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https://www.readbyqxmd.com/read/27922076/identification-of-bnayucca6-as-a-candidate-gene-for-branch-angle-in-brassica-napus-by-qtl-seq
#1
Hui Wang, Hongtao Cheng, Wenxiang Wang, Jia Liu, Mengyu Hao, Desheng Mei, Rijin Zhou, Li Fu, Qiong Hu
Oilseed rape (Brassica napus L.) is one of the most important oil crops in China as well as worldwide. Branch angle as a plant architecture component trait plays an important role for high density planting and yield performance. In this study, bulked segregant analysis (BSA) combined with next generation sequencing technology was used to fine map QTL for branch angle. A major QTL, designated as branch angle 1 (ba1) was identified on A06 and further validated by Indel marker-based classical QTL mapping in an F2 population...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27920979/transcript-profiling-in-the-milk-of-dairy-ewes-fed-extruded-linseed
#2
Tommaso Giordani, Alberto Vangelisti, Giuseppe Conte, Andrea Serra, Lucia Natali, Annamaria Ranieri, Marcello Mele, Andrea Cavallini
The identification of genes regulating milk secretion by mammary glands is a key-step for exploiting changes in milk composition induced by different diet regimens. Linseed supplementation is a reliable feeding strategy to enhance polyunsaturated fatty acid content in milk fat from sheep, increasing milk quality and nutraceutical value. To investigate the molecular bases of diet induced differences in milk composition, we collected milk from dairy ewes at 90 day of lactation and after 3 weeks of diet supplementation with extruded linseed...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/27920488/evalmsa-a-program-to-evaluate-multiple-sequence-alignments-and-detect-outliers
#3
Alvaro Chiner-Oms, Fernando González-Candelas
We present EvalMSA, a software tool for evaluating and detecting outliers in multiple sequence alignments (MSAs). This tool allows the identification of divergent sequences in MSAs by scoring the contribution of each row in the alignment to its quality using a sum-of-pair-based method and additional analyses. Our main goal is to provide users with objective data in order to take informed decisions about the relevance and/or pertinence of including/retaining a particular sequence in an MSA. EvalMSA is written in standard Perl and also uses some routines from the statistical language R...
2016: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/27918193/dna-barcodes-identify-medically-important-tick-species-in-canada
#4
Danielle A Ondrejicka, Kevin C Morey, Robert H Hanner
Medically important ticks (Acari: Ixodidae) are often difficult to identify morphologically. A standardized, molecular approach using a 658 base pair DNA barcode sequence (from the 5' region of the mitochondrial cytochrome c oxidase subunit I gene) was evaluated for its effectiveness in discriminating ticks in North America, with an emphasis on Canadian ticks. DNA barcodes were generated for 96 of 154 specimens representing 26 ixodid species. A genetic cluster analysis was performed on the barcode sequences, which separated specimens into haplogroups closely corresponding with morphologically identified species...
July 19, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/27917693/identification-of-kcnq1-compound-heterozygous-mutations-in-three-chinese-families-with-jervell-and-lange-nielsen-syndrome
#5
Cuicui Wang, Yu Lu, Jing Cheng, Lei Zhang, Wei Liu, Weihua Peng, Di Zhang, Hong Duan, Dongyi Han, Huijun Yuan
CONCLUSION: Besides expanding the spectrum of KCNQ1 mutations causing Jervell and Lange-Nielsen Syndrome (JLNS), the results showed diversity of its phenotypes, and emphasized the importance of molecular genetic analysis in confirming clinical diagnosis and making diagnosis possible before the emergency symptoms for deaf individuals. OBJECTIVES: This study aimed to investigate four patients from three Chinese families with congenital hearing loss clinically and genetically...
December 5, 2016: Acta Oto-laryngologica
https://www.readbyqxmd.com/read/27917629/identification-of-hla-class-i-misreads-dropouts-using-serological-typing-in-comparison-with-dna-based-typing
#6
Hamid Nawaz Tipu, Muhammad Mukarram Bashir, Muhammad Noman
Serology and DNA techniques are employed for Human Leukocyte Antigen (HLA) typing in different transplant centers. Results may not always correlate well and may need retyping with different technique. All the patients (with aplastic anemia, thalassemia, and immunodeficiency) and their donors, requiring HLA typing for bone marrow transplant were enrolled in the study. Serological HLA typing was done by complement-dependent lymphocytotoxicity while DNA-based typing was done with sequence specific primers (SSP)...
October 2016: Iranian Journal of Allergy, Asthma, and Immunology
https://www.readbyqxmd.com/read/27917337/identification-characterization-and-phylogenetic-analysis-of-antifungal-trichoderma-from-tomato-rhizosphere
#7
Shalini Rai, Prem Lal Kashyap, Sudheer Kumar, Alok Kumar Srivastava, Pramod W Ramteke
The use of Trichoderma isolates with efficient antagonistic activity represents a potentially effective and alternative disease management strategy to replace health hazardous chemical control. In this context, twenty isolates were obtained from tomato rhizosphere and evaluated by their antagonistic activity against four fungal pathogens (Fusarium oxysporum f. sp. lycopersici, Alternaria alternata, Colletotrichum gloeosporoides and Rhizoctonia solani). The production of extracellular cell wall degrading enzymes of tested isolates was also measured...
2016: SpringerPlus
https://www.readbyqxmd.com/read/27916703/oogenesis_pred-a-sequence-based-method-for-predicting-oogenesis-proteins-by-six-different-modes-of-chou-s-pseudo-amino-acid-composition
#8
Maryam Rahimi, Mohammad Reza Bakhtiarizadeh, Abdollah Mohammadi-Sangcheshmeh
Regarding to critical roles of oogenesis in formation of ova or unfertilized eggs from the oogonia by mitotic division and subsequent differentiation, the identification of oogenesis-related proteins is of great interest. However, the experimental determination of proteins involved in oogenesis is expensive, time consuming and labor-intensive. Therefore, a new powerful discriminating model is indispensable for classifying oogenesis/non-oogenesis-related proteins with high accuracy and precision. Hereby, for the first time we developed a support vector machine based oogenesis protein prediction method which differentiates oogenesis from non-oogenesis proteins...
December 1, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27916572/high-resolution-melting-hrm-for-genotyping-bovine-ephemeral-fever-virus-befv
#9
Oran Erster, Rotem Stram, Shopia Menasherow, Marisol Rubistein-Giuni, Binyamin Sharir, Evgeni Kchinich, Yehuda Stram
In recent years there have been several major outbreaks of bovine ephemeral disease in the Middle East, including Israel. Such occurrences raise the need for quick identification of the viruses responsible for the outbreaks, in order to rapidly identify the entry of viruses that do not belong to the Middle-East BEFV lineage. This challenge was met by the development of a high-resolution method (HRM) assay. The assay is based on the viral G gene sequence and generation of an algorithm that calculates and evaluates the GC content of various fragments...
December 1, 2016: Virus Research
https://www.readbyqxmd.com/read/27915305/dna-barcoding-coupled-with-high-resolution-melting-analysis-enables-rapid-and-accurate-distinction-of-aspergillus-species
#10
Gabor Fidler, Sandor Kocsube, Eva Leiter, Sandor Biro, Melinda Paholcsek
We describe a high-resolution melting (HRM) analysis method that is rapid, reproducible, and able to identify reference strains and further 40 clinical isolates of Aspergillus fumigatus (14), A. lentulus (3), A. terreus (7), A. flavus (8), A. niger (2), A. welwitschiae (4), and A. tubingensis (2). Asp1 and Asp2 primer sets were designed to amplify partial sequences of the Aspergillus benA (beta-tubulin) genes in a closed-, single-tube system. Human placenta DNA, further Aspergillus (3), Candida (9), Fusarium (6), and Scedosporium (2) nucleic acids from type strains and clinical isolates were also included in this study to evaluate cross reactivity with other relevant pathogens causing invasive fungal infections...
December 3, 2016: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/27915089/complete-mitochondrial-genome-of-parasitic-nematode-cylicocyclus-nassatus-and-comparative-analyses-with-cylicocyclus-insigne
#11
Yuan Gao, Jian-Hua Qiu, Bing-Bing Zhang, Xin Su, Xue Fu, Dong-Mei Yue, Chun-Ren Wang
Cylicocyclus nassatus is a common and important parasite in the large intestine of equine. In this study, the complete mitochondrial (mt) genome sequence of C. nassatus was determined and comparatively analysed with Cylicocyclus insigne. The mt genome size of C. nassatus was 13,846 bp, 18 bp longer than that of C. insigne. The circular mt genome includes 12 protein-coding genes, two rRNA genes, 22 tRNA genes and two non-coding regions. All the genes are transcribed in the same direction and gene arrangement is consistent with that of gene arrangement 3 (GA3)...
November 30, 2016: Experimental Parasitology
https://www.readbyqxmd.com/read/27914047/deterministic-search-methods-for-computational-protein-design
#12
Seydou Traoré, David Allouche, Isabelle André, Thomas Schiex, Sophie Barbe
One main challenge in Computational Protein Design (CPD) lies in the exploration of the amino-acid sequence space, while considering, to some extent, side chain flexibility. The exorbitant size of the search space urges for the development of efficient exact deterministic search methods enabling identification of low-energy sequence-conformation models, corresponding either to the global minimum energy conformation (GMEC) or an ensemble of guaranteed near-optimal solutions. In contrast to stochastic local search methods that are not guaranteed to find the GMEC, exact deterministic approaches always identify the GMEC and prove its optimality in finite but exponential worst-case time...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913979/genetic-diversity-of-the-genotype-vii-newcastle-disease-virus-identification-of-a-novel-viij-sub-genotype
#13
Cong Xue, Yanlong Cong, Renfu Yin, Yixue Sun, Chan Ding, Shengqing Yu, Xiufan Liu, Shunlin Hu, Jing Qian, Qianliang Yuan, Mingxi Yang, Chunfeng Wang, Zhuang Ding
Newcastle disease (ND) is a highly contagious disease of poultry caused by Newcastle disease virus (NDV). Multiple genotypes of NDV have been circulating worldwide and NDV is continuously evolving, resulting into more diversity. Of multiple viral genotypes, VII is particularly important given that it had been associated with most recent ND outbreaks worldwide. In this study, an epidemiological investigation performed in northeastern China during 2014-2015 showed that 11 genotype VII isolates amounted to 55 percent in a total number of NDV isolates...
December 2, 2016: Virus Genes
https://www.readbyqxmd.com/read/27912812/endodontic-microbiology-and-pathobiology-current-state-of-knowledge
#14
REVIEW
Ashraf F Fouad
Newer research tools and basic science knowledge base have allowed the exploration of endodontic diseases in the pulp and periapical tissues in novel ways. The use of next generation sequencing, bioinformatics analyses, genome-wide association studies, to name just a few of these innovations, has allowed the identification of hundreds of microorganisms and of host response factors. This review addresses recent advances in endodontic microbiology and the host response and discusses the potential for future innovations in this area...
January 2017: Dental Clinics of North America
https://www.readbyqxmd.com/read/27911469/comprehensive-identification-and-clustering-of-clv3-esr-related-cle-genes-in-plants-finds-groups-with%C3%A2-potentially-shared-function
#15
David M Goad, Chuanmei Zhu, Elizabeth A Kellogg
CLV3/ESR (CLE) proteins are important signaling peptides in plants. The short CLE peptide (12-13 amino acids) is cleaved from a larger pre-propeptide and functions as an extracellular ligand. The CLE family is large and has resisted attempts at classification because the CLE domain is too short for reliable phylogenetic analysis and the pre-propeptide is too variable. We used a model-based search for CLE domains from 57 plant genomes and used the entire pre-propeptide for comprehensive clustering analysis. In total, 1628 CLE genes were identified in land plants, with none recognizable from green algae...
December 1, 2016: New Phytologist
https://www.readbyqxmd.com/read/27909575/a-step-by-step-workflow-for-low-level-analysis-of-single-cell-rna-seq-data
#16
Aaron T L Lun, Davis J McCarthy, John C Marioni
Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of individual cells. This provides biological resolution that cannot be matched by bulk RNA sequencing, at the cost of increased technical noise and data complexity. The differences between scRNA-seq and bulk RNA-seq data mean that the analysis of the former cannot be performed by recycling bioinformatics pipelines for the latter. Rather, dedicated single-cell methods are required at various steps to exploit the cellular resolution while accounting for technical noise...
2016: F1000Research
https://www.readbyqxmd.com/read/27908705/a-novel-method-for-in-silico-identification-of-regulatory-snps-in-human-genome
#17
Rong Li, Dexing Zhong, Ruiling Liu, Hongqiang Lv, Xinman Zhang, Jun Liu, Jiuqiang Han
Regulatory single nucleotide polymorphisms (rSNPs), kind of functional noncoding genetic variants, can affect gene expression in a regulatory way, and they are thought to be associated with increased susceptibilities to complex diseases. Here a novel computational approach to identify potential rSNPs is presented. Different from most other rSNPs finding methods which based on hypothesis that SNPs causing large allele-specific changes in transcription factor binding affinities are more likely to play regulatory functions, we use a set of documented experimentally verified rSNPs and nonfunctional background SNPs to train classifiers, so the discriminating features are found...
November 28, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27907159/dnabp-identification-of-dna-binding-proteins-based-on-feature-selection-using-a-random-forest-and-predicting-binding-residues
#18
Xin Ma, Jing Guo, Xiao Sun
DNA-binding proteins are fundamentally important in cellular processes. Several computational-based methods have been developed to improve the prediction of DNA-binding proteins in previous years. However, insufficient work has been done on the prediction of DNA-binding proteins from protein sequence information. In this paper, a novel predictor, DNABP (DNA-binding proteins), was designed to predict DNA-binding proteins using the random forest (RF) classifier with a hybrid feature. The hybrid feature contains two types of novel sequence features, which reflect information about the conservation of physicochemical properties of the amino acids, and the binding propensity of DNA-binding residues and non-binding propensities of non-binding residues...
2016: PloS One
https://www.readbyqxmd.com/read/27905886/multi-locus-phylogeny-using-topotype-specimens-sheds-light-on-the-systematics-of-niviventer-rodentia-muridae-in-china
#19
Bin Zhang, Kai He, Tao Wan, Peng Chen, Guozheng Sun, Shaoying Liu, Truong Son Nguyen, Liangkong Lin, Xuelong Jiang
BACKGROUND: Niviventer is a genus of white-bellied rats that are among the most common rodents in the Indo-Sundaic region. The taxonomy of the genus has undergone extensive revisions and remains controversial. The current phylogeny is unresolved and was developed primarily on the basis of mitochondrial genes. Identification is extremely difficult, and a large number of GenBank sequences seem to be problematic. We extensively sampled specimens of Niviventer in China and neighboring northern Vietnam, including topotypes of the most reported species (n = 6), subspecies (n = 8), and synonyms (n = 4)...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27905875/a-nonsense-mutation-in-the-col7a1-gene-causes-epidermolysis-bullosa-in-vorderwald-cattle
#20
Hubert Pausch, Simon Ammermüller, Christine Wurmser, Henning Hamann, Jens Tetens, Cord Drögemüller, Ruedi Fries
BACKGROUND: The widespread use of individual sires for artificial insemination promotes the propagation of recessive conditions. Inadvertent matings between unnoticed carriers of deleterious alleles may result in the manifestation of fatal phenotypes in their progeny. Breeding consultants and farmers reported on Vorderwald calves with a congenital skin disease. The clinical findings in affected calves were compatible with epidermolysis bullosa. RESULTS: Pedigree analysis indicated autosomal recessive inheritance of epidermolysis bullosa in Vorderwald cattle...
December 1, 2016: BMC Genetics
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