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https://www.readbyqxmd.com/read/29779223/gene-editing-vectors-for-studying-nicotinic-acetylcholine-receptors-in-cholinergic-transmission
#1
Can Peng, Yijin Yan, Veronica J Kim, Staci E Engle, Jennifer N Berry, J Michael McIntosh, Rachael L Neve, Ryan M Drenan
Nicotinic acetylcholine receptors (nAChRs), prototype members of the cys-loop ligand gated ion channel family, are key mediators of cholinergic transmission in the central nervous system. Despite their importance, technical gaps exist in our ability to dissect the function of individual subunits in the brain. To overcome these barriers, we designed CRISPR/Cas9 small guide RNA sequences (sgRNAs) for production of loss-of-function alleles in mouse nAChR genes. These sgRNAs were validated in vitro via deep sequencing...
May 19, 2018: European Journal of Neuroscience
https://www.readbyqxmd.com/read/29778844/identification-of-micrornas-with-heat-stress-responsive-and-immune-properties-in-marsupenaeus-japonicus-based-on-next-generation-sequencing-and-bioinformatics-analysis-essential-regulators-in-the-heat-stress-host-interactions
#2
Jinbin Zheng, Jiawen Cao, Yong Mao, Yongquan Su, Jun Wang
Summer mortality syndrome is one of the most serious issue for Marsupenaeus japonicus aquaculture in China. Since it causes massive economic loss and threatens sustainability of M. japonicus aquaculture industry, thus, there is an urgent desire to reveal the heat stress-host interactions mechanisms that lead to mass mortalities of M. japonicus in hot summer months. MicroRNAs (miRNAs) are small noncoding RNAs that involved in regulation of diverse biological processes, including stress and immune response, and might serve as potential regulators in the heat stress-host interactions...
May 17, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29778390/next-generation-sequencing-reveals-differentially-expressed-small-noncoding-rnas-in-uterine-leiomyoma
#3
Tsai-Der Chuang, Yeming Xie, Wei Yan, Omid Khorram
OBJECTIVE: To determine the expression profile of small noncoding RNAs (sncRNAs) in leiomyoma, which has not been investigated to date. DESIGN: Laboratory-based investigation. SETTING: Academic center. PATIENT(S): Women undergoing hysterectomy for benign indications. INTERVENTION(S): Next-generation sequencing and screening of an sncRNA database with confirmatory analysis by quantitative reverse-transcription polymerase chain reaction (qRT-PCR)...
May 2018: Fertility and Sterility
https://www.readbyqxmd.com/read/29777089/human-plasma-and-serum-extracellular-small-rna-reference-profiles-and-their-clinical-utility
#4
Klaas E A Max, Karl Bertram, Kemal Marc Akat, Kimberly A Bogardus, Jenny Li, Pavel Morozov, Iddo Z Ben-Dov, Xin Li, Zachary R Weiss, Azadeh Azizian, Anuoluwapo Sopeyin, Thomas G Diacovo, Catherine Adamidi, Zev Williams, Thomas Tuschl
Circulating extracellular RNAs (exRNAs) have the potential to serve as biomarkers for a wide range of medical conditions. However, limitations in existing exRNA isolation methods and a lack of knowledge on parameters affecting exRNA variability in human samples may hinder their successful discovery and clinical implementation. Using combinations of denaturants, reducing agents, proteolysis, and revised organic extraction, we developed an automated, high-throughput approach for recovery of exRNAs and exDNA from the same biofluid sample...
May 18, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29775598/selective-cytotoxicity-of-the-nampt-inhibitor-fk866-toward-gastric-cancer-cells-with-markers-of-the-epithelial-mesenchymal-transition-due-to-loss-of-naprt
#5
Jooyoung Lee, Hyosil Kim, Jae Eun Lee, Su-Jin Shin, Sejin Oh, Sungjin Kwon, Hakhyun Kim, Yoon Young Choi, Michael A White, Soonmyung Paik, Jae-Ho Cheong, Hyun Seok Kim
BACKGROUND & AIMS: Markers of the epithelial-mesenchymal transition (EMT) in gastric tumor tissues are associated with poor outcomes of patients. We performed a screen to identify pharmacologic compounds that kill gastric cancer cells with EMT-associated gene expression patterns and investigate their mechanisms. METHODS: We identified 29 gastric cancer cell lines with gene expression signature previously associated with an EMT subtype, based on data from RNA sequence analyses, and confirmed their mesenchymal phenotypes of 7 lines (Hs746T, SNU1750, MKN1, SK4, SNU484, SNU668, and YCC11), based in invasive activity and protein markers...
May 15, 2018: Gastroenterology
https://www.readbyqxmd.com/read/29774543/human-monocyte-transciptional-profiling-identifies-interleukin-18-receptor-accessory-protein-and-lactoferrin-as-novel-immune-targets-in-hypertension
#6
Matthew R Alexander, Allison E Norlander, Fernando Elijovich, Ravi V Atreya, Amadou Gaye, Juan S Gnecco, Cheryl L Laffer, Cristi L Galindo, Meena S Madhur
BACKGROUND AND PURPOSE: Monocytes play a critical role in hypertension. The purpose of our study was to use an unbiased approach to determine whether hypertensive individuals on conventional therapy exhibit an altered monocyte gene expression profile and to perform validation studies of select genes to identify novel therapeutic targets for hypertension. EXPERIMENTAL APPROACH: Next-generation RNA sequencing identified differentially expressed genes in a small discovery cohort of normotensive and hypertensive individuals...
May 18, 2018: British Journal of Pharmacology
https://www.readbyqxmd.com/read/29774288/molecular-analysis-of-giardia-duodenalis-isolates-from-symptomatic-and-asymptomatic-children-from-la-habana-cuba
#7
Luis Enrique Jerez Puebla, Fidel A Núñez, Lissette Pérez Santos, Lázara Rojas Rivero, Isabel Martínez Silva, Lucía Ayllón Valdés, Iraís Atencio Millán, Norbert Müller
Giardiasis is considered the most common intestinal parasitic disease in humans worldwide. In Cuba, this infection has particularly a strong clinical impact on the child population. Giardia duodenalis is a highly diverse protozoan, which comprises a complex of eight morphologically identical genetic assemblages, further divided into sub-assemblages. The present study used triose phosphate isomerase ( tpi ) and small-subunit ribosomal RNA (SSU rRNA) genes as genetic markers for the identification of G. duodenalis assemblages and sub-assemblages in correlation with clinical and epidemiological data in children attended at the Paediatric Hospital "William Soler" and at Pedro Kouri Institute, between 2015 and 2016...
August 2017: Parasite Epidemiology and Control
https://www.readbyqxmd.com/read/29774045/transposon-derived-non-coding-rnas-and-their-function-in-plants
#8
REVIEW
Jungnam Cho
Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans -acting regulatory roles of TE-derived RNAs have been rarely studied...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29774043/integration-of-the-pokeweed-mirna-and-mrna-transcriptomes-reveals-targeting-of-jasmonic-acid-responsive-genes
#9
Kira C M Neller, Alexander Klenov, Juan C Guzman, Katalin A Hudak
The American pokeweed plant, Phytolacca americana , displays broad-spectrum resistance to plant viruses and is a heavy metal hyperaccumulator. However, little is known about the regulation of biotic and abiotic stress responses in this non-model plant. To investigate the control of miRNAs in gene expression, we sequenced the small RNA transcriptome of pokeweed treated with jasmonic acid (JA), a hormone that mediates pathogen defense and stress tolerance. We predicted 145 miRNAs responsive to JA, most of which were unique to pokeweed...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29773992/functional-analysis-of-rna-interference-related-soybean-pod-borer-lepidoptera-genes-based-on-transcriptome-sequences
#10
Fanli Meng, Mingyu Yang, Yang Li, Tianyu Li, Xinxin Liu, Guoyue Wang, Zhanchun Wang, Xianhao Jin, Wenbin Li
RNA interference (RNAi) is useful for controlling pests of agriculturally important crops. The soybean pod borer (SPB) is the most important soybean pest in Northeastern Asia. In an earlier study, we confirmed that the SPB could be controlled via transgenic plant-mediated RNAi. Here, the SPB transcriptome was sequenced to identify RNAi-related genes, and also to establish an RNAi-of-RNAi assay system for evaluating genes involved in the SPB systemic RNAi response. The core RNAi genes, as well as genes potentially involved in double-stranded RNA (dsRNA) uptake were identified based on SPB transcriptome sequences...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/29772702/exploration-of-aba-responsive-mirnas-reveals-a-new-hormone-signaling-crosstalk-pathway-regulating-root-growth-of-populus-euphratica
#11
Conglong Lian, Kun Yao, Hui Duan, Qing Li, Chao Liu, Weilun Yin, Xinli Xia
Abscisic acid (ABA) plays an important role in the regulation of plant adaptation, seed germination, and root development in plants. However, the mechanism of ABA regulation of root development is still poorly understood, especially through the miRNA-mediated pathway . Here, small RNA (sRNA)-seq and degradome-seq were used to analyze the miRNAs' responsive to ABA in the stems and roots of P. euphratica , a model tree species for abiotic stress-resistance research. In total, 255 unique mature sequences, containing 154 known miRNAs and 101 novel miRNAs were identified, among which 33 miRNAs and 54 miRNAs were responsive to ABA in the roots and stems, respectively...
May 16, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29771354/methylation-guide-rna-evolution-in-archaea-structure-function-and-genomic-organization-of-110-c-d-box-srna-families-across-six-pyrobaculum-species
#12
Lauren M Lui, Andrew V Uzilov, David L Bernick, Andrea Corredor, Todd M Lowe, Patrick P Dennis
Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2'-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genus Pyrobaculum, particularly rich in C/D box sRNA genes...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29769334/reovirus-nonstructural-protein-%C3%AF-ns-acts-as-an-rna-stability-factor-promoting-viral-genome-replication
#13
Paula F Zamora, Liya Hu, Jonathan J Knowlton, Roni M Lahr, Rodolfo A Moreno, Andrea J Berman, B V Venkataram Prasad, Terence S Dermody
Viral nonstructural proteins, which are not packaged into virions, are essential for replication of most viruses. Reovirus, a nonenveloped, double-stranded RNA (dsRNA) virus, encodes three nonstructural proteins that are required for viral replication and dissemination in the host. Reovirus nonstructural protein σNS is a single-stranded RNA (ssRNA)-binding protein that must be expressed in infected cells for production of viral progeny. However, activities of σNS during individual steps of the reovirus replication cycle are poorly understood...
May 16, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29769273/genome-wide-posttranscriptional-dysregulation-by-micrornas-in-human-asthma-as-revealed-by-frac-seq
#14
Rocio T Martinez-Nunez, Hitasha Rupani, Manuela Platé, Mahesan Niranjan, Rachel C Chambers, Peter H Howarth, Tilman Sanchez-Elsner
MicroRNAs are small noncoding RNAs that inhibit gene expression posttranscriptionally, implicated in virtually all biological processes. Although the effect of individual microRNAs is generally studied, the genome-wide role of multiple microRNAs is less investigated. We assessed paired genome-wide expression of microRNAs with total (cytoplasmic) and translational (polyribosome-bound) mRNA levels employing subcellular fractionation and RNA sequencing (Frac-seq) in human primary bronchoepithelium from healthy controls and severe asthmatics...
May 16, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29768183/ndrg1-disruption-alleviates-cisplatin-sodium-glycididazole-induced-dna-damage-response-and-apoptosis-in-ercc1-defective-lung-cancer-cells
#15
Lang He, Kang Liu, Xiaoshan Wang, Hong Chen, Jin Zhou, Xun Wu, Tao Liu, Yongxue Yang, Xuemei Yang, Dandan Cui, Guiqin Song, Jianguo Lei, Jun Wang
BACKGROUND: Resistance to platinum-based chemotherapy becomes a major obstacle in lung cancer treatment. Compensatory activation of nucleotide excision repair (NER) pathway is the major mechanism accounting for cisplatin-resistance. We aimed at identifying additional regulators in NER-mediated chemoresistance in a hypoxic setting induced by sodium glycididazole (CMNa)-sensitized cisplatin chemotherapy of non-small cell lung cancer (NSCLC). METHODS: We performed an RNA-sequencing (RNA-Seq) analysis to identify the genes whose expression had been differentially regulated in NER-deficient cells that had been treated by cisplatin/CMNa...
May 13, 2018: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/29767361/making-and-sequencing-heavily-multiplexed-high-throughput-16s-ribosomal-rna-gene-amplicon-libraries-using-a-flexible-two-stage-pcr-protocol
#16
Ankur Naqib, Silvana Poggi, Weihua Wang, Marieta Hyde, Kevin Kunstman, Stefan J Green
Deep sequencing of polymerase chain reaction (PCR)-amplified small subunit (16S or 18S) ribosomal RNA (rRNA) genes fragments is commonly employed to characterize the composition and structure of microbial communities. Preparing genomic DNA for sequencing of such gene fragments on Illumina sequencers can be performed in a straightforward, two-stage PCR method, described herein. The protocol described allows for up to 384 samples to be sequenced simultaneously, and provides great flexibility in choice of primers...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29765537/stat3-activated-cd36-facilitates-fatty-acid-uptake-in-chronic-lymphocytic-leukemia-cells
#17
Uri Rozovski, David M Harris, Ping Li, Zhiming Liu, Preetesh Jain, Alessandra Ferrajoli, Jan Burger, Phillip Thompson, Nitin Jain, William Wierda, Michael J Keating, Zeev Estrov
Although several studies established that unlike normal B cells chronic lymphocytic leukemia (CLL) cells metabolize fatty acids (FA), how CLL cells internalize FA is poorly understood. Because in various cell types CD36 facilitates FA uptake, we wondered whether a similar mechanism is operative CLL. We found that CD36 levels are higher in CLL cells than in normal B cells, and that small interfering RNA, CD36 neutralizing antibodies or sulfosuccinimidyl oleate (SSO) that inhibits CD36 significantly reduced the oxygen consumption of CLL cells incubated with FA...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29764987/rapid-and-dynamic-alternative-splicing-impacts-the-arabidopsis-cold-response-transcriptome
#18
Cristiane P G Calixto, Wenbin Guo, Allan B James, Nikoleta A Tzioutziou, Juan C Entizne, Paige E Panter, Heather Knight, Hugh Nimmo, Runxuan Zhang, John W S Brown
Plants have adapted to tolerate and survive constantly changing environmental conditions by re-programming gene expression. The dynamics of the contribution of alternative splicing (AS) to stress responses are unknown. RNA-sequencing of a time-series of Arabidopsis thaliana plants exposed to cold determines the timing of significant AS changes. This shows a massive and rapid AS response with coincident waves of transcriptional and AS activity occurring in the first few hours of temperature reduction, and further AS throughout the cold...
May 15, 2018: Plant Cell
https://www.readbyqxmd.com/read/29764507/aldolase-a-promotes-proliferation-and-g-1-s-transition-via-the-egfr-mapk-pathway-in-non-small-cell-lung-cancer
#19
Hailu Fu, Huijun Gao, Xiaoyu Qi, Lei Zhao, Donghua Wu, Yuxin Bai, Huimin Li, Xuan Liu, Jun Hu, Shujuan Shao
BACKGROUND: Our previous study demonstrated that aldolase A (ALDOA) is overexpressed in clinical human lung squamous cell carcinoma and that ALDOA promotes epithelial-mesenchymal transition and tumorigenesis. The present study aimed to explore the function of ALDOA in the modulation of non-small cell lung cancer (NSCLC) proliferation and cell cycle progression and the potential mechanism. METHODS: ALDOA was knocked down by short hairpin RNA in H520 and H1299 cells...
May 8, 2018: Cancer communications
https://www.readbyqxmd.com/read/29764489/mir-magic-improves-quantification-accuracy-for-small-rna-seq
#20
Pamela H Russell, Brian Vestal, Wen Shi, Pratyaydipta D Rudra, Robin Dowell, Richard Radcliffe, Laura Saba, Katerina Kechris
OBJECTIVE: Many tools have been developed to profile microRNA (miRNA) expression from small RNA-seq data. These tools must contend with several issues: the small size of miRNAs, the small number of unique miRNAs, the fact that similar miRNAs can be transcribed from multiple loci, and the presence of miRNA isoforms known as isomiRs. Methods failing to address these issues can return misleading information. We propose a novel quantification method designed to address these concerns. RESULTS: We present miR-MaGiC, a novel miRNA quantification method, implemented as a cross-platform tool in Java...
May 15, 2018: BMC Research Notes
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