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Phylogenetics

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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/28330322/de-novo-transcriptome-sequencing-in-monsonia-burkeana-revealed-putative-genes-for-key-metabolic-pathways-involved-in-tea-quality-and-medicinal-value
#2
Adugna A Woldesemayat, Khayalethu Ntushelo, David M Modise
Monsonia (Monsonia burkeana Planch. ex Harv) is one of the most valuable tea and traditional medicinal plants used in Southern Africa. In spite of this, there is no sequence information regarding this plant in literature. To provide understanding of the naturally occurring tea and drug-specific products and the key pathways for the biosynthesis of these molecules, we sequenced the leaf transcriptome using Illumina MiSeq platform and generated 2,590,652 paired-end reads that were assembled de novo into 45,450 high-quality transcripts...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330314/bioremediation-of-heavy-metals-using-an-endophytic-bacterium-paenibacillus-sp-rm-isolated-from-the-roots-of-tridax-procumbens
#3
M Govarthanan, R Mythili, T Selvankumar, S Kamala-Kannan, A Rajasekar, Young-Cheol Chang
The aim of the present study was to assess the bioremediation potential of endophytic bacteria isolated from roots of Tridax procumbens plant. Five bacterial endophytes were isolated and subsequently tested for minimal inhibitory concentration (MIC) against different heavy metals. Amongst the five isolates, strain RM exhibited the highest resistance to copper (750 mg/l), followed by zinc (500 mg/l), lead (450 mg/l), and arsenic (400 mg/l). Phylogenetic analysis of the 16S rDNA sequence suggested that strain RM was a member of genus Paneibacillus...
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
#4
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/28330262/biodegradation-of-isoproturon-by-pseudoxanthomonas-sp-isolated-from-herbicide-treated-wheat-fields-of-tarai-agro-ecosystem-pantnagar
#5
Krishna Giri, Shailseh Pandey, Rajesh Kumar, J P N Rai
A gram-negative, rod-shaped, isoproturon (IPU) utilizing bacterium was isolated from herbicide-applied wheat fields of Tarai agro-ecosystem, Pantnagar. The phylogenetic sequence analysis based on 16S rRNA sequence revealed that the isolate could be a distinct species within the genus Pseudomonas. The isolate was a close relative of Pseudoxanthomonas japonensis (95 % similarity) and designated as K2. The bacterial isolate showed positive reaction for oxidase, catalase, and 20 carbohydrates using KB009 Part A and B HiCarbohydrate™ Kit...
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/28330205/dna-record-of-some-traditional-small-millet-landraces-in-india-and-nepal
#7
Subramanyam Ragupathy, Shanmughanandhan Dhivya, Kirit Patel, Abiran Sritharan, Kathirvelu Sambandan, Hom Gartaula, Ramalingam Sathishkumar, Kamal Khadka, Balasubramanian C Nirmala, A Nirmala Kumari, Steven G Newmaster
Despite the extensive use of small millet landraces as an important source of nutrition for people living in semi-arid regions, they are presently marginalized and their diversity and distribution are threatened at a global scale. Local farmers have developed ancient breeding programs entrenched in traditional knowledge (TK) that has sustained rural cultures for thousands of years. The convention on biological diversity seeks fair and equitable sharing of genetic resources arising from local knowledge and requires signatory nations to provide appropriate policy and legal framework to farmers' rights over plant genetic resources and associated TK...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330168/metabolism-of-waste-engine-oil-by-pseudomonas-species
#8
Lateef B Salam
Two bacterial strains phylogenetically identified as Pseudomonas aeruginosa strains RM1 and SK1 displayed extensive degradation ability on waste engine oil (SAE 40W) in batch cultures. Spectrophotometric analysis revealed the presence of various heavy metals such as lead, chromium and nickel in the waste engine oil. The rate of degradation of waste engine oil by the isolates, for the first 12 days and the last 9 days were 66.3, 31.6 mg l(-1) day(-1)  and 69.6, 40.0 mg l(-1) day(-1) for strains RM1 and SK1, respectively...
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
#9
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/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/28330142/an-overview-of-physico-chemical-mechanisms-of-biogas-production-by-microbial-communities-a-step-towards-sustainable-waste-management
#11
REVIEW
Ramansu Goswami, Pritam Chattopadhyay, Arunima Shome, Sambhu Nath Banerjee, Amit Kumar Chakraborty, Anil K Mathew, Shibani Chaudhury
Biogas is a combination of methane, CO2, nitrogen, H2S and traces of few other gases. Almost any organic waste can be biologically transformed into biogas and other energy-rich organic compounds through the process of anaerobic digestion (AD) and thus helping in sustainable waste management. Although microbes are involved in each step of AD, knowledge about those microbial consortia is limited due to the lack of phylogenetic and metabolic data of predominantly unculturable microorganisms. However, culture-independent methods like PCR-based ribotyping has been successfully employed to get information about the microbial consortia involved in AD...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330115/phylogenetic-and-metabolic-diversity-of-tunisian-forest-wood-degrading-fungi-a-wealth-of-novelties-and-opportunities-for-biotechnology
#12
Dalel Daâssi, Héla Zouari-Mechichi, Lassaad Belbahri, Jorge Barriuso, María Jesús Martínez, Moncef Nasri, Tahar Mechichi
In this study, 51 fungal strains were isolated from decaying wood samples collected from forests located in the Northwest of Tunisia in the vicinity of Bousalem, Ain Draham and Kef. Phylogenetic analysis based on the sequences of the internal transcribed spacers of the ribosomal DNA showed a high diversity among the 51 fungal isolates collection. Representatives of 25 genera and 29 species were identified, most of which were members of one of the following phyla (Ascomycota, Basidiomycota and Zygomycota). In addition to the phylogenetic diversity, a high diversity of secreted enzyme profiles was also detected among the fungal isolates...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330100/molecular-characterization-and-amplified-ribosomal-dna-restriction-analysis-of-entomopathogenic-bacteria-associated-with-rhabditis-oscheius-spp
#13
Balakrishnan Geetha Sangeetha, Cheruvandasseri Arumughan Jayaprakas, Jinachandrannair Vijayakumari Siji, Moochattil Rajitha, Basheerkutty Shyni, Chellappan Mohandas
Bacterial strains associated with entomopathogenic nematodes (EPNs) Rhabditis (Oscheius) spp. were isolated from infected cadavers of Galleria mellonella. The obtained 18 isolates were subdivided into nine phylogenetically different genera based on comparative sequence analysis of their 16S rRNA genes. The isolates were affiliated to three different class namely γ-proteobacteria (Enterobacter, Proteus, Providencia, Pseudomonas, Stenotrophomonas), β-proteobacteria (Alcaligenes) and Bacilli (Bacillus, Enterococcus, Lysinibacillus)...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330094/characterization-of-antibiotic-resistant-and-enzyme-producing-bacterial-strains-isolated-from-the-arabian-sea
#14
Preeti N Tallur, Dayanand B Sajjan, Sikandar I Mulla, Manjunatha P Talwar, A Pragasam, Vinayak M Nayak, Harichandra Z Ninnekar, Shivanand S Bhat
Marine bacteria are known to produce many bioactive molecules and extracellular enzymes of commercial importance. We have investigated the bacterial diversity of the coastal area of Karwar, Karnataka State, India. Among these bacterial isolates, five bacterial strains were selected and identified by their morphological, biochemical characteristics and phylogenetic analysis based on 16S rRNA gene sequences. The identified bacterial isolates, Bacillus toyonensis PNTB1, Lysinibacillus sphaericus PTB, Vibrio vulnificus PMD, Shewanella MPTDBS, and Pseudomonas chlororaphis PNTB were characterized for their tolerance to salt and antibiotics...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330078/potential-of-trichoderma-harzianum-for-control-of-banana-leaf-fungal-pathogens-when-applied-with-a-food-source-and-an-organic-adjuvant
#15
Suren Samuelian
Trichoderma isolates were obtained from diseased leaves and fruit collected from plantations in the main banana production area in Northern Queensland. Phylogenetic analyses identified the Trichoderma isolates as T. harzianum and T. virens. The Trichoderma spp. were found to be antagonistic against the banana leaf pathogens Mycosphaerella musicola, Cordana musae, and Deightoniella torulosa in vitro. Several products used by the banana industry to increase production, including molasses, Fishoil and Seasol, were tested as food source for the Trichoderma isolates...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329933/-study-on-hiv-1-subtype-among-elderly-male-clients-and-female-sex-workers-of-low-cost-venues-in-guangxi-zhuang-autonomous-region-china
#16
Y Q Deng, J J Li, N Y Fang, B Wang, J W Wang, S S Liang, Z Y Shen, G H Lan, H M Zhang, X H Wu, H X Lu, X M Ge
Objective: To understand HIV-1 subtype characteristics and transmission clusters in elderly male clients and female sex workers (FSWs) of low-cost commercial sex venues in Guangxi Zhuang Autonomous Region, China. Methods: A cross sectional survey was conducted in FSWs and elderly male clients (≥50 years) of low-cost commercial sex venues in 4 cities and 9 counties in Guangxi Zhuang Autonomous Region by convenient sampling in 2012. The blood sample was collected from each case for HIV-1 antibody detection...
March 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28329448/a-novel-nhad-type-na-h-antiporter-from-the-moderate-halophile-and-alkaliphile-halomonas-alkaliphila
#17
Yanhong Wang, Na Song, Lina Yang, Heba Abdel-Motaal, Rui Zhang, Zhenglai Zhang, Fankui Meng, Juquan Jiang
In this study, a NhaD-type Na+/H+ antiporter gene designated Ha-nhaD was obtained by selection of genomic DNA from the moderate halophile and alkaliphile Halomonas alkaliphila in Escherichia coli KNabc lacking three major Na+/H+ antiporters. The presence of Ha-NhaD conferred tolerance of E. coli KNabc to up to 0.6 M NaCl and 0.2 M LiCl and an alkaline pH. pH-dependent Na+(Li+)/H+ antiport activity was detected from everted membrane vesicles prepared from E. coli KNabc/pUC-nhaD but not those from KNabc/pUC18...
March 22, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28329402/novel-orthopoxvirus-infection-in-an-alaska-resident
#18
Yuri P Springer, Christopher H Hsu, Zachary R Werle, Link E Olson, Michael P Cooper, Louisa J Castrodale, Nisha Fowler, Andrea M McCollum, Cynthia S Goldsmith, Ginny L Emerson, Kimberly Wilkins, Jeffrey B Doty, Jillybeth Burgado, JinXin Gao, Nishi Patel, Matthew R Mauldin, Mary G Reynolds, Panayampalli S Satheshkumar, Whitni Davidson, Yu Li, Joseph B McLaughlin
Background.: Human infection by orthopoxviruses is being reported with increasing frequency, attributed in part to the cessation of smallpox vaccination and concomitant waning of population-level immunity. In July 2015, a female resident of interior Alaska, presented to an urgent care clinic with a dermal lesion consistent with poxvirus infection. Laboratory testing of a virus isolated from the lesion confirmed infection by an Orthopoxvirus. Methods.: The virus isolate was characterized by using electron microscopy and nucleic acid sequencing...
March 15, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28329390/high-rates-of-transmission-of-drug-resistant-hiv-in-aruba-resulting-in-reduced-susceptibility-to-the-who-recommended-first-line-regimen-in-nearly-half-of-newly-diagnosed-hiv-infected-patients
#19
L Marije Hofstra, Elena Sánchez Rivas, Monique Nijhuis, Leonie E A Bank, Eduan Wilkinson, Karina Kelly, Tania Mudrikova, Rob Schuurman, Tulio de Oliveira, Jaclyn de Kort, Annemarie M J Wensing
Background.: In Western countries emergence of human immunodeficiency virus (HIV) drug resistance has tremendously decreased, and transmission of drug resistance has merely stabilized in recent years. However, in many endemic settings with limited resources rates of emerging and transmitted drug resistance are not regularly assessed. Methods.: We performed a survey including all HIV-infected individuals who received resistance testing in 2010-2015 in Aruba, a highly endemic HIV area in the Caribbean...
March 9, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28329010/phylogenetic-reconstruction-of-syntermitinae-isoptera-termitidae-based-on-morphological-and-molecular-data
#20
Mauricio M Rocha, Adriana C Morales-Corrêa E Castro, Carolina Cuezzo, Eliana M Cancello
The subfamily Syntermitinae comprises a group of Neotropical termites with 18 genera and 101 species described. It has been considered a natural group, but relationships among the genera within the subfamily remain uncertain, and some genera appear to be non-monophyletic. Here, we provide a comprehensive phylogeny including six Neotropical species of Termitinae as outgroup, 42 Syntermitinae species as ingroup, 92 morphological characters (from external and internal anatomy of soldier and worker castes) and 117 molecular sequences (109 obtained for this study and 8 from GenBank) of 4 gene regions (41 and 22 from Cytochrome Oxidase I and II respectively, 19 from Cytochrome b, and 35 from 16S rDNA)...
2017: PloS One
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