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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
#1
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/28330315/characterization-and-development-of-est-ssr-markers-in-sweet-potato-ipomoea-batatas-l-lam
#2
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/28330309/molecular-characterization-of-phytoplasmas-of-clover-proliferation-group-associated-with-three-ornamental-plant-species-in-india
#3
Ekta Khasa, Gopala, Aido Taloh, T Prabha, Madhupriya, G P Rao
Suspected phytoplasma symptoms of little leaf, yellowing, chlorosis, phyllody, witches' broom, and stunting were observed on ten different ornamental plant species at New Delhi, Andhra Pradesh, Haryana, Bengaluru, and Pune, India, during March to July 2016. To investigate the possibility of phytoplasma etiology, PCR assays were performed using universal primer pairs (P1/P7 followed by 3Far/3Rev) specific to the phytoplasma 16Sr RNA gene. First round PCR amplification with primer pair P1/P7 did not yield expected 1...
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
#4
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/28330276/molecular-diversity-of-annona-species-and-proximate-fruit-composition-of-selected-genotypes
#5
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/28330242/phylogenetical-coherence-of-pseudomonas-in-unexplored-soils-of-himalayan-region
#6
Stuti Sah, Rajni Singh
Pseudomonas, an enormously diverse genus of the γ-Proteobacteria, is an important member of soil microbial communities. In this study, genetic heterogeneity and plant growth promotory property of Pseudomonas was compared within the group Pseudomonas sensu stricto isolated from the lesser explored niches of Himalayan region. A significant difference (P < 0.001 in total Pseudomonas count) was observed among the six types of soil samples collected from oak forest, fine forest, and agricultural soil. The highest numbers of bacteria were isolated from oak forest soil followed by pine forest soil and agricultural soil...
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
#7
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/28330178/emergence-of-mixed-infection-of-beijing-non-beijing-strains-among-multi-drug-resistant-mycobacterium-tuberculosis-in-pakistan
#8
Samar Mustafa, Hasnain Javed, Jawairia Hashmi, Nazia Jamil, Zarfishan Tahir, Abdul Majeed Akhtar
Tuberculosis (TB) remains as one of the deadliest diseases after HIV globally with 95 % of deaths confined to low-and-middle income countries. Pakistan is fifth among the 22 high-burden TB countries with the incidence rate of 230/100,000 persons, however, studies related to prevalent Mycobacterium tuberculosis strains and their spread, drug resistance pattern and evolutionary genetics are inadequate. The present study was undertaken to highlight the circulation of M. tuberculosis strains causing drug resistant TB in our community by targeting the molecular marker IS6110 and then characterization of these strains as Beijing and Non-Beijing genotypes...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330170/an-efficient-and-cost-effective-method-of-rna-extraction-from-mucilage-phenol-and-secondary-metabolite-rich-bark-tissue-of-tossa-jute-c-olitorius-l-actively-developing-phloem-fiber
#9
S B Choudhary, M Kumar, I Chowdhury, R K Singh, S P Pandey, H K Sharma, P G Karmakar
Tossa jute is an important natural fiber crop of Southeast Asian countries including India, Bangladesh, China, Thailand, Myanmar etc. Traditional industrial application of jute fiber is limited to the packaging products like hessians, sacks, etc. and the fiber found unsuitable for textile industries largely due to significantly high lignin content. Therefore, understanding genetic factors underlying lignin biosynthesis in tossa jute holds promise for jute based product diversification. The major limiting factor in undertaking such study is unavailability of efficient protocol for RNA extraction at secondary growth active stage of tossa jute...
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
#10
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/28330127/diversity-of-toxic-and-phytopathogenic-fusarium-species-occurring-on-cereals-grown-in-karnataka-state-india
#11
H Nagaraja, G Chennappa, K Poorna Chandra Rao, G Mahadev Prasad, M Y Sreenivasa
A total of 198 cereal samples (53 maize, 54 sorghum, 37 paddy and 54 wheat) were collected from 11 districts of Karnataka to understand the percent infection (PI), relative density (RD) and their frequency (Fr) caused by Fusarium spp. All samples were screened by agar plating method using MGA 2.5 agar media and incubated at 25 ± 2 °C for 3-5 days. The study revealed the association of 10 different Fusarium species known trichothecene producers such as Fusarium acuminatum, F. avenaceum, F. crookwellense, F...
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/28330092/development-of-molecular-method-for-sex-identification-in-date-palm-phoenix-dactylifera-l-plantlets-using-novel-sex-linked-microsatellite-markers
#14
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/28330075/a-novel-multiplex-pcr-method-for-the-detection-of-virulence-associated-genes-of-escherichia-coli-o157-h7-in-food
#15
Vo Van Giau, Thuy Trang Nguyen, Thi Kim Oanh Nguyen, Thi Thuy Hang Le, Tien Dung Nguyen
Shiga toxin-producing Escherichia coli O157:H7 (E. coli O157:H7) strains are foodborne infectious agents that cause a number of life-threatening diseases, including hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS). Shiga toxin 1 (stx1), shiga toxin 2 (stx2), or a combination of both are responsible for most clinical symptoms of these diseases. Hence, various diagnostic methods have been developed so far to detect shiga toxins such as cell culture, ELISA, Rapid Latex Agglutination (RPLA) and hybridization, but due to high costs and labor time in addition to low sensitivity, they have not received much attention...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28327639/evaluation-of-different-oligonucleotide-base-substitutions-at-cpg-binding-sites-in-multiplex-bisulfite-pcr-sequencing
#16
Jennifer Lu, Kelin Ru, Ida Candiloro, Alexander Dobrovic, Darren Korbie, Matt Trau
Multiplex bisulfite-PCR sequencing is a convenient and scalable method for the quantitative determination of the methylation state of target DNA regions. A challenge of this application is the presence of CpGs in the same region where primers are being placed. A common solution to the presence of CpGs within a primer-binding region is to substitute a base degeneracy at the cytosine position. However, the efficacy of different substitutions and the extent to which bias towards methylated or unmethylated templates may occur has never been evaluated in bisulfite multiplex sequencing applications...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28326314/case-study-of-somaclonal-variation-in-resistance-genes-mlo-and-pme3-in-flaxseed-linum-usitatissimum-l-induced-by-nanoparticles
#17
Inese Kokina, Ilona Mickeviča, Marija Jermaļonoka, Linda Bankovska, Vjačeslavs Gerbreders, Andrejs Ogurcovs, Inese Jahundoviča
Nanoparticles influence on genome is investigated worldwide. The appearance of somaclonal variation is a cause of great concern for any micropropagation system. Somaclonal variation describes the tissue-culture-induced phenotypic and genotypic variations. This paper shows the results of somaclonal variation in two resistance genes pectin methylesterase and Mlo-like protein in all tissue culture development stages, as donor plant, calluses, and regenerants of Linum usitatissimum induced by gold and silver nanoparticles...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28325909/nmr-monitoring-of-the-selex-process-to-confirm-enrichment-of-structured-rna
#18
Ryo Amano, Kazuteru Aoki, Shin Miyakawa, Yoshikazu Nakamura, Tomoko Kozu, Gota Kawai, Taiichi Sakamoto
RNA aptamers are RNA molecules that bind to a target molecule with high affinity and specificity using uniquely-folded tertiary structures. RNA aptamers are selected from an RNA pool typically comprising up to 10(15) different sequences generated by iterative steps of selection and amplification known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Over several rounds of SELEX, the diversity of the RNA pool decreases and the aptamers are enriched. Hence, monitoring of the enrichment of these RNA pools is critical for the successful selection of aptamers, and several methods for monitoring them have been developed...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28324847/species-identification-in-forensic-samples-using-the-spindel-approach-a-ghep-isfg-inter-laboratory-collaborative-exercise
#19
Cíntia Alves, Rui Pereira, Lourdes Prieto, Mercedes Aler, Cesar R L Amaral, Cristina Arévalo, Gabriela Berardi, Florencia Di Rocco, Mariela Caputo, Cristian Hernandez Carmona, Laura Catelli, Heloísa Afonso Costa, Pavla Coufalova, Sandra Furfuro, Óscar García, Anibal Gaviria, Ana Goios, Juan José Builes Gómez, Alexis Hernández, Eva Del Carmen Betancor Hernández, Luís Miranda, David Parra, Susana Pedrosa, Maria João Anjos Porto, Maria de Lurdes Rebelo, Matteo Spirito, María Del Carmen Villalobos Torres, António Amorim, Filipe Pereira
DNA is a powerful tool available for forensic investigations requiring identification of species. However, it is necessary to develop and validate methods able to produce results in degraded and or low quality DNA samples with the high standards obligatory in forensic research. Here, we describe a voluntary collaborative exercise to test the recently developed Species Identification by Insertions/Deletions (SPInDel) method. The SPInDel kit allows the identification of species by the generation of numeric profiles combining the lengths of six mitochondrial ribosomal RNA (rRNA) gene regions amplified in a single reaction followed by capillary electrophoresis...
March 7, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28324500/analysis-of-yeast-telomerase-by-primer-extension-assays
#20
Min Hsu, Neal F Lue
Telomeres are specialized nucleoprotein structures located at eukaryotic chromosomal termini, which are required for chromosome stability and are maintained by a reverse transcriptase named telomerase. Budding yeast has served as an extremely useful model system for analyzing telomere maintenance because the organism offers a wide range of genetic and biochemical tools. Several milestones in telomerase research have been reached through investigation of the yeast system. For example, the consequence of telomerase loss was first characterized in the budding yeast Saccharomyces cerevisiae...
2017: Methods in Molecular Biology
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