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https://www.readbyqxmd.com/read/28717530/comparative-and-integrative-analysis-of-rna-structural-profiling-data-current-practices-and-emerging-questions
#1
Krishna Choudhary, Fei Deng, Sharon Aviran
BACKGROUND: Structure profiling experiments provide single-nucleotide information on RNA structure. Recent advances in chemistry combined with application of high-throughput sequencing have enabled structure profiling at transcriptome scale and in living cells, creating unprecedented opportunities for RNA biology. Propelled by these experimental advances, massive data with ever-increasing diversity and complexity have been generated, which give rise to new challenges in interpreting and analyzing these data...
March 2017: Quantitative Biology
https://www.readbyqxmd.com/read/28717350/properties-of-native-high-density-lipoproteins-inspire-synthesis-of-actively-targeted-in-vivo-sirna-delivery-vehicles
#2
Kaylin M McMahon, Michael P Plebanek, C Shad Thaxton
Efficient systemic administration of therapeutic short interfering RNA (siRNA) is challenging. High-density lipoproteins (HDL) are natural in vivo RNA delivery vehicles. Specifically, native HDLs: 1) Load single-stranded RNA; 2) Are anionic, which requires charge reconciliation between the RNA and HDL, and 3) Actively target scavenger receptor type B-1 (SR-B1) to deliver RNA. Emphasizing these particular parameters, we employed templated lipoprotein particles (TLP), mimics of spherical HDLs, and self-assembled them with single-stranded complements of, presumably, any highly unmodified siRNA duplex pair after formulation with a cationic lipid...
November 15, 2016: Advanced Functional Materials
https://www.readbyqxmd.com/read/28715399/integration-free-derivation-of-human-induced-pluripotent-stem-cells-using-laminin-521-matrix
#3
Elias Uhlin, Ana Marin Navarro, Harriet Rönnholm, Kelly Day, Malin Kele, Anna Falk
Xeno-free and fully defined conditions are key parameters for robust and reproducible generation of homogenous human induced pluripotent stem (hiPS) cells. Maintenance of hiPS cells on feeder cells or undefined matrices are susceptible to batch variances, pathogenic contamination and risk of immunogenicity. Utilizing the defined recombinant human laminin 521 (LN-521) matrix in combination with xeno-free and defined media formulations reduces variability and allows for the consistent generation of hiPS cells...
July 7, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28714868/interval-dosing-with-the-hdac-inhibitor-vorinostat-effectively-reverses-hiv-latency
#4
Nancie M Archin, Jennifer L Kirchherr, Julia Am Sung, Genevieve Clutton, Katherine Sholtis, Yinyan Xu, Brigitte Allard, Erin Stuelke, Angela D Kashuba, Joann D Kuruc, Joseph Eron, Cynthia L Gay, Nilu Goonetilleke, David M Margolis
BACKGROUND: The histone deacetylase (HDAC) inhibitor vorinostat (VOR) can increase HIV RNA expression in vivo within resting CD4+ T cells of aviremic HIV+ individuals. However, while studies of VOR or other HDAC inhibitors have reported reversal of latency, none has demonstrated clearance of latent infection. We sought to identify the optimal dosing of VOR for effective serial reversal of HIV latency. METHODS: In a study of 16 HIV-infected, aviremic individuals, we measured resting CD4+ T cell-associated HIV RNA ex vivo and in vivo following a single exposure to VOR, and then in vivo after a pair of doses separated by 48 or 72 hours, and finally following a series of 10 doses given at 72-hour intervals...
July 17, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28711492/species-specific-real-time-rt-pcr-analysis-of-expression-of-stromal-cell-genes-in-a-tumor-xenotransplantation-model-in-mice
#5
Evzen Krepela, Petr Busek, Marek Hilser, Zdislava Vanickova, Aleksi Sedo
Human tumor xenografts in mice together with the species-specific analysis of expressed genes allow to study the molecular processes driving tumor growth and progression in vivo and help to develop and evaluate anticancer therapies. In the present work, we designed and validated species-specific real-time RT-PCR assays for discrimination and quantitation of expression of human and mouse transcripts in cancer and stromal cells including dipeptidyl peptidase (DPP) 4, DPP8, DPP9, fibroblast activation protein (FAP) and CXC chemokine receptor 4 in mixed human-mouse biological samples...
July 12, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28711491/copper-chaperone-atox1-regulates-pluripotency-factor-oct4-in-preimplantation-mouse-embryos
#6
Emanuele Celauro, Amisa Mukaj, Juan Carlos Fierro-González, Pernilla Wittung-Stafshede
Despite of the importance of copper (Cu) during pregnancy, the roles of Cu-binding proteins during early embryonic development are unknown. The Cu chaperone ATOX1 was recently suggested to have additional functions related to transcription and cancer. When we analyzed single-cell RNA transcript data from early mouse embryos, Atox1 transcript levels increased dramatically at the 8-cell stage and, at 16- and 32-cell embryo stages, matched those of Oct4 which expresses a transcription factor essential for pluripotency in the inner cell mass...
July 12, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28710314/sarcomatoid-renal-cell-carcinoma-has-a-distinct-molecular-pathogenesis-driver-mutation-profile-and-transcriptional-landscape
#7
Zixing Wang, Tae Beom Kim, Bo Peng, Jose A Karam, Chad J Creighton, Aron Y Joon, Fumi Kawakami, Patricia Trevisan, Eric Jonasch, Chi-Wan Chow, Jaime Rodriguez-Canales, Pheroze Tamboli, Nizar M Tannir, Christopher G Wood, Federico A Monzon, Keith A Baggerly, Marileila Varella-Garcia, Bogdan Czerniak, Ignacio I Wistuba, Gordon B Mills, Kenna Shaw, Ken Chen, Kanishka Sircar
Sarcomatoid renal cell carcinoma (SRCC) ranks among the most aggressive clinicopathologic phenotypes of RCC. However, the paucity of high-quality, genome-wide molecular examinations of SRCC has hindered our understanding of this entity.<br /><br />Experimental Design: We interrogated the mutational, copy number, and transcriptional characteristics of SRCC and compared these data with those of non-sarcomatoid RCC (RCC). We evaluated whole exome sequencing, single nucleotide polymorphism, and RNA sequencing data from patients with SRCC (n=65) and RCC (n=598) across different parent RCC subtypes, including clear cell RCC, papillary RCC, and chromophobe RCC subtypes...
July 14, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28709640/genome-wide-identification-of-genes-essential-for-podocyte-cytoskeletons-based-on-single-cell-rna%C3%A2-sequencing
#8
Yuqiu Lu, Yuting Ye, Wenduona Bao, Qianqian Yang, Jinquan Wang, Zhihong Liu, Shaolin Shi
Gene expression differs substantially among individual cells of the same type. We speculate that genes that are expressed in all but a portion of cells of a given cell type would be likely essential and required for either the cell survival (housekeeping) or for the cell type's unique structure and function, enabling the organism to survive. Here, we performed RNA-seq of 20 mouse podocytes using the Fluidigm C1 system and identified 335 genes that were expressed in all of them. Among them, 239 genes were also expressed in mesangial and endothelial cells and were involved in energy metabolism, protein synthesis, etc...
July 11, 2017: Kidney International
https://www.readbyqxmd.com/read/28706995/disabling-cas9-by-an-anti-crispr-dna-mimic
#9
Jiyung Shin, Fuguo Jiang, Jun-Jie Liu, Nicolas L Bray, Benjamin J Rauch, Seung Hyun Baik, Eva Nogales, Joseph Bondy-Denomy, Jacob E Corn, Jennifer A Doudna
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 gene editing technology is derived from a microbial adaptive immune system, where bacteriophages are often the intended target. Natural inhibitors of CRISPR-Cas9 enable phages to evade immunity and show promise in controlling Cas9-mediated gene editing in human cells. However, the mechanism of CRISPR-Cas9 inhibition is not known, and the potential applications for Cas9 inhibitor proteins in mammalian cells have not been fully established...
July 2017: Science Advances
https://www.readbyqxmd.com/read/28706128/transcriptome-analysis-reveals-a-role-for-the-endothelial-anp-gc-a-signaling-in-interfering-with-pre-metastatic-niche-formation-by-solid-cancers
#10
Takashi Nojiri, Miki Arai, Yutaka Suzuki, Motofumi Kumazoe, Takeshi Tokudome, Koichi Miura, Jun Hino, Hiroshi Hosoda, Mikiya Miyazato, Meinoshin Okumura, Shinpei Kawaoka, Kenji Kangawa
Cancer establishes a microenvironment called the pre-metastatic niche in distant organs where disseminated cancer cells can efficiently metastasize. Pre-metastatic niche formation requires various genetic factors. Previous studies suggest that inhibiting a single niche-factor is insufficient to completely block pre-metastatic niche formation especially in human patients. Here we show that the atrial natriuretic peptide (ANP), an endogenous hormone produced by the heart, inhibits pre-metastatic niche formation and metastasis of murine solid cancer models when pharmacologically supplied in vivo...
May 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28705680/characterization-of-significant-molecular-determinants-of-virulence-of-enterovirus-71-sub-genotype-b4-in-rhabdomyosarcoma-cells
#11
Pinn Tsin Isabel Yee, Reham Ahmed Hashim Mohamed, Seng-Kai Ong, Kuan Onn Tan, Chit Laa Poh
One of the leading causes of the hand, foot and mouth disease (HFMD) is Enterovirus 71 (EV-A71), displaying symptoms such as fever and ulcers in children but some strains can produce cardiopulmonary oedema which leads to death. There is no FDA-approved vaccine for prevention of severe HFMD. The molecular determinants of virulence for EV-A71 are unclear. It could be a single or a combination of amino acids that determines virulence in different EV-A71 genotype/sub-genotypes. Several EV-A71 strains bearing single nucleotide (nt) mutations were constructed and the contribution of each mutation to virulence was evaluated...
July 10, 2017: Virus Research
https://www.readbyqxmd.com/read/28705213/the-therapeutic-landscape-of-hiv-1-via-genome-editing
#12
REVIEW
Alexander Kwarteng, Samuel Terkper Ahuno, Godwin Kwakye-Nuako
Current treatment for HIV-1 largely relies on chemotherapy through the administration of antiretroviral drugs. While the search for anti-HIV-1 vaccine remain elusive, the use of highly active antiretroviral therapies (HAART) have been far-reaching and has changed HIV-1 into a manageable chronic infection. There is compelling evidence, including several side-effects of ARTs, suggesting that eradication of HIV-1 cannot depend solely on antiretrovirals. Gene therapy, an expanding treatment strategy, using RNA interference (RNAi) and programmable nucleases such as meganuclease, zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR-Cas9) are transforming the therapeutic landscape of HIV-1...
July 14, 2017: AIDS Research and Therapy
https://www.readbyqxmd.com/read/28704922/transcriptome-differences-in-porcine-alveolar-macrophages-from-tongcheng-and-large-white-pigs-in-response-to-highly-pathogenic-porcine-reproductive-and-respiratory-syndrome-virus-prrsv-infection
#13
Wan Liang, Likai Ji, Yu Zhang, Yueran Zhen, Qingde Zhang, Xuewen Xu, Bang Liu
Porcine reproductive and respiratory syndrome virus (PRRSV) is a single-stranded positive-sense RNA virus that can cause devastating reproductive failure and respiratory tract lesions, which has led to serious damage to the swine industry worldwide. Our previous studies have indicated that Tongcheng (TC) pigs, a Chinese local breed, have stronger resistance or tolerance to PRRSV infection than Large White (LW) pigs. This study aims to investigate their host transcriptome differences in porcine alveolar macrophages (PAMs) at 7 days post challenge...
July 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28702647/an-enhanced-htert-promoter-driven-crispr-cas9-system-selectively-inhibits-the-progression-of-bladder-cancer-cells
#14
Xinbo Huang, Chengle Zhuang, Changshui Zhuang, Tiefu Xiong, Yawen Li, Yaoting Gui
The current therapies for treating tumors are lacking in efficacy and specificity. Synthetic biology principles may bring some new possible methods for curing cancer. Here we present a synthetic logic circuit based on the CRISPR/Cas9 system. The CRISPR/Cas9 technology has been applied in many biological fields, including cancer research. In this study, the expression of Cas9 nuclease was controlled indirectly by an enhanced hTERT promoter using the GAL4/upstream activating sequence (UAS) binding system. Cas9 was driven by 5XUAS, single guide RNA (sgRNA) was used to target mutant or wild-type HRAS, and the fusion gene GAL4-P65 was driven by the enhanced hTERT promoter...
July 12, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28702151/human-enteroviruses-in-cerebrospinal-fluid-of-children-with-suspected-aseptic-meningitis-a-study-in-northern-iran
#15
Farzin Sadeghi, Masoumeh Talebi-Nesami, Rahim Barari-Savadkouhi, Ali Bijani, Elahe Ferdosi-Shahandashti, Yousef Yahyapour
BACKGROUND: Enterovirus (EV) infections are one of the most common causes of aseptic meningitis in pediatrics. To diagnose EV meningitis, virus isolation in cell cultures is often time consuming and lacks sensitivity to be of clinical relevance. This makes the virus culture results difficult to interpret. The rapid detection of EVs in cerebrospinal fluid (CSF) by molecular diagnostic techniques may improve the management of patients with aseptic meningitis. The purpose of the present study was to develop a more convenient and sensitive alternative technique to viral culture...
2017: Caspian Journal of Internal Medicine
https://www.readbyqxmd.com/read/28702049/endurance-exercise-ability-in-the-horse-a-trait-with-complex-polygenic-determinism
#16
Anne Ricard, Céline Robert, Christine Blouin, Fanny Baste, Gwendoline Torquet, Caroline Morgenthaler, Julie Rivière, Nuria Mach, Xavier Mata, Laurent Schibler, Eric Barrey
Endurance horses are able to run at more than 20 km/h for 160 km (in bouts of 30-40 km). This level of performance is based on intense aerobic metabolism, effective body heat dissipation and the ability to endure painful exercise. The known heritabilities of endurance performance and exercise-related physiological traits in Arabian horses suggest that adaptation to extreme endurance exercise is influenced by genetic factors. The objective of the present genome-wide association study (GWAS) was to identify single nucleotide polymorphisms (SNPs) related to endurance racing performance in 597 Arabian horses...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28701394/single-particle-detection-of-transcription-following-rotavirus-entry
#17
Eric N Salgado, Srigokul Upadhyayula, Stephen C Harrison
Infectious rotavirus particles are triple-layered, icosahedral assemblies. The outer layer proteins, VP4 (cleaved to VP8* and VP5*) and VP7, surround a transcriptionally competent, double-layer particle (DLP), which they deliver into the cytosol. During entry of rhesus rotavirus, VP8* interacts with cell-surface gangliosides, allowing engulfment into a membrane vesicle by a clathrin-independent process. Escape into the cytosol and outer-layer shedding depend on interaction of a hydrophobic surface on VP5* with the membrane bilayer and on a large-scale conformational change...
July 12, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28701189/stromal-derived-factor-1-mediates-the-lung-regenerative-effects-of-mesenchymal-stem-cells-in-a-rodent-model-of-bronchopulmonary-dysplasia
#18
Joel Reiter, Shelley Drummond, Ibrahim Sammour, Jian Huang, Victoria Florea, Polliana Dornas, Joshua M Hare, Claudia O Rodrigues, Karen C Young
BACKGROUND: Mesenchymal stem cells (MSCs) attenuate lung injury in experimental models of bronchopulmonary dysplasia (BPD). Stromal derived factor-1 (SDF-1), a chemokine secreted by MSCs, modulates angiogenesis and stem cell recruitment. Here we tested the hypothesis that SDF-1 mediates MSC protective effects in experimental BPD by modulating angiogenesis. METHODS: SDF-1 was knocked down in MSCs using lentiviral vectors carrying anti-SDF-1 short hairpin RNA (MSC-SDF KD)...
July 12, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28698542/genome-wide-differential-mrna-expression-profiles-in-follicles-of-two-breeds-and-at-two-stages-of-estrus-cycle-of-gilts
#19
Qingpo Chu, Bo Zhou, Feilong Xu, Ruonan Chen, Chunyan Shen, Tingting Liang, Yuan Li, Allan P Schinckel
Estrus expression by gilts and sows is hereditable and important for heat detection. To better understand the molecular biological mechanisms of estrus expression in gilts, the mRNA expression profiles of follicular tissue from Large White gilts in diestrus (LD, n = 3) and estrus (LE, n = 3), and Chinese indigenous Mi gilts in diestrus (MD, n = 2) and estrus (ME, n = 3) were investigated using RNA sequencing. We detected 122,804-335,295 SNPs, 6,140-14,947 InDel and 12 types of AS events (39...
July 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28698276/a-novel-single-cell-fish-flow-assay-identifies-effector-memory-cd4-t-cells-as-a-major-niche-for-hiv-1-transcription-in-hiv-infected-patients
#20
Judith Grau-Expósito, Carla Serra-Peinado, Lucia Miguel, Jordi Navarro, Adrià Curran, Joaquin Burgos, Imma Ocaña, Esteban Ribera, Ariadna Torrella, Bibiana Planas, Rosa Badía, Josep Castellví, Vicenç Falcó, Manuel Crespo, Maria J Buzon
Cells that actively transcribe HIV-1 have been defined as the "active viral reservoir" in HIV-infected individuals. However, important technical limitations have precluded the characterization of this specific viral reservoir during both treated and untreated HIV-1 infections. Here, we used a novel single-cell RNA fluorescence in situ hybridization-flow cytometry (FISH-flow) assay that requires only 15 million unfractionated peripheral blood mononuclear cells (PBMCs) to characterize the specific cell subpopulations that transcribe HIV RNA in different subsets of CD4(+) T cells...
July 11, 2017: MBio
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