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https://www.readbyqxmd.com/read/28109084/mir-5195-3p-inhibits-proliferation-and-invasion-of-human-bladder-cancer-cells-by-directly-targeting-oncogene-klf5
#1
Zhangjie Jiang, Yida Zhang, Runfu Cao, Li Li, Kezhao Zhong, Qingsheng Chen, Jianjun Xiao
MiRNAs played key roles in carcinogenesis of many cancers including bladder cancer. In current study, the role of miR-5195-3p, a quite recently discovered and poorly studied miRNA, in the proliferation and invasion of human bladder cancer cells was investigated. Our data displayed that, compared with the healthy volunteers (control) and SU-HUC-1 human normal bladder epithelial cells, miR-5195-3p was sharply down-regulated in the bladder cancer patients and 5 human bladder cancer cell lines. Then, the oligo miR-5195-3p mimic or miR-5195-3p antagomir was respectively transfected into both T24 and BIU-87 bladder cancer cell lines...
January 20, 2017: Oncology Research
https://www.readbyqxmd.com/read/28109076/microrna-409-3p-represses-glioma-cell-invasion-and-proliferation-by-targeting-high-mobility-group-nucleosome-binding-domain-5
#2
Yidong Cao, Liang Zhang, Minghao Wei, Xue Jiang, Dong Jia
Emerging evidence has suggested that aberrantly expressed microRNAs (miRNAs) are associated with glioma development andprogression. The aberrant expression of miR-409-3p has been reported in several human cancers. However, little is known about the function of miR-409-3p in gliomas. The aim of this study was to investigate the specific role and molecular mechanism of miR-409-3p in gliomas. In the present study, we found that miR-409-3p was downregulated in glioma tissue and cell lines. Overexpression of miR-409-3p inhibited glioma cell invasion and proliferation, whereas suppression of miR-409-3p promoted glioma cell invasion and proliferation...
January 20, 2017: Oncology Research
https://www.readbyqxmd.com/read/28108672/stromal-interaction-molecule-1-stim1-regulates-growth-cell-cycle-and-apoptosis-of-human-tongue-squamous-carcinoma-cells
#3
Xiaobo Cui, Laixiao Song, Yunfei Bai, Yaping Wang, Boqian Wang, Wei Wang
Oral tongue squamous carcinoma (OTSCC) is the most common type of cancer of oral carcinomas. However, the molecular mechanism by which OTSCC development is not fully identified. Stromal interaction molecule 1 (STIM1) is a transmembrane protein, mainly located in the endoplasmic reticulum (ER). STIM1 is involved in several types of cancers. Here we report that STIM1 contributes to the development of human OTSCC. We knocked down STIM1 in OTSCC cell line Tca-8113 with lentivirus-mediated shRNA and found that SITM1 knockdown repressed the proliferation of Tca-8113 cells...
January 20, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28108556/confirmation-of-five-novel-susceptibility-loci-for-systemic-lupus-erythematosus-sle-and-integrated-network-analysis-of-82-sle-susceptibility-loci
#4
Julio E Molineros, Wanling Yang, Xu-Jie Zhou, Celi Sun, Yukinori Okada, Huoru Zhang, Kek Heng Chua, Yu-Lung Lau, Yuta Kochi, Akari Suzuki, Kazuhiko Yamamoto, Jianyang Ma, So-Young Bang, Hye-Soon Lee, Kwangwoo Kim, Sang-Cheol Bae, Hong Zhang, Nan Shen, Loren L Looger, Swapan K Nath
We recently identified ten novel SLE susceptibility loci in Asians and uncovered several additional suggestive loci requiring further validation. This study aimed to replicate five of these suggestive loci in a Han Chinese cohort from Hong Kong, followed by meta-analysis (11,656 cases and 23,968 controls) on previously reported Asian and European populations, and perform bioinformatic analyses on all 82 reported SLE loci to identify shared regulatory signatures. We performed a battery of analyses for these five loci, as well as joint analyses on all 82 SLE loci...
January 20, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28108518/a-transposon-based-analysis-reveals-rasa1-is-involved-in-triple-negative-breast-cancer
#5
Cristian Suárez-Cabrera, Rita M Quintana, Ana Bravo, M LLanos Casanova, Angustias Page, Josefa P Alameda, Jesus M Paramio, Alicia Maroto, Javier Salamanca, Adam J Dupuy, Angel Ramírez, Manuel Navarro
RAS genes are mutated in 20% of human tumors, but these mutations are very rare in breast cancer. Here we used a mouse model to generate tumors upon activation of a mutagenic T2Onc2 transposon via expression of a transposase driven by the keratin K5 promoter in a p53+/- background. These animals mainly developed mammary tumors, most of which had transposon insertions in one of two RASGAP genes, neurofibromin1 (NF1) and RAS p21 protein activator (Rasa1). Immunohistochemical analysis of a collection of human breast tumors confirmed that low expression of RASA1 is frequent in basal (triple-negative) and ER-negative tumors...
January 20, 2017: Cancer Research
https://www.readbyqxmd.com/read/28108469/blood-rna-biomarkers-in-prodromal-park4-and-rem-sleep-behavior-disorder-show-role-of-complexin-1-loss-for-risk-of-parkinson-s-disease
#6
Suna Lahut, Suzana Gispert, Özgür Ömür, Candan Depboylu, Kay Seidel, Jorge Antolio Domínguez-Bautista, Nadine Brehm, Hülya Tireli, Karl Hackmann, Caroline Pirkevi, Barbara Leube, Vincent Ries, Kerstin Reim, Nils Brose, Wilfred F den Dunnen, Madrid Johnson, Zsuzsanna Wolf, Marc Schindewolf, Wiebke Schrempf, Kathrin Reetz, Peter Young, David Vadasz, Achilleas S Frangakis, Evelin Schröck, Helmuth Steinmetz, Marina Jendrach, Udo Rüb, Ayşe Nazlı Başak, Wolfgang Oertel, Georg Auburger
Parkinson's disease (PD) is a frequent neurodegenerative process at old age. Accumulation and aggregation of the lipid-binding SNARE complex component alpha-synuclein (SNCA) underlies this vulnerability and defines stages of disease progression. Determinants of SNCA levels and mechanisms of SNCA neurotoxicity are intensely investigated. In view of physiological SNCA roles in blood to modulate vesicle release, we studied blood samples from a new large pedigree with SNCA gene duplication (PARK4 mutation), to identify effects of SNCA gain-of-function as potential disease biomarkers...
January 20, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28108449/quantification-of-fibrous-spatial-point-patterns-from-single-molecule-localization-microscopy-smlm-data
#7
Ruby Peters, Marta Benthem Muñiz, Juliette Griffié, David J Williamson, George W Ashdown, Christian D Lorenz, Dylan M Owen
MOTIVATION: Unlike conventional microscopy which produces pixelated images, SMLM produces data in the form of a list of localization coordinates - a spatial point pattern (SPP). Often, such SPPs are analyzed using cluster analysis algorithms to quantify molecular clustering within, for example, the plasma membrane. While SMLM cluster analysis is now well developed, techniques for analyzing fibrous structures remain poorly explored. RESULTS: Here, we demonstrate statistical methodology, based on Ripley's K-function to quantitatively assess fibrous structures in 2D SMLM data sets...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108448/arnapipe-a-balanced-efficient-and-distributed-pipeline-for-processing-rna-seq-data-in-high-performance-computing-environments
#8
Arnald Alonso, Brittany N Lasseigne, Kelly Williams, Josh Nielsen, Ryne C Ramaker, Andrew A Hardigan, Bobbi Johnston, Brian S Roberts, Sara J Cooper, Sara Marsal, Richard M Myers
The wide range of RNA-seq applications and their high computational needs require the development of pipelines orchestrating the entire workflow and optimizing usage of available computational resources. We present aRNApipe, a project-oriented pipeline for processing of RNA-seq data in high performance cluster environments. aRNApipe is highly modular and can be easily migrated to any high performance computing (HPC) environment. The current applications included in aRNApipe combine the essential RNA-seq primary analyses, including quality control metrics, transcript alignment, count generation, transcript fusion identification, alternative splicing, and sequence variant calling...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108447/mirmine-a-database-of-human-mirna-expression-profiles
#9
Bharat Panwar, Gilbert S Omenn, Yuanfang Guan
MOTIVATION: MicroRNAs (miRNAs) are small non-coding RNAs that are involved in post-transcriptional regulation of gene expression. In this high-throughput sequencing era, a tremendous amount of RNA-seq data is accumulating, and full utilization of publicly available miRNA data is an important challenge. These data are useful to determine expression values for each miRNA, but quantification pipelines are in a primitive stage and still evolving; there are many factors that affect expression values significantly...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108446/chaincleaner-improves-genome-alignment-specificity-and-sensitivity
#10
Hernando G Suarez, Bjoern E Langer, Pradnya Ladde, Michael Hiller
MOTIVATION: Accurate alignments between entire genomes are crucial for comparative genomics. However, computing sensitive and accurate genome alignments is a challenging problem, complicated by genomic rearrangements. RESULTS: Here we present a fast approach, called chainCleaner, that improves the specificity in genome alignments by accurately detecting and removing local alignments that obscure the evolutionary history of genomic rearrangements. Systematic tests on alignments between the human and other vertebrate genomes show that chainCleaner (i) improves the alignment of numerous orthologous genes, (ii) exposes alignments between exons of orthologous genes that were masked before by alignments to pseudogenes, and (iii) recovers hundreds of kilobases in local alignments that otherwise would fall below a minimum score threshold...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108217/cdk3-is-a-major-target-of-mir-150-in-cell-proliferation-and-anti-cancer-effect
#11
Liang Wang, Yongyong Xi, Chengcao Sun, Feng Zhang, Heng Jiang, Qiqiang He, Dejia Li
MiR-150, a member of small non-coding RNAs, has been proven to dysregulate in different types of tumor and bear on carcinogenesis and cancer prognosis by regulating the expression of a series of gene including utrophin. Given that utrophin can compensate for dystrophin's absence and be regarded as a promising therapeutic target for Duchenne Muscular Dystrophy (DMD), we further detected the deep role of miR-150 in dystrophic muscle. Using a range of bioinformatic, molecular and cell biology techniques, we declared that miR-150 directly targets cyclin-dependent kinase 3 (CDK3) and leads to the regulation of CDK3 gene expression in both muscle-derived and non-muscle cells...
January 17, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28108031/ifpa-meeting-2016-workshop-report-i-genomic-communication-bioinformatics-trophoblast-biology-and-transport-systems
#12
Christiane Albrecht, Julie C Baker, Cassidy Blundell, Shawn L Chavez, Lucia Carbone, Larry Chamley, Roberta L Hannibal, Nick Illsley, Peter Kurre, Louise C Laurent, Charles McKenzie, Diana Morales-Prieto, Priyadarshini Pantham, Alison Paquette, Katie Powell, Nathan Price, Balaji M Rao, Yoel Sadovsky, Carlos Salomon, Geetu Tuteja, Samantha Wilson, P F O'Tierney-Ginn
Workshops are an important part of the IFPA annual meeting as they allow for discussion of specialized topics. At IFPA meeting 2016 there were twelve themed workshops, four of which are summarized in this report. These workshops covered innovative technologies applied to new and traditional areas of placental research: 1) genomic communication; 2) bioinformatics; 3) trophoblast biology and pathology; 4) placental transport systems.
January 11, 2017: Placenta
https://www.readbyqxmd.com/read/28107695/antibacterial-activity-computational-analysis-and-host-toxicity-study-of-thymol-sulfonamide-conjugates
#13
Shasank S Swain, Sudhir K Paidesetty, Rabindra N Padhy
Methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococcus faecalis (VRE) are notorious pathogenic multidrug resistant (MDR) bacteria in both hospital and community sectors, and today the first antibacterial drug sulfamethoxazole is ineffective. The monoterpene phenol, thymol was conjugated with seven sulfa drug derivatives individually, adopting the dye-azo synthesis protocol, and conjugates were characterized using spectral analysis techniques such as, UV, FTIR, MS, HPLC, (1)H NMR, (13)C NMR and SEM...
January 17, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28107688/sequencing-and-de-novo-assembly-of-visceral-mass-transcriptome-of-the-critically-endangered-land-snail-satsuma-myomphala-annotation-and-ssr-discovery
#14
Se Won Kang, Bharat Bhusan Patnaik, Hee-Ju Hwang, So Young Park, Jong Min Chung, Dae Kwon Song, Hongray Howrelia Patnaik, Jae Bong Lee, Changmu Kim, Soonok Kim, Young-Su Park, Hong Seog Park, Seung-Hwan Park, Yeon Soo Han, Jun Sang Lee, Yong Seok Lee
Satsuma myomphala is critically endangered through loss of natural habitats, predation by natural enemies, and indiscriminate collection. It is a protected species in Korea but lacks genomic resources for an understanding of varied functional processes attributable to evolutionary success under natural habitats. For assessing the genetic information of S. myomphala, we performed for the first time, de novo transcriptome sequencing and functional annotation of expressed sequences using Illumina Next-Generation Sequencing (NGS) platform and bioinformatics analysis...
October 29, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28107418/nf-kappab-is-involved-in-the-regulation-of-emt-genes-in-breast-cancer-cells
#15
Bruno R B Pires, Andre L Mencalha, Gerson M Ferreira, Waldemir F de Souza, José A Morgado-Díaz, Amanda M Maia, Stephany Corrêa, Eliana S F W Abdelhay
The metastatic process in breast cancer is related to the expression of the epithelial-to-mesenchymal transition transcription factors (EMT-TFs) SNAIL, SLUG, SIP1 and TWIST1. EMT-TFs and nuclear factor-κB (NF-κB) activation have been associated with aggressiveness and metastatic potential in carcinomas. Here, we sought to examine the role of NF-κB in the aggressive properties and regulation of EMT-TFs in human breast cancer cells. Blocking NF-κB/p65 activity by reducing its transcript and protein levels (through siRNA-strategy and dehydroxymethylepoxyquinomicin [DHMEQ] treatment) in the aggressive MDA-MB-231 and HCC-1954 cell lines resulted in decreased invasiveness and migration, a downregulation of SLUG, SIP1, TWIST1, MMP11 and N-cadherin transcripts and an upregulation of E-cadherin transcripts...
2017: PloS One
https://www.readbyqxmd.com/read/28107202/correlation-of-five-secretory-proteins-with-the-nasopharyngeal-carcinoma-metastasis-and-the-clinical-applications
#16
Ya Tao, Kun Wang, Zhen Chen, Lu Long, Qiong Wu, Facai Cui, Lepan Zhu, Manlin Xiang, Yuan Jiang, Yunlai Liang, Shiyang Qiu, Zhiqiang Xiao, Bin Yi
In our previous study, five different secretory proteins, including GSN, ADAMTSL4, CALR, PPIA and TXN, have been identified to be associated with the nasopharyngeal carcinoma (NPC) metastasis.In this work, the 5 proteins were further investigated. Bioinformatics analysis suggested that they might play an important role in the process of NPC development.Western blotting analysis showed that all of these 5 targets could be secreted into extracellular by both high metastatic NPC 5-8F cells and non-metastatic NPC 6-10B cells...
January 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28106390/tubulin-binding-and-polymerization-promoting-properties-of-tppp-proteins-are-evolutionarily-conserved
#17
Judit Oláh, Tibor Szénási, Adél Szabó, Kinga Kovács, Péter Lőw, Mauro Stifanic, Ferenc Orosz
Tubulin Polymerization Promoting Proteins (TPPPs) constitute a new eukaryotic protein family. There are three TPPP paralogs in the human genome; denoted as TPPP1, TPPP2 and TPPP3. TPPP1 and TPPP3 are intrinsically unstructured proteins (IUPs) that bind and polymerize tubulin and stabilize microtubules but TPPP2 does not. Vertebrate TPPPs originated from the ancient invertebrate TPPP by two-round whole-genome-duplication thus it was an open question whether the tubulin/microtubule binding function of TPPP1 and TPPP3 is a newly acquired property or it was present in the invertebrate orthologs (generally one TPPP/species)...
January 20, 2017: Biochemistry
https://www.readbyqxmd.com/read/28106375/acinetodin-and-klebsidin-rna-polymerase-targeting-lasso-peptides-produced-by-human-isolates-of-acinetobacter-gyllenbergii-and-klebsiella-pneumoniae
#18
Mikhail Metelev, Anatolii Arseniev, Leah B Bushin, Konstantin Kuznedelov, Tatiana O Artamonova, Ruslan Kondratenko, Mikhail Khodorkovskii, Mohammad R Seyedsayamdost, Konstantin Severinov
We report the bioinformatic prediction and structural validation of two lasso peptides, acinetodin and klebsidin, encoded by the genomes of several human-associated strains of Acinetobacter and Klebsiella. Computation of the three-dimensional structures of these peptides using NMR NOESY constraints verifies that they contain a lasso motif. Despite the lack of sequence similarity to each other or to microcin J25, a prototypical lasso peptide and transcription inhibitor from Escherichia coli, acinetodin and klebsidin also inhibit transcript elongation by the E...
January 20, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28105979/human-dental-pulp-stem-cells-are-more-effective-than-human-bone-marrow-derived-mesenchymal-stem-cells-in-cerebral-ischemic-injury
#19
Miyeoun Song, Jae-Hyung Lee, Jinhyun Bae, Youngmin Bu, Eun-Cheol Kim
We compared the therapeutic effects and mechanism of transplanted human dental pulp stem cells (hDPSCs) and human bonemarrow-derived mesenchymal stem cells (hMSCs) in a stroke model of rats and an <i>in vitro</i> ischemic model. Both hDPSCs- and hMSCs- intravenously injected rats 24&#8201;h after middle cerebral artery occlusion showed improved functional recovery and reduced infarct volume versus control rats, but the hDPSCs group showed greater reduction in infarct volume than hMSCs. The positive area for the endothelial cell marker was greater in the lesion boundary areas in the hDPSCs group than with hMSCs...
January 20, 2017: Cell Transplantation
https://www.readbyqxmd.com/read/28105928/computer-aided-identification-of-a-hevein-like-antimicrobial-peptide-of-bell-pepper-leaves-for-biotechnological-use
#20
Patrícia Dias Games, Elói Quintas Gonçalves daSilva, Meire de Oliveira Barbosa, Hebréia Oliveira Almeida-Souza, Patrícia Pereira Fontes, Marcos Jorge deMagalhães-Jr, Paulo Roberto Gomes Pereira, Maura Vianna Prates, Gloria Regina Franco, Alessandra Faria-Campos, Sérgio Vale Aguiar Campos, Maria Cristina Baracat-Pereira
BACKGROUND: Antimicrobial peptides from plants present mechanisms of action that are different from those of conventional defense agents. They are under-explored but have a potential as commercial antimicrobials. Bell pepper leaves ('Magali R') are discarded after harvesting the fruit and are sources of bioactive peptides. This work reports the isolation by peptidomics tools, and the identification and partially characterization by computational tools of an antimicrobial peptide from bell pepper leaves, and evidences the usefulness of records and the in silico analysis for the study of plant peptides aiming biotechnological uses...
December 15, 2016: BMC Genomics
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