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https://www.readbyqxmd.com/read/27933532/precise-network-modeling-of-systems-genetics-data-using-the-bayesian-network-webserver
#1
Jesse D Ziebarth, Yan Cui
The Bayesian Network Webserver (BNW, http://compbio.uthsc.edu/BNW ) is an integrated platform for Bayesian network modeling of biological datasets. It provides a web-based network modeling environment that seamlessly integrates advanced algorithms for probabilistic causal modeling and reasoning with Bayesian networks. BNW is designed for precise modeling of relatively small networks that contain less than 20 nodes. The structure learning algorithms used by BNW guarantee the discovery of the best (most probable) network structure given the data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27932893/let-7a-enhances-the-sensitivity-of-hepatocellular-carcinoma-cells-to-cetuximab-by-regulating-stat3-expression
#2
Fei Xue, Yanhui Liu, Hongwei Zhang, Yu Wen, Lei Yan, Qiang Tang, Erhui Xiao, Dongyi Zhang
BACKGROUND: Let-7 miRNAs are reported to play an inhibitory role in carcinogenesis, tumor progression, recurrence, and pluripotency of cancer. However, few studies have reported the relationship between let-7 and drug sensitivity, especially for let-7a (a subtype of let-7). This study aimed to investigate the function of let-7a in regulating the sensitivity of hepatocellular carcinoma (HCC) cell lines to cetuximab. METHODS: The cytotoxicity of cetuximab on HCC cell lines (Huh7, Hep3B, HepG2, SNU449, and SNU387) was evaluated using a cell viability assay (the Cell Counting Kit-8 assay) and a cell proliferation assay (the Click-iT EdU Imaging Kit) in the presence of a control, a let-7a mimic, and a let-7a inhibitor...
2016: OncoTargets and Therapy
https://www.readbyqxmd.com/read/27932760/-satb1-promotes-the-malignant-of-human-non-hodgkin-lymphoma-by-activating-the-ribonucleotide-reductase-%C3%A2-small-subunit-m2
#3
Dayong Yan, Wei Wang
To explore the role of the special AT rich sequence binding protein-1 (SATB1) and ribonucleotide reductase M2 (RRM2) in enhancing malignant progression of non-Hodgkin lymphoma (NHL). 
 Methods: A total of 42 NHL and 42 chronic lymphadenitis patients were recruited. The protein expressions of SATB1 and RRM2 in cervical lymph nodes were determined by Western blot. After overexpression of SATB1, siSATB1 or siRRM2, the mRNA levels of SATB1 and RRM2 in cells were analyzed via RT-PCR, the cell proliferation was evaluated via MTT and EdU assays, while the migration and invasion of cells were assessed by transwell assays...
November 28, 2016: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
https://www.readbyqxmd.com/read/27928192/approvals-submission-and-important-labeling-changes-for-us-marketed-pharmaceuticals
#4
(no author information available yet)
This monthly feature will help readers keep current on new drug, new indications, dosage forms and safety-related changes in labeling or use. Efforts have been made to assure the accuracy of this information; however, if there are any questions, please let us know at jgeneral@ku.edu.
November 2016: Hospital Pharmacy
https://www.readbyqxmd.com/read/27928184/ismp-adverse-drug-reactions-chronic-marijuana-use-associated-with-recurrent-diabetic-ketoacidosis-lamotrigine-induced-cataplexy-trimethoprim-sulfamethoxazole-induced-hyponatremia-ziprasidone-induced-sleepwalking-and-sleep-related-eating-metabolic-acidosis-associated
#5
Michael A Mancano
The purpose of this feature is to heighten awareness of specific adverse drug reactions (ADRs), discuss methods of prevention, and promote reporting of ADRs to the US Food and Drug Administration's (FDA's) MedWatch program (800-FDA-1088). If you have reported an interesting, preventable ADR to MedWatch, please consider sharing the account with our readers. Write to Dr. Mancano at ISMP, 200 Lakeside Drive, Suite 200, Horsham, PA 19044 (phone: 215-707-4936; e-mail: mmancano@temple.edu). Your report will be published anonymously unless otherwise requested...
November 2016: Hospital Pharmacy
https://www.readbyqxmd.com/read/27926534/irna-ai-identifying-the-adenosine-to-inosine-editing-sites-in-rna-sequences
#6
Wei Chen, Pengmian Feng, Hui Yang, Hui Ding, Hao Lin, Kuo-Chen Chou
Catalyzed by adenosine deaminase (ADAR), the adenosine to inosine (A-to-I) editing in RNA is not only involved in various important biological processes, but also closely associated with a series of major diseases. Therefore, knowledge about the A-to-I editing sites in RNA is crucially important for both basic research and drug development. Given an uncharacterized RNA sequence that contains many adenosine (A) residues, can we identify which one of them can be of A-to-I editing, and which one cannot? Unfortunately, so far no computational method whatsoever has been developed to address such an important problem based on the RNA sequence information alone...
December 1, 2016: Oncotarget
https://www.readbyqxmd.com/read/27926382/prediction-of-anti-cancer-drug-response-by-kernelized-multi-task-learning
#7
Mehmet Tan
MOTIVATION: Chemotherapy or targeted therapy are two of the main treatment options for many types of cancer. Due to the heterogeneous nature of cancer, the success of the therapeutic agents differs among patients. In this sense, determination of chemotherapeutic response of the malign cells is essential for establishing a personalized treatment protocol and designing new drugs. With the recent technological advances in producing large amounts of pharmacogenomic data, in silico methods have become important tools to achieve this aim...
October 2016: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/27924042/planttfdb-4-0-toward-a-central-hub-for-transcription-factors-and-regulatory-interactions-in-plants
#8
Jinpu Jin, Feng Tian, De-Chang Yang, Yu-Qi Meng, Lei Kong, Jingchu Luo, Ge Gao
With the goal of providing a comprehensive, high-quality resource for both plant transcription factors (TFs) and their regulatory interactions with target genes, we upgraded plant TF database PlantTFDB to version 4.0 (http://planttfdb.cbi.pku.edu.cn/). In the new version, we identified 320 370 TFs from 165 species, presenting a more comprehensive genomic TF repertoires of green plants. Besides updating the pre-existing abundant functional and evolutionary annotation for identified TFs, we generated three new types of annotation which provide more directly clues to investigate functional mechanisms underlying: (i) a set of high-quality, non-redundant TF binding motifs derived from experiments; (ii) multiple types of regulatory elements identified from high-throughput sequencing data; (iii) regulatory interactions curated from literature and inferred by combining TF binding motifs and regulatory elements...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924039/flyrnai-org-the-database-of-the-drosophila-rnai-screening-center-and-transgenic-rnai-project-2017-update
#9
Yanhui Hu, Aram Comjean, Charles Roesel, Arunachalam Vinayagam, Ian Flockhart, Jonathan Zirin, Lizabeth Perkins, Norbert Perrimon, Stephanie E Mohr
The FlyRNAi database of the Drosophila RNAi Screening Center (DRSC) and Transgenic RNAi Project (TRiP) at Harvard Medical School and associated DRSC/TRiP Functional Genomics Resources website (http://fgr.hms.harvard.edu) serve as a reagent production tracking system, screen data repository, and portal to the community. Through this portal, we make available protocols, online tools, and other resources useful to researchers at all stages of high-throughput functional genomics screening, from assay design and reagent identification to data analysis and interpretation...
October 23, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924038/farna-knowledgebase-of-inferred-functions-of-non-coding-rna-transcripts
#10
Tanvir Alam, Mahmut Uludag, Magbubah Essack, Adil Salhi, Haitham Ashoor, John B Hanks, Craig Kapfer, Katsuhiko Mineta, Takashi Gojobori, Vladimir B Bajic
Non-coding RNA (ncRNA) genes play a major role in control of heterogeneous cellular behavior. Yet, their functions are largely uncharacterized. Current available databases lack in-depth information of ncRNA functions across spectrum of various cells/tissues. Here, we present FARNA, a knowledgebase of inferred functions of 10,289 human ncRNA transcripts (2,734 microRNA and 7,555 long ncRNA) in 119 tissues and 177 primary cells of human. Since transcription factors (TFs) and TF co-factors (TcoFs) are crucial components of regulatory machinery for activation of gene transcription, cellular processes and diseases in which TFs and TcoFs are involved suggest functions of the transcripts they regulate...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924033/chipbase-v2-0-decoding-transcriptional-regulatory-networks-of-non-coding-rnas-and-protein-coding-genes-from-chip-seq-data
#11
Ke-Ren Zhou, Shun Liu, Wen-Ju Sun, Ling-Ling Zheng, Hui Zhou, Jian-Hua Yang, Liang-Hu Qu
The abnormal transcriptional regulation of non-coding RNAs (ncRNAs) and protein-coding genes (PCGs) is contributed to various biological processes and linked with human diseases, but the underlying mechanisms remain elusive. In this study, we developed ChIPBase v2.0 (http://rna.sysu.edu.cn/chipbase/) to explore the transcriptional regulatory networks of ncRNAs and PCGs. ChIPBase v2.0 has been expanded with ∼10 200 curated ChIP-seq datasets, which represent about 20 times expansion when comparing to the previous released version...
October 23, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924023/methsmrt-an-integrative-database-for-dna-n6-methyladenine-and-n4-methylcytosine-generated-by-single-molecular-real-time-sequencing
#12
Pohao Ye, Yizhao Luan, Kaining Chen, Yizhi Liu, Chuanle Xiao, Zhi Xie
DNA methylation is an important type of epigenetic modifications, where 5- methylcytosine (5mC), 6-methyadenine (6mA) and 4-methylcytosine (4mC) are the most common types. Previous efforts have been largely focused on 5mC, providing invaluable insights into epigenetic regulation through DNA methylation. Recently developed single-molecule real-time (SMRT) sequencing technology provides a unique opportunity to detect the less studied DNA 6mA and 4mC modifications at single-nucleotide resolution. With a rapidly increased amount of SMRT sequencing data generated, there is an emerging demand to systematically explore DNA 6mA and 4mC modifications from these data sets...
October 18, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924020/lincsnp-2-0-an-updated-database-for-linking-disease-associated-snps-to-human-long-non-coding-rnas-and-their-tfbss
#13
Shangwei Ning, Ming Yue, Peng Wang, Yue Liu, Hui Zhi, Yan Zhang, Jizhou Zhang, Yue Gao, Maoni Guo, Dianshuang Zhou, Xin Li, Xia Li
We describe LincSNP 2.0 (http://bioinfo.hrbmu.edu.cn/LincSNP), an updated database that is used specifically to store and annotate disease-associated single nucleotide polymorphisms (SNPs) in human long non-coding RNAs (lncRNAs) and their transcription factor binding sites (TFBSs). In LincSNP 2.0, we have updated the database with more data and several new features, including (i) expanding disease-associated SNPs in human lncRNAs; (ii) identifying disease-associated SNPs in lncRNA TFBSs; (iii) updating LD-SNPs from the 1000 Genomes Project; and (iv) collecting more experimentally supported SNP-lncRNA-disease associations...
October 23, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923875/accounting-for-protein-subcellular-localization-a-compartmental-map-of-the-rat-liver-proteome
#14
Michel Jadot, Marielle Boonen, Jacqueline Thirion, Nan Wang, Jinchuan Xing, Caifeng Zhao, Abla Tannous, Meiqian Qian, Haiyan Zheng, John K Everett, Dirk F Moore, David E Sleat, Peter Lobel
Accurate knowledge of the intracellular location of proteins is important for numerous areas of biomedical research including assessing fidelity of putative protein-protein interactions, modeling cellular processes at a system-wide level and investigating metabolic and disease pathways. Many proteins have not been localized, or have been incompletely localized, partly because most studies do not account for entire subcellular distribution. Thus, proteins are frequently assigned to one organelle while a significant fraction may reside elsewhere...
December 6, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27923350/coneva-a-toolbox-for-comprehensive-assessment-of-protein-contacts
#15
Badri Adhikari, Jackson Nowotny, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng
BACKGROUND: In recent years, successful contact prediction methods and contact-guided ab initio protein structure prediction methods have highlighted the importance of incorporating contact information into protein structure prediction methods. It is also observed that for almost all globular proteins, the quality of contact prediction dictates the accuracy of structure prediction. Hence, like many existing evaluation measures for evaluating 3D protein models, various measures are currently used to evaluate predicted contacts, with the most popular ones being precision, coverage and distance distribution score (Xd)...
December 7, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27922095/co-expression-network-analyses-identify-functional-modules-associated-with-development-and-stress-response-in-gossypium-arboreum
#16
Qi You, Liwei Zhang, Xin Yi, Kang Zhang, Dongxia Yao, Xueyan Zhang, Qianhua Wang, Xinhua Zhao, Yi Ling, Wenying Xu, Fuguang Li, Zhen Su
Cotton is an economically important crop, essential for the agriculture and textile industries. Through integrating transcriptomic data, we discovered that multi-dimensional co-expression network analysis was powerful for predicting cotton gene functions and functional modules. Here, the recently available transcriptomic data on Gossypium arboreum, including data on multiple growth stages of tissues and stress treatment samples were applied to construct a co-expression network exploring multi-dimensional expression (development and stress) through multi-layered approaches...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27921202/endogenous-stem-cells-were-recruited-by-defocused-low-energy-shock-wave-in-treating-diabetic-bladder-dysfunction
#17
Yang Jin, Lina Xu, Yong Zhao, Muwen Wang, Xunbo Jin, Haiyang Zhang
Defocused low-energy shock wave (DLSW) has been shown effects on activating mesenchymal stromal cells (MSCs) in vitro. In this study, recruitment of endogenous stem cells was firstly examined as an important pathway during the healing process of diabetic bladder dysfunction (DBD) treated by DLSW in vivo. Neonatal rats received intraperitoneal injection of 5-ethynyl-2-deoxyuridine (EdU) and then DBD rat model was created by injecting streptozotocin. Four weeks later, DLSW treatment was performed. Afterward, their tissues were examined by histology...
December 5, 2016: Stem Cell Reviews
https://www.readbyqxmd.com/read/27919220/deepqa-improving-the-estimation-of-single-protein-model-quality-with-deep-belief-networks
#18
Renzhi Cao, Debswapna Bhattacharya, Jie Hou, Jianlin Cheng
BACKGROUND: Protein quality assessment (QA) useful for ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, estimating the quality of a single protein model, which is important for selecting a few good models out of a large model pool consisting of mostly low-quality models, is still a largely unsolved problem. RESULTS: We introduce a novel single-model quality assessment method DeepQA based on deep belief network that utilizes a number of selected features describing the quality of a model from different perspectives, such as energy, physio-chemical characteristics, and structural information...
December 5, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27918592/microrna-497-induces-apoptosis-and-suppresses-proliferation-via-the-bcl-2-bax-caspase9-caspase3-pathway-and-cyclin-d2-protein-in-huvecs
#19
Ridong Wu, Shi Tang, Mian Wang, Xiangdong Xu, Chen Yao, Shenming Wang
INTRODUCTION: MicroRNAs play crucial roles in various types of diseases. However, to date, no information about the role of miR-497 in the development of atherosclerosis has been reported. This study investigated the possible role of miR-497 in vascular endothelial cell injury during the early stage of atherosclerosis. MATERIALS AND METHODS: The expression level of miR-497 in human umbilical vein endothelial cells (HUVECs) exposed to ox-LDL was detected using qRT-PCR...
2016: PloS One
https://www.readbyqxmd.com/read/27915346/mir-181a-targets-phlpp2-to-augment-akt-signaling-and-regulate-proliferation-and-apoptosis-in-human-keloid-fibroblasts
#20
Zhen Rang, Zong-Yang Wang, Qiu-Yu Pang, You-Wei Wang, Ge Yang, Fan Cui
BACKGROUND/AIMS: Keloids are fibrous overgrowths induced by cutaneous injury. MicroRNAs (miRNAs) have recently emerged as post-transcriptional gene repressors and participants in a diverse array of pathophysiological processes leading to skin disease. The purpose of the current study was to explore the precise functions of miR-181a in human keloid development and the underlying mechanisms. METHODS: A miRNA microarray analysis was performed to compare expression profiles between keloid and normal skin tissues...
December 5, 2016: Cellular Physiology and Biochemistry
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