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https://www.readbyqxmd.com/read/28463400/using-3drna-for-rna-3-d-structure-prediction-and-evaluation
#1
Jian Wang, Yi Xiao
This unit describes how to use 3dRNA to predict RNA 3-D structures from their sequences and secondary (2-D) structures, and how to use 3dRNAscore to evaluate the predicted structures. The predicted RNA 3-D structures can be used to predict or understand their functions and can also be used to find the interactions between the RNA and other molecules. © 2017 by John Wiley & Sons, Inc.
May 2, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28450173/a-method-for-the-improved-detection-of-aerosolized-influenza-viruses-and-the-male-specific-f-rna-coliphage-ms2
#2
J C Chandler, J W Schaeffer, M Davidson, S L Magzamen, A Pérez-Méndez, S J Reynolds, L D Goodridge, J Volckens, A B Franklin, S A Shriner, B Bisha
The detection of aerosolized viruses can serve as an important surveillance and control tool in agriculture, human health, and environmental settings. Here, we adapted an anion exchange resin-based method, initially developed to concentrate negatively charged viruses from water, to liquid impingement-based bioaerosol sampling. In this method, aerosolized viruses are collected in a 20ml liquid sample contained within widely used impingers, BioSamplers (SKC Inc., Eighty Four, PA), and further concentrated via adsorption to an anion exchange resin that is suspended within this liquid...
April 24, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28444712/the-urinary-microbiome-and-its-contribution-to-lower-urinary-tract-symptoms-ici-rs-2015
#3
REVIEW
Marcus J Drake, Nicola Morris, Apostolos Apostolidis, Mohammad S Rahnama'i, Julian R Marchesi
AIMS: The microbiome is the term used for the symbiotic microbial colonisation of healthy organs. Studies have found bacterial identifiers within voided urine which is apparently sterile on conventional laboratory culture, and accordingly there may be health and disease implications. METHODS: The International Consultation on Incontinence Research Society (ICI-RS) established a literature review and expert consensus discussion focussed on the increasing awareness of the urinary microbiome, and potential research priorities...
April 2017: Neurourology and Urodynamics
https://www.readbyqxmd.com/read/28419777/micrornas-as-biomarkers-for-psychiatric-disorders-with-a-focus-on-autism-spectrum-disorder-current-progress-in-genetic-association-studies-expression-profiling-and-translational-research
#4
REVIEW
Yubin Hu, Erik A Ehli, Dorret I Boomsma
MicroRNAs (miRNAs) are a group of small noncoding RNA molecules, 18-25 nucleotides in length, which can negatively regulate gene expression at the post-transcriptional level by binding to messenger RNAs. About half of all identified miRNAs in humans are expressed in the brain and display regulatory functions important for many biological processes related to the development of the central nervous system (CNS). Disruptions in miRNA biogenesis and miRNA-target interaction have been related to CNS diseases, including psychiatric disorders...
April 17, 2017: Autism Research: Official Journal of the International Society for Autism Research
https://www.readbyqxmd.com/read/28370415/top2b-is-involved-in-the-formation-of-outer-segment-and-synapse-during-late-stage-photoreceptor-differentiation-by-controlling-key-genes-of-photoreceptor-transcriptional-regulatory-network
#5
Ying Li, Hailing Hao, Mavis R Swerdel, Hyeon-Yeol Cho, Ki-Bum Lee, Ronald P Hart, Yi Lisa Lyu, Li Cai
Topoisomerase II beta (Top2b) is an enzyme that alters the topologic states of DNA during transcription. Top2b deletion in early retinal progenitor cells causes severe defects in neural differentiation and affects cell survival in all retinal cell types. However, it is unclear whether the observed severe phenotypes are the result of cell-autonomous/primary defects or non-cell-autonomous/secondary defects caused by alterations of other retinal cells. Using photoreceptor cells as a model, we first characterized the phenotypes in Top2b conditional knockout...
March 30, 2017: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/28370177/blood-safety-implications-of-donors-using-hiv-pre-exposure-prophylaxis
#6
C R Seed, H Yang, J F Lee
HIV pre-exposure prophylaxis (PrEP) is the use of one or more antiretroviral medications (in combination) to prevent HIV infection. The most commonly used PrEP medication (Truvada(®) , Gilead Sciences, Inc.) acts by inhibiting HIV-1 reverse transcriptase. If someone who is using PrEP unknowingly becomes HIV infected (termed 'PrEP breakthrough infection'), there may be suppressed viral replication resulting in a virus level undetectable by the most sensitive HIV NAT. Failure to seroconvert and seroreversion (loss of previously detectable HIV antibodies) have also both been observed with 2nd, 3rd and 4th generation screening immunoassays, as well as Western blot assays...
March 31, 2017: Vox Sanguinis
https://www.readbyqxmd.com/read/28369676/transcriptome-wide-identification-of-rna-binding-protein-binding-sites-using-photoactivatable-ribonucleoside-enhanced-crosslinking-immunoprecipitation-par-clip
#7
Henrike Maatz, Marcin Kolinski, Norbert Hubner, Markus Landthaler
RNA-binding proteins (RBPs) mediate important co- and post-transcriptional gene regulation by binding pre-mRNA in a sequence- and/or structure-specific manner. For a comprehensive understanding of RBP function, transcriptome-wide mapping of the RNA-binding sites is essential, and CLIP-seq methods have been developed to elucidate protein/RNA interactions at high resolution. CLIP-seq combines protein/RNA UV-crosslinking with immunoprecipitation (CLIP) followed by high-throughput sequencing of crosslinked RNA fragments...
April 3, 2017: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/28349780/ganoderic-acid-targeting-nuclear-factor-erythroid-2-related-factor-2-in-lung-cancer
#8
Balraj Singh Gill, Sanjeev Kumar, Navgeet
Lung cancer causes huge mortality worldwide, and targeting new pathway may provide an alternative in modulating signaling in cancer. Nuclear factor erythroid 2-related factor 2 is the major regulator of endogenous and exogenous stress by activating numerous antioxidant genes critical in cancer, Alzheimer's, Parkinson's, and inflammatory bowel diseases. Ganoderic acid is a triterpene from basiodiomycetes fungus Ganoderma lucidum with numerous therapeutic effects. In this study, ganoderic acid and its 50 isomers and natural activators were docked by receptor-based molecular docking using Maestro 9...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28323041/quantitative-analyses-of-the-3d-nuclear-landscape-recorded-with-super-resolved-fluorescence-microscopy
#9
Volker J Schmid, Marion Cremer, Thomas Cremer
Recent advancements of super-resolved fluorescence microscopy have revolutionized microscopic studies of cells, including the exceedingly complex structural organization of cell nuclei in space and time. In this paper we describe and discuss tools for (semi-) automated, quantitative 3D analyses of the spatial nuclear organization. These tools allow the quantitative assessment of highly resolved different chromatin compaction levels in individual cell nuclei, which reflect functionally different regions or sub-compartments of the 3D nuclear landscape, and measurements of absolute distances between sites of different chromatin compaction...
March 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28256719/rna-whole-mount-in-situ-hybridization-proximity-ligation-assay-rish-pla-an-assay-for-detecting-rna-protein-complexes-in-intact-cells
#10
Ioannis M Roussis, Fiona A Myers, Garry P Scarlett
Techniques for studying RNA-protein interactions have lagged behind those for DNA-protein interactions as a consequence of the complexities associated with working with RNA. This unit describes a method for the adaptation of the In Situ Hybridization-Proximity Ligation Assay (ISH-PLA) to the study of RNA regulation (rISH-PLA). The rISH-PLA assay allows the identification of a given RNA-protein complex at subcellular and single-cell resolution, thus avoiding the lack of spatial resolution and sensitivity associated with assaying heterogeneous cell populations from which conventional RNA-protein interaction detection techniques suffer...
March 3, 2017: Current Protocols in Cell Biology
https://www.readbyqxmd.com/read/28252184/using-morpholinos-to-control-gene-expression
#11
Jon D Moulton
Morpholino oligonucleotides are stable, uncharged, water-soluble molecules used to block complementary sequences of RNA, preventing processing, read-through, or protein binding at those sites. Morpholinos are typically used to block translation of mRNA and to block splicing of pre-mRNA, though they can block other interactions between biological macromolecules and RNA. Morpholinos are effective, specific, and lack non-antisense effects. They work in any cell that transcribes and translates RNA, but must be delivered into the nuclear/cytosolic compartment to be effective...
March 2, 2017: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/28252182/synthesis-of-geranyl-2-thiouridine-modified-rna
#12
Rui Wang, Phensinee Haruehanroengra, Jia Sheng
This unit describes the chemical synthesis of the S-geranyl-2-thiouridine (ges(2) U) phosphoramidite and its incorporation into RNA oligonucleotides through solid-phase synthesis. Starting from the 2-thiouracil nucleobase and the protected ribose, the 2-thiouridine is synthesized and the geranyl functionality is introduced into the 2-thio position by using geranyl bromide as the geranylating reagent before the conversion of this modified nucleoside into a phosphoramidite building block. The modified phosphoramidite is used to make the geranyl-RNA oligonucleotides with a solid-phase DNA synthesizer...
March 2, 2017: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/28252179/deformability-calculation-for-estimation-of-the-relative-stability-of-chemically-modified-rna-duplexes
#13
Yoshiaki Masaki, Mitsuo Sekine, Kohji Seio
Chemical modification of RNA duplexes alters their stability. We have attempted to develop a computational approach to estimate the thermal stability of chemically modified duplexes. These studies revealed that the deformability of chemically modified RNA duplexes, calculated from molecular dynamics simulations, could be used as a good indicator for estimating the effect of chemical modification on duplex thermal stability. This unit describes how deformability calculation can be applied to estimate the relative stability of chemically modified RNA duplexes...
March 2, 2017: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/28244141/claudin-domain-containing-1-contributing-to-endothelial-cell-adhesion-decreases-in-presence-of-cerebellar-hemorrhage
#14
Masatoshi Ohnishi, Hiroyuki Ochiai, Kohei Matsuoka, Marina Akagi, Yuta Nakayama, Akiho Shima, Arisa Uda, Hiroshi Matsuoka, Jun Kamishikiryo, Akihiro Michihara, Atsuko Inoue
The claudin family comprises four-pass transmembrane proteins involved in the formation of tight junctions (TJs). Relatively recently, claudin domain containing (CLDND) 1, also known as claudin-25, was identified as a novel member of the claudin family. In the present study, we revealed that in the adult murine brain, CLDND1 is abundant in the cerebellum among common sites of intracerebral hemorrhage. Thus, the dynamics of CLDND1 after cerebellar hemorrhage were examined. Both CLDND1 mRNA and protein levels transiently decreased at 24 hr after hemorrhagic insult...
February 28, 2017: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/28213929/exploration-of-the-brn4-regulated-genes-enhancing-adult-hippocampal-neurogenesis-by-rna-sequencing
#15
Jingjing Guo, Xiang Cheng, Lei Zhang, Linmei Wang, Yongxin Mao, Guixiang Tian, Wenhao Xu, Yuhao Wu, Zhi Ma, Jianbing Qin, Meiling Tian, Guohua Jin, Wei Shi, Xinhua Zhang
Adult hippocampal neurogenesis is essential for learning and memory, and its dysfunction is involved in neurodegenerative diseases. However, the molecular mechanisms underlying adult hippocampal neurogenesis are still largely unknown. Our previous studies indicated that the transcription factor Brn4 was upregulated and promoted neuronal differentiation of neural stem cells (NSCs) in the surgically denervated hippocampus in rats. In this study, we use high-throughput RNA sequencing to explore the molecular mechanisms underlying the enhancement of adult hippocampal neurogenesis induced by lentivirus-mediated Brn4 overexpression in vivo...
February 18, 2017: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/28179023/optimization-of-dna-extraction-for-advancing-coral-microbiota-investigations
#16
Laura Weber, Emelia DeForce, Amy Apprill
BACKGROUND: DNA-based sequencing approaches are commonly used to identify microorganisms and their genes and document trends in microbial community diversity in environmental samples. However, extraction of microbial DNA from complex environmental samples like corals can be technically challenging, and extraction methods may impart biases on microbial community structure. METHODS: We designed a two-phase study in order to propose a comprehensive and efficient method for DNA extraction from microbial cells present in corals and investigate if extraction method influences microbial community composition...
February 8, 2017: Microbiome
https://www.readbyqxmd.com/read/28166383/efficient-genome-editing-in-the-oomycete-phytophthora-sojae-using-crispr-cas9
#17
Yufeng Fang, Linkai Cui, Biao Gu, Felipe Arredondo, Brett M Tyler
Phytophthora is a filamentous fungus-like microorganism, but belongs to the oomycetes, in the kingdom Stramenopila. Phytophthora species are notorious as plant destroyers, causing multibillion-dollar damage to agriculture and natural ecosystems worldwide annually. For a long time, genome editing has been unattainable in oomycetes, because of their extremely low rate of homologous recombination. The recent implementation of the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) system in the soybean pathogen Phytophthora sojae, an experimental model for oomycetes, has opened up a powerful new research capability for the oomycete community...
February 6, 2017: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/28150861/quantitation-of-dna-and-rna-with-absorption-and-fluorescence-spectroscopy
#18
Sean R Gallagher
Quantitation of nucleic acids is a fundamental tool in molecular biology that requires accuracy, reliability, and the use of increasingly smaller sample volumes. This unit describes the traditional absorbance measurement at 260 nm and three more sensitive fluorescence techniques employing Hoechst 33258, ethidium bromide, and PicoGreen. The range of the assays covers 25 pg/ml to 50 µg/ml. Absorbance at 260 nm has an effective range from 1 to 50 µg/ml; Hoechst 33258 from 0.01 to 15 µg/ml; ethidium bromide from 0...
February 2, 2017: Current Protocols in Immunology
https://www.readbyqxmd.com/read/28139025/a-de-novo-splice-site-mutation-in-cask-causes-fg-syndrome-4-and-congenital-nystagmus
#19
P Dunn, G P Prigatano, S Szelinger, J Roth, A L Siniard, A M Claasen, R F Richholt, M De Both, J J Corneveaux, A M Moskowitz, C Balak, I S Piras, M Russell, A L Courtright, N Belnap, S Rangasamy, K Ramsey, J M Opitz, D W Craig, V Narayanan, M J Huentelman, I Schrauwen
Mutations in CASK cause X-linked intellectual disability, microcephaly with pontine and cerebellar hypoplasia, optic atrophy, nystagmus, feeding difficulties, GI hypomotility, and seizures. Here we present a patient with a de novo carboxyl-terminus splice site mutation in CASK (c.2521-2A>G) and clinical features of the rare FG syndrome-4 (FGS4). We provide further characterization of genotype-phenotype correlations in CASK mutations and the presentation of nystagmus and the FGS4 phenotype. There is considerable variability in clinical phenotype among patients with a CASK mutation, even among variants predicted to have similar functionality...
January 31, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28101966/the-free-energy-of-locking-a-ring-changing-a-deoxyribonucleoside-to-a-locked-nucleic-acid
#20
You Xu, Alessandra Villa, Lennart Nilsson
Locked nucleic acid (LNA), a modified nucleoside which contains a bridging group across the ribose ring, improves the stability of DNA/RNA duplexes significantly, and therefore is of interest in biotechnology and gene therapy applications. In this study, we investigate the free energy change between LNA and DNA nucleosides. The transformation requires the breaking of the bridging group across the ribose ring, a problematic transformation in free energy calculations. To address this, we have developed a 3-step (easy to implement) and a 1-step protocol (more efficient, but more complicated to setup), for single and dual topologies in classical molecular dynamics simulations, using the Bennett Acceptance Ratio method to calculate the free energy...
June 5, 2017: Journal of Computational Chemistry
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