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https://www.readbyqxmd.com/read/29245011/oncogenic-role-of-thor-a-conserved-cancer-testis-long-non-coding-rna
#1
Yasuyuki Hosono, Yashar S Niknafs, John R Prensner, Matthew K Iyer, Saravana M Dhanasekaran, Rohit Mehra, Sethuramasundaram Pitchiaya, Jean Tien, June Escara-Wilke, Anton Poliakov, Shih-Chun Chu, Sahal Saleh, Keerthana Sankar, Fengyun Su, Shuling Guo, Yuanyuan Qiao, Susan M Freier, Huynh-Hoa Bui, Xuhong Cao, Rohit Malik, Timothy M Johnson, David G Beer, Felix Y Feng, Weibin Zhou, Arul M Chinnaiyan
Large-scale transcriptome sequencing efforts have vastly expanded the catalog of long non-coding RNAs (lncRNAs) with varying evolutionary conservation, lineage expression, and cancer specificity. Here, we functionally characterize a novel ultraconserved lncRNA, THOR (ENSG00000226856), which exhibits expression exclusively in testis and a broad range of human cancers. THOR knockdown and overexpression in multiple cell lines and animal models alters cell or tumor growth supporting an oncogenic role. We discovered a conserved interaction of THOR with IGF2BP1 and show that THOR contributes to the mRNA stabilization activities of IGF2BP1...
December 14, 2017: Cell
https://www.readbyqxmd.com/read/29244859/the-second-molecular-epidemiological-study-of-hiv-infection-in-mongolia-between-2010-and-2016
#2
Davaalkham Jagdagsuren, Tsunefusa Hayashida, Misao Takano, Erdenetuya Gombo, Setsen Zayasaikhan, Naomi Kanayama, Kiyoto Tsuchiya, Shinichi Oka
OBJECTIVE: Our previous 2005-2009 molecular epidemiological study in Mongolia identified a hot spot of HIV-1 transmission in men who have sex with men (MSM). To control the infection, we collaborated with NGOs to promote safer sex and HIV testing since mid-2010. In this study, we carried out the second molecular epidemiological survey between 2010 and 2016 to determine the status of HIV-1 infection in Mongolia. METHODS: The study included 143 new cases of HIV-1 infection...
2017: PloS One
https://www.readbyqxmd.com/read/29244808/fgmd-a-novel-approach-for-functional-gene-module-detection-in-cancer
#3
Daeyong Jin, Hyunju Lee
With the increasing availability of multi-dimensional biological datasets for the same samples (i.e., gene expression, microRNAs, copy numbers, mutations, methylations), it has now become possible to systematically understand the regulatory mechanisms operating in a cancer cell. For this task, it is important to discover a set of co-expressed genes with functions, representing a so-called functional gene module, because co-expressed genes tend to be co-regulated by the same regulators, including transcription factors, microRNAs, and copy number aberrations...
2017: PloS One
https://www.readbyqxmd.com/read/29244728/transcriptome-analysis-of-paraburkholderia-phymatum-under-nitrogen-starvation-and-during-symbiosis-with-phaseolus-vulgaris
#4
Martina Lardi, Yilei Liu, Gabriela Purtschert, Samanta Bolzan de Campos, Gabriella Pessi
Paraburkholderia phymatum belongs to the β-subclass of proteobacteria. It has recently been shown to be able to nodulate and fix nitrogen in symbiosis with several mimosoid and papilionoid legumes. In contrast to the symbiosis of legumes with α-proteobacteria, very little is known about the molecular determinants underlying the successful establishment of this mutualistic relationship with β-proteobacteria. In this study, we performed an RNA-sequencing (RNA-seq) analysis of free-living P. phymatum growing under nitrogen-replete and -limited conditions, the latter partially mimicking the situation in nitrogen-deprived soils...
December 15, 2017: Genes
https://www.readbyqxmd.com/read/29244143/impact-of-hiv-1-minority-variants-on-the-virus-response-to-a-rilpivirine-based-first-line-regimen
#5
Stéphanie Raymond, Florence Nicot, Coralie Pallier, Pantxika Bellecave, Anne Maillard, Mary Anne Trabaud, Laurence Morand-Joubert, Audrey Rodallec, Corinne Amiel, Thomas Mourez, Laurence Bocket, Agnès Beby-Defaux, Magali Bouvier-Alias, Sidonie Lambert-Niclot, Charlotte Charpentier, Brice Malve, Audrey Mirand, Julia Dina, Hélène Le Guillou-Guillemette, Stéphanie Marque-Juillet, Anne Signori-Schmuck, Francis Barin, Ali Si-Mohamed, Véronique Avettand Fenoel, Catherine Roussel, Vincent Calvez, Karine Saune, Anne Geneviève Marcelin, Christophe Rodriguez, Diane Descamps, Jacques Izopet
Background: Minority resistant variants of HIV-1 could influence the virological response to treatment based on non-nucleoside reverse transcriptase (RT) inhibitors. Data on minority rilpivirine-resistant variants are scarce. This study used next-generation sequencing (NGS) to identify patients harbouring minority resistant variants to nucleos(t)ide and non-nucleoside RT inhibitors and to assess their influence on the virological response (VR). Methods: All the subjects, 541 HIV-1-infected patients being treated at 24 French virology laboratories, started their first line regimen containing rilpivirine between 2012 and 2015...
December 13, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29244142/an-autofluorescence-based-method-for-the-isolation-of-highly-purified-ventricular-cardiomyocytes
#6
Veronica Larcher, Paolo Kunderfranco, Marco Vacchiano, Pierluigi Carullo, Marco Erreni, Irene Salamon, Federico Simone Colombo, Enrico Lugli, Marta Mazzola, Achille Anselmo, Gianluigi Condorelli
Aims: The aim of our study was to set up a simple and reliable isolation method of living ventricular cardiomyocytes (vCMs) for molecular and biological studies. Methods: A standard technique for the retrograde perfusion of an enzymatic solution was used to isolate cardiac cells from adult mouse heart. Fluorescence-activated cell sorting (FACS) on adult murine cardiac ventricle cells was performed, comparing the intrinsic autofluorescence in the FITC channel and the forward scatter (FSC) parameter in order to isolate highly fluorescent cells...
December 13, 2017: Cardiovascular Research
https://www.readbyqxmd.com/read/29244011/a-deep-learning-method-for-lincrna-detection-using-auto-encoder-algorithm
#7
Ning Yu, Zeng Yu, Yi Pan
BACKGROUND: RNA sequencing technique (RNA-seq) enables scientists to develop novel data-driven methods for discovering more unidentified lincRNAs. Meantime, knowledge-based technologies are experiencing a potential revolution ignited by the new deep learning methods. By scanning the newly found data set from RNA-seq, scientists have found that: (1) the expression of lincRNAs appears to be regulated, that is, the relevance exists along the DNA sequences; (2) lincRNAs contain some conversed patterns/motifs tethered together by non-conserved regions...
December 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29244009/inference-of-genetic-relatedness-between-viral-quasispecies-from-sequencing-data
#8
Olga Glebova, Sergey Knyazev, Andrew Melnyk, Alexander Artyomenko, Yury Khudyakov, Alex Zelikovsky, Pavel Skums
BACKGROUND: RNA viruses such as HCV and HIV mutate at extremely high rates, and as a result, they exist in infected hosts as populations of genetically related variants. Recent advances in sequencing technologies make possible to identify such populations at great depth. In particular, these technologies provide new opportunities for inference of relatedness between viral samples, identification of transmission clusters and sources of infection, which are crucial tasks for viral outbreaks investigations...
December 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29244008/a-divide-and-conquer-algorithm-for-large-scale-de-novo-transcriptome-assembly-through-combining-small-assemblies-from-existing-algorithms
#9
Sing-Hoi Sze, Jonathan J Parrott, Aaron M Tarone
BACKGROUND: While the continued development of high-throughput sequencing has facilitated studies of entire transcriptomes in non-model organisms, the incorporation of an increasing amount of RNA-Seq libraries has made de novo transcriptome assembly difficult. Although algorithms that can assemble a large amount of RNA-Seq data are available, they are generally very memory-intensive and can only be used to construct small assemblies. RESULTS: We develop a divide-and-conquer strategy that allows these algorithms to be utilized, by subdividing a large RNA-Seq data set into small libraries...
December 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29243809/obesity-induced-mitochondrial-dysfunction-in-porcine-adipose-tissue-derived-mesenchymal-stem-cells
#10
Yu Meng, Alfonso Eirin, Xiang-Yang Zhu, Hui Tang, Pritha Chanana, Amir Lerman, Andre J van Wijnen, Lilach O Lerman
BACKGROUND: Transplantation of autologous mesenchymal stem cells (MSCs) may be a viable option for treatment of several diseases. MSCs efficacy depends on adequate function of their mitochondria, which might be impaired in a noxious milieu. OBJECTIVES: We hypothesized that obesity compromises MSCs mitochondrial structure and function, possibly via micro-RNA (miRNA)-based mechanisms. METHODS: MSCs were collected from swine abdominal adipose tissue after 16 weeks of Lean or Obese diet (n = 7 each)...
December 15, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29243374/molecular-classification-of-autofluorescence-excision-margins-in-oral-potentially-malignant-disorders
#11
Camile S Farah, Farzaneh Kordbacheh, Keziah John, Nigel Bennett, Simon A Fox
OBJECTIVE: To define molecular differences between autofluorescence and white light defined excision margins in oral potentially malignant disorders (OPMD) using transcriptome expression profiles. MATERIALS AND METHODS: Excisional biopsy specimens were taken from 11 patients at three different sites for each lesion: centre, white light margin, and autofluorescence margin. The lesions were diagnosed histopathologically as oral epithelial dysplasia, oral lichenoid dysplasia, oral lichen planus or other...
December 14, 2017: Oral Diseases
https://www.readbyqxmd.com/read/29242829/molecular-mechanisms-for-microbe-recognition-and-defense-by-the-red-seaweed-laurencia-dendroidea
#12
Louisi Souza de Oliveira, Diogo Antonio Tschoeke, Ana Carolina Rubem Magalhães Lopes, Daniela Bueno Sudatti, Pedro Milet Meirelles, Cristiane C Thompson, Renato Crespo Pereira, Fabiano L Thompson
The ability to recognize and respond to the presence of microbes is an essential strategy for seaweeds to survive in the marine environment, but understanding of molecular seaweed-microbe interactions is limited. Laurencia dendroidea clones were inoculated with the marine bacterium Vibrio madracius. The seaweed RNA was sequenced, providing an unprecedentedly high coverage of the transcriptome of Laurencia, and the gene expression levels were compared between control and inoculated samples after 24, 48, and 72 h...
November 2017: MSphere
https://www.readbyqxmd.com/read/29242757/differential-gene-transcription-of-extracellular-matrix-components-in-response-to-in-vivo-corneal-crosslinking-cxl-in-rabbit-corneas
#13
Sabine Kling, Arthur Hammer, Emilio A Torres Netto, Farhad Hafezi
Purpose: We studied changes in gene transcription after corneal crosslinking (CXL) in the rabbit cornea in vivo and identified potential molecular signaling pathways. Methods: A total of 15 corneas of eight male New-Zealand-White rabbits were de-epithelialized and equally divided into five groups. Group 1 served as an untreated control. Groups 2 to 5 were soaked with 0.1% riboflavin for 20 minutes, which in Groups 3 to 5 was followed by UV-A irradiation at a fluence of 5...
December 2017: Translational Vision Science & Technology
https://www.readbyqxmd.com/read/29242583/hybrid-splicing-minigene-and-antisense-oligonucleotides-as-efficient-tools-to-determine-functional-protein-rna-interactions
#14
Piotr Cywoniuk, Katarzyna Taylor, Łukasz J Sznajder, Krzysztof Sobczak
Alternative splicing is a complex process that provides a high diversity of proteins from a limited number of protein-coding genes. It is governed by multiple regulatory factors, including RNA-binding proteins (RBPs), that bind to specific RNA sequences embedded in a specific structure. The ability to predict RNA-binding regions recognized by RBPs using whole-transcriptome approaches can deliver a multitude of data, including false-positive hits. Therefore, validation of the global results is indispensable...
December 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29242501/high-throughput-rna-sequencing-reveals-distinct-gene-signatures-in-active-igg4-related-disease
#15
Brandon W Higgs, Yanying Liu, Jianping Guo, Yinong Sebastian, Chris Morehouse, Wei Zhu, Limin Ren, Mengru Liu, Yan Du, Guangyan Yu, Lingli Dong, Hong Hua, Pan Wei, Yi Wang, Zhengang Wang, Yihong Yao, Zhan-Guo Li
We aimed to characterize the molecular differences and effects from prednisone treatment among IgG4-related disease with salivary gland lesions (RD-SG), without SG lesions (RD-nonSG), and IgG4-related retroperitoneal fibrosis (RF). RNA sequencing was conducted on blood from 25 RD-SG, 11 RD-nonSG, 3 RF and 10 control subjects. Among these, 8 RD-nonSG and 12 RD-SG patients were subjected to treatment with prednisone and/or glucocorticoid-sparing agents. Six RD patients had a longitudinal time point. The mRNA levels of IgG4 and IgE, genes specific for Th2 cells, eosinophils, and neutrophils were over-expressed in RD-SG and RD-nonSG...
December 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29242457/the-complete-mitochondrial-genome-of-the-korean-endemic-millipede-i-anaulaciulus-i-i-koreanus-i-verhoeff-1937-with-notes-on-the-gene-arrangement-of-millipede-orders
#16
Hyung Jik Woo, Anh D Nguyen, Kuem Hee Jang, Eun Hwa Choi, Shi Hyun Ryu, Ui Wook Hwang
The millipede Anaulaciulus koreanus (Verhoeff, 1937), belonging to the family Julidae, is an endemic species of the Korean fauna. In this study, we sequence and annotate the mitochondrial genome of A. koreanus. The complete mitochondrial genome of this species is 14,916 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes (16S and 12S rRNA), and a large non-coding region. The genome has a very high A+T content (71.1%), less than of the species Brachycybe lecontii Wood, 1864 (order Platydesmida; 76...
October 10, 2017: Zootaxa
https://www.readbyqxmd.com/read/29242407/central-role-of-the-p53-pathway-in-the-noncoding-rna-response-to-oxidative-stress
#17
Paola Fuschi, Matteo Carrara, Christine Voellenkle, Jose Manuel Garcia-Manteiga, Paolo Righini, Biagina Maimone, Elena Sangalli, Francesco Villa, Claudia Specchia, Mario Picozza, Giovanni Nano, Carlo Gaetano, Gaia Spinetti, Annibale A Puca, Alessandra Magenta, Fabio Martelli
Oxidative stress plays a fundamental role in many conditions. Specifically, redox imbalance inhibits endothelial cell (EC) growth, inducing cell death and senescence. We used global transcriptome profiling to investigate the involvement of noncoding-RNAs in these phenotypes. By RNA-sequencing, transcriptome changes were analyzed in human ECs exposed to H2O2, highlighting a pivotal role of p53-signaling. Bioinformatic analysis and validation in p53-silenced ECs, identified several p53-targets among both mRNAs and long noncoding-RNAs (lncRNAs), including MALAT1 and NEAT1...
December 12, 2017: Aging
https://www.readbyqxmd.com/read/29242298/a-29-gene-and-cytogenetic-score-for-the-prediction-of-resistance-to-induction-treatment-in-acute-myeloid-leukemia
#18
Tobias Herold, Vindi Jurinovic, Aarif M N Batcha, Stefanos A Bamopoulos, Maja Rothenberg-Thurley, Bianka Ksienzyk, Luise Hartmann, Philipp A Greif, Julia Phillippou-Massier, Stefan Krebs, Helmut Blum, Susanne Amler, Stephanie Schneider, Nikola Konstandin, Maria Cristina Sauerland, Dennis Görlich, Wolfgang E Berdel, Bernhard J Wörmann, Johanna Tischer, Marion Subklewe, Stefan K Bohlander, Jan Braess, Wolfgang Hiddemann, Klaus H Metzeler, Ulrich Mansmann, Karsten Spiekermann
Primary therapy resistance is a major problem in acute myeloid leukemia treatment. We set out to develop a powerful and robust predictor for therapy resistance for intensively treated adult patients. We used two large gene expression data sets (n=856) to develop a predictor of therapy resistance, which was validated in an independent cohort analyzed by RNA sequencing (n=250). In addition to gene expression markers, standard clinical and laboratory variables as well as the mutation status of 68 genes were considered during construction of the model...
December 14, 2017: Haematologica
https://www.readbyqxmd.com/read/29242273/rbpj-mediates-uterine-repair-in-the-mouse-and-is-reduced-in-women-with-recurrent-pregnancy-loss
#19
Michael R Strug, Ren-Wei Su, Tae Hoon Kim, Alessandro Mauriello, Carlo Ticconi, Bruce A Lessey, Steven L Young, Jeong Mook Lim, Jae-Wook Jeong, Asgerally T Fazleabas
Unexplained recurrent pregnancy loss (uRPL) is associated with repeated embryo loss and endometrial repair with elevated endometrial expression of inflammatory cytokines, including IFN-γ. Notch signaling through its transcription factor recombination signal binding protein Jκ (RBPJ) regulates mechanisms including the immune response and repair after tissue injury. Initially, null mutation of RBPJ in the mouse uterus (Pgrcre/+Rbpjf/f ; Rbpj c-KO) results in subfertility, but we have found that these mice become infertile after pregnancy as a result of dysfunctional postpartum uterine repair, including delayed endometrial epithelial and myometrial regeneration...
December 14, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29242225/first-report-of-a-whole-genome-shotgun-sequence-of-a-clinical-enterococcus-faecalis-sequence-type-6-strain-from-south-africa
#20
Nontombi Marylucy Mbelle, Nontuthuko Excellent Maningi, Vhudzani Tshisevhe, Lesedi Modipane, Daniel Gyamfi Amoako, John Osei Sekyere
Enterococcus faecalis is a lactic acid-producing Gram-positive bacterium commonly found in the intestinal tract of humans and animals; it is implicated in multidrug-resistant nosocomial infections. The draft genome of this E. faecalis sequence type 6 (ST6) strain consists of 3,215,228 bp, with 37.20% GC content, 3,048 predicted coding sequences, and 61 RNA genes.
December 14, 2017: Genome Announcements
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