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https://www.readbyqxmd.com/read/28323406/affinity-selection-mass-spectrometry-identifies-a-novel-antibacterial-rna-polymerase-inhibitor
#1
Scott S Walker, David Degen, Elliott Nickbarg, Donna Carr, Aileen Soriano, Mihir Baran Mandal, Ronald E Painter, Payal R Sheth, Li Xiao, Xinwei Sher, Nicholas Murgolo, Jing Su, David B Olsen, Richard H Ebright, Katherine Young
The growing prevalence of drug-resistant Gram-negative bacteria is a significant global threat to human health. Rifampicin, an RNA polymerase-targeting agent, is an important part of the antibacterial armamentarium; however the emergence of resistance requires that it be used against only certain infections and usually in combination with another antibiotic. While rifampicin has significant clinical limitations, it does show that bacterial RNA polymerase can be an effective target for antibacterial intervention...
March 21, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28318822/genome-wide-analysis-of-rna-polymerase-ii-termination-at-protein-coding-genes
#2
Carlo Baejen, Jessica Andreani, Phillipp Torkler, Sofia Battaglia, Bjoern Schwalb, Michael Lidschreiber, Kerstin C Maier, Andrea Boltendahl, Petra Rus, Stephanie Esslinger, Johannes Söding, Patrick Cramer
At the end of protein-coding genes, RNA polymerase (Pol) II undergoes a concerted transition that involves 3'-processing of the pre-mRNA and transcription termination. Here, we present a genome-wide analysis of the 3'-transition in budding yeast. We find that the 3'-transition globally requires the Pol II elongation factor Spt5 and factors involved in the recognition of the polyadenylation (pA) site and in endonucleolytic RNA cleavage. Pol II release from DNA occurs in a narrow termination window downstream of the pA site and requires the "torpedo" exonuclease Rat1 (XRN2 in human)...
March 6, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28318486/structural-basis-of-transcription-arrest-by-coliphage-hk022-nun-in-an-escherichia-coli-rna-polymerase-elongation-complex
#3
Jin Young Kang, Paul Dominic B Olinares, James Chen, Elizabeth A Campbell, Arkady Mustaev, Brian T Chait, Max E Gottesman, Seth A Darst
Coliphage HK022 Nun blocks superinfection by coliphage λ by stalling RNA polymerase (RNAP) translocation specifically on λΔNA.To provide a structural framework to understand how Nun blocks RNAP translocation, we determined structures of Escherichia coli RNAP ternary elongation complexes (TECs) with and without Nun by single-particle cryo-electron microscopy. Nun fits tightly into the TEC by taking advantage of gaps between the RNAP and the nucleic acids. The C-terminal segment of Nun interacts with the RNAP β and β' subunits inside the RNAP active site cleft as well as with nearly every element of the nucleic-acid scaffold, essentially crosslinking the RNAP and the nucleic acids to prevent translocation, a mechanism supported by the effects of Nun amino acid substitutions...
March 20, 2017: ELife
https://www.readbyqxmd.com/read/28318412/effects-of-lithium-and-2-4-dichlorophenol-on-zebrafish-circadian-rhythm-disorder-and-molecular-effects
#4
Bo Xiao, Li-Qiang Cui, Cheng Ding, Han Wang
The aim of this study was to investigate lithium and 2,4-dichlorophenol (2,4-DCP)-induced circadian rhythm disorder and their genome-wide effects in zebrafish. Zebrafish larvae were exposed to 250 ppm LiCl (n = 40) or 20 ppm 2,4-DCP. RNA was subsequently extracted and determined quantitatively. The mRNA levels of circadian clock-related genes, including clock1a, bmal1b, per2, and per1b, were determined. Microarray datasets were generated and the differentially expressed genes (DEGs) were identified. The mRNA levels of some upregulated and downregulated DEGs were examined by quantitative real-time polymerase chain reaction (RT-PCR)...
March 20, 2017: Zebrafish
https://www.readbyqxmd.com/read/28318165/-effects-of-rhoa-silencing-on-proliferation-of-tongue-squamous-cancer-cells
#5
Yan Guoxin, Fan Bing, Zou Ronghai, Zhang Jian, Sun Xiaofeng, Tong Lei, Wang Qimin, Han Jinhong, Lu Xufei, Wang Ying, Zhou Yuan, He Zongxuan, Liao Yixiang, Li Ning, Cao Lei, Chen Zhenggang
OBJECTIVE: This study investigated the effect of RhoA silencing through RNA interference on proliferation and growth of tongue cancer cells, as well as explored the possible mechanisms of this effect. METHODS: SSC-4 tongue cancer cells were cultured in vitro and then transfected with small interfering RNA to knock down RhoA expression. The tested cells were divided into three groups: experimental group (experimental group 1: transfected with RhoA-siRNA-1; experi-mental group 2: transfected with RhoA-siRNA-2), negative control group (transfected by random sequence NC-siRNA), and blank control group (transfected with Lipofectamine)...
December 1, 2016: Hua Xi Kou Qiang Yi Xue za Zhi, Huaxi Kouqiang Yixue Zazhi, West China Journal of Stomatology
https://www.readbyqxmd.com/read/28317540/endophytic-botryosphaeriaceae-including-five-new-species-associated-with-mangrove-trees-in-south-africa
#6
J Alexander Osorio, Casparus J Crous, Z Wilhelm de Beer, Michael J Wingfield, Jolanda Roux
Little is known regarding the fungi, especially fungal pathogens, associated with mangroves in Africa. This includes fungi in the Botryosphaeriaceae that comprise numerous opportunistic, stress-associated pathogens often associated with trees affected by environmental and anthropogenically generated stresses, such as those affecting mangroves. We investigated the occurrence of endophytic Botryosphaeriaceae along the entire distribution of mangroves in South Africa. Asymptomatic branches were collected from ten localities and six mangrove species...
April 2017: Fungal Biology
https://www.readbyqxmd.com/read/28316886/identification-of-dysregulated-genes-in-rheumatoid-arthritis-based-on-bioinformatics-analysis
#7
Ruihu Hao, Haiwei Du, Lin Guo, Fengde Tian, Ning An, Tiejun Yang, Changcheng Wang, Bo Wang, Zihao Zhou
BACKGROUND: Rheumatoid arthritis (RA) is a chronic auto-inflammatory disorder of joints. The present study aimed to identify the key genes in RA for better understanding the underlying mechanisms of RA. METHODS: The integrated analysis of expression profiling was conducted to identify differentially expressed genes (DEGs) in RA. Moreover, functional annotation, protein-protein interaction (PPI) network and transcription factor (TF) regulatory network construction were applied for exploring the potential biological roles of DEGs in RA...
2017: PeerJ
https://www.readbyqxmd.com/read/28316163/-effects-of-silencing-smad-ubiquitination-regulatory-factor-2-on-the-function-of-human-hypertrophic-scar-derived-fibroblasts
#8
Z Zhang, F Kuang, C L Liu, B Chen, W B Tang, X J Li
Objective: To explore the effects of silencing Smad ubiquitination regulatory factor 2 (Smurf2) on the secretion of transforming growth factor beta 1 (TGF-β(1)), alpha-smooth muscle actin (α-SMA), and collagen type Ⅰ by human hypertrophic scar-derived fibroblasts. Methods: The human normal skin-derived fibroblasts and hypertrophic scar-derived fibroblasts were cultured with explant culture technique from the normal skin and hypertrophic scar tissue, which was obtained from 9 patients with hypertrophic scars after burn...
March 20, 2017: Zhonghua Shao Shang za Zhi, Zhonghua Shaoshang Zazhi, Chinese Journal of Burns
https://www.readbyqxmd.com/read/28316131/evaluation-of-potential-rna-interference-target-genes-to-control-cotton-mealybug-phenacoccus-solenopsis-hemiptera-pseudococcuidae
#9
Arif M Khan, Muhammad Ashfaq, Azhar A Khan, Muhammad T Naseem, Shahid Mansoor
RNA interference (RNAi) of vital insect genes is a potential tool for targeted pest control. However, selection of the right target genes is a challenge because the RNAi efficacy is known to vary among insect species. Cotton mealybug, Phenacoccus solenopsis, is a phloem-feeding economically important crop pest. We evaluated the RNAi of two vital genes, Bursicon (PsBur) and V-ATPase (PsV-ATPase) as potential targets in P. solenopsis for its control. PCR fragments of PsBur and PsV-ATPase were amplified using cDNA synthesized from the total RNA...
March 18, 2017: Insect Science
https://www.readbyqxmd.com/read/28316018/a-novel-vitivirus-like-sequence-found-in-arracacia-xanthorrhiza-plants-by-high-throughput-sequencing
#10
Layssa M Oliveira, Anelise F Orílio, Alice K Inoue-Nagata, Tatsuya Nagata, Rosana Blawid
High throughput sequencing (HTS) is a very powerful tool for detecting and discovering novel viral-like sequences without prior knowledge of the sequence. Here we describe the complete genome of a new vitivirus-like sequence that was found in arracacha (Arracacia xanthorrhiza) plants using HTS technology. The complete genome sequence was validated by Sanger sequencing. The genomic organization of the new putative vitivirus resembles that of grapevine virus B (GVB) and grapevine virus D (GVD). The putative coat protein showed 41 to 49% identity with similar proteins of known vitiviruses, while the RNA-dependent RNA polymerase shared 52 to 55% identity with those encoded by grapevine vitiviruses...
March 18, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28316014/rescue-of-recombinant-newcastle-disease-virus-a-short-history-of-how-it-all-started
#11
REVIEW
Aidin Molouki, Ben Peeters
Reverse genetics of viruses has come a long way, and many recombinant viruses have been generated since the first successful "rescues" were reported in the late 1970s. Recombinant Newcastle disease virus (rNDV), a non-segmented negative-sense RNA virus (NSNSV), was first rescued in 1999 using a reverse genetics approach similar to that reported for other recombinant viruses of the order Mononegavirales a few years before. The route from an original NDV isolate to the generation of its recombinant counterpart requires many steps that have to be sequentially and carefully completed...
March 18, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28315476/comparative-analysis-of-protein-evolution-in-the-genome-of-pre-epidemic-and-epidemic-zika-virus
#12
Arunachalam Ramaiah, Lei Dai, Deisy Contreras, Sanjeev Sinha, Ren Sun, Vaithilingaraja Arumugaswami
Zika virus (ZIKV) causes microcephaly in congenital infection, neurological disorders, and poor pregnancy outcome and no vaccine is available for use in humans or approved. Although ZIKV was first discovered in 1947, the exact mechanism of virus replication and pathogenesis remains unknown. Recent outbreaks of Zika virus in the Americas clearly suggest a human-mosquito cycle or urban cycle of transmission. Understanding the conserved and adaptive features in the evolution of ZIKV genome will provide a hint on the mechanism of ZIKV adaptation to a new cycle of transmission...
March 14, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28315051/development-of-antibody-modified-chitosan-nanoparticles-for-the-targeted-delivery-of-sirna-across-the-blood-brain-barrier-as-a-strategy-for-inhibiting-hiv-replication-in-astrocytes
#13
Jijin Gu, Karam Al-Bayati, Emmanuel A Ho
RNA interference (RNAi)-mediated gene silencing offers a novel treatment and prevention strategy for human immunodeficiency virus (HIV) infection. HIV was found to infect and replicate in human brain cells and can cause neuroinfections and neurological deterioration. We designed dual-antibody-modified chitosan/small interfering RNA (siRNA) nanoparticles to deliver siRNA across the blood-brain barrier (BBB) targeting HIV-infected brain astrocytes as a strategy for inhibiting HIV replication. We hypothesized that transferrin antibody and bradykinin B2 antibody could specifically bind to the transferrin receptor (TfR) and bradykinin B2 receptor (B2R), respectively, and deliver siRNA across the BBB into astrocytes as potential targeting ligands...
March 17, 2017: Drug Delivery and Translational Research
https://www.readbyqxmd.com/read/28315015/characterization-of-a-novel-strain-of-botryosphaeria-dothidea-chrysovirus-1-from-the-apple-white-rot-pathogen-botryosphaeria-dothidea
#14
Zheng Ding, Tao Zhou, Li-Yun Guo
A novel strain of Botryosphaeria dothidea chrysovirus 1 was identified. It encodes a shortened RNA-dependent RNA polymerase and an elongated coat protein, and it might cause hypovirulence of the host fungal strain.
March 17, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28314879/a-study-on-associations-of-single-nucleotide-polymorphisms-within-h19-and-hox-transcript-antisense-rna-hotair-with-genetic-susceptibility-to-rheumatoid-arthritis-in-a-chinese-population
#15
Jian-Zhe Zhou, Jing-Jing Li, Dong-Jin Hua, Si-Chao Huang, Qing-Qing Sun, Hua Huang, Xia-Fei Xin, Han Cen
OBJECTIVE: The purpose of our study was to examine whether the H19 rs2839698, rs217727, and HOX transcript antisense RNA (HOTAIR) rs12826786 polymorphisms were associated with genetic susceptibility to rheumatoid arthritis (RA) in a Chinese population. METHODS: A total of 777 participants were enrolled in this study, including 328 RA patients and 449 healthy controls. The H19 rs2839698, rs217727, and HOTAIR rs12826786 polymorphisms were detected by the ligase detection reaction-polymerase chain reaction (LDR-PCR) technology...
March 17, 2017: Inflammation Research: Official Journal of the European Histamine Research Society ... [et Al.]
https://www.readbyqxmd.com/read/28306719/chromosome-19q13-disruption-alters-expressions-of-cyp2a7-mia-and-mia-rab4b-lncrna-and-contributes-to-fap-like-phenotype-in-apc-mutation-negative-familial-colorectal-cancer-patients
#16
Lai Fun Thean, Yu Hui Wong, Michelle Lo, Carol Loi, Min Hoe Chew, Choong Leong Tang, Peh Yean Cheah
Familial adenomatous polyposis (FAP) is an autosomal-dominantly inherited form of colorectal cancer (CRC) caused by mutation in the adenomatous polyposis coli (APC) gene. Our ability to exhaustively screen for APC mutations identify microsatellite-stable and APC-mutation negative familial CRC patients, enabling us to search for novel genes. We performed genome-wide scan on two affected siblings of one family and 88 ethnicity- and gender-matched healthy controls to identify deletions shared by the siblings. Combined loss of heterozygosity, copy number and allelic-specific copy number analysis uncovered 5 shared deletions...
2017: PloS One
https://www.readbyqxmd.com/read/28306505/identification-of-an-rna-polymerase-iii-regulator-linked-to-disease-associated-protein-aggregation
#17
Olga Sin, Tristan de Jong, Alejandro Mata-Cabana, Michelle Kudron, Mohamad Amr Zaini, Francesco A Aprile, Renée I Seinstra, Esther Stroo, Roméo Willinge Prins, Céline N Martineau, Hai Hui Wang, Wytse Hogewerf, Anne Steinhof, Erich E Wanker, Michele Vendruscolo, Cornelis F Calkhoven, Valerie Reinke, Victor Guryev, Ellen A A Nollen
Protein aggregation is associated with age-related neurodegenerative disorders, such as Alzheimer's and polyglutamine diseases. As a causal relationship between protein aggregation and neurodegeneration remains elusive, understanding the cellular mechanisms regulating protein aggregation will help develop future treatments. To identify such mechanisms, we conducted a forward genetic screen in a C. elegans model of polyglutamine aggregation and identified the protein MOAG-2/LIR-3 as a driver of protein aggregation...
March 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28304334/kdm2-family-members-are-regulated-by-hif-1-in-hypoxia
#18
Michael Batie, Jimena Druker, Laura D'Ignazio, Sonia Rocha
Hypoxia is not only a developmental cue but also a stress and pathological stimulus in many human diseases. The response to hypoxia at the cellular level relies on the activity of the transcription factor family, hypoxia inducible factor (HIF). HIF-1 is responsible for the acute response and transactivates a variety of genes involved in cellular metabolism, cell death, and cell growth. Here, we show that hypoxia results in increased mRNA levels for human lysine (K)-specific demethylase 2 (KDM2) family members, KDM2A and KDM2B, and also for Drosophila melanogaster KDM2, a histone and protein demethylase...
March 17, 2017: Cells
https://www.readbyqxmd.com/read/28304296/pcsk9-promotes-oxldl-induced-pc12-cell-apoptosis-through-the-bcl-2-bax-caspase-9-3-signaling-pathway
#19
Lu-Shan Liu, Xue-Qin Bai, Ya Gao, Qi Wu, Zhong Ren, Qing Li, Li-Hong Pan, Ni-Ya He, Juan Peng, Zhi-Han Tang
BACKGROUND: Hyperlipidemia is a risk factor for neurodegenerative diseases. Proprotein convertase subtilisin / Kexin type 9 (PCSK9) degrades hepatic low-density lipoprotein receptor (LDLR) to regulate lipid metabolism. It is unclear if PCSK9 plays a role in neurodegenerative diseases. OBJECTIVE: This study was designed to determine whether PCSK9 is crucial between hyperlipidemia and Alzheimer's disease. The interrelationship between PCSK9 and neuronal apoptosis was explored in PC12 cells in response to treatment with oxidized low-density lipoprotein (oxLDL)...
March 10, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28303856/effect-of-matrix-metallopeptidase-13-on-the-function-of-mouse-bone-marrow-derived-dendritic-cells
#20
Xiao-Dong Li, Xin-Rui Zhang, Zhi-Hao Li, Yang Yang, Duo Zhang, Heng Zheng, Shu-Ying Dong, Juan Chen, Xian-Dong Zeng
BACKGROUND: Dendritic cells are professional antigen-presenting cells found in an immature state in epithelia and interstitial space, where they capture antigens such as pathogens or damaged tissue. Matrix metallopeptidase 13 (MMP-13), a member of the collagenase subfamily, is involved in many different cellular processes and is expressed in murine bone marrow-derived dendritic cells (DCs). The function of MMP-13 in DCs is not well understood. Here, we investigated the effect of MMP-13 on DC maturation, apoptosis, and phagocytosis...
March 20, 2017: Chinese Medical Journal
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