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Suhyung Cho, Donghui Choe, Eunju Lee, Sun Chang Kim, Bernhard Ø Palsson, Byung-Kwan Cho
Along with functional advances in the use of CRISPR/Cas9 for genome editing, endonuclease-deficient Cas9 (dCas9) has provided a versatile molecular tool for exploring gene functions. In principle, differences in cell phenotypes that result from the RNA-guided modulation of transcription levels by dCas9 are critical for inferring with gene function; however, the effect of intracellular dCas9 expression on bacterial morphology has not been systematically elucidated. Here, we observed unexpected morphological changes in Escherichia coli mediated by dCas9, which were then characterized using RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq)...
March 15, 2018: ACS Synthetic Biology
Alessandra Livigni, Laura O'Hara, Marta E Polak, Tim Angus, Derek W Wright, Lee B Smith, Tom C Freeman
A major endeavor of systems biology is the construction of graphical and computational models of biological pathways as a means to better understand their structure and function. Here, we present a protocol for a biologist-friendly graphical modeling scheme that facilitates the construction of detailed network diagrams, summarizing the components of a biological pathway (such as proteins and biochemicals) and illustrating how they interact. These diagrams can then be used to simulate activity flow through a pathway, thereby modeling its dynamic behavior...
April 2018: Nature Protocols
Valentina Morsan, Carlo Fantoni, Maria Anna Tallandini
AIM: To verify whether it is appropriate to use age correction for infants born preterm in all the developmental domains (cognitive, linguistic, and motor) considered by the Bayley Scales of Infant and Toddler Development, Third Edition (Bayley-III). METHOD: Seventy-three infants born preterm (26-35wks) without major neurological sequelae and 67 infants born at term were assessed at 12 months (corrected age for infants born preterm). The performance of the infants born preterm was assessed with two different evaluations: scores based on uncorrected age and scores based on corrected age...
March 14, 2018: Developmental Medicine and Child Neurology
Shashank Gandhi, Florian Razy-Krajka, Lionel Christiaen, Alberto Stolfi
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 has emerged as a revolutionary tool for fast and efficient targeted gene knockouts and genome editing in almost any organism. The laboratory model tunicate Ciona is no exception. Here, we describe our latest protocol for the design, implementation, and evaluation of successful CRISPR/Cas9-mediated gene knockouts in somatic cells of electroporated Ciona embryos. Using commercially available reagents, publicly accessible plasmids, and free web-based software applications, any Ciona researcher can easily knock out any gene of interest in their favorite embryonic cell lineage...
2018: Advances in Experimental Medicine and Biology
Keita Yoshida, Nicholas Treen
Targeted mutagenesis of genes-of-interest is a powerful method of addressing the functions of genes. Genome editing techniques, such as transcriptional activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 systems, have enabled this approach in various organisms because of their ease of use. In the ascidian, Ciona intestinalis, recent studies show that TALEN-based knockout can be applied to establishing both mutant lines and tissue-specific knockout for addressing gene functions...
2018: Advances in Experimental Medicine and Biology
Weizhi Yu, Hong Xu, Ying Xue, Dong An, Huairui Li, Wei Chen, Deqin Yu, Yiping Sun, Jianmei Ma, Yiyuan Tang, Zhaoyang Xiao, Shengming Yin
Introduction: Social isolation enhances the aggressive behavior of animals, but the detailed mechanism remains unclear. Epigenetic studies have suggested that Htr2c RNA editing is closely related to aggressive behavior. This study aims to obtain a fundamental understanding of how social isolation impacts adenosine deaminase acting on RNA 1 (ADAR1, RNA editing enzyme) and Htr2c RNA editing, leading to aggressive behavior, and explore the effective solutions for the recovery of this behavior...
March 2018: Brain and Behavior
Betty Kollia, Corey H Basch, Christina Mouser, Aurea J Deleon
Background: Considering how many people obtain information about their health online, the aim of this study was to describe the content of the currently most widely viewed YouTube videos related to concussions and to test the hypothesis that consumer videos would be anecdotal, while other sources would be more informational. Methods: The term "concussion" was used to search for videos with 100,000 or more views on YouTube that were posted in English or Spanish...
2018: International Journal of Preventive Medicine
Shuping Yang, Xin Li, Xinfeng Liu, Xiangbin Ding, Xiangbo Xin, Congfei Jin, Sheng Zhang, Guangpeng Li, Hong Guo
MSTN -encoded myostatin is a negative regulator of skeletal muscle development. Here, we utilized the gluteus tissues from MSTN gene editing and wild type Luxi beef cattle which are native breed of cattle in China, performed tandem mass tag (TMT) -based comparative proteomics and phosphoproteomics analyses to investigate the regulatory mechanism of MSTN related to cellular metabolism and signaling pathway in muscle development. Out of 1,315 proteins, 69 differentially expressed proteins (DEPs) were found in global proteomics analysis...
February 16, 2018: Oncotarget
Mathew A Cherian, Sydney Olson, Hemalatha Sundaramoorthi, Kitra Cates, Xiaogang Cheng, John Harding, Andrew Martens, Grant A Challen, Manoj Tyagi, Lee Ratner, Daniel Rauch
The human T cell leukemia virus-1 (HTLV-1) oncoprotein Tax drives cell proliferation and resistance to apoptosis early in the pathogenesis of adult T-cell leukemia (ATL). Subsequently, likely as a result of specific immuno-editing, Tax expression is downregulated and functionally replaced by somatic driver mutations of the host genome. Both amplification and point mutations of interferon regulatory factor 4 (IRF4) have been previously detected in ATL, and the K59R mutation is the most common single-nucleotide variation in IRF4 and is found exclusively in ATL...
March 14, 2018: Journal of Biological Chemistry
Alexander B Olawaiye, David G Mutch
No abstract text is available yet for this article.
March 12, 2018: Gynecologic Oncology
Neftali Vazquez, Lilia Sanchez, Rebecca Marks, Eduardo Martinez, Victor Fanniel, Alma Lopez, Andrea Salinas, Itzel Flores, Jesse Hirschmann, Robert Gilkerson, Erin Schuenzel, Robert Dearth, Reginald Halaby, Wendy Innis-Whitehouse, Megan Keniry
BACKGROUND: Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided adaptive immune systems are found in prokaryotes to defend cells from foreign DNA. CRISPR Cas9 systems have been modified and employed as genome editing tools in wide ranging organisms. Here, we provide a detailed protocol to truncate genes in mammalian cells using CRISPR Cas9 editing. We describe custom donor vector construction using Gibson assembly with the commonly utilized pcDNA3 vector as the backbone...
March 14, 2018: BMC Molecular Biology
Tafadzwa Mlambo, Sandra Nitsch, Markus Hildenbeutel, Marianna Romito, Maximilian Müller, Claudia Bossen, Sven Diederichs, Tatjana I Cornu, Toni Cathomen, Claudio Mussolino
Targeted modulation of gene expression represents a valuable approach to understand the mechanisms governing gene regulation. In a therapeutic context, it can be exploited to selectively modify the aberrant expression of a disease-causing gene or to provide the target cells with a new function. Here, we have established a novel platform for achieving precision epigenome editing using designer epigenome modifiers (DEMs). DEMs combine in a single molecule a DNA binding domain based on highly specific transcription activator-like effectors (TALEs) and several effector domains capable of inducing DNA methylation and locally altering the chromatin structure to silence target gene expression...
March 10, 2018: Nucleic Acids Research
Eva K Brinkman, Arne N Kousholt, Tim Harmsen, Christ Leemans, Tao Chen, Jos Jonkers, Bas van Steensel
Template-directed CRISPR/Cas9 editing is a powerful tool for introducing subtle mutations in genomes. However, the success rate of incorporation of the desired mutations at the target site is difficult to predict and therefore must be empirically determined. Here, we adapted the widely used TIDE method for quantification of templated editing events, including point mutations. The resulting TIDER method is a rapid, cheap and accessible tool for testing and optimization of template-directed genome editing strategies...
March 10, 2018: Nucleic Acids Research
Caroline Dos Santos Costa, Thaynã Ramos Flores, Andrea Wendt, Rosália Garcia Neves, Maria Cecília Formoso Assunção, Iná S Santos
The aim of this cross-sectional study was to investigate the association between sedentary behavior and consumption of ultra-processed foods (UPF) among Brazilian adolescents. The study used data from the 2015 edition of the Brazilian National School Health Survey (PeNSE). Daily consumption of at least one group of UPF was the outcome, and the principal exposure was daily time spent in sedentary behavior (hours spent sitting, except for time sitting at school). We calculated prevalence rates, prevalence ratios, and 95% confidence intervals (95%CI)...
March 8, 2018: Cadernos de Saúde Pública
Stephanie F Polites, Rachel M Nygaard, Pooja N Reddy, Martin D Zielinski, Chad J Richardson, Terri A Elsbernd, Branden M Petrun, Sean L Weinberg, Sherrie Murphy, Donald D Potter, Denise B Klinkner, Christopher R Moir
BACKGROUND: The 9th edition of ATLS recommends up to three crystalloid boluses in pediatric trauma patients with consideration of transfusion after the second bolus however this approach is debated. We aimed to determine if requirement of more than one fluid bolus predicts the need for transfusion. METHODS: 2010-2016 highest tier activation patients <15 years of age from two ACS Level I pediatric trauma centers were identified from prospectively maintained trauma databases...
March 12, 2018: Journal of Trauma and Acute Care Surgery
Lin Xie, Jay Onysko, Howard Morrison
INTRODUCTION: Surveillance of childhood cancer incidence trends can inform etiologic research, policy and programs. This study presents the first population-based report on demographic and geographic variations in incidence trends of detailed pediatric diagnostic groups in Canada. METHODS: The Canadian Cancer Registry data were used to calculate annual age-standardized incidence rates (ASIRs) from 1992 to 2010 among children less than 15 years of age by sex, age and region for the 12 main diagnostic groups and selected subgroups of the International Classification of Childhood Cancer (ICCC), 3rd edition...
March 2018: Health Promotion and Chronic Disease Prevention in Canada
Shruti Varadarajan
No abstract text is available yet for this article.
March 2018: Family Medicine
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