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https://www.readbyqxmd.com/read/29131534/universal-target-enrichment-baits-for-anthozoan-cnidaria-phylogenomics-new-approaches-to-long-standing-problems
#1
A M Quattrini, B C Faircloth, L F Dueñas, T C L Bridge, M R Brugler, I F Calixto-Botía, D M DeLeo, S Forêt, S Herrera, S Lee, D J Miller, C Prada, G Rádis-Baptista, C Ramírez-Portilla, J A Sánchez, E Rodríguez, C S McFadden
Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the ~7500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequenced across a diversity of taxa. We designed and tested 16,306 RNA baits to capture 720 Ultraconserved Element loci and 1,071 exon loci. Library preparation and target enrichment was performed on 33 taxa from all orders within the class Anthozoa...
November 13, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29125846/characterization-of-the-lycium-barbarum-fruit-transcriptome-and-development-of-est-ssr-markers
#2
Chunling Chen, Meilong Xu, Cuiping Wang, Gaixia Qiao, Wenwen Wang, Zhaoyun Tan, Tiantian Wu, Zhengsheng Zhang
Lycium barbarum, commonly known as goji, is important in Chinese herbal medicine and its fruit is a very important agricultural and biological product. However, the molecular mechanism of formation of its fruit and associated medicinal and nutritional components is unexplored. Moreover, this species lacks SSR markers due to lack of genomic and transcriptomic information. In this study, a total of 139,333 unigenes with average length of 1049 bp and N50 of 1579 bp are obtained by trinity assembly from Illumina sequencing reads...
2017: PloS One
https://www.readbyqxmd.com/read/29120386/high-quality-unigenes-and-microsatellite-markers-from-tissue-specific-transcriptome-and-development-of-a-database-in-clusterbean-cyamopsis-tetragonoloba-l-taub
#3
Hukam C Rawal, Shrawan Kumar, Amitha Mithra S V, Amolkumar U Solanke, Deepti Nigam, Swati Saxena, Anshika Tyagi, Sureshkumar V, Neelam R Yadav, Pritam Kalia, Narendra Pratap Singh, Nagendra Kumar Singh, Tilak Raj Sharma, Kishor Gaikwad
Clusterbean (Cyamopsis tetragonoloba L. Taub), is an important industrial, vegetable and forage crop. This crop owes its commercial importance to the presence of guar gum (galactomannans) in its endosperm which is used as a lubricant in a range of industries. Despite its relevance to agriculture and industry, genomic resources available in this crop are limited. Therefore, the present study was undertaken to generate RNA-Seq based transcriptome from leaf, shoot, and flower tissues. A total of 145 million high quality Illumina reads were assembled using Trinity into 127,706 transcripts and 48,007 non-redundant high quality (HQ) unigenes...
November 9, 2017: Genes
https://www.readbyqxmd.com/read/29113841/immunotherapy-with-checkpoint-blockade-in-the-treatment-of-urothelial-carcinoma
#4
REVIEW
Arlene O Siefker-Radtke, Andrea B Apolo, Trinity J Bivalacqua, Philippe E Spiess, Peter C Black
PURPOSE: Although immunotherapy has a long history in the treatment of urothelial carcinoma, its use was limited to intravesical therapy for non-muscle-invasive disease. The development of immune checkpoint blockers for systemic delivery has expanded the application of immunotherapy to advanced metastatic urothelial cancers. MATERIALS AND METHODS: The PubMed database was searched for publications regarding immune checkpoint blockers for the treatment of patients with urothelial carcinoma...
November 4, 2017: Journal of Urology
https://www.readbyqxmd.com/read/29109919/the-unexpected-depths-of-genome-skimming-data-a-case-study-examining-goodeniaceae-floral-symmetry-genes
#5
Brent A Berger, Jiahong Han, Emily B Sessa, Andrew G Gardner, Kelly A Shepherd, Vincent A Ricigliano, Rachel S Jabaily, Dianella G Howarth
Premise of the study: The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae. Methods: Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes...
October 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/29100493/k-mer-clustering-algorithm-using-a-mapreduce-framework-application-to-the-parallelization-of-the-inchworm-module-of-trinity
#6
Chang Sik Kim, Martyn D Winn, Vipin Sachdeva, Kirk E Jordan
BACKGROUND: De novo transcriptome assembly is an important technique for understanding gene expression in non-model organisms. Many de novo assemblers using the de Bruijn graph of a set of the RNA sequences rely on in-memory representation of this graph. However, current methods analyse the complete set of read-derived k-mer sequence at once, resulting in the need for computer hardware with large shared memory. RESULTS: We introduce a novel approach that clusters k-mers as the first step...
November 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29098789/gene-expression-differs-in-co-dominant-prairie-grasses-under-drought
#7
Ava M Hoffman, Melinda D Smith
Grasslands of the Central US are expected to experience severe droughts and other climate extremes in the future, yet we know little about how these grasses will respond in terms of gene expression. We compared gene expression in Andropogon gerardii and Sorghastrum nutans, two closely related co-dominant C4 grasses responsible for the majority of ecosystem function, using RNA-seq. We compared Trinity assemblies within each species to determine annotated functions of transcripts responding to drought. Subsequently, we compared homologous annotated gene-groups across the two species using cross-species meta-level analysis and functional clustering based on key terms...
November 3, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29092955/lesiontracker-extensible-open-source-zero-footprint-web-viewer-for-cancer-imaging-research-and-clinical-trials
#8
Trinity Urban, Erik Ziegler, Rob Lewis, Chris Hafey, Cheryl Sadow, Annick D Van den Abbeele, Gordon J Harris
Oncology clinical trials have become increasingly dependent upon image-based surrogate endpoints for determining patient eligibility and treatment efficacy. As therapeutics have evolved and multiplied in number, the tumor metrics criteria used to characterize therapeutic response have become progressively more varied and complex. The growing intricacies of image-based response evaluation, together with rising expectations for rapid and consistent results reporting, make it difficult for site radiologists to adequately address local and multicenter imaging demands...
November 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/29083435/dairy-intakes-in-older-irish-adults-and-effects-on-vitamin-micronutrient-status-data-from-the-tuda-study
#9
E Laird, M C Casey, M Ward, L Hoey, C F Hughes, K McCarroll, C Cunningham, J J Strain, H McNulty, A M Molloy
BACKGROUND: Consumption of dairy products has been associated with positive health outcomes including a lower risk of hypertension, improved bone health and a reduction in the risk of type 2 diabetes. The suggested dairy intake for health in older adults is three servings per day but recent analysis of the NHANES data for older adults reported 98% were not meeting these recommendations. No studies have investigated the consequences of such declines in the dairy intakes of Irish older adults and the subsequent effects on vitamin micronutrient status...
2017: Journal of Nutrition, Health & Aging
https://www.readbyqxmd.com/read/29071295/data-of-first-de-novo-transcriptome-assembly-of-a-non-model-species-hawksbill-sea-turtle-eretmochelys-imbricate-nesting-of-the-colombian-caribean
#10
Javier Hernández-Fernández
The hawksbill sea turtle, Eretmochelys imbricata, is an endangered species of the Caribbean Colombian coast due to anthropic and natural factors that have decreased their population levels. Little is known about the genes that are involved in their immune system, sex determination, aging and others important functions. The data generated represents RNA sequencing and the first de-novo assembly of transcripts expressed in the blood of the hawksbill sea turtle. The raw FASTQ files were deposited in the NCBI SRA database with accession number SRX2653641...
December 2017: Data in Brief
https://www.readbyqxmd.com/read/29068303/three-turbulent-spots-that-could-ground-value-based-care
#11
Michael D Dalzell
Many of today's value-based care models trace their roots to the Institute for Healthcare Improvement's Triple Aim. Arguably, their sustainability may hinge on how true they stay to that trinity of improving population health, the patient experience, and per capita costs.
September 2017: Managed Care
https://www.readbyqxmd.com/read/29067547/low-levels-of-psma-expression-limit-the-utility-of-18-f-dcfpyl-pet-ct-for-imaging-urothelial-carcinoma
#12
Scott P Campbell, Alexander S Baras, Mark W Ball, Max Kates, Noah M Hahn, Trinity J Bivalacqua, Michael H Johnson, Martin G Pomper, Mohamad E Allaf, Steven P Rowe, Michael A Gorin
OBJECTIVE: To explore the clinical utility of PSMA-targeted (18)F-DCFPyL PET/CT in patients with metastatic urothelial carcinoma. METHODS: Three patients with metastatic urothelial carcinoma were imaged with (18)F-DCFPyL PET/CT. All lesions with perceptible radiotracer uptake above background were considered positive. Maximum standardized uptake values were recorded for each detected lesion and findings on (18)F-DCFPyL PET/CT were compared to those on conventional imaging studies...
October 24, 2017: Annals of Nuclear Medicine
https://www.readbyqxmd.com/read/29066225/urinary-tissue-engineering-challenges-and-opportunities
#13
REVIEW
Anirudha Singh, Trinity J Bivalacqua, Nikolai Sopko
INTRODUCTION: In this review, we discuss major advancements and common challenges in constructing and regenerating a neo-urinary conduit (NUC). First, we focus on the need for regenerating the urothelium, the hallmark the urine barrier, unique to urinary tissues. Second, we focus on clinically feasible scaffolds based on decellularized matrices and molded collagen that are currently of great research interest. AIM: To discuss the major advancements in constructing a tissue-engineered NUC (TE-NUC) and the challenges involved in their successful clinical translation...
October 21, 2017: Sexual Medicine Reviews
https://www.readbyqxmd.com/read/29062051/gene-expression-atlas-of-fruit-ripening-and-transcriptome-assembly-from-rna-seq-data-in-octoploid-strawberry-fragaria%C3%A2-%C3%A3-%C3%A2-ananassa
#14
José F Sánchez-Sevilla, José G Vallarino, Sonia Osorio, Aureliano Bombarely, David Posé, Catharina Merchante, Miguel A Botella, Iraida Amaya, Victoriano Valpuesta
RNA-seq has been used to perform global expression analysis of the achene and the receptacle at four stages of fruit ripening, and of the roots and leaves of strawberry (Fragaria × ananassa). About 967 million reads and 191 Gb of sequence were produced, using Illumina sequencing. Mapping the reads in the related genome of the wild diploid Fragaria vesca revealed differences between the achene and receptacle development program, and reinforced the role played by ethylene in the ripening receptacle. For the strawberry transcriptome assembly, a de novo strategy was followed, generating separate assemblies for each of the ten tissues and stages sampled...
October 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29052505/transcriptome-assembly-in-suaeda-aralocaspica-to-reveal-the-distinct-temporal-gene-mirna-alterations-between-the-dimorphic-seeds-during-germination
#15
Lei Wang, Hong-Ling Wang, Lan Yin, Chang-Yan Tian
BACKGROUND: Dimorphic seeds from Suaeda aralocaspica exhibit different germination behaviors that are thought to be a bet-hedging strategy advantageous in harsh and unpredictable environments. To understand the molecular mechanisms of Suaeda aralocaspica dimorphic seed germination, we applied RNA sequencing and small RNA sequencing for samples collected at three germination stages. RESULTS: A total of 79,414 transcripts were assembled using Trinity, of which 57...
October 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29032237/hospital-charges-and-length-of-stay-following-radical-cystectomy-in-the-eras-era
#16
Alice Semerjian, Niv Milbar, Max Kates, Michael A Gorin, Hiten D Patel, Heather J Chalfin, Steven M Frank, Christopher L Wu, William W Yang, Deb Hobson, Lindsay Robertson, Elizabeth Wick, Mark P Schoenberg, Phillip M Pierorazio, Michael H Johnson, C J Stimson, Trinity J Bivalacqua
OBJECTIVE: To report our center's experience with Enhanced Recovery after Surgery (ERAS) pathway for radical cystectomy (RC), specifically evaluating complications, LOS, 30- and 90-day readmissions, and hospital charges. Pathways of this type have been shown to decrease length of stay (LOS) and post-operative ileus. However, concerns persist that ERAS is costly and increases readmissions. To date, limited studies have evaluated these concerns. MATERIALS AND METHODS: Our ERAS protocol was implemented for RC in December 2015...
October 12, 2017: Urology
https://www.readbyqxmd.com/read/29030342/the-sex-specific-impact-of-aging-on-the-blood-pressure-response-to-exercise
#17
Joel D Trinity, Gwenael Layec, Corey R Hart, Russell S Richardson
An exaggerated blood pressure (BP) response to exercise has been linked to cardiovascular disease (CVD), but little is known about the impact of age and sex on this response. Therefore, this study examined the hemodynamic and skeletal muscle metabolic response to dynamic plantar flexion exercise, at 40% of WRmax, in 40 physical activity-matched young (n=20, 23±1 yr) and old (n=20, 73±2 yr), equally distributed, male and female subjects. Central hemodynamics and BP (finometer), popliteal artery (PA) blood flow (Doppler ultrasound), and skeletal muscle metabolism (phosphorous magnetic resonance spectroscopy, (31)P-MRS) were measured during 5 mins of plantar flexion exercise...
October 13, 2017: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/29028004/geobiological-feedbacks-and-the-evolution-of-thermoacidophiles
#18
Daniel R Colman, Saroj Poudel, Trinity L Hamilton, Jeff R Havig, Matthew J Selensky, Everett L Shock, Eric S Boyd
Oxygen-dependent microbial oxidation of sulfur compounds leads to the acidification of natural waters. How acidophiles and their acidic habitats evolved, however, is largely unknown. Using 16S rRNA gene abundance and composition data from 72 hot springs in Yellowstone National Park, Wyoming, we show that hyperacidic (pH<3.0) hydrothermal ecosystems are dominated by a limited number of archaeal lineages with an inferred ability to respire O2. Phylogenomic analyses of 584 existing archaeal genomes revealed that hyperacidophiles evolved independently multiple times within the Archaea, each coincident with the emergence of the ability to respire O2, and that these events likely occurred in the recent evolutionary past...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/28977394/development-of-a-liquid-chromatography-tandem-mass-spectrometry-method-for-the-simultaneous-determination-of-four-cannabinoids-in-umbilical-cord-tissue
#19
Fang Wu, Triniti L Scroggin, Torri D Metz, Gwendolyn A McMillin
In utero exposure to marijuana may cause various short- and long-term health problems, such as stillbirth, low birth weight and decreased cognitive function. Detection of in utero marijuana exposure with a relatively new specimen type, umbilical cord tissue, can be used to plan treatment and guide social management. In this study, a liquid chromatography-tandem mass spectrometry (LC-MS-MS) assay was developed for the simultaneous identification of four cannabinoids in umbilical cord tissue, including ∆9-tetrahydrocannabinol (THC), 11-nor-9-carboxy-∆9--THC (THC-COOH), 11-hydroxy-∆9-THC (11-OH-THC) and cannabinol (CBN)...
September 15, 2017: Journal of Analytical Toxicology
https://www.readbyqxmd.com/read/28953888/cg-dinucleotide-suppression-enables-antiviral-defence-targeting-non-self-rna
#20
Matthew A Takata, Daniel Gonçalves-Carneiro, Trinity M Zang, Steven J Soll, Ashley York, Daniel Blanco-Melo, Paul D Bieniasz
Vertebrate genomes exhibit marked CG suppression-that is, lower than expected numbers of 5'-CG-3' dinucleotides. This feature is likely to be due to C-to-T mutations that have accumulated over hundreds of millions of years, driven by CG-specific DNA methyl transferases and spontaneous methyl-cytosine deamination. Many RNA viruses of vertebrates that are not substrates for DNA methyl transferases mimic the CG suppression of their hosts. This property of viral genomes is unexplained. Here we show, using synonymous mutagenesis, that CG suppression is essential for HIV-1 replication...
October 5, 2017: Nature
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