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https://www.readbyqxmd.com/read/28822148/-dna-barcoding-identification-of-endangered-medicinal-plants-of-orchidaceae
#1
Huan Tang, Li Xiang, Xi-Wen Li, Wei Sun, Mei-Na Wang, Yun-Feng Huang, Meng Ye
In this study, DNA barcoding was used to validate the traditional morphological classification of medicinal plants of Orchidaceae. The 163 samples of 135 species belong to 49 genera which have been confirmed by morphological identification were collected. Candidate sequences, including matK, psbA-trnH and ITS2 sequences, were amplified, bidirectionally sequenced, and assembled. All the sequences were blasted to GenBank database at NCBI, then analyzed using Neighbor-joining tree method by MEGA 7.0. The results showed that the DNAs of 163 samples were successfully extracted...
June 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28818099/biosemantics-guided-gene-expression-profiling-of-sj%C3%A3-gren-s-syndrome-a-comparative-analysis-with-systemic-lupus-erythematosus-and-rheumatoid-arthritis
#2
Nirav R Shah, Braxton D Noll, Craig B Stevens, Michael T Brennan, Farah B Mougeot, Jean-Luc C Mougeot
BACKGROUND: Sjögren's syndrome (SS) shares many clinical and pathological similarities with systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). These autoimmune diseases mostly affect women. In this study, concept profile analysis (CPA) and gene expression meta-analysis were used to identify genes potentially involved in SS pathogenesis. METHODS: Human genes associated with SS, SLE, and RA were identified using the CPA tool, Anni 2.1. The differential mRNA expression of genes common to SS and SLE (SS-SLE) was determined in female peripheral blood mononuclear cells (PBMCs) using NCBI-GEO2R...
August 17, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28808804/identification-of-a-new-liver-specific-c-type-mrna-transcriptional-variant-for-mouse-st3gal5-gm3-gm4-synthase
#3
Fumi Shishido, Satoshi Uemura, Takahiro Nitta, Jin-Ichi Inokuchi
GM3, a major lipid component of the plasma membrane outer leaflet in mammalian cells, is synthesized in the luminal side of Golgi by ST3GAL5 protein (ST3G5), a type II membrane protein. Two strains of St3Gal5 knockout mice have been established for studies of GM3 physiological function: St3Gal5-Ex5-KO (lacking exon 5, which contains the catalytic domain of ST3G5), and St3Gal5-Ex3-KO (lacking exon 3, which contains the initiation codons). Results of the present study demonstrate that GM3 synthesis is still present, at a low level, in liver of St3Gal5-Ex3-KO mice...
August 14, 2017: Glycoconjugate Journal
https://www.readbyqxmd.com/read/28808380/identification-and-analysis-of-jasmonate-pathway-genes-in-coffea-canephora-robusta-coffee-by-in-silico-approach
#4
Kosaraju Bharathi, H L Sreenath
BACKGROUND: Coffea canephora is the commonly cultivated coffee species in the world along with Coffea arabica. Different pests and pathogens affect the production and quality of the coffee. Jasmonic acid (JA) is a plant hormone which plays an important role in plants growth, development, and defense mechanisms, particularly against insect pests. The key enzymes involved in the production of JA are lipoxygenase, allene oxide synthase, allene oxide cyclase, and 12-oxo-phytodienoic reductase...
July 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/28806931/draft-de-novo-transcriptome-assembly-and-proteome-characterization-of-the-electric-lobe-of-tetronarce-californica-a-molecular-tool-for-the-study-of-cholinergic-neurotransmission-in-the-electric-organ
#5
Maria Stavrianakou, Ricardo Perez, Cheng Wu, Matthew S Sachs, Rodolfo Aramayo, Mark Harlow
BACKGROUND: The electric organ of Tetronarce californica (an electric ray formerly known as Torpedo californica) is a classic preparation for biochemical studies of cholinergic neurotransmission. To broaden the usefulness of this preparation, we have performed a transcriptome assembly of the presynaptic component of the electric organ (the electric lobe). We combined our assembled transcriptome with a previous transcriptome of the postsynaptic electric organ, to define a MetaProteome containing pre- and post-synaptic components of the electric organ...
August 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28803679/systematic-review-of-the-methods-predictive-of-the-functionality-of-kidney-transplantation
#6
E Miret Alomar, E Trilla Herrera, D Lorente Garcia, L Regis Placido, R López Del Campo, M Cuadras Solé, T Pont Castellana, F Moreso Mateos, D Serón Micas, J Morote Robles
CONTEXT: Kidney transplantation from donors with expanded criteria has increased the pool of kidneys at the cost of a higher risk of short and long-term graft dysfunction. The main issue lies in determining which kidneys will offer acceptable function and survival compared with the risk represented by surgery and subsequent immunosuppression. OBJECTIVE: The objective of our article is to review the current evidence on the tools for predicting the functionality of kidney transplantation from cadaveric donors with expanded criteria and determining the validity for their use in standard practice...
August 10, 2017: Actas Urologicas Españolas
https://www.readbyqxmd.com/read/28800846/saprotrophic-proteomes-of-biotypes-of-the-witches-broom-pathogen-moniliophthora-perniciosa
#7
Sandra Pierre, Gareth W Griffith, Russell M Morphew, Luis A J Mur, Ian M Scott
Nine geographically diverse Moniliophthora perniciosa (witches' broom disease pathogen) isolates were cultured in vitro. They included six C-biotypes differing in virulence on cacao (Theobroma cacao), two S-biotypes (solanaceous hosts), and an L-biotype (liana hosts). Mycelial growth rates and morphologies differed considerably, but no characters were observed to correlate with virulence or biotype. In plant inoculations using basidiospores, one C-biotype caused symptoms on tomato (an S-biotype host), adding to evidence of limited host adaptation in these biotypes...
September 2017: Fungal Biology
https://www.readbyqxmd.com/read/28800773/rattus-norvegicus-bn-shr-liver-and-heart-left-ventricle-ribosomal-rna-depleted-directional-rna-sequencing
#8
Emanuel Wyler, Sebastiaan van Heesch, Eleonora Adami, Norbert Hubner, Markus Landthaler
OBJECTIVE: The spontaneously hypertensive rat strain is a frequently used disease model. In a previous study, we measured translational efficiency from this strain and BN-Lx animals. Here, we describe long RNA sequencing reads from ribosomal RNA depleted samples from the same animals. This data can be used to investigate splicing-related events. RESULTS: RNA was extracted from rat liver and heart left ventricle from BN-Lx and SHR/Ola rats in biological replicates...
August 11, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28800601/sequence-homology-between-hla-bound-cytomegalovirus-and-human-peptides-a-potential-trigger-for-alloreactivity
#9
Charles E Hall, Vishal N Koparde, Maximilian Jameson-Lee, Abdelrhman G Elnasseh, Allison F Scalora, David J Kobulnicky, Myrna G Serrano, Catherine H Roberts, Gregory A Buck, Michael C Neale, Daniel E Nixon, Amir A Toor
Human cytomegalovirus (hCMV) reactivation may often coincide with the development of graft-versus-host-disease (GVHD) in stem cell transplantation (SCT). Seventy seven SCT donor-recipient pairs (DRP) (HLA matched unrelated donor (MUD), n = 50; matched related donor (MRD), n = 27) underwent whole exome sequencing to identify single nucleotide polymorphisms (SNPs) generating alloreactive peptide libraries for each DRP (9-mer peptide-HLA complexes); Human CMV CROSS (Cross-Reactive Open Source Sequence) database was compiled from NCBI; HLA class I binding affinity for each DRPs HLA was calculated by NetMHCpan 2...
2017: PloS One
https://www.readbyqxmd.com/read/28799009/genome-wide-survey-and-characterization-of-fatty-acid-desaturase-gene-family-in-brassica-napus-and-its-parental-species
#10
Yufei Xue, Baojun Chen, Rui Wang, Aung Naing Win, Jiana Li, Yourong Chai
Rapeseed (Brassica napus) is an important oilseed crop worldwide, and fatty acid (FA) compositions determine the nutritional and economic value of its seed oil. Fatty acid desaturases (FADs) play a pivotal role in regulating FA compositions, but to date, no comprehensive genome-wide analysis of FAD gene family in rapeseed and its parent species has been reported. In this study, using homology searches, 84, 45, and 44 FAD genes were identified in rapeseed, Brassica rapa, and Brassica oleracea genomes, respectively...
August 10, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28795103/rna-seq-data-of-oryza-sativa-cultivar-kuku-belang-under-peg-treatment
#11
Bernadette Toni, Hossein Hosseini Monfared, Mohd Noor Mat Isa, Nurulhikma Md Isa, Ismanizan Ismail, Zamri Zainal
Drought stress is the main abiotic factor affecting rice production. Rain-fed upland rice which is grown on unbounded fields and totally dependent on rainfall for moisture is more prone to drought stress compared to rice from other ecosystems. However, upland rice has adapted to this limited water condition, thus are more drought tolerant than rice from other ecosystems. We performed the first transcriptome sequencing of drought tolerant indica upland rice cultivar Kuku Belang to identify differentially expressed genes related to drought tolerance mechanism...
October 2017: Data in Brief
https://www.readbyqxmd.com/read/28794989/comparative-metagenomics-reveals-alterations-in-the-soil-bacterial-community-driven-by-n-fertilizer-and-amino-16%C3%A2-application-in-lettuce
#12
Apostolos Kalivas, Ioannis Ganopoulos, Fotis Psomopoulos, Ioannis Grigoriadis, Aliki Xanthopoulou, Evangelos Hatzigiannakis, Maslin Osathanunkul, Athanasios Tsaftaris, Panagiotis Madesis
Nutrients in the form of fertilizers and/or other additives such as amino acids, dramatically influence plant development and growth, plant nutrient composition and the level of soil pollution. Moreover, the treatment of soil microbiota is emerging as a new strategy in plant breeding to achieve desirable traits. Thus, integrated study of fertilizer application and soil microbiota might lead to a better understanding of soil-plant interactions and inform the design of novel ways to fertilize plants. Herein we report metagenomics data for soil microbiota in lettuce (Lactuca sativa) treated with fertilizer, amino acids or their combinations as follows: N-fertilizer + Amino16®, Amino16®, N-fertilizer and no treatment control...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28794988/whole-genome-sequencing-of-microbacterium-sp-aiso3-from-polluted-san-jacinto-river-sediment-reveals-high-bacterial-mobility-metabolic-versatility-and-heavy-metal-resistance
#13
Rupa Iyer, Ashish Damania, Brian Iken
The genus Microbacterium is composed of high GC content, Gram-positive bacteria of the phylum Acintobacteria known for their antibiotic production. Microbacterium species commonly colonize agricultural rhizospheres and more infrequently have been found to colonize and infect human tissues as well. Here we report the 3,696,310 bp draft genome (chromosome and plasmids) sequence assembled at the scaffold level from 232 contigs of Microbacterium sp. strain AISO3, isolated from polluted San Jacinto River sediment in Channelview, Texas...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28794987/whole-genome-of-klebsiella-aerogenes-px01-isolated-from-san-jacinto-river-sediment-west-of-baytown-texas-reveals-the-presence-of-multiple-antibiotic-resistance-determinants-and-mobile-genetic-elements
#14
Rupa Iyer, Brian Iken, Ashish Damania
Klebsiella aerogenes is a Gram-negative bacterium of the family Enterobacteriaceae which is widely distributed in water, air and soil. It also forms part of the normal microbiota found in human and animal gastrointestinal tracts. Here we report the draft genome sequence (chromosome and 1 plasmid) of K. aerogenes strain PX01 compiled at the scaffold level from 97 contigs totaling 5,262,952 bp. K. aerogenes PX01 was isolated from sediment along the northern face of Burnet Bay west of Baytown, Texas. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession NJBB00000000...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28791183/alterations-in-gene-expression-of-components-of-the-renin-angiotensin-system-and-its-related-enzymes-in-lung-cancer
#15
Benjamin Goldstein, Malav Trivedi, Robert C Speth
OBJECTIVES: The study assessed the existence and significance of associations between the expression of fifteen renin-angiotensin system component genes and lung adenocarcinoma. MATERIALS AND METHODS: NCBI's built-in statistical tool, GEO2R, was used to calculate Student's t-tests for the associations found in a DNA expression study of adenocarcinoma and matched healthy lung tissue samples. The raw data was processed with GeneSpring™ and then used to generate figures with and without Sidak's multiple comparison correction...
2017: Lung Cancer International
https://www.readbyqxmd.com/read/28777847/-study-of-a-family-with-epidermolysis-bullosa-simplex-resulting-from-a-novel-mutation-of-krt14-gene
#16
Lanlan Meng, Juan Du, Wen Li, Guangxiu Lu, Yueqiu Tan
OBJECTIVE: To determine the molecular etiology for a Chinese pedigree affected with epidermolysis bullosa simplex (EBS). METHODS: Target region sequencing using a hereditary epidermolysis bullosa capture array combined with Sanger sequencing and bioinformatics analysis were used. Mutation taster, PolyPhen-2, Provean, and SIFT software and NCBI online were employed to assess the pathogenicity and conservation of detected mutations. One hundred healthy unrelated individuals were used as controls...
August 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28771471/the-genomic-observatories-metadatabase-geome-a-new-repository-for-field-and-sampling-event-metadata-associated-with-genetic-samples
#17
John Deck, Michelle R Gaither, Rodney Ewing, Christopher E Bird, Neil Davies, Christopher Meyer, Cynthia Riginos, Robert J Toonen, Eric D Crandall
The Genomic Observatories Metadatabase (GeOMe, http://www.geome-db.org/) is an open access repository for geographic and ecological metadata associated with biosamples and genetic data. Whereas public databases have served as vital repositories for nucleotide sequences, they do not accession all the metadata required for ecological or evolutionary analyses. GeOMe fills this need, providing a user-friendly, web-based interface for both data contributors and data recipients. The interface allows data contributors to create a customized yet standard-compliant spreadsheet that captures the temporal and geospatial context of each biosample...
August 2017: PLoS Biology
https://www.readbyqxmd.com/read/28768485/a-systematic-review-of-genetic-mutations-in-pulmonary-arterial-hypertension
#18
Gerardo Garcia-Rivas, Carlos Jerjes-Sánchez, David Rodriguez, José Garcia-Pelaez, Victor Trevino
BACKGROUND: Pulmonary arterial hypertension (PAH) is a group of vascular diseases that produce right ventricular dysfunction, heart failure syndrome, and death. Although the majority of patients appear idiopathic, accumulated research work combined with current sequencing technology show that many gene variants could be an important component of the disease. However, current guidelines, clinical practices, and available gene panels focus the diagnosis of PAH on a relatively low number of genes and variants associated with the bone morphogenic proteins and transforming Growth Factor-β pathways, such as the BMPR2, ACVRL1, CAV1, ENG, and SMAD9...
August 2, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28765569/locus-of-adhesion-and-autoaggregation-laa-a-pathogenicity-island-present-in-emerging-shiga-toxin-producing-escherichia-coli-strains
#19
David A Montero, Juliana Velasco, Felipe Del Canto, Jose L Puente, Nora L Padola, David A Rasko, Mauricio Farfán, Juan C Salazar, Roberto Vidal
Shiga Toxin-producing Escherichia coli (STEC) are a group of foodborne pathogens associated with diarrhea, dysentery, hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS). Shiga toxins are the major virulence factor of these pathogens, however adhesion and colonization to the human intestine is required for STEC pathogenesis. A subset of STEC strains carry the Locus of Enterocyte Effacement (LEE) pathogenicity island (PAI), which encodes genes that mediate the colonization of the human intestine. While LEE-positive STEC strains have traditionally been associated with human disease, the burden of disease caused by STEC strains that lacks LEE (LEE-negative) has increased recently in several countries; however, in the absence of LEE, the molecular pathogenic mechanisms by STEC strains are unknown...
August 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28761826/the-inhibitory-effect-of-ginger-extract-on-ovarian-cancer-cell-line-application-of-systems-biology
#20
Roghiyeh Pashaei-Asl, Fatima Pashaei-Asl, Parvin Mostafa Gharabaghi, Khodadad Khodadadi, Mansour Ebrahimi, Esmaeil Ebrahimie, Maryam Pashaiasl
Purpose: Ginger is a natural compound with anti-cancer properties. The effects of ginger and its mechanism on ovarian cancer and its cell line model, SKOV-3, are unclear. In this study, we have evaluated the effect of ginger extract on SKOV-3. Methods: SKOV-3 cells were incubated with ginger extract for 24, 48 and 72 hours. Cell toxicity assay was performed. Different data mining algorithms were applied to highlight the most important features contributing to ginger inhibition on the SKOV-3 cell proliferation...
June 2017: Advanced Pharmaceutical Bulletin
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