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https://www.readbyqxmd.com/read/28213929/exploration-of-the-brn4-regulated-genes-enhancing-adult-hippocampal-neurogenesis-by-rna-sequencing
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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...
January 19, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28087069/safety-tolerability-and-antiviral-effect-of-rg-101-in-patients-with-chronic-hepatitis-c-a-phase-1b-double-blind-randomised-controlled-trial
#7
Meike H van der Ree, J Marleen de Vree, Femke Stelma, Sophie Willemse, Marc van der Valk, Svend Rietdijk, Richard Molenkamp, Janke Schinkel, Ad C van Nuenen, Ulrich Beuers, Salah Hadi, Marten Harbers, Eva van der Veer, Kai Liu, John Grundy, Amy K Patick, Adam Pavlicek, Jacqueline Blem, Michael Huang, Paul Grint, Steven Neben, Neil W Gibson, Neeltje A Kootstra, Hendrik W Reesink
BACKGROUND: miR-122 is an important host factor for hepatitis C virus (HCV) replication. The aim of this study was to assess the safety and tolerability, pharmacokinetics, and antiviral effect of a single dose of RG-101, a hepatocyte targeted N-acetylgalactosamine conjugated oligonucleotide that antagonises miR-122, in patients with chronic HCV infection with various genotypes. METHODS: In this randomised, double-blind, placebo-controlled, multicentre, phase 1B study, patients were randomly assigned to RG-101 or placebo (7:1)...
January 10, 2017: Lancet
https://www.readbyqxmd.com/read/28060411/scarless-cas9-assisted-recombineering-no-scar-in-escherichia-coli-an-easy-to-use-system-for-genome-editing
#8
Christopher R Reisch, Kristala L J Prather
The discovery and development of genome editing systems that leverage the site-specific DNA endonuclease system CRISPR/Cas9 has fundamentally changed the ease and speed of genome editing in many organisms. In eukaryotes, the CRISPR/Cas9 system utilizes a "guide" RNA to enable the Cas9 nuclease to make a double-strand break at a particular genome locus, which is repaired by non-homologous end joining (NHEJ) repair enzymes, often generating random mutations in the process. A specific alteration of the target genome can also be generated by supplying a DNA template in vivo with a desired mutation, which is incorporated by homology-directed repair...
January 5, 2017: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/28055115/measurement-of-t-cell-telomere-length-using-amplified-signal-fish-staining-and-flow-cytometry
#9
Andrea L Henning, Danielle E Levitt, Jakob L Vingren, Brian K McFarlin
Exposure to pathogen-associated molecular patterns (PAMPS), damage-associated molecular patterns (DAMPS), and physiologically challenging stimuli either positively or negatively affect leukocyte maturity. Cellular maturity has implications for the effectiveness of host response to bacterial or viral infection and/or tissue injury. Thus, the ability to accurately assess cellular maturity and health is important to fully understand immune status and function. The most common technique for measuring cellular maturity is to measure telomere length; however, existing techniques are not optimized for single-cell measurements using flow cytometry...
January 5, 2017: Current Protocols in Cytometry
https://www.readbyqxmd.com/read/28036033/mec1-atr-the-program-manager-of-nucleic-acids-inc
#10
REVIEW
Wenyi Feng
Eukaryotic cells are equipped with surveillance mechanisms called checkpoints to ensure proper execution of cell cycle events. Among these are the checkpoints that detect DNA damage or replication perturbations and coordinate cellular activities to maintain genome stability. At the forefront of damage sensing is an evolutionarily conserved molecule, known respectively in budding yeast and humans as Mec1 (Mitosis entry checkpoint 1) and ATR (Ataxia telangiectasia and Rad3-related protein). Through phosphorylation, Mec1/ATR activates downstream components of a signaling cascade to maintain nucleotide pool balance, protect replication fork integrity, regulate activation of origins of replication, coordinate DNA repair, and implement cell cycle delay...
December 28, 2016: Genes
https://www.readbyqxmd.com/read/28026860/pioglitazone-together-with-imatinib-in-chronic-myeloid-leukemia-a-proof-of-concept-study
#11
Philippe Rousselot, Stéphane Prost, Joelle Guilhot, Lydia Roy, Gabriel Etienne, Laurence Legros, Aude Charbonnier, Valérie Coiteux, Pascale Cony-Makhoul, Francoise Huguet, Emilie Cayssials, Jean-Michel Cayuela, Francis Relouzat, Marc Delord, Heriberto Bruzzoni-Giovanelli, Laure Morisset, François-Xavier Mahon, François Guilhot, Philippe Leboulch
BACKGROUND: We recently reported that peroxisome proliferator-activated receptor γ agonists target chronic myeloid leukemia (CML) quiescent stem cells in vitro by decreasing transcription of STAT5. Here in the ACTIM phase 2 clinical trial, we asked whether pioglitazone add-on therapy to imatinib would impact CML residual disease, as assessed by BCR-ABL1 transcript quantification. METHODS: CML patients were eligible if treated with imatinib for at least 2 years at a stable daily dose, having yielded major molecular response (MMR) but not having achieved molecular response 4...
December 27, 2016: Cancer
https://www.readbyqxmd.com/read/27991686/co-expression-changes-of-lncrnas-and-mrnas-in-the-cervical-sympathetic-ganglia-in-diabetic-cardiac-autonomic-neuropathic-rats
#12
Guilin Li, Xuan Sheng, Yurong Xu, Huaide Jiang, Chaoran Zheng, Jingjing Guo, Shanshan Sun, Zhihua Yi, Shulan Qin, Shuangmei Liu, Yun Gao, Chunping Zhang, Hong Xu, Bing Wu, Lifang Zou, Shangdong Liang, Gaochun Zhu
Cardiac autonomic neuropathy in Type 2 diabetes (T2D) is often a devastating complication. Long non-coding RNAs (lncRNAs) have important effects on both normal development and disease pathogenesis. In this study, we explored the expression profiles of some lncRNAs involved in inflammation which may be co-expressed with messenger RNA (mRNA) in superior cervical and stellate ganglia after type 2 diabetic injuries. Total RNA isolated from 10 pairs of superior cervical and stellate ganglia in diabetic and normal male rats was hybridized to lncRNA arrays for detections...
December 19, 2016: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/27976414/low-testosterone-alters-the-activity-of-mouse-prostate-stem-cells
#13
Ye Zhou, Ben Copeland, Maya Otto-Duessel, Miaoling He, Susan Markel, Tim W Synold, Jeremy O Jones
BACKGROUND: Low serum testosterone (low T) has been repeatedly linked to worse outcomes in men with newly diagnosed prostate cancer (PC). How low T contributes to these outcomes is unknown. Here we demonstrate that exposure to low T causes significant changes in the mouse prostate and prostate stem cells. METHODS: Mice were castrated and implanted with capsules to achieve castrate, normal, or sub-physiological levels of T. After 6 weeks of treatment, LC-MS/MS was used to quantify the levels of T and dihydrotestosterone (DHT) in serum and prostate tissue...
December 14, 2016: Prostate
https://www.readbyqxmd.com/read/27933721/shared-molecular-networks-in-orofacial-and-neural-tube-development
#14
Youssef A Kousa, Tamer A Mansour, Haitham Seada, Samaneh Matoo, Brian C Schutte
BACKGROUND: Single genetic variants can affect multiple tissues during development. Thus it is possible that disruption of shared gene regulatory networks might underlie syndromic presentations. In this study, we explore this idea through examination of two critical developmental programs that control orofacial and neural tube development and identify shared regulatory factors and networks. Identification of these networks has the potential to yield additional candidate genes for poorly understood developmental disorders and assist in modeling and perhaps managing risk factors to prevent morbidly and mortality...
December 9, 2016: Birth Defects Research. Part A, Clinical and Molecular Teratology
https://www.readbyqxmd.com/read/27925666/enriching-s-4-u-rna-using-methane-thiosulfonate-mts-chemistry
#15
Erin E Duffy, Matthew D Simon
Metabolic labeling of cellular RNA is a useful approach to study RNA biology. 4-Thiouridine (s(4) U) is a convenient nucleoside for metabolic labeling because it is cell permeable and is incorporated into newly transcribed RNA, and the sulfur moiety provides a handle for biochemical purification. However, a critical step in the purification of s(4) U-RNA is the efficiency of the chemistry used to enrich s(4) U-RNA. Here, we present a protocol for s(4) U-RNA enrichment that includes efficient and reversible covalent chemistry to biotinylate s(4) U-RNA using the activated disulfide methane thiosulfonate conjugated to biotin (MTS-biotin), followed by enrichment on streptavidin beads...
December 7, 2016: Current Protocols in Chemical Biology
https://www.readbyqxmd.com/read/27925173/potential-of-long-non-coding-rnas-in-cancer-patients-from-biomarkers-to-therapeutic-targets
#16
REVIEW
Subash Chandra Gupta, Yashoda Nandan Tripathi
Because of high specificity and easy detection in the tissues, serum, plasma, urine and saliva, interest in exploring the potential of long non-coding RNAs (lncRNAs) in cancer patients continues to increase. LncRNAs have shown potential as a biomarker in the diagnosis and prognosis of bladder cancer, prostate cancer, gastric cancer, pancreatic cancer, breast cancer and many other cancer types. Some lncRNAs have also been used as adjunct to improve the specificity and sensitivity of existing biomarkers. The molecular tools such as RNA-seq, RNA-FISH, ic-SHAPE and quantitative real-time PCR have been used for examining the lncRNAs' potential...
December 7, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27911495/synthesis-and-evaluation-of-caged-sirna-with-terminal-single-vitamin-e-modification
#17
Jiali Yang, Lijia Yu, Liangliang Zhang, Xingsu Long, Yuzhuo Ji, Xinjing Tang
RNA-induced gene silencing has been widely applied as a powerful research tool in drug development due to its sequence-specific degradation of target mRNA. Conditional regulation of gene functions with small interfering RNAs (siRNAs) is highly useful, especially when specific gene expression regulation with spatiotemporal resolution and amplitude is desired. Here, the synthesis of a series of new caged siRNAs with vitamin E (vitE) modification and/or a single photolabile linker at the 5' terminal is described...
December 1, 2016: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/27911494/determining-functional-aptamer-protein-interaction-by-biolayer-interferometry
#18
Xinhui Lou, Martin Egli, Xianbin Yang
Short single-stranded nucleic acids called aptamers are widely being explored as recognition molecules of high affinity and specificity for binding a wide range of target molecules, particularly protein targets. In biolayer interferometry (BLI), a simple Dip-and-Read approach in which the aptamer-coated biosensors are dipped into microplate wells is used to study the interactions between an aptamer and its target protein. Here we describe the protocol for the analysis of the interaction between a well-characterized anti-thrombin RNA aptamer with thrombin (Basic Protocol)...
December 1, 2016: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/27911493/rna-secondary-structure-prediction
#19
David H Mathews, Douglas H Turner, Richard M Watson
In this unit, protocols are provided for predicting RNA secondary structure with the user-friendly RNAstructure desktop computer program and the RNAstructure Web server. The minimum free energy structure and a set of suboptimal structures with similar free energies are predicted. Prediction of high-affinity oligonucleotide binding sites to a structured RNA target is also presented. © 2016 by John Wiley & Sons, Inc.
December 1, 2016: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/27900797/evidence-for-feedback-regulation-following-cholesterol-lowering-therapy-in-a-prostate-cancer-xenograft-model
#20
Elizabeth M Masko, Mahmoud A Alfaqih, Keith R Solomon, William T Barry, Christopher B Newgard, Michael J Muehlbauer, Nikolaos A Valilis, Tameika E Phillips, Susan H Poulton, Alexis R Freedland, Stephanie Sun, Shweta K Dambal, Sergio E Sanders, Everardo Macias, Michael R Freeman, Mark W Dewhirst, Salvatore V Pizzo, Stephen J Freedland
BACKGROUND: Epidemiologic data suggest cholesterol-lowering drugs may prevent the progression of prostate cancer, but not the incidence of the disease. However, the association of combination therapy in cholesterol reduction on prostate or any cancer is unclear. In this study, we compared the effects of the cholesterol lowering drugs simvastatin and ezetimibe alone or in combination on the growth of LAPC-4 prostate cancer in vivo xenografts. METHODS: Proliferation assays were conducted by MTS solution and assessed by Student's t-test...
November 30, 2016: Prostate
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