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https://www.readbyqxmd.com/read/28330329/diversity-of-bacteria-and-archaea-in-the-rhizosphere-of-bioenergy-crop-jatropha-curcas
#1
Garima Dubey, Bharati Kollah, Vijay Kumar Gour, Arvind Kumar Shukla, Santosh Ranjan Mohanty
Plant-microbial interaction in rhizosphere plays vital role in shaping plant's growth and ecosystem function. Most of the rhizospheric microbial diversity studies are restricted to bacteria. In natural ecosystem, archaea also constitutes a major component of the microbial population. However, their diversity is less known compared to bacteria. Experiments were carried out to examine diversity of bacteria and archaea in the rhizosphere of bioenergy crop Jatropha curcas (J. curcas). Samples were collected from three locations varying widely in the soil physico-chemical properties...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330327/role-of-gnb3-net-kcnj11-tcf7l2-and-grl-genes-single-nucleotide-polymorphism-in-the-risk-prediction-of-type-2-diabetes-mellitus
#2
REVIEW
Saliha Rizvi, Syed Tasleem Raza, Qamar Rahman, Farzana Mahdi
Type 2 diabetes (T2DM) is a polygenic metabolic disorder characterized by hyperglycemia occurring as a result of impaired insulin secretion or insulin resistance. Various environmental and genetic factors interact and increase the risk of T2DM and its complications. Among the various genetic factors associated with T2DM, single nucleotide polymorphism in different candidate genes have been studied intensively and the resulting genetic variants have been found to have either positive or negative association with T2DM thereby increasing or decreasing the risk of T2DM, respectively...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330315/characterization-and-development-of-est-ssr-markers-in-sweet-potato-ipomoea-batatas-l-lam
#3
Jin-Hee Kim, Jun-Hoi Kim, Won-Sam Jo, Jeong-Gwan Ham, Il Kyung Chung, Kyung-Min Kim
In this study, a cDNA library was constructed from the total RNA of sweet potato leaves. A total of 789 copies of the cDNA were cloned in Escherichia coli by employing the pGEM-T Easy vector. Sequencing was carried out by Solgent Co. (Korea). As many as 579 expressed sequence tag-simple sequence repeat (EST-SSR) markers were designed (73.38%) from the known cDNA nucleotide base sequences. The lengths of the developed EST-SSR markers ranged from 100 to 499 bp (average length 238 bp). Their motif sequence types were varied, with most being dinucleotides and pentanucleotides, and the most commonly found motifs were CAGAAT (29...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330276/molecular-diversity-of-annona-species-and-proximate-fruit-composition-of-selected-genotypes
#4
Hirdayesh Anuragi, Haresh L Dhaduk, Sushil Kumar, Jitendra J Dhruve, Mithil J Parekh, Amar A Sakure
Understanding the genetic variation in germplasm is of utmost importance for crop improvement. Therefore, efforts were made to analyse the molecular marker based genetic diversity of 20 Annona genotypes from five different species of family Annonaceae. During analysis, a set of 11 RAPD primers yielded a total of 152 bands with 80.01 % polymorphism and PIC for RAPD ranged from 0.86 to 0.92 with a mean of 0.89. With 93.05 % polymorphism, 12 SSR primers produced 39 amplicons. The PIC for SSRs ranged from 0.169 to 0...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330250/deciphering-the-evolutionary-affiliations-among-bacterial-strains-pseudomonas-and-frankia-sp-inhabiting-same-ecological-niche-using-virtual-rflp-and-simulation-based-approaches
#5
Meenakshi Srivastava, Manish Singh Kaushik, Amrita Srivastava, Anumeha Singh, Ekta Verma, Arun Kumar Mishra
To decipher an evolutionary lineage between two different but important bacterial groups, i.e., Pseudomonas strain (γ-Proteobacteria) and Frankia strain (actinobacteria) growing in the same ecological niche in and around of an actinorhizal plant Hippophae salicifolia D. Don, genetic diversity and comparative molecular phylogeny have been investigated using 16S rRNA gene sequences and computer-simulated and virtually directed restriction fragment length polymorphism (RFLP) through 10 restriction enzymes. Bayesian and coalescent analyses on the basis of 16S rRNA gene sequences suggested three major groups with close proximity between Pseudomonas and Frankia isolates...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330228/development-of-novel-ssr-markers-for-evaluation-of-genetic-diversity-and-population-structure-in-tribulus-terrestris-l-zygophyllaceae
#6
Kuljit Kaur, Vikas Sharma, Vijay Singh, Mohammad Saleem Wani, Raghbir Chand Gupta
Tribulus terrestris L., commonly called puncture vine and gokhru, is an important member of Zygophyllaceae. The species is highly important in context to therapeutic uses and provides important active principles responsible for treatment of various diseases and also used as tonic. It is widely distributed in tropical regions of India and the world. However, status of its genetic diversity remained concealed due to lack of research work in this species. In present study, genetic diversity and structure of different populations of T...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330165/genetic-characterization-and-population-structure-of-indian-rice-cultivars-and-wild-genotypes-using-core-set-markers
#7
Malathi Surapaneni, Divya Balakrishnan, Sukumar Mesapogu, Addanki Krishnam Raju, Yadavalli Venkateswara Rao, Sarla Neelamraju
Genetic diversity among 23 rice genotypes including wild species and cultivars of indica, japonica, aus and aromatic type was investigated using 165 genomewide core set microsatellite (SSR) markers. This genotypic characterization was undertaken to know the genetic similarity among the parental lines to be used in developing a set of chromosome segment substitution lines. In all, 253 alleles were identified using 77 polymorphic SSRs, and polymorphism information content ranged from 0.31 to 0.97 with a mean of 0...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330150/phylogenetic-relationships-of-fluorescent-pseudomonads-deduced-from-the-sequence-analysis-of-16s-rrna-pseudomonas-specific-and-rpod-genes
#8
Asmita Rajwar, Manvika Sahgal
Phylogenetic relationship of 22 FLPs was revealed on the basis of polymorphism in three genes namely 16S rDNA, Pseudomonas-specific and rpoD gene regions. The primers for 16S rDNA, Pseudomonas-specific region and rpoD gene region were amplifying a region of 1492, 990 and 760 bp, respectively, from all the isolates investigated. The RFLP analysis of the PCR products resulted in a classification of these fluorescent pseudomonads which was best answered by rpoD-based RFLP analysis. The 22 FLPs were placed in two major clusters and seven subclusters suggesting that these were genotypically heterogenous and might belong to several species within Pseudomonas sensu stricto...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330146/mapping-of-stripe-rust-resistance-qtl-in-cappelle-desprez%C3%A2-%C3%A3-%C3%A2-pbw343-ril-population-effective-in-northern-wheat-belt-of-india
#9
Sushma Kumari Pawar, Davinder Sharma, Joginder Singh Duhan, Mahender Singh Saharan, Ratan Tiwari, Indu Sharma
Stripe rust caused by Puccinia striiformis f. sp. tritici is most important and devastating disease of wheat worldwide, which affects the grain yields, quality and nutrition. To elucidate, the genetic basis of resistance, a mapping population of recombinant inbred lines was developed from a cross between resistant Cappelle-Desprez and susceptible cultivar PBW343 using single-seed descent. Variety PBW343 had been one of the most popular cultivars of North Western Plains Zone, for more than a decade, before succumbing to the stripe rust...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330138/vdap-gui-a-user-friendly-pipeline-for-variant-discovery-and-annotation-of-raw-next-generation-sequencing-data
#10
Ramesh Menon, Namrata V Patel, Amitbikram Mohapatra, Chaitanya G Joshi
Even though next-generation sequencing (NGS) has become an invaluable tool in molecular biology, several laboratories with NGS facilities lack trained Bioinformaticians for data analysis. Here, focusing on the variant detection application of NGS analysis, we have developed a fully automated pipeline, namely Variant Discovery and Annotation Tool-Graphical User Interface (VDAP-GUI), which detects and annotates single nucleotide polymorphisms and insertions/deletions from raw sequence reads. VDAP-GUI consolidates several proven methods in each step such as quality control, trimming, mapping, variant detection and annotation...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330135/confamiliar-transferability-of-simple-sequence-repeat-ssr-markers-from-cotton-gossypium-hirsutum-l-and-jute-corchorus-olitorius-l-to-twenty-two-malvaceous-species
#11
Pratik Satya, Pramod Kumar Paswan, Swagata Ghosh, Snehalata Majumdar, Nasim Ali
Cross-species transferability is a quick and economic method to enrich SSR database, particularly for minor crops where little genomic information is available. However, transferability of SSR markers varies greatly between species, genera and families of plant species. We assessed confamiliar transferability of SSR markers from cotton (Gossypium hirsutum) and jute (Corchorus olitorius) to 22 species distributed in different taxonomic groups of Malvaceae. All the species selected were potential industrial crop species having little or no genomic resources or SSR database...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330125/detection-of-genetic-variation-in-sandalwood-using-various-dna-markers
#12
Dimple M Patel, Ranbir S Fougat, Amar A Sakure, Sushil Kumar, Mukesh Kumar, Jigar G Mistry
In the present study, 20 sandalwood (Santalum album L.) genotypes were characterized using RAPD, ISSR and SSR markers. Twenty-five RAPD and twenty-one ISSR primers that generated clear and reproducible banding patterns amplified 225 and 208 bands, respectively, among 20 sandalwood genotypes. Out of 225, 181 (83.13 %) RAPD bands were polymorphic while out of 208, 156 (75.77 %) ISSR bands were polymorphic. The average polymorphism information content (PIC) for RAPD and ISSR was 0.84 and 0.86, respectively...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330120/assessment-of-genetic-purity-in-rice-oryza-sativa-l-hybrids-using-microsatellite-markers
#13
Anjana Bora, Partha Ray Choudhury, Veena Pande, Asit B Mandal
The objective of the present study is to detect genetic impurity in the seed lots of CMS lines, restorers and hybrids and to identify signature markers to differentiate parents and hybrids through DNA-based assays. Furthermore, attempts have been made to find out an alternative to Grow-Out-Test, which is very tedious, time consuming and used conventionally for seed genetic purity testing since beginning of quality seed multiplication chain. Fifty-one rice-specific sequence tagged microsatellite (STMS) primer pairs distributed throughout the rice genome were employed for fingerprinting of eight rice hybrids and their parental lines with a view to assess variation within parental lines and to test the genetic purity of the commercial seed lots...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330108/identification-of-novel-snps-in-differentially-expressed-genes-and-its-association-with-horn-cancer-of-bos-indicus-bullocks-by-next-generation-sequencing
#14
P G Koringa, S J Jakhesara, D N Rank, C G Joshi
The use of polymorphic markers like SNPs promises to provide comprehensive tool for analysing genome and identifying genomic regions that contribute to cancer phenotype. Horn cancer is the most common cancer among Bos indicus animals. Increased expression of some genes due to polymorphisms increases risk of HC incidence. We successfully amplified 91 SNPs located in 69 genes in 52 samples, each of HC and HN. Equimolar concentration of amplicons from 69 PCR products of each sample was pooled and subjected to sequencing using Ion Torrent PGM...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330092/development-of-molecular-method-for-sex-identification-in-date-palm-phoenix-dactylifera-l-plantlets-using-novel-sex-linked-microsatellite-markers
#15
Maryam, Muhammad Jafar Jaskani, Faisal Saeed Awan, Saeed Ahmad, Iqrar A Khan
Microsatellite markers containing simple sequence repeats (SSRs) are a valuable tool for genetic analysis. Date palm is a dioecious and slow flowering and is very difficult to identify the gender of the trees until it reaches the reproductive age (5-10 years). A total of 12 microsatellite primers were used with 30 date palm samples, 14 parents (8 male + 6 females) and 16 progeny (developed from parents breeding) which showed that microsatellites were highly polymorphic, having a great number of alleles. A total of 124 alleles were characterized in 12 SSR loci...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329770/antigen-presentation-profiling-reveals-recognition-of-lymphoma-immunoglobulin-neoantigens
#16
Michael S Khodadoust, Niclas Olsson, Lisa E Wagar, Ole A W Haabeth, Binbin Chen, Kavya Swaminathan, Keith Rawson, Chih Long Liu, David Steiner, Peder Lund, Samhita Rao, Lichao Zhang, Caleb Marceau, Henning Stehr, Aaron M Newman, Debra K Czerwinski, Victoria E H Carlton, Martin Moorhead, Malek Faham, Holbrook E Kohrt, Jan Carette, Michael R Green, Mark M Davis, Ronald Levy, Joshua E Elias, Ash A Alizadeh
Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells. However, the personalized identification and validation of neoantigens remains a major challenge. Here we discover neoantigens in human mantle-cell lymphomas by using an integrated genomic and proteomic strategy that interrogates tumour antigen peptides presented by major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically characterize MHC ligands from 17 patients...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28329746/genotyping-platelet-activation-and-cardiovascular-outcome-in-patients-after-percutaneous-coronary-intervention-two-pieces-of-the-puzzle-of-clopidogrel-resistance
#17
Gerasimos Siasos, Evangelos Oikonomou, Manolis Vavuranakis, Eleni Kokkou, Konstantinos Mourouzis, Sotiris Tsalamandris, Marina Zaromitidou, Stamatios Kioufis, Vasiliki Tsigkou, Spyridon Defteros, Christodoulos Stefanadis, Dimitris Tousoulis
OBJECTIVES: Individual platelet responses to antiplatelet therapy depend on genetic, cellular, and clinical factors. CYP2C19 and P2Y12 receptor polymorphisms are implicated in platelet responses to antiplatelet treatment. We aimed to evaluate the impact of CYP2C19 and C34T P2Y12 genotyping on platelet reactivity and cardiovascular outcome in patients after percutaneous coronary intervention (PCI) on clopidogrel treatment. METHODS: We enrolled 408 patients with stable coronary artery disease (CAD) receiving aspirin and clopidogrel (75 mg/day) 1 month after PCI...
March 22, 2017: Cardiology
https://www.readbyqxmd.com/read/28329314/sirt1-polymorphisms-and-serum-induced-sirt1-protein-expression-in-aging-and-frailty-the-champ-study
#18
Shajjia Razi, Victoria C Cogger, Marina Kennerson, Vicky L Benson, Aisling C McMahon, Fiona M Blyth, David J Handelsman, Markus J Seibel, Vasant Hirani, Vasikaran Naganathan, Louise Waite, Rafael de Cabo, Robert G Cumming, David G Le Couteur
The nutrient sensing protein, SIRT1 influences aging and nutritional interventions such as caloric restriction in animals, however, the role of SIRT1 in human aging remains unclear. Here, the role of SIRT1 single-nucleotide polymorphisms (SNPs) and serum-induced SIRT1 protein expression (a novel assay that detects circulating factors that influence SIRT1 expression in vitro) were studied in the Concord Health and Ageing in Men Project (CHAMP), a prospective cohort of community dwelling men aged 70 years and older...
March 14, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28329290/association-of-btbd9-and-map2k5-skor1-with-restless-legs-syndrome-in-chinese-population
#19
Gen Li, Huidong Tang, Cheng Wang, Xuemei Qi, Jie Chen, Shengdi Chen, Jianfang Ma
Objective: The aim of the study was to investigate the relationship between genetic factors and primary restless legs syndrome (RLS) in Chinese population. Methods: Totally, 116 RLS patients and 200 controls were recruited and the diagnosis of RLS was based on the criteria of International RLS Study Group. Polymer chain reaction (PCR) and sequencing were used to detect 19 single nucleotide polymorphisms (SNPs) in six genetic loci (MEIS1, BTBD9, PTPRD, MAP2K5/SKOR1, TOX3, and Intergenic region of 2p14)...
February 24, 2017: Sleep
https://www.readbyqxmd.com/read/28329160/maternal-microchimerism-predicts-increased-infection-but-decreased-disease-due-to-p-falciparum-during-early-childhood
#20
Whitney E Harrington, Sami B Kanaan, Atis Muehlenbachs, Robert Morrison, Philip Stevenson, Michal Fried, Patrick E Duffy, J Lee Nelson
BACKGROUND: A mother's infection with placental malaria (PM) can affect her child's susceptibility to malaria, although the mechanism remains unclear. The fetus acquires a small amount of maternal cells and DNA known as maternal microchimerism (MMc), and we hypothesized that PM increases MMc and that MMc alters risk of P. falciparum malaria during infancy. METHODS: In a nested cohort from Muheza, Tanzania, we evaluated the presence and level of cord blood MMc in offspring of women with and without PM...
March 15, 2017: Journal of Infectious Diseases
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