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https://www.readbyqxmd.com/read/29346801/early-gene-expression-profile-in-retinal-ganglion-cell-layer-after-optic-nerve-crush-in-mice
#1
Satoru Ueno, Azusa Yoneshige, Yoshiki Koriyama, Man Hagiyama, Yoshikazu Shimomura, Akihiko Ito
Purpose: Optic nerve crush (ONC) induces retinal ganglion cell (RGC) death, which causes vision loss in glaucoma. To investigate early events leading to apoptosis of RGCs, we performed gene expression analysis of injured retinas in the period before RGC loss. Methods: The temporal changes of gene profiles at 0, 1, and 4 days after ONC were determined by DNA microarray. To verify the gene expression changes in RGCs, we enriched RGCs by laser-captured microdissection and performed real-time RT-PCR of 14 selected genes...
January 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29346775/brd4-promotes-dna-repair-and-mediates-the-formation-of-tmprss2-erg-gene-rearrangements-in-prostate-cancer
#2
Xiangyi Li, GuemHee Baek, Susmita G Ramanand, Adam Sharp, Yunpeng Gao, Wei Yuan, Jon Welti, Daniel N Rodrigues, David Dolling, Ines Figueiredo, Semini Sumanasuriya, Mateus Crespo, Adam Aslam, Rui Li, Yi Yin, Bipasha Mukherjee, Mohammed Kanchwala, Ashley M Hughes, Wendy S Halsey, Cheng-Ming Chiang, Chao Xing, Ganesh V Raj, Sandeep Burma, Johann de Bono, Ram S Mani
BRD4 belongs to the bromodomain and extraterminal (BET) family of chromatin reader proteins that bind acetylated histones and regulate gene expression. Pharmacological inhibition of BRD4 by BET inhibitors (BETi) has indicated antitumor activity against multiple cancer types. We show that BRD4 is essential for the repair of DNA double-strand breaks (DSBs) and mediates the formation of oncogenic gene rearrangements by engaging the non-homologous end joining (NHEJ) pathway. Mechanistically, genome-wide DNA breaks are associated with enhanced acetylation of histone H4, leading to BRD4 recruitment, and stable establishment of the DNA repair complex...
January 16, 2018: Cell Reports
https://www.readbyqxmd.com/read/29346762/transcriptome-and-dna-methylome-analysis-in-a-mouse-model-of-diet-induced-obesity-predicts-increased-risk-of-colorectal-cancer
#3
Ruifang Li, Sara A Grimm, Deepak Mav, Haiwei Gu, Danijel Djukovic, Ruchir Shah, B Alex Merrick, Daniel Raftery, Paul A Wade
Colorectal cancer (CRC) tends to occur at older age; however, CRC incidence rates have been rising sharply among young age groups. The increasing prevalence of obesity is recognized as a major risk, yet the mechanistic underpinnings remain poorly understood. Using a diet-induced obesity mouse model, we identified obesity-associated molecular changes in the colonic epithelium of young and aged mice, and we further investigated whether the changes were reversed after weight loss. Transcriptome analysis indicated that obesity-related colonic cellular metabolic switch favoring long-chain fatty acid oxidation happened in young mice, while obesity-associated downregulation of negative feedback regulators of pro-proliferative signaling pathways occurred in older mice...
January 16, 2018: Cell Reports
https://www.readbyqxmd.com/read/29346705/effect-of-dys-1-mutation-on-gene-expression-profile-in-space-flown-c-elegans
#4
Dan Xu, Ying Gao, Lin Guo, Chenggang Lin, Yeqing Sun
INTRODUCTION: Dystrophin-like dys-1 gene expression increases in the body-wall muscles of Caenorhabditis elegans (C. elegans) after spaceflight. Here, we utilized a dys-1(cx18) mutant to analyze the molecular adaptive responses of C. elegans to spaceflight. METHODS: DNA microarrays were performed to identify differentially expressed genes between wild-type and dys-1 mutant worms after spaceflight. We performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses, predicted human diseases and screened out key genes for human muscle diseases with NextBio...
January 18, 2018: Muscle & Nerve
https://www.readbyqxmd.com/read/29346669/regulation-of-mitotic-recombination-between-dna-repeats-in-centromeres
#5
Faria Zafar, Akiko K Okita, Atsushi T Onaka, Jie Su, Yasuhiro Katahira, Jun-Ichi Nakayama, Tatsuro S Takahashi, Hisao Masukata, Takuro Nakagawa
No abstract text is available yet for this article.
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29346632/diagnostic-and-prognostic-value-of-jc-virus-dna-in-plasma-in-progressive-multifocal-leukoencephalopathy
#6
Francesca Ferretti, Arabella Bestetti, Constantin T Yiannoutsos, Beverly S Musick, Simonetta Gerevini, Laura Passeri, Simona Bossolasco, Antonio Boschini, Diego Franciotta, Adriano Lazzarin, Paola Cinque
Background: Progressive multifocal leukoencephalopathy (PML) is a severe demyelinating disease caused by the polyomavirus JC (JCV) affecting subjects with impaired immune system. While JCV-DNA detection in cerebrospinal fluid (CSF) is diagnostic of PML, the clinical significance of plasma JCV-DNA is still uncertain. Methods: We retrospectively analyzed plasma samples drawn from patients with PML close to disease onset, and controls without PML. In PML patients, we compared plasma JCV DNA detection and levels to: JCV DNA in the other biological samples, clinical and laboratory parameters and patients' survival...
January 15, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29346625/complete-genomic-and-transcriptional-landscape-analysis-using-third-generation-sequencing-a-case-study-of-saccharomyces-cerevisiae-cen-pk113-7d
#7
Piroon Jenjaroenpun, Thidathip Wongsurawat, Rui Pereira, Preecha Patumcharoenpol, David W Ussery, Jens Nielsen, Intawat Nookaew
Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along the chromosomes and short read lengths of second-generation sequencing. Saccharomyces cerevisiae strain CEN.PK113-7D, widely used as a model organism and a cell factory, was selected for this study to demonstrate the superior capability of very long sequence reads for de novo genome assembly. We generated long reads using two common third-generation sequencing technologies (Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)) and used short reads obtained using Illumina sequencing for error correction...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29346604/unique-genetic-profiles-from-cerebrospinal-fluid-cell-free-dna-in-leptomeningeal-metastases-of-egfr-mutant-non-small-cell-lung-cancer-a-new-medium-of-liquid-biopsy
#8
Y S Li, B Y Jiang, J J Yang, X C Zhang, Z Zhang, J Y Ye, W Z Zhong, H Y Tu, H J Chen, Z Wang, C R Xu, B C Wang, H J Du, S Chuai, H Han-Zhang, J Su, Q Zhou, X N Yang, W B Guo, H H Yan, Y H Liu, L X Yan, B Huang, M M Zheng, Y L Wu
Background: Leptomeningeal metastases (LM) are more frequent in non-small cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) mutations. Due to limited access to leptomeningeal lesions, the purpose of this study was to explore the potential role of cerebrospinal fluid (CSF) as a source of liquid biopsy in patients with LM. Patients and methods: Primary tumor, CSF, and plasma in NSCLC with LM were tested by next-generation sequencing. In total, 45 patients with suspected LM underwent lumbar puncture, and those with EGFR mutations diagnosed with LM were enrolled...
January 15, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29346578/effect-of-daidzein-and-equol-on-dna-replication-in-mcf-7-cells
#9
Mako Tsuji, Tomoki Tanaka, Ryosuke Nagashima, Yuka Sagisaka, Yuko Tousen, Yoriko Nishide, Yoshiko Ishimi, Yukio Ishimi
It has been reported that daidzein and equol stimulate DNA replication and proliferation of MCF-7 cells. However, their molecular mechanisms of action are still unclear. We examined the effects of daidzein and equol on DNA replication of MCF-7 cells, focusing on MCM2-7 proteins, which function as the replicative helicase. In the presence of either 1 μM of daidzein or equol, the number of cells in S-phase, which was determined by detecting bromodeoxyuridine incorporated into replicated DNA, almost doubled...
January 15, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/29346571/natural-course-of-htlv-1-proviral-dna-levels-in-carriers-during-pregnancy
#10
Naoki Fuchi, Kiyonori Miura, Takashi Tsukiyama, Daisuke Sasaki, Kaori Ishihara, Kazuto Tsuruda, Hiroo Hasegawa, Shoko Miura, Katsumi Yanagihara, Hideaki Masuzaki
The measurement of human T-cell leukemia virus type 1 (HTLV-1) proviral DNA levels using polymerase chain reaction has been beneficial for confirming HTLV-1 infection during pregnancy. However, the influence of pregnancy on HTLV-1 infection and proviral DNA levels among pregnant women with HTLV-1 has not been clarified. We prospectively gathered blood samples from 36 pregnant women who were previously diagnosed as HTLV-1 carriers and sequentially measured their proviral DNA levels. The HTLV-1 proviral DNA levels remained in a plateau during pregnancy but were elevated after delivery...
January 16, 2018: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29346513/pancancer-analysis-identifies-prognostic-high-apobec1-expression-level-implicated-in-cancer-in-frame-insertions-and-deletions
#11
Ahmadreza Niavarani, Asieh Shahrabi Farahani, Maryam Sharafkhah, Minoo Rassoulzadegan
Genome insertions and deletions (indels) show tremendous functional impacts despite they are much less common than single nucleotide variants, which are at the center of studies assessing cancer mutational signatures. We studied 8,891 tumor samples of 32 types from The Cancer Genome Atlas in order to explore those genes which are potentially implicated in cancer indels. Survival analysis identified in-frame indels as the most important variants predicting adverse outcome. Transcriptome-wide association study identified 16 genes overexpressed in both tumor samples and tumor types with high number of in-frame indels, of whom four (APOBEC1, BCL2L15, FOXL1, and PDX1) were identified with gene products distributed within the nucleus...
January 13, 2018: Carcinogenesis
https://www.readbyqxmd.com/read/29346508/oroxylin-a%C3%AF-a-natural-compound-mitigates-the-negative-effects-of-tnf%C3%AE-treated-acute-myelogenous-leukemia-cells
#12
Hui Li, Na Lu, Xiaoxuan Yu, Xiao Liu, Po Hu, Yu Zhu, Le Shen, Jingyan Xu, Zhiyu Li, Qinglong Guo, Hui Hui
Tumor necrosis factor alpha (TNFα) is a complicated cytokine which is involved in proliferation and differentiation of acute myelogenous leukemia (AML) cells through a poorly understood mechanism. Mechanistic studies indicate that TNFα induced binding of PI3K subunit p85α to N-terminal truncated nuclear receptor RXRα (tRXRα) proteins, and activated AKT. The activated PI3K/AKT pathway negatively regulated differentiation of AML cells through the up-regulation of c-Myc. In addition, TNFα also induced activation of nuclear factor κB (NF-κB), a nuclear transcription factor which was shown to promote cell proliferation...
January 13, 2018: Carcinogenesis
https://www.readbyqxmd.com/read/29346438/colonization-of-the-cervicovaginal-space-with-gardnerella-vaginalis-leads-to-local-inflammation-and-cervical-remodeling-in-pregnant-mice
#13
Luz-Jeannette Sierra, Amy G Brown, Guillermo O Barilá, Lauren Anton, Carrie E Barnum, Snehal S Shetye, Louis J Soslowsky, Michal A Elovitz
The role of the cervicovaginal (CV) microbiome in regulating cervical function during pregnancy is poorly understood. Gardnerella vaginalis (G. vaginalis) is the most common bacteria associated with the diagnosis of bacterial vaginosis (BV). While BV has been associated with preterm birth (PTB), clinical trials targeting BV do not decrease PTB rates. It remains unknown if G. vaginalis is capable of triggering molecular, biomechanical and cellular events that could lead to PTB. The objective of this study was to determine if cervicovaginal colonization with G...
2018: PloS One
https://www.readbyqxmd.com/read/29346433/vault-rnas-partially-induces-drug-resistance-of-human-tumor-cells-mcf-7-by-binding-to-the-rna-dna-binding-protein-psf-and-inducing-oncogene-gage6
#14
Jianjun Chen, Hui OuYang, Xuemei An, Shixi Liu
BACKGROUND: Vault is the largest nonicosahedral cytosolic nucleoprotein particle, which is widely involved in induction of chemoresistance and lead to failure in long-term chemotherapy. Vault contains three different major vault proteins (MVPs) and four vault RNAs paralogues (vtRNAs, vtRNA1-1, vtRNA1-2, vtRNA1-3 and vtRNA2-1). Disruption of the MVPs do not induce hypersensitivity while expression of vtRNAs contributes to cells' drug resistance, indicates that vtRNAs, but not MVPs play an important role in causing drug resistance...
2018: PloS One
https://www.readbyqxmd.com/read/29346412/a-comparative-analysis-of-preservation-techniques-for-the-optimal-molecular-detection-of-hookworm-dna-in-a-human-fecal-specimen
#15
Marina Papaiakovou, Nils Pilotte, Ben Baumer, Jessica Grant, Kristjana Asbjornsdottir, Fabian Schaer, Yan Hu, Raffi Aroian, Judd Walson, Steven A Williams
BACKGROUND: Proper collection and storage of fecal samples is necessary to guarantee the subsequent reliability of DNA-based soil-transmitted helminth diagnostic procedures. Previous research has examined various methods to preserve fecal samples for subsequent microscopic analysis or for subsequent determination of overall DNA yields obtained following DNA extraction. However, only limited research has focused on the preservation of soil-transmitted helminth DNA in stool samples stored at ambient temperature or maintained in a cold chain for extended periods of time...
January 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29346402/gene-regulation-in-kluyveromyces-marxianus-in-the-context-of-chromosomes
#16
Du Toit W P Schabort, Stephanus G Kilian, James C du Preez
Eukaryotes, including the unicellular eukaryotes such as yeasts, employ multiple levels of gene regulation. Regulation of chromatin structure through chromatin compaction cascades, and influenced by transcriptional insulators, might play a role in the coordinated regulation of genes situated at adjacent loci and expressed as a co-regulated cluster. Subtelomeric gene silencing, which has previously been described in the yeast Saccharomyces cerevisiae, is an example of this phenomenon. Transcription from a common regulatory element located around a shared intergenic region is another factor that could coordinate the transcription of genes at adjacent loci...
2018: PloS One
https://www.readbyqxmd.com/read/29346345/the-cytosolic-sensor-sting-is-required-for-intestinal-homeostasis-and-control-of-inflammation
#17
M C C Canesso, L Lemos, T C Neves, F M Marim, T B R Castro, É S Veloso, C P Queiroz, J Ahn, H C Santiago, F S Martins, J Alves-Silva, E Ferreira, D C Cara, A T Vieira, G N Barber, S C Oliveira, A M C Faria
STING (stimulator of interferon genes) is a cytosolic sensor for cyclic dinucleotides and also an adaptor molecule for intracellular DNA receptors. Although STING has important functions in the host defense against pathogens and in autoimmune diseases, its physiological relevance in intestinal homeostasis is largely unknown. In this study, we show that STING-/- mice presented defective protective mechanisms of intestinal mucosa, including decreased number of goblet cells, diminished mucus production, and lower levels of secretory IgA, when compared with wild-type (WT) mice...
December 20, 2017: Mucosal Immunology
https://www.readbyqxmd.com/read/29346292/isoform-sequencing-and-state-of-art-applications-for-unravelling-complexity-of-plant-transcriptomes
#18
REVIEW
Dong An, Hieu X Cao, Changsheng Li, Klaus Humbeck, Wenqin Wang
Single-molecule real-time (SMRT) sequencing developed by PacBio, also called third-generation sequencing (TGS), offers longer reads than the second-generation sequencing (SGS). Given its ability to obtain full-length transcripts without assembly, isoform sequencing (Iso-Seq) of transcriptomes by PacBio is advantageous for genome annotation, identification of novel genes and isoforms, as well as the discovery of long non-coding RNA (lncRNA). In addition, Iso-Seq gives access to the direct detection of alternative splicing, alternative polyadenylation (APA), gene fusion, and DNA modifications...
January 18, 2018: Genes
https://www.readbyqxmd.com/read/29346287/development-of-zika-virus-vaccines
#19
REVIEW
Huda Makhluf, Sujan Shresta
Zika virus (ZIKV) is a mosquito-borne flavivirus that emerged as a global threat following the most recent outbreak in Brazil in 2015. ZIKV infection of pregnant women is associated with fetal abnormalities such as microcephaly, and infection of adults can lead to Guillain-Barré syndrome, an autoimmune disease characterized by neurological deficits. Although there are currently licensed vaccines for other flaviviruses, there remains an urgent need for preventative vaccines against ZIKV infection. Herein we describe the current efforts to accelerate the development of ZIKV vaccines using various platforms, including live attenuated virus, inactivated virus, DNA and RNA, viral vectors, and in silico-predicted immunogenic viral epitopes...
January 18, 2018: Vaccines
https://www.readbyqxmd.com/read/29346277/vaccinia-virus-in-blood-samples-of-humans-domestic-and-wild-mammals-in-brazil
#20
Marina G Peres, Thais S Bacchiega, Camila M Appolinário, Acácia F Vicente, Mateus de Souza Ribeiro Mioni, Bruna L D Ribeiro, Clóvis R S Fonseca, Vanessa C Pelícia, Fernando Ferreira, Graziele P Oliveira, Jonatas S Abrahão, Jane Megid
Outbreaks of Vaccinia virus (VACV) affecting cattle and humans have been reported in Brazil in the last 15 years, but the origin of outbreaks remains unknown. Although VACV DNA have been already detected in mice (Mus musculus), opossums (Didelphis albiventris) and dogs during VACV zoonotic outbreaks, no transmission to cattle or humans from any of these were reported during Brazilian outbreaks. In this work, we assessed the PCR positivity to VACV in blood samples of cows and other domestic mammals, wild rodents and other wild mammals, and humans from areas with or without VACV infection reports...
January 18, 2018: Viruses
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