keyword
MENU ▼
Read by QxMD icon Read
search

Inc RNA

keyword
https://www.readbyqxmd.com/read/27911495/synthesis-and-evaluation-of-caged-sirna-with-terminal-single-vitamin-e-modification
#1
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
#2
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
#3
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
#4
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
https://www.readbyqxmd.com/read/27898186/human-papillomavirus-dna-detection-in-fine-needle-aspirates-as-indicator-of-human-papillomavirus-positive-oropharyngeal-squamous-cell-carcinoma-a-prospective-study
#5
Lars Sivars, David Landin, Linnea Haeggblom, Nikolaos Tertipis, Nathalie Grün, Cinzia Bersani, Linda Marklund, Mehran Ghaderi, Anders Näsman, Torbjörn Ramqvist, Cecilia Nordfors, Eva Munck-Wikland, Edneia Tani, Tina Dalianis
BACKGROUND: Human papillomavirus (HPV)-positive oropharyngeal squamous cell carcinoma (SCC) has a better outcome than most head neck squamous cell carcinomas (HNSCCs) and an HPV-positive lymph node metastasis likely has an HPV-positive oropharyngeal SCC origin. Determining HPV-status in cervical lymph nodes by fine-needle aspiration cytology (FNAC) may be useful for diagnosis. METHODS: FNACs from 66 patients with neck masses were prospectively examined for HPV DNA and HPV16 mRNA by a polymerase chain reaction (PCR)-based assay, and the data correlated to diagnosis and HPV-status obtained from histopathological specimens...
November 29, 2016: Head & Neck
https://www.readbyqxmd.com/read/27870441/sexual-divergence-in-activity-dependent-neuroprotective-protein-impacting-autism-schizophrenia-and-alzheimer-s-disease
#6
REVIEW
Illana Gozes
Discovered in our laboratory, activity-dependent neuroprotective protein (ADNP) interacts with key regulatory proteins, including the chromatin remodeling complex SWI/SNF, proteins associated with RNA splicing, RNA translation, microtubule dynamics, and autophagy. ADNP regulates > 400 genes during mouse embryonic development and is essential for neural tube closure. ADNP key functions extend from mice to men, with mutations causing ADNP-related ID/autism syndrome, also known as the Helsmoortel-Van der Aa syndrome...
January 2, 2017: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/27859387/molecular-simulations-to-delineate-functional-conformational-transitions-in-the-hcv-polymerase
#7
Ester Sesmero, Jodian A Brown, Ian F Thorpe
Hepatitis C virus (HCV) is a global health concern for which there is no vaccine available. The HCV polymerase is responsible for the critical function of replicating the RNA genome of the virus. Transitions between at least two conformations (open and closed) are necessary to allow the enzyme to replicate RNA. In this study, molecular dynamic simulations were initiated from multiple crystal structures to understand the free energy landscape (FEL) explored by the enzyme as it interconverts between these conformations...
November 12, 2016: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/27858971/molecular-identification-and-subtype-analysis-of-blastocystis
#8
C Rune Stensvold, C Graham Clark
Several typing methods have been used in studies aiming to unravel the molecular epidemiology of Blastocystis, which is one of the most common intestinal parasites in human and many non-human hosts. Such studies have the potential to add to knowledge on Blastocystis transmission, host specificity, phylogeography, and clinical and public health significance, but rely on robust, standardized methods by which data can be generated and compared directly between studies. One of the most used methods is "barcoding,", which involves single-round PCR amplification and sequencing of partial small subunit ribosomal RNA genes of the parasites...
November 18, 2016: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/27857825/evaluation-of-the-upgraded-version-2-0-of-the-roche-cobas-%C3%A2-ampliprep-cobas-%C3%A2-taqman-hiv-1-qualitative-assay-in-central-african-children
#9
C D Mossoro-Kpinde, M A Jenabian, J C Gody, L Robin, P Talla, Jdd Longo, G Grésenguet, L Belec
BACKGROUND: Several commercially available molecular techniques were developed based on subtype B of HIV-1, which represents only 10% of HIV strains worldwide. Indeed, in sub-Saharan Africa, non-B subtypes of HIV-1 are predominant. The aim of this study was to evaluate the performances of the COBAS(®) AmpliPrep/COBAS(®) (CAP/CTM) HIV-1 Qualitative assays to detect the broad range of HIV-1 variants circulating in Central Africa and compare to the outgoing CAP/CTM HIV-1 Quantitative test v2...
2016: Open AIDS Journal
https://www.readbyqxmd.com/read/27800642/p110%C3%AE-inhibition-reduces-histone-h3k4-di-methylation-in-prostate-cancer
#10
Jun Pang, Yue-Wu Yang, Yiling Huang, Jun Yang, Hao Zhang, Ruibao Chen, Liang Dong, Yan Huang, Dongying Wang, Jihong Liu, Benyi Li
INTRODUCTION AND AIMS: Epigenetic alteration plays a major role in the development and progression of human cancers, including prostate cancer. Histones are the key factors in modulating gene accessibility to transcription factors and post-translational modification of the histone N-terminal tail including methylation is associated with either transcriptional activation (H3K4me2) or repression (H3K9me3). Furthermore, phosphoinositide 3-kinase (PI3 K) signaling and the androgen receptor (AR) are the key determinants in prostate cancer development and progression...
November 1, 2016: Prostate
https://www.readbyqxmd.com/read/27785895/transcriptome-analysis-of-zebrafish-embryos-exposed-to-deltamethrin
#11
Tsung-Cheng Chueh, Li-Sung Hsu, Chin-Ming Kao, Tung-Wei Hsu, Hung-Yu Liao, Kuan-Yi Wang, Ssu Ching Chen
Deltamethrin (DTM), a type II pyrethroid, is one of the most commonly used insecticides. The increased use of pyrethroid leads to potential adverse effects, particularly in sensitive populations such as children and pregnant women. None of the related studies was focused on the transcriptome responses in zebrafish embryos after treatment with DTM; therefore, RNA-seq, a high-throughput method, was performed to analyze the global expression of differential expressed genes (DEGs) in zebrafish embryos treated with DTM (40 and 80 μg/L) from fertilization to 48 h postfertilization (hpf) as compared with that in the control group (without DTM treatment)...
October 27, 2016: Environmental Toxicology
https://www.readbyqxmd.com/read/27775175/genetic-risk-mechanisms-of-posttraumatic-stress-disorder-in-the-human-brain
#12
Rahul A Bharadwaj, Andrew E Jaffe, Qiang Chen, Amy Deep-Soboslay, Aaron L Goldman, Michelle I Mighdoll, John A Cotoia, Anna C Brandtjen, JooHeon Shin, Thomas M Hyde, Venkata S Mattay, Daniel R Weinberger, Joel E Kleinman
Posttraumatic stress disorder (PTSD) follows exposure to a traumatic event in susceptible individuals. Recently, genome-wide association studies have identified a number of genetic sequence variants that are associated with the risk of developing PTSD. To follow up on identifying the molecular mechanisms of these risk variants, we performed genotype to RNA sequencing-derived quantitative expression (whole gene, exon, and exon junction levels) analysis in the dorsolateral prefrontal cortex (DLPFC) of normal postmortem human brains...
October 24, 2016: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/27769309/analytical-characteristics-and-comparative-evaluation-of-aptima-hiv-1-quant-dx-assay-with-ampliprep-cobas-taqman-hiv-1-test-v2-0
#13
Angelos Hatzakis, Helen Papachristou, Sangeetha J Nair, Jacqueline Fortunko, Tracy Foote, HeeCheol Kim, Tashi L Peling, Andrew J Worlock
BACKGROUND: Quantitation of HIV-RNA is critically important for diagnosis, prognosis, treatment, monitoring and assessment of infectivity in HIV-1 infection. The objective of this study was to assess performance characteristics of the Aptima HIV-1 Quant Dx assay (Aptima), a new transcription mediated amplification (TMA), fully integrated and automated assay from Hologic Inc., San Diego, CA, USA. The analytical sensitivity, analytical specificity, precision and detection of HIV-1 subtypes were tested based on commercially available international standards or panels...
October 21, 2016: Virology Journal
https://www.readbyqxmd.com/read/27753212/methamphetamine-induced-psychosis-is-associated-with-dna-hypomethylation-and-increased-expression-of-akt1-and-key-dopaminergic-genes
#14
Shabnam Nohesara, Mohammad Ghadirivasfi, Mahmood Barati, Mohammad-Reza Ghasemzadeh, Samira Narimani, Zohreh Mousavi-Behbahani, Mohammadtaghi Joghataei, Mansoureh Soleimani, Mozhgan Taban, Soraya Mehrabi, Sam Thiagalingam, Hamid Mostafavi Abdolmaleky
Methamphetamine, one of the most frequently used illicit drugs worldwide, can induce psychosis in a large fraction of abusers and it is becoming a major problem for the health care institutions. There is some evidence that genetic and epigenetic factors may play roles in methamphetamine psychosis. In this study, we examined methamphetamine-induced epigenetic and expression changes of several key genes involved in psychosis. RNA and DNA extracted from the saliva samples of patients with methamphetamine dependency with and without psychosis as well as control subjects (each group 25) were analyzed for expression and promoter DNA methylation status of DRD1, DRD2, DRD3, DRD4, MB-COMT, GAD1, and AKT1 using qRT-PCR and q-MSP, respectively...
December 2016: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/27740722/detection-of-airborne-respiratory-syncytial-virus-in-a-pediatric-acute-care-clinic
#15
Stephanie A Grayson, Pamela S Griffiths, Miriam K Perez, Giovanni Piedimonte
OBJECTIVE: Respiratory syncytial virus (RSV) is the most common cause of respiratory illness in infants and young children, but this virus is also capable of re-infecting adults throughout life. Universal precautions to prevent its transmission consist of gown and glove use, but masks and goggles are not routinely required because it is believed that RSV is unlikely to be transmitted by the airborne route. Our hypothesis was that RSV is present in respirable-size particles aerosolized by patients seen in a pediatric acute care setting...
October 14, 2016: Pediatric Pulmonology
https://www.readbyqxmd.com/read/27729940/the-analytical-validation-of-the-oncotype-dx-recurrence-score-assay
#16
Frederick L Baehner
In vitro diagnostic multivariate index assays are highly complex molecular assays that can provide clinically actionable information regarding the underlying tumour biology and facilitate personalised treatment. These assays are only useful in clinical practice if all of the following are established: analytical validation (i.e., how accurately/reliably the assay measures the molecular characteristics), clinical validation (i.e., how consistently/accurately the test detects/predicts the outcomes of interest), and clinical utility (i...
2016: Ecancermedicalscience
https://www.readbyqxmd.com/read/27723745/c9orf72-interaction-with-cofilin-modulates-actin-dynamics-in-motor-neurons
#17
Rajeeve Sivadasan, Daniel Hornburg, Carsten Drepper, Nicolas Frank, Sibylle Jablonka, Anna Hansel, Xenia Lojewski, Jared Sterneckert, Andreas Hermann, Pamela J Shaw, Paul G Ince, Matthias Mann, Felix Meissner, Michael Sendtner
Intronic hexanucleotide expansions in C9ORF72 are common in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia, but it is unknown whether loss of function, toxicity by the expanded RNA or dipeptides from non-ATG-initiated translation are responsible for the pathophysiology. We determined the interactome of C9ORF72 in motor neurons and found that C9ORF72 was present in a complex with cofilin and other actin binding proteins. Phosphorylation of cofilin was enhanced in C9ORF72-depleted motor neurons, in patient-derived lymphoblastoid cells, induced pluripotent stem cell-derived motor neurons and post-mortem brain samples from ALS patients...
October 10, 2016: Nature Neuroscience
https://www.readbyqxmd.com/read/27723087/strand-specific-transcriptome-sequencing-using-smart-technology
#18
Magnolia Bostick, Nathalie Bolduc, Alisa Lehman, Andrew Farmer
Next-generation sequencing is empowering a deeper understanding of biology by enabling RNA expression analysis over the entire transcriptome with high sensitivity and a wide dynamic range. One powerful application within this field is stranded RNA sequencing (RNA-seq), which is necessary to distinguish overlapping genes and to conduct comprehensive annotation and quantification of long non-coding RNAs. Commonly used methods for generating strand-specific RNA-seq libraries are often complicated by protocols that require several rounds of enzymatic treatments and clean-up steps, making them time-intensive, insensitive, and unsuitable for processing several samples simultaneously...
October 10, 2016: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/27723086/transcriptome-analysis-at-the-single-cell-level-using-smart-technology
#19
Rachel N Fish, Magnolia Bostick, Alisa Lehman, Andrew Farmer
RNA sequencing (RNA-seq) is a powerful method for analyzing cell state, with minimal bias, and has broad applications within the biological sciences. However, transcriptome analysis of seemingly homogenous cell populations may in fact overlook significant heterogeneity that can be uncovered at the single-cell level. The ultra-low amount of RNA contained in a single cell requires extraordinarily sensitive and reproducible transcriptome analysis methods. As next-generation sequencing (NGS) technologies mature, transcriptome profiling by RNA-seq is increasingly being used to decipher the molecular signature of individual cells...
October 10, 2016: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/27723083/protein-interaction-profile-sequencing-pip-seq
#20
Shawn W Foley, Brian D Gregory
Every eukaryotic RNA transcript undergoes extensive post-transcriptional processing from the moment of transcription up through degradation. This regulation is performed by a distinct cohort of RNA-binding proteins which recognize their target transcript by both its primary sequence and secondary structure. Here, we describe protein interaction profile sequencing (PIP-seq), a technique that uses ribonuclease-based footprinting followed by high-throughput sequencing to globally assess both protein-bound RNA sequences and RNA secondary structure...
October 10, 2016: Current Protocols in Molecular Biology
keyword
keyword
76948
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"