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https://www.readbyqxmd.com/read/28440736/levistilide-a-inhibits-angiogenesis-in-liver-fibrosis-via-vascular-endothelial-growth-factor-signaling-pathway
#1
Zhi-Min Zhao, Hong-Liang Liu, Xin Sun, Tao Guo, Li Shen, Yan-Yan Tao, Cheng-Hai Liu
Levistilide A (C24H28O4, molecular weight = 380.48) derived from Angelica sinensis (Danggui) has been reported to inhibit hepatic stellate cell proliferation. This study investigated the effects of levistilide A on liver fibrosis relating to angiogenesis, particularly on the characteristic change in liver sinusoidal endothelial cells. LX-2 cells were activated by TGF-β1, and the human hepatic sinusoidal endothelial cells (HHSECs) were induced by endothelial cell growth supplement. Cell viability was detected using a methylthiazoldiphenyl-tetrazolium bromide assay; F-actin was visualized through the fluorescence probe method; cell proliferation was examined using the EdU kit; antiangiogenesis activity was assessed using the tube formation assay and transgenic zebrafish model...
May 2017: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28439139/approvals-submission-and-important-labeling-changes-for-us-marketed-pharmaceuticals
#2
(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.
March 2017: Hospital Pharmacy
https://www.readbyqxmd.com/read/28439130/ismp-adverse-drug-reactions
#3
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...
March 2017: Hospital Pharmacy
https://www.readbyqxmd.com/read/28437450/esprit-forest-parallel-clustering-of-massive-amplicon-sequence-data-in-subquadratic-time
#4
Yunpeng Cai, Wei Zheng, Jin Yao, Yujie Yang, Volker Mai, Qi Mao, Yijun Sun
The rapid development of sequencing technology has led to an explosive accumulation of genomic sequence data. Clustering is often the first step to perform in sequence analy- sis, and hierarchical clustering is one of the most commonly used approaches for this purpose. However, it is currently computationally expensive to perform hierarchical clustering of extremely large sequence datasets due to its quadratic time and space complexities. In this paper we developed a new algorithm called ESPRIT-Forest for parallel hierarchical clustering of sequences...
April 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28436919/a-machine-learning-method-for-fast-and-accurate-characterization-of-depth-of-interaction-gamma-cameras
#5
Stefano Pedemonte, Larry Pierce, Koen Van Leemput
Measuring the depth-of-interaction (DOI) of gamma photons enables increasing the resolution of emission imaging systems. Several design variants of DOI-sensitive detectors have been recently introduced to improve the performance of scanners for Positron Emission Tomography (PET). However, the accurate characterization of the response of DOI detectors, necessary to accurately measure the DOI, remains an unsolved problem. Numerical simulations are, at the state of the art, imprecise, while measuring directly the characteristics of DOI detectors experimentally is hindered by the impossibility to impose the depth-of-interaction in an experimental set-up...
April 24, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28435097/defining-the-most-probable-location-of-the-parahippocampal-place-area-using-cortex-based-alignment-and-cross-validation
#6
REVIEW
Kevin S Weiner, Michael Barnett, Nathan Witthoft, Golijeh Golarai, Anthony Stigliani, Kendrick N Kay, Jesse Gomez, Vaidehi S Natu, Katrin Amunts, Karl Zilles, Kalanit Grill-Spector
The parahippocampal place area (PPA) is a widely studied high-level visual region in the human brain involved in place and scene processing. The goal of the present study was to identify the most probable location of place-selective voxels in medial ventral temporal cortex. To achieve this goal, we first used cortex-based alignment (CBA) to create a probabilistic place-selective region of interest (ROI) from one group of 12 participants. We then tested how well this ROI could predict place selectivity in each hemisphere within a new group of 12 participants...
April 18, 2017: NeuroImage
https://www.readbyqxmd.com/read/28435071/er-%C3%AE-36-mediates-estrogen-stimulated-mapk-erk-activation-and-regulates-migration-invasion-proliferation-in-cervical-cancer-cells
#7
Qing Sun, Ying Liang, Tianli Zhang, Kun Wang, Xingsheng Yang
OBJECTIVE: Estrogen receptor alpha 36 (ER-α36), a truncated variant of ER-α, is different from other nuclear receptors of the ER-α family. Previous findings indicate that ER-α36 might be involved in cell growth, proliferation, and differentiation in carcinomas and primarily mediates non-genomic estrogen signaling. However, studies on ER-α36 and cervical cancer are rare. This study aimed to detect the expression of ER-α36 in cervical cancer; the role of ER-α36 in 17-β-estradiol (E2)-induced invasion, migration and proliferation of cervical cancer; and their probable molecular mechanisms...
April 20, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28431583/overexpression-of-mir-584-5p-inhibits-proliferation-and-induces-apoptosis-by-targeting-ww-domain-containing-e3-ubiquitin-protein-ligase-1-in-gastric-cancer
#8
Qing Li, Zheng Li, Song Wei, Weizhi Wang, Zheng Chen, Lei Zhang, Liang Chen, Bowen Li, Guangli Sun, Jianghao Xu, Qiang Li, Lu Wang, Zhipeng Xu, Yiwen Xia, Diancai Zhang, Hao Xu, Zekuan Xu
BACKGROUND: MicroRNAs are endogenously expressed, small non-coding RNAs that modulate gene expression by targeting specific mRNAs, resulting in translational repression or mRNA degradation. Although miR-584-5p has been reported to play a vital role in various malignancies, its role and the molecular mechanisms underlying the effects of miR-584-5p in gastric cancer (GC) remain to be clarified. In this study, we investigated the role of miR-584-5p in GC. METHODS: The expression of miR-584-5p and its specific target gene were determined in human GC specimens and cell lines by microRNA real-time polymerase chain reaction (RT-PCR), quantitative RT-PCR (qRT-PCR) and Western blot...
April 21, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/28431131/dnaprodb-an-interactive-tool-for-structural-analysis-of-dna-protein-complexes
#9
Jared M Sagendorf, Helen M Berman, Remo Rohs
Many biological processes are mediated by complex interactions between DNA and proteins. Transcription factors, various polymerases, nucleases and histones recognize and bind DNA with different levels of binding specificity. To understand the physical mechanisms that allow proteins to recognize DNA and achieve their biological functions, it is important to analyze structures of DNA-protein complexes in detail. DNAproDB is a web-based interactive tool designed to help researchers study these complexes. DNAproDB provides an automated structure-processing pipeline that extracts structural features from DNA-protein complexes...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28431087/a-method-for-learning-a-sparse-classifier-in-the-presence-of-missing-data-for-high-dimensional-biological-datasets
#10
Kristen Severson, Brinda Monian, J Christopher Love, Richard D Braatz
Motivation: This work addresses two common issues in building classification models for biological or medical studies: learning a sparse model, where only a subset of a large number of possible predictors is used, and training in the presence of missing data. This work focuses on supervised generative binary classification models, specifically linear discriminant analysis (LDA). The parameters are determined using an expectation maximization algorithm to both address missing data and introduce priors to promote sparsity...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28430977/deep-mining-heterogeneous-networks-of-biomedical-linked-data-to-predict-novel-drug-target-associations
#11
Nansu Zong, Hyeoneui Kim, Victoria Ngo, Olivier Harismendy
Motivation: A heterogeneous network topology possessing abundant interactions between biomedical entities has yet to be utilized in similarity-based methods for predicting drug-target associations based on the array of varying features of drugs and their targets. Deep learning reveals features of vertices of a large network that can be adapted in accommodating the similarity-based solutions to provide a flexible method of drug-target prediction. Results: We propose a similarity-based drug-target prediction method that enhances existing association discovery methods by using a topology-based similarity measure...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28430949/capturing-non-local-interactions-by-long-short-term-memory-bidirectional-recurrent-neural-networks-for-improving-prediction-of-protein-secondary-structure-backbone-angles-contact-numbers-and-solvent-accessibility
#12
Rhys Heffernan, Yuedong Yang, Kuldip Paliwal, Yaoqi Zhou
Motivation: The accuracy of predicting protein local and global structural properties such as secondary structure and solvent accessible surface area has been stagnant for many years because of the challenge of accounting for non-local interactions between amino acid residues that are close in three-dimensional structural space but far from each other in their sequence positions. All existing machine-learning techniques relied on a sliding window of 10-20 amino acid residues to capture some "short to intermediate" non-local interactions...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28430868/most-visualization-software-for-producing-automated-textbook-style-maps-of-genome-scale-metabolic-networks
#13
James J Kelley, Shay Maor, Min Kyung Kim, Anatoliy Lane, Desmond S Lun
Summary: Visualization of metabolites, reactions and pathways in genome-scale metabolic networks (GEMs) can assist in understanding cellular metabolism. Three attributes are desirable in software used for visualizing GEMs: 1. automation, since GEMs can be quite large; 2. production of understandable maps that provide ease in identification of pathways, reactions, and metabolites; and 3. visualization of the entire network to show how pathways are interconnected. No software currently exists for visualizing GEMs that satisfies all three characteristics, but MOST-Visualization, an extension of the software package MOST (Metabolic Optimization and Simulation Tool), satisfies (1), and by using a pre-drawn overview map of metabolism based on the Roche map satisfies (2) and comes close to satisfying (3)...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28430527/herc4-is-overexpressed-in-hepatocellular-carcinoma-and-contributes-to-the-proliferation-and-migration-of-hepatocellular-carcinoma-cells
#14
Yi Zheng, Jie Li, Chenwei Pan, Guangyao Zhou, Lu Zhuge, Lingxiang Jin, Peipei Fang
Recently, more and more evidences unveiled that ubiquitin-proteasome system (UPS) makes an important contribution to the occurrence and development of cancer. HERC4 is one identified Ubiqutin ligase E3, a member of UPS. Although some studies showed that HERC4 abnormally expresses in many cancer cells, till now, nothing has been reported about the function of HERC4 in the development of hepatoma carcinoma. To this end, in this study, we studied the function of HERC4 for the first time in hepatoma carcinoma cells...
April 21, 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28427077/mybl2-is-a-potential-prognostic-marker-that-promotes-cell-proliferation-in-gallbladder-cancer
#15
Hai-Bin Liang, Yang Cao, Qiang Ma, Yi-Jun Shu, Zheng Wang, Fei Zhang, Yuan-Yuan Ye, Huai-Feng Li, Shan-Shan Xiang, Xiao-Ling Song, Yi Xu, Yi-Chi Zhang, Run-Fa Bao, Rui-Yan Yuan, Yi-Jian Zhang, Yun-Ping Hu, Lin Jiang, Mao-Lan Li, Xu-An Wang, Xiang-Song Wu, Wen-Guang Wu, Shuai Zhao, Yong Fand, Xiao-Peng Cui, Yun-Shu Lu, Jian Zhou, Lei Zheng, Wei Gong, Ying-Bin Liu
BACKGROUND: Gallbladder cancer (GBC) is an aggressive and highly lethal biliary tract malignancy, with extremely poor prognosis. In the present study, we analyzed the potential involvement of MYBL2, a member of the Myb transcription factor family, in the carcinogenesis of human GBC. METHODS: MYBL2 expression levels were measured in GBC and cholecystitis tissue specimens using quantitative real-time PCR (qRT-PCR) and immunohistochemical (IHC) assays. The effects of MYBL2 on cell proliferation and DNA synthesis were evaluated using Cell Counting Kit-8 assay (CCK-8), colony formation, and 5-ethynyl-2'-deoxyuridine (EdU) retention assay, flow cytometry analysis, western blot, and a xenograft model of GBC cells in nude mice...
April 17, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28426719/transcriptome-of-interstitial-cells-of-cajal-reveals-unique-and-selective-gene-signatures
#16
Moon Young Lee, Se Eun Ha, Chanjae Park, Paul J Park, Robert Fuchs, Lai Wei, Brian G Jorgensen, Doug Redelman, Sean M Ward, Kenton M Sanders, Seungil Ro
Transcriptome-scale data can reveal essential clues into understanding the underlying molecular mechanisms behind specific cellular functions and biological processes. Transcriptomics is a continually growing field of research utilized in biomarker discovery. The transcriptomic profile of interstitial cells of Cajal (ICC), which serve as slow-wave electrical pacemakers for gastrointestinal (GI) smooth muscle, has yet to be uncovered. Using copGFP-labeled ICC mice and flow cytometry, we isolated ICC populations from the murine small intestine and colon and obtained their transcriptomes...
2017: PloS One
https://www.readbyqxmd.com/read/28425468/transcriptome-analysis-of-mango-mangifera-indica-l-fruit-epidermal-peel-to-identify-putative-cuticle-associated-genes
#17
Julio C Tafolla-Arellano, Yi Zheng, Honghe Sun, Chen Jiao, Eliel Ruiz-May, Miguel A Hernández-Oñate, Alberto González-León, Reginaldo Báez-Sañudo, Zhangjun Fei, David Domozych, Jocelyn K C Rose, Martín E Tiznado-Hernández
Mango fruit (Mangifera indica L.) are highly perishable and have a limited shelf life, due to postharvest desiccation and senescence, which limits their global distribution. Recent studies of tomato fruit suggest that these traits are influenced by the expression of genes that are associated with cuticle metabolism. However, studies of these phenomena in mango fruit are limited by the lack of genome-scale data. In order to gain insight into the mango cuticle biogenesis and identify putative cuticle-associated genes, we analyzed the transcriptomes of peels from ripe and overripe mango fruit using RNA-Seq...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28423357/mir-29b-inhibits-the-growth-of-glioma-via-mycn-dependent-way
#18
Guan Sun, Jingmin Lu, Chuang Zhang, Ran You, Lei Shi, Nan Jiang, Dekang Nie, Jian Zhu, Min Li, Jun Guo
MiR-29b is widely involved in diverse cancers. We plan to study its role in glioma. The expression of miR-29b was detected by real-time polymerase chain reaction (PCR) and we found the expression of miR-29b was decreased in glioma. Cell proliferation was evaluated by cell counting kit (CCK8) and 5-Ethynyl-2'- deoxyuridine (EdU) and cell apoptosis was assayed with flow cytometry assay (FCA), which indicated miR-29b can inhibit the proliferation and promote the apoptosis of glioma cells. The target of miR-29b was predicted using miRanda, TargetScan and PicTar sofeware and we also found MYCN was a direct target of miR-29b in glioma cells and miR-29b inhibited the proliferation of glioma cells via MYCN dependent way...
April 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28420402/sser-species-specific-essential-reactions-database
#19
Abraham A Labena, Yuan-Nong Ye, Chuan Dong, Fa-Z Zhang, Feng-Biao Guo
BACKGROUND: Essential reactions are vital components of cellular networks. They are the foundations of synthetic biology and are potential candidate targets for antimetabolic drug design. Especially if a single reaction is catalyzed by multiple enzymes, then inhibiting the reaction would be a better option than targeting the enzymes or the corresponding enzyme-encoding gene. The existing databases such as BRENDA, BiGG, KEGG, Bio-models, Biosilico, and many others offer useful and comprehensive information on biochemical reactions...
April 19, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28420207/t%C3%AE-rii-regulates-the-proliferation-of-metanephric-mesenchyme-cells-through-six2-in-vitro
#20
Zhaomin Mao, Zhongshi Lyu, Liyuan Huang, Qin Zhou, Yaguang Weng
The transforming growth factor-β (TGFβ) family signaling pathways play an important role in regulatory cellular networks and exert specific effects on developmental programs during embryo development. However, the function of TGFβ signaling pathways on the early kidney development remains unclear. In this work, we aim to detect the underlying role of TGFβ type II receptor (TβRII) in vitro, which has a similar expression pattern as the crucial regulator Six2 during early kidney development. Firstly, the 5-ethynyl-2'-deoxyuridine (EdU) assay showed knock down of TβRII significantly decreased the proliferation ratio of metanephric mesenchyme (MM) cells...
April 18, 2017: International Journal of Molecular Sciences
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