keyword
MENU ▼
Read by QxMD icon Read
search

Genome

keyword
https://www.readbyqxmd.com/read/28330333/extraction-and-bioactive-profile-of-the-compounds-produced-by-rhodococcus-sp-vld-10
#1
Bokka Yellamanda, Muvva Vijayalakshmi, Alapati Kavitha, Dorigondla Kumar Reddy, Yenamandra Venkateswarlu
A potent actinobacterial strain isolated from the marine samples of Bheemunipatnam beach, Visakhapatnam, India, was identified as Rhodococcus sp. VLD-10 using the conventional and genomic (16S rRNA) approaches. Bioactive compounds responsible for the antimicrobial activity of the strain were elucidated by cultivating the strain VLD-10 in a modified yeast extract-malt extract-lactose broth followed by subsequent chromatographic and spectroscopic analyses. Extraction, purification, and structural confirmation of five compounds, viz...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330331/identification-and-quantification-of-novel-rna-isoforms-in-horn-cancer-of-bos-indicus-by-comprehensive-rna-seq
#2
Subhash J Jakhesara, Prakash G Koringa, Neelam M Nathani, Chaitanya G Joshi
Horn cancer (HC) is a squamous cell carcinoma of horn, commonly observed in Bos indicus of the Asian countries. To elucidate the complexity of alternative splicing present in the HC, high-throughput sequencing and analysis of HC and matching horn normal (HN) tissue were carried out. A total of 535,067 and 849,077 reads were analysed after stringent quality filtering for HN and HC, respectively. Cufflinks pipeline for transcriptome analysis revealed 4786 novel splice isoforms comprising 2432 exclusively in HC, 2055 exclusively in HN and 298 in both the conditions...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330330/a-combined-chloroplast-atpb-rbcl-and-trnl-f-phylogeny-unveils-the-ancestry-of-balsams-impatiens-spp-in-the-western-ghats-of-india
#3
P P Shajitha, N R Dhanesh, P J Ebin, Joseph Laly, Devassy Aneesha, John Reshma, Jomy Augustine, Mathew Linu
Only a few Impatiens spp. from South India (one of the five centers of diversity for Impatiens species) were included in the published datum of molecular phylogeny of the family Balsaminaceae. The present investigation is a novel attempt to reveal the phylogenetic association of Impatiens species of South India, by placing them in the global phylogeny of Impatiens based on a combined analysis of two chloroplast genes. Thirty species of genus Impatiens were collected from different locations of South India. Total genomic DNA was extracted from fresh plant leaf, and polymerase chain reaction was carried out using atpB-rbcL and trnL-F intergenic spacer-specific forward and reverse primers...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330305/studies-on-coexistence-of-mec-gene-is256-and-novel-sasx-gene-among-human-clinical-coagulase-negative-staphylococci
#4
K R Soumya, Sheela Sugathan, Jyothis Mathew, E K Radhakrishnan
Methicillin-resistant coagulase-negative staphylococci (MRCoNS) are major nosocomial pathogens which cause device-related infections. Presence of various virulence factors along with methicillin resistance favor improved CoNS pathogenicity and their dissemination among population. In the present study, mec gene prevalence was analyzed along with SCC mec diversity among 55 human clinical CoNS isolates. PCR screening of insertion sequence (IS256) was also conducted to elucidate their association with methicillin resistance among selected CoNS species...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330292/comparative-assessment-of-methods-for-metagenomic-dna-isolation-from-soils-of-different-crop-growing-fields
#5
Aiman Tanveer, Sangeeta Yadav, Dinesh Yadav
The isolation of good quality metagenomic DNA from diverse soil, in appreciable amount, is a prerequisite for metagenomics. The availability of commercial kits for isolation of genomic DNAs from soil has drastically expedited the application of metagenomics approach for identifying novel sources of industrially important enzymes. The quantitative and qualitative assessment of metagenomic DNA isolated using either the manual method or the kit-based method should be performed prior to its use in downstream applications...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330289/progress-in-genome-sequencing-will-accelerate-molecular-breeding-in-cotton-gossypium-spp
#6
REVIEW
Rong Yan, Chengzhen Liang, Zhigang Meng, Waqas Malik, Tao Zhu, Xuefeng Zong, Sandui Guo, Rui Zhang
Cotton (Gossypium spp.) is the single most important spinning fiber that has economic significance worldwide. Cotton is one of the most value-added crops and an excellent model system for the analysis of polyploidization and cell development. Thus, the Cotton Genome Consortium has made rapid and significant progress in whole genome sequencing studies in the last decade. Developments in cotton genome sequencing and assembly provide powerful tools for dissecting the genetic and molecular bases of agronomically important traits and establishing regulatory networks on these processes, which leads to molecular breeding...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330272/biodegradation-of-endocrine-disruptor-dibutyl-phthalate-dbp-by-a-newly-isolated-methylobacillus-sp-v29b-and-the-dbp-degradation-pathway
#7
Vinay Kumar, S S Maitra
Bacteria of the genus Methylobacillus are methanotrophs, a metabolic feature that is widespread in the phylum Proteobacteria. The study demonstrates the isolation and characterization of a newly isolated Methylobacillus sp. V29b. which grows on methanol, protocatechuate, monobutyl phthalate, dibutyl phthalate, diethyl phthalate, benzyl butyl phthalate, dioctyl phthalate and diisodecyl phthalate. Methylobacillus sp. V29b was characterized with scanning electron microscopy, transmission electron microscopy, Gram staining, antibiotics sensitivity tests and biochemical characterization...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330264/construction-of-recombinant-sestc-saccharomyces-cerevisiae-for-consolidated-bioprocessing-cellulase-characterization-and-ethanol-production-by-in-situ-fermentation
#8
Peizhou Yang, Haifeng Zhang, Shaotong Jiang
Bioethanol is an important oil substitute produced by the sugar fermentation process. To improve the efficiency of cellulase expression of Saccharomyces cerevisiae, a eukaryotic expression vector harboring a single-enzyme-system-three-cellulase gene (sestc) was integrated into the S. cerevisiae genome by the protoplast method. Using PCR screening, RT-PCR, and "transparent circle" detection, several recombinant S. cerevisiae strains, capable of efficiently expressing the heterogeneous cellulase, were selected...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330232/high-quality-metagenomic-dna-from-marine-sediment-samples-for-genomic-studies-through-a-preprocessing-approach
#9
Solly Solomon, Bhavya Kachiprath, G Jayanath, T P Sajeevan, I S Bright Singh, Rosamma Philip
Recent advances in culture-independent studies of microbes had proved to be more reliable and efficient than the conventional ones. The isolation of good quality and quantity of total community DNA are one of the major hurdles in this endeavour. Shearing of DNA during the extraction process and the co-extraction of inhibitory compounds reduce the quality of the isolated nucleic acids making it unsuitable for the construction of large insert metagenomic libraries. In the present study, a multi-level filtration step was brought in which efficiently isolated total bacterial DNA from three different environment samples...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330225/metagenomics-analysis-of-microbial-communities-associated-with-a-traditional-rice-wine-starter-culture-xaj-pitha-of-assam-india
#10
Sudipta Sankar Bora, Jyotshna Keot, Saurav Das, Kishore Sarma, Madhumita Barooah
This is the first report on the microbial diversity of xaj-pitha, a rice wine fermentation starter culture through a metagenomics approach involving Illumine-based whole genome shotgun (WGS) sequencing method. Metagenomic DNA was extracted from rice wine starter culture concocted by Ahom community of Assam and analyzed using a MiSeq(®) System. A total of 2,78,231 contigs, with an average read length of 640.13 bp, were obtained. Data obtained from the use of several taxonomic profiling tools were compared with previously reported microbial diversity studies through the culture-dependent and culture-independent method...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330193/a-rapid-method-for-isolation-of-genomic-dna-from-food-borne-fungal-pathogens
#11
S Umesha, H M Manukumar, Sri Raghava
Food contaminated with fungal pathogens can cause extremely harmful effects to human even when present in low concentrations. Researchers now pay more attention towards rapid DNA extraction for the quick screening, which is highly demanded in diverse research field. Molecular description of many fungal species is identified by different molecular characteristics. Hence, the efficient isolation of genomic DNA and amplification using PCR is a prerequisite for molecular characterization. Here, we used an improved Sodium dodecyl sulfate-Cetyltrimethyl ammonium bromide-Chloroform-isoamyl alcohol method by combining Sodium dodecyl sulfate with cetyl methylammonium bromide without addition of proteinase K, RNase K, and β-mercaptoethanol...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330167/genetic-characterization-of-moroccan-and-the-exotic-bread-wheat-cultivars-using-functional-and-random-dna-markers-linked-to-the-agronomic-traits-for-genomics-assisted-improvement
#12
Fatima Henkrar, Jamal El-Haddoury, Hassan Ouabbou, Najib Bendaou, Sripada M Udupa
Genetic characterization, diversity analysis and estimate of the genetic relationship among varieties using functional and random DNA markers linked to agronomic traits can provide relevant guidelines in selecting parents and designing new breeding strategies for marker-assisted wheat cultivar improvement. Here, we characterize 20 Moroccan and 19 exotic bread wheat (Triticum aestivum L.) cultivars using 47 functional and 7 linked random DNA markers associated with 21 loci of the most important traits for wheat breeding...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330166/a-molecular-phylogenetic-framework-for-bacillus-subtilis-using-genome-sequences-and-its-application-to-bacillus-subtilis-subspecies-stecoris-strain-d7xpn1-an-isolate-from-a-commercial-food-waste-degrading-bioreactor
#13
Joseph Adelskov, Bharat K C Patel
A thermophilic, heterotrophic and facultatively anaerobic bacterium designated strain D7XPN1 was isolated from Baku BakuKing™, a commercial food-waste degrading bioreactor (composter). The strain grew optimally at 45 °C (growth range between 24 and 50 °C) and pH 7 (growth pH range between pH 5 and 9) in Luria Broth supplemented with 0.3 % glucose. Strain D7XPN1 tolerated up to 7 % NaCl and showed amylolytic and xylanolytic activities. 16S rRNA gene analysis placed strain D7XPN1 in the cluster represented by Bacillus subtilis and the genome analysis of the 4...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330159/in-silico-characterization-and-differential-expression-pattern-analysis-of-conserved-hmg-coa-reductase-domain-isolated-from-aconitum-balfourii-stapf
#14
Eti Sharma, Saurabh Pandey, A K Gaur
The 3-hydroxy-3-methyl glutaryl CoA reductase (HMGR) is the key enzyme of mevalonate pathway in plants. A partial genomic DNA fragment encoding HMGR conserved domain (denoted as AbHMGR) is isolated from Aconitum balfourii Stapf. It comprises 871 bp encoding 290 amino acids. In silico analysis reveals that it had extensive similarities to other plant HMGR gene. Domain analysis of AbHMGR showed two highly conserved NADPH and HMG CoA domains. Docking study predicted inhibitor, substrate and cofactor binding sites in the protein...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330158/a-simple-and-efficient-agrobacterium-tumefaciens-mediated-plant-transformation-of-brassica-rapa-ssp-pekinensis
#15
Venkidasamy Baskar, Baniekal H Gangadhar, Se Won Park, Shivraj Hariram Nile
The present study aims to investigate the numerous factors influencing Agrobacterium tumefaciens-mediated genetic transformation of Chinese cabbage (Brassica rapa ssp. pekinensis). Factors affecting transformation efficiency, such as age of explants, Agrobacterium concentration, and effect of acetosyringone, pre-cultivation, infection and co-cultivation time of Agrobacterium were examined. The pre-cultured hypocotyls from young seedlings prior to exposure to Agrobacterium showed higher shoot regeneration. The plant transformation with the modest A...
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
#16
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/28330144/upcot-an-integrated-pipeline-tool-for-clustering-upstream-dna-sequences-of-orthologous-genes-in-prokaryotic-genomes
#17
P V Parvati Sai Arun, Jogadhenu S S Prakash
UpCoT is a pipeline tool developed by automating the series of steps involved in prediction of cis-regulatory elements. UpCoT generates orthologs for each gene in target genome using bi-directional best blast hit against the reference genomes, then identifies potential orthologous transcriptional units using intergenic distance. Finally it generates the FASTA files containing upstream sequences of orthologous transcriptional units of each gene in target genome. The inputs of UpCoT are protein sequence files (*...
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
#18
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/28330131/an-efficient-protocol-for-isolation-of-inhibitor-free-nucleic-acids-even-from-recalcitrant-plants
#19
Mohammad Hossein Rezadoost, Mojtaba Kordrostami, Hassan Hassani Kumleh
For fast and easy isolation of inhibitor-free genomic DNA even from the toughest plant leaf samples, including those high in polyphenols and polysaccharides, a protocol has been developed. To prevent the solubility of polysaccharides in the DNA extract, high salt concentration (1.4 M) was used in the extraction buffer. Polyvinylpyrrolidone (PVP) was used for the removal of polyphenols as polymerase chain reaction (PCR) inhibitors. Proteins like various enzymes were degraded by proteinase K and removed by centrifugation from plant extracts during the isolation process resulting in pure DNA and RNA ready to use in downstream applications including PCR, quantitative polymerase chain reaction (qPCR), ligation, restriction and sequencing...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330120/assessment-of-genetic-purity-in-rice-oryza-sativa-l-hybrids-using-microsatellite-markers
#20
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
keyword
keyword
658
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"