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https://www.readbyqxmd.com/read/28812932/celebrating-wobble-decoding-half-a-century-and-still-much-is-new
#1
Paul F Agris, Emily R Eruysal, Amithi Narendran, Ville Y P Väre, Sweta Vangaveti, Srivathsan V Ranganathan
A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons...
August 16, 2017: RNA Biology
https://www.readbyqxmd.com/read/28812316/literacy-acquisition-influences-children-s-rapid-automatized-naming
#2
Robin L Peterson, Anne B Arnett, Bruce F Pennington, Brian Byrne, Stefan Samuelsson, Richard K Olson
Previous research has established that learning to read improves children's performance on reading-related phonological tasks, including phoneme awareness (PA) and nonword repetition. Few studies have investigated whether literacy acquisition also promotes children's rapid automatized naming (RAN). We tested the hypothesis that literacy acquisition should influence RAN in an international, longitudinal population sample of twins. Cross-lagged path models evaluated the relationships among literacy, PA, and RAN across four time points from pre-kindergarten through grade 4...
August 15, 2017: Developmental Science
https://www.readbyqxmd.com/read/28811315/quantitative-whole-genome-sequencing-of-circulating-tumor-cells-enables-personalized-combination-therapy-of-metastatic-cancer
#3
Natali Gulbahce, Mark Jesus M Magbanua, Robert Chin, Misha R Agarwal, Xuhao Luo, Jia Liu, Daniel M Hayden, Qing Mao, Serban Ciotlos, Zhenyu Li, Yanxiang Chen, Xingpeng Chen, Yuxiang Li, Rebecca Yu Zhang, Katharine Lee, Rick Tearle, Emily Park, Snezana Drmanac, Hope S Rugo, John W Park, Radoje Drmanac, Brock A Peters
Much effort has been dedicated to developing circulating tumor cells (CTC) as a noninvasive cancer biopsy, but with limited success as yet. In this study, we combine a method for isolation of highly pure CTCs using immunomagnetic enrichment/fluorescence-activated cell sorting with advanced whole genome sequencing (WGS), based on long fragment read technology, to illustrate the utility of an accurate, comprehensive, phased, and quantitative genomic analysis platform for CTCs. Whole genomes of 34 CTCs from a patient with metastatic breast cancer were analyzed as 3,072 barcoded subgenomic compartments of long DNA...
August 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28811246/microbial-metagenomics-mock-scenario-based-sample-simulation-m3s3
#4
Yair Motro, Jacob Moran-Gilad
OBJECTIVES: Shotgun sequencing in increasingly applied in clinical microbiology for unbiased culture-independent diagnosis. While software solutions for metagenomics proliferate, integration of metagenomics in clinical care, requires method standardisation and validation. Virtual metagenomics samples could underpin validation by substituting real samples and thus we sought to develop a novel solution for simulation of metagenomics samples based on user-defined clinical scenarios. METHODS: We designed the Microbial Metagenomics Mock Scenario-based Sample Simulation (M3S3) workflow, which allows users to generate virtual samples from raw reads or assemblies...
August 12, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28811053/burns-first-aid-treatment-in-remote-northern-australia
#5
David J Read, Swee Chin Tan, Linda Ward, Kathleen McDermott
BACKGROUND AND OBJECTIVE: It is well demonstrated that adequate burns first aid treatment (BFAT) improves clinical outcomes for the injured but adequacy remains low in many studies. This study presents a twelve month assessment of the adequacy of burns first aid treatment for patients managed by the Burns Service, Royal Darwin Hospital (RDH). METHODS: Prospective study design of all patients managed by the Burns Service, Royal Darwin Hospital. Data were collated from two sources; RDH Burns Registry, and the Burns Registry of Australia and New Zealand (BRANZ)...
August 12, 2017: Burns: Journal of the International Society for Burn Injuries
https://www.readbyqxmd.com/read/28809013/a-step-by-step-guide-to-assemble-a-reptilian-genome
#6
Asier Ullate-Agote, Yingguang Frank Chan, Athanasia C Tzika
Multiple technologies and software are now available facilitating the de novo sequencing and assembly of any vertebrate genome. Yet the quality of most available sequenced genomes is substantially poorer than that of the golden standard in the field: the human genome. Here, we present a step-by-step protocol for the successful sequencing and assembly of a high-quality snake genome that can be applied to any other reptilian or avian species. We combine the great sequencing depth and accuracy of short reads with the use of different insert size libraries for extended scaffolding followed by optical mapping...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28808417/down-regulation-of-aminopeptidase-n-and-abc-transporter-subfamily-g-transcripts-in-cry1ab-and-cry1ac-resistant-asian-corn-borer-ostrinia-furnacalis-lepidoptera-crambidae
#7
Tiantao Zhang, Brad S Coates, Yueqin Wang, Yidong Wang, Shuxiong Bai, Zhenying Wang, Kanglai He
The Asian corn borer (ACB), Ostrinia furnacalis (Lepidoptera: Crambidae), is a highly destructive pest of cultivated maize throughout East Asia. Bacillus thuringiensis (Bt) crystalline protein (Cry) toxins cause mortality by a mechanism involving pore formation or signal transduction following toxin binding to receptors along the midgut lumen of susceptible insects, but this mechanism and mutations therein that lead to resistance are not fully understood. In the current study, quantitative comparisons were made among midgut expressed transcripts from O...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/28808019/next-step-in-the-ongoing-arms-race-between-myxoma-virus-and-wild-rabbits-in-australia-is-a-novel-disease-phenotype
#8
Peter J Kerr, Isabella M Cattadori, June Liu, Derek G Sim, Jeff W Dodds, Jason W Brooks, Mary J Kennett, Edward C Holmes, Andrew F Read
In host-pathogen arms races, increases in host resistance prompt counteradaptation by pathogens, but the nature of that counteradaptation is seldom directly observed outside of laboratory models. The best-documented field example is the coevolution of myxoma virus (MYXV) in European rabbits. To understand how MYXV in Australia has continued to evolve in wild rabbits under intense selection for genetic resistance to myxomatosis, we compared the phenotypes of the progenitor MYXV and viral isolates from the 1950s and the 1990s in laboratory rabbits with no resistance...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28806977/a-tandem-simulation-framework-for-predicting-mapping-quality
#9
Ben Langmead
Read alignment is the first step in most sequencing data analyses. Because a read's point of origin can be ambiguous, aligners report a mapping quality, which is the probability that the reported alignment is incorrect. Despite its importance, there is no established and general method for calculating mapping quality. I describe a framework for predicting mapping qualities that works by simulating a set of tandem reads. These are like the input reads in important ways, but the true point of origin is known...
August 10, 2017: Genome Biology
https://www.readbyqxmd.com/read/28806713/activity-groups-for-persons-with-dementia-personal-predictors-of-participation-engagement-and-mood
#10
Jiska Cohen-Mansfield
This study examined the relationship between personal characteristics and attendance, engagement, sleep, and mood outcomes of persons with dementia participating in group activities. The purpose of this study is to examine which persons with dementia benefit most from group interventions. Sixty-nine persons with dementia were observed by research and therapeutic recreation staff during 10 types of group activities (reading aloud with discussion, choral-singing, baking, creative storytelling, brain games, active games, exercise, reminiscence poetry, holiday newsletter, and holiday discussions) on multiple outcomes (attendance duration, sleep, engagement, active participation, attitude, and positive mood)...
July 25, 2017: Psychiatry Research
https://www.readbyqxmd.com/read/28802455/from-control-to-causation-validating-a-complex-systems-model-of-running-related-injury-development-and-prevention
#11
A Hulme, P M Salmon, R O Nielsen, G J M Read, C F Finch
INTRODUCTION: There is a need for an ecological and complex systems approach for better understanding the development and prevention of running-related injury (RRI). In a previous article, we proposed a prototype model of the Australian recreational distance running system which was based on the Systems Theoretic Accident Mapping and Processes (STAMP) method. That model included the influence of political, organisational, managerial, and sociocultural determinants alongside individual-level factors in relation to RRI development...
November 2017: Applied Ergonomics
https://www.readbyqxmd.com/read/28801936/normative-data-and-psychometric-properties-of-a-farsi-translation-of-the-strange-stories-test
#12
Zahra Shahrivar, Mehdi Tehrani-Doost, Anahita Khorrami Banaraki, Azar Mohammadzadeh, Francesca Happe
BACKGROUND AND OBJECTIVE: The Strange Stories test is one of the most commonly used tests to evaluate advanced "theory of mind," i.e. attribution of mental states. Normative data and psychometric properties of a new Farsi translation of this test were evaluated in a large community-based sample of Iranian school-aged children. METHODS: Through randomized cluster sampling, 398 children aged 9-11 years studying at 20 elementary schools were recruited from 4 central regions of Tehran, Iran...
August 11, 2017: Autism Research: Official Journal of the International Society for Autism Research
https://www.readbyqxmd.com/read/28801410/radiographic-features-of-importance-in-the-national-institute-for-occupational-safety-and-health-administered-coal-workers-health-surveillance-program-characterising-the-use-of-the-other-symbols
#13
Cara N Halldin, Janet M Hale, David J Blackley, A Scott Laney
OBJECTIVE: The National Institute for Occupation Safety and Health-administered Coal Workers' Health Surveillance Program (CWHSP) provides radiographic pneumoconiosis screening for US coal miners. Radiographs are classified by readers according to International Labour Office criteria. In addition to pneumoconiotic parenchymal and pleural lung abnormalities, readers document radiographic features of importance (other symbols). Other symbols are not meant to imply a diagnosis or interpretation but are relevant as they provide information beyond a pneumoconiosis classification for features related to dust exposure and other aetiologies...
August 11, 2017: BMJ Open
https://www.readbyqxmd.com/read/28797240/a-comparison-of-illumina-and-ion-torrent-sequencing-platforms-in-the-context-of-differential-gene-expression
#14
Nicholas F Lahens, Emanuela Ricciotti, Olga Smirnova, Erik Toorens, Eun Ji Kim, Giacomo Baruzzo, Katharina E Hayer, Tapan Ganguly, Jonathan Schug, Gregory R Grant
BACKGROUND: Though Illumina has largely dominated the RNA-Seq field, the simultaneous availability of Ion Torrent has left scientists wondering which platform is most effective for differential gene expression (DGE) analysis. Previous investigations of this question have typically used reference samples derived from cell lines and brain tissue, and do not involve biological variability. While these comparisons might inform studies of tissue-specific expression, marked by large-scale transcriptional differences, this is not the common use case...
August 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28797083/the-transcriptional-response-to-the-olive-fruit-fly-bactrocera-oleae-reveals-extended-differences-between-tolerant-and-susceptible-olive-olea-europaea-l-varieties
#15
Filomena Grasso, Mariangela Coppola, Fabrizio Carbone, Luciana Baldoni, Fiammetta Alagna, Gaetano Perrotta, Antonio J Pérez-Pulido, Antonio Garonna, Paolo Facella, Loretta Daddiego, Loredana Lopez, Alessia Vitiello, Rosa Rao, Giandomenico Corrado
The olive fruit fly Bactrocera oleae (Diptera: Tephritidae) is the most devastating pest of cultivated olive (Olea europaea L.). Intraspecific variation in plant resistance to B. oleae has been described only at phenotypic level. In this work, we used a transcriptomic approach to study the molecular response to the olive fruit fly in two olive cultivars with contrasting level of susceptibility. Using next-generation pyrosequencing, we first generated a catalogue of more than 80,000 sequences expressed in drupes from approximately 700k reads...
2017: PloS One
https://www.readbyqxmd.com/read/28796552/diagnostic-accuracy-of-mri-versus-ct-for-the-evaluation-of-acute-appendicitis-in-children-and-young-adults
#16
Sonja Kinner, Perry J Pickhardt, Erica L Riedesel, Kara G Gill, Jessica B Robbins, Douglas R Kitchin, Timothy J Ziemlewicz, John B Harringa, Scott B Reeder, Michael D Repplinger
OBJECTIVE: Appendicitis is frequently diagnosed in the emergency department, most commonly using CT. The purpose of this study was to compare the diagnostic accuracy of contrast-enhanced MRI with that of contrast-enhanced CT for the diagnosis of appendicitis in adolescents when interpreted by abdominal radiologists and pediatric radiologists. SUBJECTS AND METHODS: Our study included a prospectively enrolled cohort of 48 patients (12-20 years old) with nontraumatic abdominal pain who underwent CT and MRI...
August 10, 2017: AJR. American Journal of Roentgenology
https://www.readbyqxmd.com/read/28794957/prevalence-of-metabolic-syndrome-and-metabolic-syndrome-components-in-young-adults-a-pooled-analysis
#17
Paul B Nolan, Graeme Carrick-Ranson, James W Stinear, Stacey A Reading, Lance C Dalleck
Metabolic syndrome (MetSyn) represents a clustering of different metabolic abnormalities. MetSyn prevalence is present in approximately 25% of all adults with increased prevalence in advanced ages. The presence of one component of MetSyn increases the risk of developing MetSyn later in life and likely represents a high lifetime burden of cardiovascular disease risk. Therefore we pooled data from multiple studies to establish the prevalence of MetSyn and MetSyn component prevalence across a broad range of ethnicities...
September 2017: Preventive Medicine Reports
https://www.readbyqxmd.com/read/28794062/high-quality-de-novo-genome-assembly-of-the-dekkera-bruxellensis-yeast-isolate-using-nanopore-minion-sequencing
#18
Téo Fournier, Jean-Sébastien Gounot, Kelle Freel, Corinne Cruaud, Arnaud Lemainque, Jean-Marc Aury, Patrick Wincker, Joseph Schacherer, Anne Friedrich
Genetic variation in natural populations represents the raw material for phenotypic diversity. Species-wide characterization of genetic variants is crucial to have a deeper insight into the genotype-phenotype relationship. With the advent of new sequencing strategies and more recently the release of long-read sequencing platforms, it is now possible to explore the genetic diversity of any non-model organisms, representing a fundamental resource for biological research. In the frame of population genomic surveys, a first step is to obtain the complete sequence and high quality assembly of a reference genome...
August 9, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28794037/reverse-genetics-system-demonstrates-that-rotavirus-non-structural-protein-nsp6-is-not-essential-for-viral-replication-in-cell-culture
#19
Satoshi Komoto, Yuta Kanai, Saori Fukuda, Masanori Kugita, Takahiro Kawagishi, Naoto Ito, Makoto Sugiyama, Yoshiharu Matsuura, Takeshi Kobayashi, Koki Taniguchi
The use of overlapping open reading frames (ORFs) to synthesize more than one unique protein from a single mRNA has been described for several viruses. Segment 11 of the rotavirus genome encodes two non-structural proteins, NSP5 and NSP6. The NSP6 ORF is present in the vast majority of rotavirus strains, and therefore the NSP6 protein would be expected to have a function in viral replication. However, there is no direct evidence of its function or requirement in the viral replication cycle yet. Here, taking advantage of a recently established plasmid only-based reverse genetics system that allows rescue of recombinant rotaviruses entirely from cloned cDNAs, we generated NSP6-deficient viruses to directly address its significance in the viral replication cycle...
August 9, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28792546/host-plant-driven-transcriptome-plasticity-in-the-salivary-glands-of-the-cabbage-looper-trichoplusia-ni
#20
Loren J Rivera-Vega, David A Galbraith, Christina M Grozinger, Gary W Felton
Generalist herbivores feed on a wide array of plants and need to adapt to varying host qualities and defenses. One of the first insect derived secretions to come in contact with the plant is the saliva. Insect saliva is potentially involved in both the pre-digestion of the host plant as well as induction/suppression of plant defenses, yet how the salivary glands respond to changes in host plant at the transcriptional level is largely unknown. The objective of this study was to determine how the labial salivary gland transcriptome varies according to the host plant on which the insect is feeding...
2017: PloS One
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