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https://www.readbyqxmd.com/read/28224052/compacting-and-correcting-trinity-and-oases-rna-seq-de-novo-assemblies
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/28140388/de-novo-transcriptome-assemblies-of-four-accessions-of-the-metal-hyperaccumulator-plant-noccaea-caerulescens
#9
Daniel Blande, Pauliina Halimaa, Arja I Tervahauta, Mark G M Aarts, Sirpa O Kärenlampi
Noccaea caerulescens of the Brassicaceae family has become the key model plant among the metal hyperaccumulator plants. Populations/accessions of N. caerulescens from geographic locations with different soil metal concentrations differ in their ability to hyperaccumulate and hypertolerate metals. Comparison of transcriptomes in several accessions provides candidates for detailed exploration of the mechanisms of metal accumulation and tolerance and local adaptation. This can have implications in the development of plants for phytoremediation and improved mineral nutrition...
January 31, 2017: Scientific Data
https://www.readbyqxmd.com/read/28135047/biomanufacturing-seamless-tubular-and-hollow-collagen-scaffolds-with-unique-design-features-and-biomechanical-properties
#10
Anirudha Singh, David Lee, Nikolai Sopko, Hotaka Matsui, Praveena Sabnekar, Xiaopu Liu, Jennifer Elisseeff, Mark P Schoenberg, Kenneth Pienta, Trinity J Bivalacqua
A versatile process to develop designer collagen scaffolds for hollow and tubular tissue engineering applications is presented. This process creates seamless and biomechanically tunable scaffolds ranging from ureter-like microsized tubings to structures with highly customized lumens that resemble intestinal villi, fluid bladders, and alveolar sacs that together with stem cells can potentially be used in preclinical and clinical settings.
January 30, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28133714/towards-a-building-typology-and-terminology-for-irish-hospitals
#11
REVIEW
T Grey, S Kennelly, P de Freine, S Mahon, V Mannion, D O'Neill
BACKGROUND: The physical form of the hospital environment shapes the care setting and influences the relationship of the hospital to the community. Due to ongoing demographic change, evolving public health needs, and advancing medical practice, typical hospitals are frequently redeveloped, retrofitted, or expanded. It is argued that multi-disciplinary and multi-stakeholder approaches are required to ensure that hospital design matches these increasingly complex needs. To facilitate such a conversation across different disciplines, experts, and community stakeholders, it is helpful to establish a hospital typology and associated terminology as part of any collaborative process...
January 30, 2017: Irish Journal of Medical Science
https://www.readbyqxmd.com/read/28131434/reply
#12
Meera R Chappidi, Max Kates, Trinity J Bivalacqua
No abstract text is available yet for this article.
January 25, 2017: Urology
https://www.readbyqxmd.com/read/28130926/penile-transplantation-an-emerging-option-for-genitourinary-reconstruction
#13
Sami H Tuffaha, Damon S Cooney, Nikolai A Sopko, Trinity J Bivalacqua, Denver M Lough, Carisa M Cooney, Gerald Brandacher, W P Andrew Lee, Arthur L Burnett, Richard J Redett
Penile transplantation is an emerging option for patients with severe genital defects not amenable to traditional reconstructive options. In this article, we discuss the burgeoning problem of severe male genitourinary trauma in the military, the limitations of traditional reconstructive options in addressing these problems, and the potential for penile transplantation to provide improved outcomes. We also review the preclinical research and limited worldwide experience with penile transplantation to date, including lessons learned, and discuss the many important technical, logistical and ethical considerations pertaining to penile transplantation that must be addressed to maximize the likelihood of successful implementation...
January 28, 2017: Transplant International: Official Journal of the European Society for Organ Transplantation
https://www.readbyqxmd.com/read/28121438/rna-seq-analysis-of-developing-pecan-carya-illinoinensis-embryos-reveals-parallel-expression-patterns-among-allergen-and-lipid-metabolism-genes
#14
Christopher P Mattison, Ruhi Rai, Robert E Settlage, Doug J Hinchliffe, Crista Madison, John M Bland, Suzanne Brashear, Charles J Graham, Matthew R Tarver, Christopher Florane, Peter J Bechtel
The pecan nut is a nutrient-rich part of a healthy diet full of beneficial fatty acids and antioxidants, but can also cause allergic reactions in people suffering from food allergy to the nuts. The transcriptome of a developing pecan nut was characterized to identify the gene expression occurring during the process of nut development and to highlight those genes involved in fatty acid metabolism and those that commonly act as food allergens. Pecan samples were collected at several time points during the embryo development process including the water, gel, dough, and mature nut stages...
February 13, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28111206/de-novo-assembly-and-characterization-of-the-transcriptome-of-the-newly-described-dinoflagellate-ansanella-granifera-spotlight-on-flagellum-associated-genes
#15
Se Hyeon Jang, Hae Jin Jeong, Jae Kyung Chon, Sung Yeon Lee
Many dinoflagellates are known to cause red tides and often outgrow non-motile diatoms and motile small flagellates through active vertical migration between well-lit surface and eutrophic deep waters and/or by locating and ingesting prey cells. Their flagella play important roles in these two critical behaviors. However, the structural and functional genes of dinoflagellate flagella are very little known. Thus, a de novo assembly and characterization of the transcriptome of the fast-swimming dinoflagellate Ansanella granifera were conducted and its flagellum genes were compared with those of other dinoflagellates, motile small flagellates, and non-motile protist species...
January 19, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28104421/assessing-cancer-progression-and-stable-disease-after-neoadjuvant-chemotherapy-for-organ-confined-muscle-invasive-bladder-cancer
#16
Meera R Chappidi, Max Kates, Aaron Brant, Alexander S Baras, George J Netto, Phillip M Pierorazio, Noah M Hahn, Trinity J Bivalacqua
OBJECTIVE: To propose and validate a new approach to stratify clinically staged, organ-confined, muscle-invasive bladder cancer patients (cT2N0M0) who are pathologic non-responders to neoadjuvant chemotherapy (NAC) to better characterize NAC non-response. METHODS: We retrospectively identified radical cystectomy patients with cT2N0M0 disease at our institution (2005-2014) and in the National Cancer Database (2004-2012) for external validation. Patients were stratified as stable (pT2N0M0) or progressors (>pT2 or pN+)...
January 16, 2017: Urology
https://www.readbyqxmd.com/read/28097264/lymph-node-density-predicts-recurrence-and-death-after-inguinal-lymph-node-dissection-for-penile-cancer
#17
Mark W Ball, Zeyad R Schwen, Joan S Ko, Alexa Meyer, George J Netto, Arthur L Burnett, Trinity J Bivalacqua
PURPOSE: To determine the impact of lymph node density (LND) on survival after inguinal lymph node dissection (ILND) for penile cancer. MATERIALS AND METHODS: Our institutional penile cancer database was queried for patients who underwent ILND. Clinicopathologic characteristics including LND and total number of positive lymph nodes (LNs) were analyzed to determine impact on recurrence-free survival (RFS) and overall survival (OS). LND, or the percent of positive LN out of total LN, was calculated as a categorical variable at varying thresholds...
January 2017: Investigative and Clinical Urology
https://www.readbyqxmd.com/read/28095660/draft-genome-of-toxocara-canis-a-pathogen-responsible-for-visceral-larva-migrans
#18
Jinhwa Kong, Jungim Won, Jeehee Yoon, UnJoo Lee, Jong-Il Kim, Sun Huh
This study aimed at constructing a draft genome of the adult female worm Toxocara canis using next-generation sequencing (NGS) and de novo assembly, as well as to find new genes after annotation using functional genomics tools. Using an NGS machine, we produced DNA read data of T. canis. The de novo assembly of the read data was performed using SOAPdenovo. RNA read data were assembled using Trinity. Structural annotation, homology search, functional annotation, classification of protein domains, and KEGG pathway analysis were carried out...
December 2016: Korean Journal of Parasitology
https://www.readbyqxmd.com/read/28086804/comparative-analysis-of-the-root-transcriptomes-of-cultivated-sweetpotato-ipomoea-batatas-l-lam-and-its-wild-ancestor-ipomoea-trifida-kunth-g-don
#19
Sathish K Ponniah, Jyothi Thimmapuram, Ketaki Bhide, Venu Kal Kalavacharla, Muthusamy Manoharan
BACKGROUND: The complex process of formation of storage roots (SRs) from adventitious roots affects sweetpotato yield. Identifying the genes that are uniquely expressed in the SR forming cultivated species, Ipomoea batatas (Ib), and its immediate ancestral species, Ipomoea trifida (It), which does not form SRs, may provide insights into the molecular mechanisms underlying SR formation in sweetpotato. RESULTS: Illumina paired-end sequencing generated ~208 and ~200 million reads for Ib and It, respectively...
January 13, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28073196/mri-us-fusion-prostate-biopsy-our-initial-experience
#20
Vito Lacetera, Bernardo Cervelli, Antonio Cicetti, Giuliana Gabrielloni, Michele Montesi, Roberto Morcellini, Gianni Parri, Emilio Recanatini, Gianluca Giglioni, Andrea Benedetto Galosi, Valerio Beatrici
AIM: The objective of this study is to present our initial experience with magnetic resonance imaging/ultrasound (MRI/US) fusion biopsy using the Koelis Trinity device after the first consecutive 59 patients. MATERIALS AND METHODS: 59 consecutive patients with suspected prostate cancer (PCA) underwent prostate biopsy using Trinity Koelis® (Koelis, Grenoble, France). We divided the patients into 2 groups: patients with a previous negative mapping underwent to a MRI/US fusion re-biopsy (Group A); and biopsy-naïve patients who underwent to a first stereotactic 3-D mapping of the prostate (Group B)...
December 30, 2016: Archivio Italiano di Urologia, Andrologia
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