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Zhitong Li, Wenjing Li, Jinmiao Zha, Huihui Chen, Christopher J Martyniuk, Xuefang Liang
Benzotriazole ultraviolet stabilizers (BUVSs) are widely applied ultraviolet absorbing compounds in industrial materials and personal care products. Due to their ubiquitous use and reports of bio-accumulation in aquatic organisms, these compounds are significant environmental pollutants; however, data are limited for BUVSs toxicity. In this study, juvenile zebrafish (Danio rerio) were exposed to 4 commonly used BUVSs (UV-234, UV-326, UV-329, and UV-P) at one dose of 10 or 100 μg/L for 28 days. To characterize the underlying mechanisms of different BUVSs-induced toxicities, we performed global transcriptome sequencing (RNA-Seq) in the brain (100 μg/L)...
October 13, 2018: Environmental Toxicology
Tetsushi Sakuma, Takashi Yamamoto
Genome editing includes various edits of the genome, such as short insertions and deletions, substitutions, and chromosomal rearrangements including inversions, duplications, and translocations. These varieties are based on single or multiple DNA double strand break (DSB)-triggered in cellulo repair machineries. In addition to these "conventional" genome editing strategies, tools enabling customized, site-specific recognition of particular nucleic acid sequences have been coming into wider use, e...
October 13, 2018: Cancer Science
Xiao-Xiao Gong, Bing-Yu Yan, Jin Hu, Cui-Ping Yang, Yi-Jian Li, Jin-Ping Liu, Wen-Bin Liao
Tropical plant rubber tree (Hevea brasiliensis) is the sole source of commercial natural rubber and low-temperature stress is the most important limiting factor for its cultivation. To characterize the gene expression profiles of H. brasiliensis under the cold stress and discover the key cold stress-induced genes. Three cDNA libraries, CT (control), LT2 (cold treatment at 4 °C for 2 h) and LT24 (cold treatment at 4 °C for 24 h) were constructed for RNA sequencing (RNA-Seq) and gene expression profiling...
November 2018: Genes & Genomics
Justyna Augustyniak, Jacek Lenart, Paweł Gaj, Monika Kolanowska, Krystian Jazdzewski, Piotr Pawel Stepien, Leonora Buzanska
Bezafibrate (BZ) regulates mitochondrial biogenesis by activation of PPAR's receptors and enhancing the level of PGC-1α coactivator. In this report, we investigated the effect of BZ on the expression of genes (1) that are linked to different pathways involved in mitochondrial biogenesis, e.g., regulated by PPAR's receptors or PGC-1α coactivator, and (2) involved in neuronal or astroglial fate, during neural differentiation of hiPSC. The tested cell populations included hiPSC-derived neural stem cells (NSC), early neural progenitors (eNP), and neural progenitors (NP)...
October 13, 2018: Molecular Neurobiology
Deepanshi Mishra, Gita Satpathy, Rohan Chawla, Pradeep Venkatesh, Nishat Hussain Ahmed, Subrat Kumar Panda
BACKGROUND: Endophthalmitis, a sight-threatening intraocular infection, can be of postsurgical, post-traumatic or endogenous origin. Laboratory diagnosis-based appropriate therapy can be vision-saving. Conventional culture-based laboratory diagnosis takes time and lacks sensitivity. In this study a broad-range PCR assay was assessed against conventional and automated culture methods in vitreous specimens for accurate microbiological diagnosis. AIMS: To use broad-range PCR assay targeting 16S ribosomal RNA (rRNA) region of bacteria and to assess its performance vis-à-vis conventional and automated culture methods in the laboratory diagnosis of endophthalmitis...
October 12, 2018: British Journal of Ophthalmology
Michela Zamboni, Donato Civitareale
In non-small lung cancer, the expression of the transcription factor TTF-1/Nkx2.1 correlates with the presence of EGFR mutations, therefore TTF-1/Nkx2.1 expression is used to optimize an EGFR testing strategy and to guide clinical treatment. We investigate the molecular mechanisms underlying the functional connection between EGFR and TTF-1/Nkx2.1 gene expression in lung adenocarcinoma. Using the H1975 cell line as a non-small cell lung cancer model system and short hairpin RNA, we have selected clones with TTF-1/Nkx2...
October 9, 2018: Biochemical and Biophysical Research Communications
Magalla Bastian Chalitha Lakmal Somarathne, Yasanthi Illika Nilmini Silva Gunawardene, Naduvilath Vishvanath Chandrasekharan, Arjuna Nisantha Bandara Ellepola, Ranil Samantha Dassanayake
BACKGROUND: Functional analysis of animal parasitic nematode genes is often quite challenging due to the unavailability of standardised in vitro culture conditions and lack of adequate tools to manipulate these genes. Therefore, this study was undertaken to investigate the suitability of Culex quinquefasciatus, as an in vivo culture platform for Setaria digitata larvae and RNA interference (RNAi), as a post-transcriptional gene silencing tool to study the roles of a vital gene that encodes a novel parasitic nematode-specific protein (SDNP)...
October 10, 2018: Parasites & Vectors
Alexander J Stockdale, Collins Mitambo, Dean Everett, Anna Maria Geretti, Melita A Gordon
BACKGROUND: Viral hepatitis is an important public health issue in sub-Saharan Africa. Due to rising mortality from cirrhosis and hepatocellular carcinoma and limited implementation of screening and treatment programmes, it has been characterised as a neglected tropical disease. Synthesis of the existing evidence on the epidemiology of viral hepatitis B, C and D in Malawi is required to inform policy and identify research gaps. METHODS: We searched Pubmed, EMBASE and Scopus for studies reporting the epidemiology of viral hepatitis B, C and D in Malawi from 1990 to 2018...
October 12, 2018: BMC Infectious Diseases
Pawel Karpinski, Pawel Skiba, Magdalena Kosinska, Marta Rosiek-Biegus, Emilia Królewicz, Nikolaus Blin, Eckart Meese, Bernard Panaszek, Marita Nittner-Marszalska, Maria Malgorzata Sasiadek
BACKGROUND: Insect venom immunotherapy (VIT) is used to protect patients against Hymenoptera insects' venom allergy (HVA), which can result in severe systemic or even life-threatening conditions. Molecular mechanisms triggered by VIT remain largely unknown. OBJECTIVE: To compare genome-wide gene expression of patients with severe HVA prior to VIT and 12 months after. METHODS: Whole blood RNA samples were analyzed on an expression array. Results from differential expression obtained on a microarray platform were confirmed by quantitative real -time PCR (qRT-PCR)...
October 9, 2018: Immunology Letters
Yan Guo, Hui Yu, David C Samuels, Wei Yue, Scott Ness, Ying-Yong Zhao
Through analysis of paired high-throughput DNA-Seq and RNA-Seq data, researchers quickly recognized that RNA-Seq can be used for more than just gene expression quantification. The alternative applications of RNA-Seq data are abundant, and we are particularly interested in its usefulness for detecting single-nucleotide variants, which arise from RNA editing, genomic variants and other RNA modifications. A stunning discovery made from RNA-Seq analyses is the unexpectedly high prevalence of RNA-editing events, many of which cannot be explained by known RNA-editing mechanisms...
October 12, 2018: Briefings in Functional Genomics
Massimiliano Lanzafame, Stefano Nicole, Sebastiano Rizzardo, Daniela Piacentini, Sheila Chiesi, Emanuela Lattuada, Erica Diani, Maria Carelli, Sandro Vento, Davide Gibellini
Combination abacavir/lamivudine/dolutegravir (ABC/3TC/DTG) is approved as a first-line treatment for antiretroviral naïve patients. This report investigated the immunovirological outcome and total HIV-1 DNA decay in a small cohort of naïve HIV-1-positive patients treated with this regimen. In the presence of viral suppression and increased lymphocyte T CD4+ cells, the quantitative analysis of total HIV-1 DNA content revealed a significant decay after 12 months of treatment. Subsequently, we deintensificated the treatment of these patients from (ABC/3TC/DTG) to lamivudine plus dolutegravir (3TC/DTG) after 12 months of virological suppression, as a strategy of "induction-maintenance" therapy...
October 12, 2018: New Microbiologica
Martin Morovic, Olga Østrup, Frantisek Strejcek, Michal Benc, Matej Murin, Katarina Jedlickova, Alexandra Bartkova, Andrea Lucas-Hahn, Lazo Pendovski, Jozef Laurincik
SummaryThe present study examines the role of RNA polymerase I (RPI)-mediated transcription, maternally inherited rRNA and nucleolar proteins in the resumption of fibrillogranular nucleoli during embryonic genome activation (EGA) in porcine embryos. Late 4-cell embryos were incubated in the absence (control) or presence of actinomycin D (AD) (0.2 μg/ml for inhibition of RPI; 2.0 μg/ml for inhibition of total transcription) and late 2-cell embryos were cultured to the late 4-cell stage with 0.2 μg/ml AD to block EGA...
October 12, 2018: Zygote: the Biology of Gametes and Early Embryos
Lukas Trixl, Alexandra Lusser
It is a well-known fact that RNA is the target of a plethora of modifications which currently amount to over a hundred. The vast majority of these modifications was observed in the two most abundant classes of RNA, rRNA and tRNA. With the recent advance in mapping technologies, modifications have been discovered also in mRNA and in less abundant non-coding RNA species. These developments have sparked renewed interest in elucidating the nature and functions of those "epitransciptomic" modifications in RNA...
October 11, 2018: Wiley Interdisciplinary Reviews. RNA
Yanping Hu, Xiaojing Teng, Linlin Wu, Wei Liu, Jianduo An
BACKGROUND: Esophageal squamous cell precursor lesions remain one of the most controversial topics in pathology and clinical management. AIMS: To analyze the dysregulation of human telomerase RNA component (hTERC) in esophageal squamous cell precursor lesions and the clinicopathological correlations with the characteristics of esophageal squamous cell precursor lesions. METHODS: Florescence in situ hybridization was performed to detect hTERC amplification in different gradings of esophageal squamous cell precursor lesions...
October 11, 2018: Digestive Diseases and Sciences
Jing Hu, Hao Qian, Yuanchao Xue, Xiang-Dong Fu
PTB was initially discovered as a polypyrimidine tract-binding protein (hence the name), which corresponds to a specific RNA-binding protein associated with heterogeneous ribonucleoprotein particle (hnRNP I). The PTB family consists of three members in mammalian genomes, with PTBP1 (PTB) expressed in most cell types, PTBP2 (also known as nPTB or brPTB) exclusively found in the nervous system, and PTBP3 (also known as ROD1) predominately detected in immune cells. During neural development, PTB is down-regulated, which induces nPTB, and the expression of both PTB and nPTB becomes diminished when neurons mature...
2018: Biophysics Reports
Ya-Yun Liu, Xue-Song Liang
As alternative indexes of hepatitis B virus (HBV), covalently closed circular DNA (cccDNA) transcriptional activity, hepatitis B surface antigen (HBsAg), hepatitis B core-related antigen (HBcrAg), and peripheral blood RNA known as pgRNA, have been advocated as novel serum markers for prediction of prognosis and treatment response in chronic hepatitis B (CHB). Since the availability of commercial quantitative assays of HBsAg in 2011, HBsAg has been widely used for predicting treatment response of patients with CHB...
September 27, 2018: World Journal of Hepatology
Eleni Gigi, Vasileios I Lagopoulos, Eleni Bekiari
Hepatitis C virus (HCV) chronic infection induces liver fibrosis and cirrhosis but is also responsible for a significant portion of hepatocellular carcinoma (HCC) occurrence. Since it was recognized as a causative factor of chronic hepatitis, there have been multiple efforts towards viral eradication, leading to the first-generation HCV treatment that was based on interferon (IFN)-α and its analogs, mainly PEGylated interferon-α (PEG IFNα). Sustained virological response (SVR), defined as the absence of detectable RNA of HCV in blood serum for at least 24 wk after discontinuing the treatment, was accepted as a marker of viral clearance and was achieved in approximately one-half of patients treated with PEG IFNα regimens...
September 27, 2018: World Journal of Hepatology
Jun Young Choi, Woo Bin Yun, Ji Eun Kim, Mi Rim Lee, Jin Ju Park, Bo Ram Song, Hye Ryeong Kim, Ji Won Park, Mi Ju Kang, Byeong Cheol Kang, Han-Woong Lee, Dae Youn Hwang
To evaluate the carcinogenicity of p27 knockout (KO) mice with RNA-guided endonuclease (RGENs)-mediated p27 mutant exon I gene (IΔ), alterations in the carcinogenic phenotypes including tumor spectrum, tumor suppressor proteins, apoptotic proteins and cell cycle regulators were observed in p27 (IΔ) KO mice after treatment with 7,12-Dimethylbenz[a]anthracene (DMBA) and 12-O-tetradecanoylphorbol-13-acetate (TPA)(DT) for 5 months. The target region (544~571 nt) in exon I of the p27 gene was successfully disrupted in p27 (IΔ) KO mice using the RGEN-induced non-homologous end joining (NHEJ) technique...
September 2018: Laboratory Animal Research
Tae Hee Lee, Joo-Hee Hwang, Woo Kon Lee, Min-Kyoung Shin, Hye Ryun Woo, Kyung Min Chung, Chang-Seop Lee
Pathogenic gram-negatives that produce 16S ribosomal RNA methyltransferases (16S RMTases) have already been distributed all over the world. To investigate the predominance of aminoglycoside resistance associated with 16S RMTases in Korea, we collected a total of 222 amikacin resistant Gram-negative clinical isolates from patient specimens between 1999 and 2015 from three hospital banks across Korea. ArmA and rmtB were the predominant 16S RMTase genes responsible for aminoglycoside-resistant isolates circulating in Korean community settings although only one rmtA -producing isolate was detected in 2006...
October 15, 2018: Journal of Korean Medical Science
Tomasz Krzywkowski, Malte Kühnemund, Mats Nilsson
Many approaches exist to detect RNA using complementary oligonucleotides. DNA ligation-based techniques can improve discrimination of subtle sequence variations, but they have been difficult to implement for direct RNA analysis due to the infidelity and inefficiency of most DNA ligases on RNA. In this report, we have systematically studied if ribonucleotide substitutions in padlock probes can provide higher catalytic efficiencies for Chlorella virus DNA ligase (PBCV-1 DNA ligase) and T4RNA ligase 2 (T4Rnl2) on RNA...
October 11, 2018: RNA
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