformatic analyses, we show here that the maize core subunit of chromatin remodeling complex, ZmCHB101, plays essential roles in growth and development of maize at both vegetative and reproductive stages...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917589/the-petale-study-late-adverse-effects-and-biomarkers-in-childhood-acute-lymphoblastic-leukemia-survivors
#15
Sophie Marcoux, Simon Drouin, Caroline Laverdière, Nathalie Alos, Gregor U Andelfinger, Laurence Bertout, Daniel Curnier, Matthias G Friedrich, Ekaterini A Kritikou, Geneviève Lefebvre, Emile Levy, Sarah Lippé, Valérie Marcil, Marie-Josée Raboisson, Frank Rauch, Philippe Robaey, Mariia Samoilenko, Chantal Séguin, Serge Sultan, Maja Krajinovic, Daniel Sinnett
BACKGROUND: Childhood cancer survivorship issues represent an established public health challenge. Most late adverse effects (LAEs) have been demonstrated to be time and treatment dependent. The PETALE study is a multidisciplinary research project aiming to comprehensively characterize LAEs and identify associated predictive biomarkers in childhood acute lymphoblastic leukemia (cALL) survivors. METHODS: cALL survivors treated at Sainte-Justine University Health Center with Dana-Farber Cancer Institution-ALL protocols 87-01 through 2005-01 were eligible...
December 4, 2016: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/27917288/towards-an-open-grapevine-information-system
#16
REVIEW
A-F Adam-Blondon, M Alaux, C Pommier, D Cantu, Z-M Cheng, G R Cramer, C Davies, S Delrot, L Deluc, G Di Gaspero, J Grimplet, A Fennell, J P Londo, P Kersey, F Mattivi, S Naithani, P Neveu, M Nikolski, M Pezzotti, B I Reisch, R Töpfer, M A Vivier, D Ware, H Quesneville
Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the framework of the International Grapevine Genome Program (www...
2016: Horticulture Research
https://www.readbyqxmd.com/read/27917188/crispr-cas9-tool-for-qualitative-and-quantitative-plant-genome-editing
#17
REVIEW
Ali Noman, Muhammad Aqeel, Shuilin He
Recent developments in genome editing techniques have aroused substantial excitement among agricultural scientists. These techniques offer new opportunities for developing improved plant lines with addition of important traits or removal of undesirable traits. Increased adoption of genome editing has been geared by swiftly developing Clustered regularly interspaced short palindromic repeats (CRISPR). This is appearing as driving force for innovative utilization in diverse branches of plant biology. CRISPR-Cas9 mediated genome editing is being used for rapid, easy and efficient alteration of genes among diverse plant species...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27917185/fire-and-brimstone-molecular-interactions-between-sulfur-and-glucosinolate-biosynthesis-in-model-and-crop-brassicaceae
#18
REVIEW
Priyakshee Borpatragohain, Terry J Rose, Graham J King
Glucosinolates (GSLs) represent one of the most widely studied classes of plant secondary metabolite, and have a wide range of biological activities. Their unique properties also affect livestock and human health, and have been harnessed for food and other end-uses. Since GSLs are sulfur (S)-rich there are many lines of evidence suggesting that plant S status plays a key role in determining plant GSL content. However, there is still a need to establish a detailed knowledge of the distribution and remobilization of S and GSLs throughout the development of Brassica crops, and to represent this in terms of primary and secondary sources and sinks...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27917181/nitric-oxide-responsive-heavy-metal-associated-gene-athmad1-contributes-to-development-and-disease-resistance-in-arabidopsis-thaliana
#19
Q Muhammad Imran, Noreen Falak, Adil Hussain, Bong-Gyu Mun, Arti Sharma, Sang-Uk Lee, Kyung-Min Kim, Byung-Wook Yun
Exposure of plants to different biotic and abiotic stress condition instigates significant change in the cellular redox status; resulting in the elevation of reactive nitrogen species that play signaling role in mediating defense responses. Heavy metal associated (HMA) domain containing genes are required for spatio-temporal transportation of metal ions that bind with various enzymes and co-factors within the cell. To uncover the underlying mechanisms mediated by AtHMA genes, we identified 14 Arabidopsis HMA genes that were differentially expressed in response to nitrosative stress through RNA-seq analysis...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27916957/snake-genome-sequencing-results-and-future-prospects
#20
REVIEW
Harald M I Kerkkamp, R Manjunatha Kini, Alexey S Pospelov, Freek J Vonk, Christiaan V Henkel, Michael K Richardson
Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes...
December 1, 2016: Toxins
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