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https://www.readbyqxmd.com/read/28327966/de-novo-transcriptome-assemblies-of-four-xylem-sap-feeding-insects
#1
Erica E Tassone, Charles C Cowden, S J Castle
Background: Spittle bugs and sharpshooters are well-known xylem sap-feeding insects and vectors of the phytopathogenic bacterium Xylella fastidiosa (Wells), a causal agent of Pierce's disease of grapevines and other crop diseases. Specialized feeding on nutrient-deficient xylem sap is relatively rare among insect herbivores, and only limited genomic and transcriptomic information has been generated for xylem-sap feeders. To develop a more comprehensive understanding of biochemical adaptations and symbiotic relationships that support survival on a nutritionally austere dietary source, transcriptome assemblies for three sharpshooter species and one spittlebug species were produced...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28318100/abrogation-of-red-blood-cell-g6pd-enzyme-activity-through-heat-treatment-development-of-survey-material-for-the-uk-neqas-g6pd-scheme
#2
D R Roper, B De la Salle, V Soni, K Fletcher, J A Green
INTRODUCTION: Participation in external quality assessment (EQA) is central to the maintenance of high-quality laboratory results in patient diagnosis and clinical trials. Laboratories in the TAF112582 DETECTIVE study (ClinicalTrials.gov identifier: NCT01376167) are enrolled in the United Kingdom National Quality Assessment Scheme (UK NEQAS) for glucose-6-phosphate dehydrogenase (G6PD) quantitative assay, which utilizes ovine (sheep) blood as a readily available source of apparently G6PD-deficient survey material...
March 20, 2017: International Journal of Laboratory Hematology
https://www.readbyqxmd.com/read/28316427/evaluation-of-toxoplasma-gondii-soluble-whole-and-excretory-secretary-antigens-for-diagnosis-of-toxoplasmosis-by-elisa-test
#3
S Pishkari, S Shojaee, H Keshavarz, M Salimi, M Mohebali
The present study was performed to compare the soluble, whole and excretory/secretary antigens of Toxoplasma gondii (RH strain) in diagnosis of toxoplasmosis by ELISA method. Tachyzoites of T. gondii, RH strain were injected in intra-peritoneal cavity of BALB/c mice, after 4 days tachyzoites were harvested by peritoneal washing of the mice. For soluble antigen, exudates were centrifuged and sediment sonicated and then centrifuged at 4 °C, 1 h, supernatant collected and density of protein determined by Bradford method...
March 2017: Journal of Parasitic Diseases: Official Organ of the Indian Society for Parasitology
https://www.readbyqxmd.com/read/28292763/oxygen-delivery-and-the-restoration-of-the-muscle-energetic-balance-following-exercise-implications-for-delayed-muscle-recovery-in-patients-with-copd
#4
Gwenael Layec, Corey R Hart, Joel D Trinity, Oh-Sung Kwon, Matthew J Rossman, Ryan M Broxterman, Yann Le Fur, Eun-Kee Jeong, Russell S Richardson
Patients with chronic obstructive pulmonary disease (COPD) experience a delayed recovery from skeletal muscle fatigue following exhaustive exercise that likely contributes to their progressive loss of mobility. As this phenomenon is not well understood, this study sought to examine post-exercise peripheral oxygen (O2) transport and muscle metabolism dynamics in patients with COPD, two important determinants of muscle recovery. Twenty four subjects, 12 non-hypoxemic patients with COPD and 12 healthy subjects with a sedentary lifestyle, performed dynamic plantar flexion exercise at 40% of maximal work rate (WRmax) with phosphorus magnetic resonance spectroscopy ((31)P-MRS), near-infrared spectroscopy (NIRS), and vascular Doppler ultrasound assessments...
March 14, 2017: American Journal of Physiology. Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28288127/the-effect-of-face-patch-microstimulation-on-perception-of-faces-and-objects
#5
Sebastian Moeller, Trinity Crapse, Le Chang, Doris Y Tsao
What is the range of stimuli encoded by face-selective regions of the brain? We asked how electrical microstimulation of face patches in macaque inferotemporal cortex affects perception of faces and objects. We found that microstimulation strongly distorted face percepts and that this effect depended on precise targeting to the center of face patches. While microstimulation had no effect on the percept of many non-face objects, it did affect the percept of some, including non-face objects whose shape is consistent with a face (for example, apples) as well as somewhat facelike abstract images (for example, cartoon houses)...
March 13, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28286074/human-penile-transplantation-an-emerging-therapy-for-genitourinary-reconstruction
#6
REVIEW
Nikolai A Sopko, Sami H Tuffaha, Denver Lough, Gerald Brandacher, W P Andrew Lee, Trinity J Bivalacqua, Richard J Redett, Arthur L Burnett
PURPOSE: Reconstruction of complex functional structures is increasingly being performed with vascularized composite allo-transplantation (VCA). Penile transplantation is a novel VCA treatment option for severe penile tissue loss and disfigurement. Three allogeneic human penile transplantations have been reported. We review these cases as well as penile transplant indications, pre-clinical models, and immunosuppression therapy. MATERIALS AND METHODS: We performed a comprehensive literature review for the years 1970 to 2016 via MEDLINE, PubMed, and Google with the key words "penis transplantation", "penile rejection", "penile replantation", "penile tissue loss", and "penis vascularized composite allo-transplantation"...
March 9, 2017: Journal of Urology
https://www.readbyqxmd.com/read/28252805/postoperative-complications-following-intraoperative-radiotherapy-in-abdominopelvic-malignancy-a-single-institution-analysis-of-113-consecutive-patients
#7
Eihab Abdelfatah, Andrew Page, Justin Sacks, Phillip Pierorazio, Trinity Bivalacqua, Jonathan Efron, Stephanie Terezakis, Susan Gearhart, Sandy Fang, Bashar Safar, Timothy M Pawlik, Elwood Armour, Amy Hacker-Prietz, Joseph Herman, Nita Ahuja
BACKGROUND: Intraoperative radiotherapy (IORT) has advantages over external beam radiation therapy (EBRT). Few studies have described side effects associated with its addition. We evaluated our institution's experience with abdominopelvic IORT to assess safety by postoperative complication rates. METHODS: Prospectively collected IRB-approved database of all patients receiving abdominopelvic IORT (via high dose rate brachytherapy) at Johns Hopkins Hospital between November 2006 and May 2014 was reviewed...
March 2, 2017: Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28250805/playing-hide-and-seek-with-repeats-in-local-and-global-de-novo-transcriptome-assembly-of-short-rna-seq-reads
#8
Leandro Lima, Blerina Sinaimeri, Gustavo Sacomoto, Helene Lopez-Maestre, Camille Marchet, Vincent Miele, Marie-France Sagot, Vincent Lacroix
BACKGROUND: The main challenge in de novo genome assembly of DNA-seq data is certainly to deal with repeats that are longer than the reads. In de novo transcriptome assembly of RNA-seq reads, on the other hand, this problem has been underestimated so far. Even though we have fewer and shorter repeated sequences in transcriptomics, they do create ambiguities and confuse assemblers if not addressed properly. Most transcriptome assemblers of short reads are based on de Bruijn graphs (DBG) and have no clear and explicit model for repeats in RNA-seq data, relying instead on heuristics to deal with them...
2017: Algorithms for Molecular Biology: AMB
https://www.readbyqxmd.com/read/28248990/a-transcriptomic-survey-of-migdolus-fryanus-sugarcane-rhizome-borer-larvae
#9
Darlan Gonçalves Nakayama, Célio Dias Santos Júnior, Luciano Takeshi Kishi, Rafael Pedezzi, Adelita Carolina Santiago, Andrea Soares-Costa, Flavio Henrique-Silva
Sugarcane, a major crop grown in the tropical and subtropical areas of the world, is produced mainly for sucrose, which is used as a sweetener or for the production of bioethanol. Among the numerous pests that significantly affect the yield of sugarcane, the sugarcane rhizome borer (Migdolus fryanus, a cerambycidae beetle) is known to cause severe damage to the crops in Brazil. The absence of molecular information about this insect reinforces the need for studies and an effective method to control this pest...
2017: PloS One
https://www.readbyqxmd.com/read/28248422/methane-occurrences-in-aquifers-overlying-the-barnett-shale-play-with-a-focus-on-parker-county-texas
#10
Jean-Philippe Nicot, Patrick Mickler, Toti Larson, M Clara Castro, Roxana Darvari, Kristine Uhlman, Ruth Costley
Clusters of elevated methane concentrations in aquifers overlying the Barnett Shale play have been the focus of recent national attention as they relate to impacts of hydraulic fracturing. The objective of this study was to assess the spatial extent of high dissolved methane previously observed on the western edge of the play (Parker County) and to evaluate its most likely source. A total of 509 well water samples from 12 counties (14,500 km(2) ) were analyzed for methane, major ions, and carbon isotopes. Most samples were collected from the regional Trinity Aquifer and show only low levels of dissolved methane (85% of 457 unique locations <0...
March 1, 2017: Ground Water
https://www.readbyqxmd.com/read/28246647/evaporative-fractionation-of-zinc-during-the-first-nuclear-detonation
#11
James M D Day, Frédéric Moynier, Alex P Meshik, Olga V Pradivtseva, Donald R Petit
Volatile element and compound abundances vary widely in planets and were set during the earliest stages of solar system evolution. Experiments or natural analogs approximating these early conditions are limited. Using silicate glass formed from arkosic sands during the first nuclear detonation at the Trinity test site, New Mexico, we show that the isotopes of zinc were fractionated during evaporation. The green silicate glasses, termed "trinitite," show +0.5 ± 0.1‰/atomic mass unit isotopic fractionation from ~200 m to within 10 m of ground zero of the detonation, corresponding to an α fractionation factor between 0...
February 2017: Science Advances
https://www.readbyqxmd.com/read/28241869/de-novo-transcriptome-assembly-functional-annotation-and-differential-gene-expression-analysis-of-juvenile-and-adult-e-fetida-a-model-oligochaete-used-in-ecotoxicological-studies
#12
Michelle Thunders, Jo Cavanagh, Yinsheng Li
BACKGROUND: Earthworms are sensitive to toxic chemicals present in the soil and so are useful indicator organisms for soil health. Eisenia fetida are commonly used in ecotoxicological studies; therefore the assembly of a baseline transcriptome is important for subsequent analyses exploring the impact of toxin exposure on genome wide gene expression. RESULTS: This paper reports on the de novo transcriptome assembly of E. fetida using Trinity, a freely available software tool...
February 27, 2017: Biological Research
https://www.readbyqxmd.com/read/28224052/compacting-and-correcting-trinity-and-oases-rna-seq-de-novo-assemblies
#13
Cédric Cabau, Frédéric Escudié, Anis Djari, Yann Guiguen, Julien Bobe, Christophe Klopp
BACKGROUND: De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved...
2017: PeerJ
https://www.readbyqxmd.com/read/28220135/differential-gene-expression-analysis-in-polygonum-minus-leaf-upon-24-h-of-methyl-jasmonate-elicitation
#14
Reyhaneh Rahnamaie-Tajadod, Kok-Keong Loke, Hoe-Han Goh, Normah M Noor
Polygonum minus is an herbal plant that grows in Southeast Asian countries and traditionally used as medicine. This plant produces diverse secondary metabolites such as phenolic compounds and their derivatives, which are known to have roles in plant abiotic and biotic stress responses. Methyl jasmonate (MeJA) is a plant signaling molecule that triggers transcriptional reprogramming in secondary metabolism and activation of defense responses against many biotic and abiotic stresses. However, the effect of MeJA elicitation on the genome-wide expression profile in the leaf tissue of P...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28210265/rna-seq-of-guar-cyamopsis-tetragonoloba-l-taub-leaves-de-novo-transcriptome-assembly-functional-annotation-and-development-of-genomic-resources
#15
Umesh K Tanwar, Vikas Pruthi, Gursharn S Randhawa
Genetic improvement in industrially important guar (Cyamopsis tetragonoloba, L. Taub.) crop has been hindered due to the lack of sufficient genomic or transcriptomic resources. In this study, RNA-Seq technology was employed to characterize the transcriptome of leaf tissues from two guar varieties, namely, M-83 and RGC-1066. Approximately 30 million high-quality pair-end reads of each variety generated by Illumina HiSeq platform were used for de novo assembly by Trinity program. A total of 62,146 non-redundant unigenes with an average length of 679 bp were obtained...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28190453/an-empirical-vs-risk-based-approach-algorithm-to-intracavernosal-injection-therapy-a-prospective-study
#16
Helen Levey Bernie, Robert Segal, Brian Le, Arthur Burnett, Trinity J Bivalacqua
INTRODUCTION: Intracavernosal injection (ICI) therapy is widely used for the treatment of erectile dysfunction (ED). Its use in practice is largely empirical and has not been validated with evidence-based approaches. AIM: To compare two strategies for ICI, specifically a risk-based approach and an empiric-based approach, and assess the efficacy, patient satisfaction, and complication rates of the two treatment approaches. METHODS: After obtaining approval from the institutional review board, a prospective database of patients enrolled in the ICI program at the Johns Hopkins Hospital (Baltimore, MD, USA) from May 2012 through May 2014 was amassed...
March 2017: Sexual Medicine
https://www.readbyqxmd.com/read/28180085/de-novo-transcriptome-assembly-of-heavy-metal-tolerant-silene-dioica
#17
Radim Cegan, Vojtech Hudzieczek, Roman Hobza
Silene dioica is a dioecious plant of the family Caryophyllaceae. In the present study, we used Illumina sequencing technology (MiSeq) to sequence, de novo assembly and annotate the transcriptomes of male and female copper tolerant S. dioica individuals. We sequenced the normalized mRNA of roots, shoots, flower buds and flowers for each sex. Raw reads of the transcriptome assembly project for S. dioica male and female individual have been deposited in NCBI's Sequence Read Archive (SRA) database with the accession number SRP094611...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28163083/sexual-function-and-quality-of-life-before-and-after-penile-prosthesis-implantation-following-radial-forearm-flap-phalloplasty
#18
Ezekiel E Young, Daniel Friedlander, Kathy Lue, Uzoma A Anele, Jacob L Khurgin, Trinity J Bivalacqua, Arthur L Burnett, Richard J Redett, John P Gearhart
OBJECTIVE: To provide sexual function and quality of life outcomes in patients with severe penile deficiency who underwent radial forearm flap phalloplasty with and without penile prosthesis implantation. PATIENTS AND METHODS: Patients with history of severe penile deficiency who underwent microsurgical radial forearm flap phalloplasty with and without penile prosthesis implantation between 2007 and 2014 were identified. They completed a set of web-based validated questionnaires including the International Index of Erectile Function, the Pediatric Penile Perception Score, the Sexual Quality of Life for Men, and several items addressing general quality of life...
February 2, 2017: Urology
https://www.readbyqxmd.com/read/28161077/m1-macrophages-are-predominantly-recruited-to-the-major-pelvic-ganglion-of-the-rat-following-cavernous-nerve-injury
#19
Hotaka Matsui, Nikolai A Sopko, Johanna L Hannan, Allison A Reinhardt, Max Kates, Takahiro Yoshida, Xiaopu Liu, Fabio Castiglione, Petter Hedlund, Emmanuel Weyne, Maarten Albersen, Trinity J Bivalacqua
INTRODUCTION: Neurogenic erectile dysfunction is a common sequela of radical prostatectomy. The etiology involves injury to the autonomic cavernous nerves, which arise from the major pelvic ganglion (MPG), and subsequent neuroinflammation, which leads to recruitment of macrophages to the injury site. Currently, two macrophage phenotypes are known: neurotoxic M1 macrophages and neuroprotective M2 macrophages. AIM: To examine whether bilateral cavernous nerve injury (BCNI) in a rat model of erectile dysfunction would increase recruitment of neurotoxic M1 macrophages to the MPG...
February 2017: Journal of Sexual Medicine
https://www.readbyqxmd.com/read/28143409/improved-annotation-with-de-novo-transcriptome-assembly-in-four-social-amoeba-species
#20
Reema Singh, Hajara M Lawal, Christina Schilde, Gernot Glöckner, Geoffrey J Barton, Pauline Schaap, Christian Cole
BACKGROUND: Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcripts. RNA sequencing (RNA-seq) data can aid the annotation with empirical data. Here we present de novo transcriptome assemblies generated from RNA-seq data in four Dictyostelid species: D. discoideum, P. pallidum, D. fasciculatum and D. lacteum. The assemblies were incorporated with existing gene models to determine corrections and improvement on a whole-genome scale...
January 31, 2017: BMC Genomics
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