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https://www.readbyqxmd.com/read/28214867/the-novel-long-noncoding-rna-tusc7-inhibits-proliferation-by-sponging-mir-211-in-colorectal-cancer
#1
Jian Xu, Rui Zhang, Jian Zhao
BACKGROUND/AIMS: The novel long noncoding RNA (lncRNA) tumor suppressor candidate 7 (TUSC7) has been reported as a potential tumor suppressor, while the functional role of TUSC7 is still unknown in colorectal cancer (CRC). Here, we characterized TUSC7 expression profile in CRC patients and investigated its biological function and potential molecular mechanism. METHODS: RNA isolation, qRT-PCR, cell counter kit-8 assay, cell cycle assay, EdU assay, and western blot were performed...
February 8, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28212602/happi-2-a-comprehensive-and-high-quality-map-of-human-annotated-and-predicted-protein-interactions
#2
Jake Y Chen, Ragini Pandey, Thanh M Nguyen
BACKGROUND: Human protein-protein interaction (PPI) data is essential to network and systems biology studies. PPI data can help biochemists hypothesize how proteins form complexes by binding to each other, how extracellular signals propagate through post-translational modification of de-activated signaling molecules, and how chemical reactions are coupled by enzymes involved in a complex biological process. Our capability to develop good public database resources for human PPI data has a direct impact on the quality of future research on genome biology and medicine...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28211534/in-vitro-differentiation-of-fertile-sperm-from-cryopreserved-spermatogonia-of-the-endangered-endemic-cyprinid-honmoroko-gnathopogon-caerulescens
#3
Shogo Higaki, Manami Shimada, Kazuaki Kawamoto, Takaaki Todo, Toshihiro Kawasaki, Ikuo Tooyama, Yasuhiro Fujioka, Noriyoshi Sakai, Tatsuyuki Takada
Many endemic fish species are threatened with extinction. Conservation strategies and the restoration of endemic fish after extinction must therefore be investigated. Although sperm cryopreservation is indispensable for the conservation of endangered fishes, the limited number of mature fish and limited availability (volume and period) of sperm from small endemic fish hinders the optimization and practical use of this material. In this report, we demonstrate the in vitro differentiation of fertile sperm from cryopreserved spermatogonia of juveniles of the endangered small cyprinid honmoroko (Gnathopogon caerulescens), which is endemic to Lake Biwa in Japan...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28205268/the-effect-of-delta-like-1-homologue-on-the-proliferation-and-odontoblastic-differentiation-in-human-dental-pulp-stem-cells
#4
Shengcai Qi, Yanhong Yan, Yue Wen, Jialiang Li, Jing Wang, Fubo Chen, Xiaoshan Tang, Guangwei Shang, Yuanzhi Xu, Raorao Wang
INTRODUCTION: This study aimed to investigate the functions of delta-like homologue 1 (DLK1) in the proliferation and differentiation of human dental pulp stem cells (hDPSCs). METHODS: Immunohistochemical analysis was used to determine the expression of alkaline phosphatase (ALP), dentin sialophosphoprotein (DSPP), DLK1, NOTCH1 and p-ERK1/2 in the mouse first maxillary molar. Recombinant lentivirus was constructed to overexpress DLK1 stably in hDPSCs. The cell viability and proliferation of hDPSCs were examined by CCK8 and EdU incorporation assay respectively...
February 15, 2017: Cell Proliferation
https://www.readbyqxmd.com/read/28204814/fisetin-regulates-astrocyte-migration-and-proliferation-in%C3%A2-vitro
#5
Nan Wang, Fang Yao, Ke Li, Lanlan Zhang, Guo Yin, Mingjun Du, Bingyi Wu
Fisetin (3,3',4',7-tetrahydroxyflavone) is a plant flavonol found in fruits and vegetables that has been reported to inhibit migration and proliferation in several types of cancer. Reactive astrogliosis involves astrocyte migration and proliferation, and contributes to the formation of glial scars in central nervous system (CNS) disorders. However, the effect of fisetin on the migration and proliferation of astrocytes remains unclear. In this study, we found that fisetin inhibited astrocyte migration in a scratch-wound assay and diminished the phosphorylation of focal adhesion kinase (FAK; Tyr576/577 and paxillin (Tyr118)...
February 15, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28203233/exo-mirexplorer-a-comprehensive-resource-for-exploring-and-comparatively-analyzing-exogenous-micrornas
#6
Ling-Ling Zheng, Kai-Wen Deng, An-Cheng Deng, Jie Wu, Jian-Hua Yang, Zhao-Rong Lun, Liang-Hu Qu
MicroRNAs (miRNAs) are small regulatory RNAs that play important roles in animals, plants, and viruses. Deep-sequencing technology has been widely adopted in miRNA investigations. However, it is still a big mysterious why nearly all sequencing data contain miRNA sequences from exogenous species, called exo-miRNAs. In this study, we developed a novel platform, exo-miRExplorer, for mining and identifying exo-miRNAs from high-throughput small RNA sequencing experiments which originated from tissues and cell lines of multiple organisms...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28202528/distinct-levels-of-radioresistance-in-lgr5-colonic-epithelial-stem-cells-versus-lgr5-small-intestinal-stem-cells
#7
Guoqiang Hua, Chu Wang, Yan Pan, Zhaoshi Zeng, Sang Gyu Lee, Maria Laura Martin, Adriana Haimovitz-Friedman, Zvi Fuks, Philip B Paty, Richard N Kolesnick
While small and large intestines possess seemingly similar Wnt-driven Leucine-rich repeat-containing G protein coupled receptor 5 (Lgr5)+ adult epithelial stem cells, we report here that the two organs exhibit distinct mechanisms of tissue response to ionizing radiation. Employing Lgr5-lacZ transgenic mice and Lgr5 in situ hybridization, we found colonic epithelial stem cells (CESC) markedly more radioresistant in vivo than small intestinal crypt base columnar stem cells (CBC) (D0 6.0±0.3 Gy vs. 1.3±0.1, respectively; p0...
February 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28196472/premeta-a-tool-to-facilitate-meta-analysis-of-rare-variant-associations
#8
Zheng-Zheng Tang, Paul Bunn, Ran Tao, Zhouwen Liu, Dan-Yu Lin
BACKGROUND: Meta-analysis is essential to the discovery of rare variants that influence complex diseases and traits. Four major software packages, namely MASS, MetaSKAT, RAREMETAL, and seqMeta, have been developed to perform meta-analysis of rare-variant associations. These packages first generate summary statistics for each study and then perform the meta-analysis by combining the summary statistics. Because of incompatible file formats and non-equivalent summary statistics, the output files from the study-level analysis of one package cannot be directly used to perform meta-analysis in another package...
February 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28194231/skinsensdb-a-curated-database-for-skin-sensitization-assays
#9
Chia-Chi Wang, Ying-Chi Lin, Shan-Shan Wang, Chieh Shih, Yi-Hui Lin, Chun-Wei Tung
Skin sensitization is an important toxicological endpoint for chemical hazard determination and safety assessment. Prediction of chemical skin sensitizer had traditionally relied on data from rodent models. The development of the adverse outcome pathway (AOP) and associated alternative in vitro assays have reshaped the assessment of skin sensitizers. The integration of multiple assays as key events in the AOP has been shown to have improved prediction performance. Current computational models to predict skin sensitization mainly based on in vivo assays without incorporating alternative in vitro assays...
2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/28193234/differential-timing-of-neurogenesis-underlies-dorsal-ventral-topographic-projection-of-olfactory-sensory-neurons
#10
Eerdunfu, Naoki Ihara, Bao Ligao, Yuji Ikegaya, Haruki Takeuchi
BACKGROUND: The mammalian primary olfactory system has a spatially-ordered projection in which olfactory sensory neurons (OSNs) located in the dorsomedial (DM) and ventrolateral (VL) region of the olfactory epithelium (OE) send their axons to the dorsal and ventral region of the olfactory bulb (OB), respectively. We previously found that OSN axonal projections occur sequentially, from the DM to the VL region of the OE. The differential timing of axonal projections is important for olfactory map formation because early-arriving OSN axons secrete guidance cues at the OB to help navigate late-arriving OSN axons...
February 13, 2017: Neural Development
https://www.readbyqxmd.com/read/28188908/hive-heptagon-a-sensible-variant-calling-algorithm-with-post-alignment-quality-controls
#11
Vahan Simonyan, Konstantin Chumakov, Eric Donaldson, Konstantinos Karagiannis, Phuc VinhNguyen Lam, Hayley Dingerdissen, Alin Voskanian
: Advances in high-throughput sequencing (HTS) technologies have greatly increased the availability of genomic data and potential discovery of clinically significant genomic variants. However, numerous issues still exist with the analysis of these data, including data complexity, the absence of formally agreed upon best practices, and inconsistent reproducibility. Toward a more robust and reproducible variant-calling paradigm, we propose a series of selective noise filtrations and post-alignment quality control (QC) techniques that may reduce the rate of false variant calls...
February 7, 2017: Genomics
https://www.readbyqxmd.com/read/28187713/novel-methods-to-optimize-gene-and-statistic-test-for-evaluation-an-application-for-escherichia-coli
#12
Tran Tuan-Anh, Le Thi Ly, Ngo Quoc Viet, Pham The Bao
BACKGROUND: Since the recombinant protein was discovered, it has become more popular in many aspects of life science. The value of global pharmaceutical market was $87 billion in 2008 and the sales for industrial enzyme exceeded $4 billion in 2012. This is strong evidence showing the great potential of recombinant protein. However, native genes introduced into a host can cause incompatibility of codon usage bias, GC content, repeat region, Shine-Dalgarno sequence with host's expression system, so the yields can fall down significantly...
February 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28187413/dato-an-atlas-of-biological-databases-and-tools
#13
Qilin Li, Yincong Zhou, Yingmin Jiao, Zhao Zhang, Lin Bai, Li Tong, Xiong Yang, Björn Sommer, Ralf Hofestädt, Ming Chen
This work presents DaTo, a semi-automatically generated world atlas of biological databases and tools. It extracts raw information from all PubMed articles which contain exact URLs in their abstract section, followed by a manual curation of the abstract and the URL accessibility. DaTo features a user-friendly query interface, providing extensible URL-related annotations, such as the status, the location and the country of the URL. A graphical interaction network browser has also been integrated into the DaTo web interface to facilitate exploration of the relationship between different tools and databases with respect to their ontology-based semantic similarity...
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28186907/identifying-sigma70-promoters-with-novel-pseudo-nucleotide-composition
#14
Hao Lin, Zhi-Yong Liang, Hua Tang, Wei Chen
Promoters are DNA regulatory elements located directly upstream or at the 5' end of the transcription initiation site (TSS), which are in charge of gene transcription initiation. With the completion of a large number of microorganism genomics, it is urgent to predict promoters accurately in bacteria by using computational method. In this work, a sequence-based predictor named "iPro70-PseZNC" was designed for identifying sigma70 promoters in prokaryote. In the predictor, the samples of DNA sequences are formulated by a novel pseudo nucleotide composition, called PseZNC, into which the multi-window Z-curve composition and six local DNA structural properties are incorporated...
February 8, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28186905/hmmcas-a-web-tool-for-the-identification-and-domain-annotations-of-cas-proteins
#15
Guoshi Chai, Min Yu, Lixu Jiang, Yaocong Duan, Jian Huang
The CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) adaptive immune systems are discovered in many bacteria and most archaea. These systems are encoded by cas (CRISPR-associated) operons that have an extremely diverse architecture. The most crucial step in the depiction of cas operons composition is the identification of cas genes or Cas proteins. With the continuous increase of the newly sequenced archaeal and bacterial genomes, the recognition of new Cas proteins is becoming possible, which not only provides candidates for novel genome editing tools but also helps to understand the prokaryotic immune system better...
February 7, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28185549/correcting-the-impact-of-docking-pose-generation-error-on-binding-affinity-prediction
#16
Hongjian Li, Kwong-Sak Leung, Man-Hon Wong, Pedro J Ballester
BACKGROUND: Pose generation error is usually quantified as the difference between the geometry of the pose generated by the docking software and that of the same molecule co-crystallised with the considered protein. Surprisingly, the impact of this error on binding affinity prediction is yet to be systematically analysed across diverse protein-ligand complexes. RESULTS: Against commonly-held views, we have found that pose generation error has generally a small impact on the accuracy of binding affinity prediction...
September 22, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28183832/molecular-bases-for-phyllomorph-development-in-a-one-leaf-plant-monophyllaea-glabra
#17
Naoko Ishikawa, Hirokazu Takahashi, Mikio Nakazono, Hirokazu Tsukaya
PREMISE OF THE STUDY: The aboveground part of one-leaf plants (Gesneriaceae) consists of a unique shoot-like unit called a phyllomorph, which is composed of a growing lamina and one petiolode (a stem- and petiole-like organ). The phyllomorph has three meristems: a basal meristem (BM; involved in lamina growth), a petiolode meristem (PM; required for midrib and petiolode growth), and a groove meristem (GM; contributes to inflorescence and new phyllomorph development). Although the GM has a tunica-corpus structure like a conventional shoot apical meristem (SAM), the vegetative GM of a one-leaf plant does not form any organ primordia and has been considered a defective or suppressed SAM...
February 9, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28179744/approvals-submission-and-important-labeling-changes-for-us-marketed-pharmaceuticals
#18
(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.
January 2017: Hospital Pharmacy
https://www.readbyqxmd.com/read/28179736/ismp-adverse-drug-reactions-acute-disseminated-intravascular-coagulation-due-to-oxaliplatin-azithromycin-induced-stevens-johnson-syndrome-acute-jugular-vein-thrombosis-with-rituximab-hemorrhagic-bullae-of-the-fingers-induced-by-furosemide
#19
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...
January 2017: Hospital Pharmacy
https://www.readbyqxmd.com/read/28168878/network-marker-selection-for-untargeted-lc-ms-metabolomics-data
#20
Qingpo Cai, Jessica A Alvarez, Jian Kang, Tianwei Yu
Untargeted metabolomics using high-resolution liquid chromatography - mass spectrometry (LC-MS) is becoming one of the major areas of high-throughput biology. Functional analysis, i.e. analyzing the data based on metabolic pathways or the genome-scale metabolic network, is critical in feature selection and interpretation of metabolomics data. One of the main challenges in the functional analyses is the lack of the feature identity in the LC-MS data itself. By matching mass-to-charge ratio (m/z) values of the features to theoretical values derived from known metabolites, some features can be matched to one or more known metabolites...
February 7, 2017: Journal of Proteome Research
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