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https://www.readbyqxmd.com/read/28330309/molecular-characterization-of-phytoplasmas-of-clover-proliferation-group-associated-with-three-ornamental-plant-species-in-india
#1
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/28330224/transcriptome-wide-mining-suggests-conglomerate-of-genes-associated-with-tuberous-root-growth-and-development-in-aconitum-heterophyllum-wall
#2
Nikhil Malhotra, Hemant Sood, Rajinder Singh Chauhan
Tuberous roots of Aconitum heterophyllum constitute storage organ for secondary metabolites, however, molecular components contributing to their formation are not known. The transcriptomes of A. heterophyllum were analyzed to identify possible genes associated with tuberous root development by taking clues from genes implicated in other plant species. Out of 18 genes, eight genes encoding GDP-mannose pyrophosphorylase (GMPase), SHAGGY, Expansin, RING-box protein 1 (RBX1), SRF receptor kinase (SRF), β-amylase, ADP-glucose pyrophosphorylase (AGPase) and Auxin responsive factor 2 (ARF2) showed higher transcript abundance in roots (13-171 folds) compared to shoots...
December 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
#3
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
#4
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/28330144/upcot-an-integrated-pipeline-tool-for-clustering-upstream-dna-sequences-of-orthologous-genes-in-prokaryotic-genomes
#5
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/28330100/molecular-characterization-and-amplified-ribosomal-dna-restriction-analysis-of-entomopathogenic-bacteria-associated-with-rhabditis-oscheius-spp
#6
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/28329933/-study-on-hiv-1-subtype-among-elderly-male-clients-and-female-sex-workers-of-low-cost-venues-in-guangxi-zhuang-autonomous-region-china
#7
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/28329901/-pathophysiology-of-headaches
#8
Charly Gaul, Karl Meßlinger, Dagny Holle-Lee, Lars Neeb
Pathophysiological concepts of primary headache diseases have been developed significantly in the last decades. Nevertheless pathophysiology of single diseases is unexplained. Migraine headache arises from activation and sensibilization of trigeminal nociceptors, essential processes are located at the meninges and the meningeal vessels. Calcitonin gene-related peptide (CGRP) seems to have essential importance concerning migraine and cluster headache. Mechanisms leading to peripheral and central sensitization are relevant in chronification of migraine and tension-type headache...
March 2017: Deutsche Medizinische Wochenschrift
https://www.readbyqxmd.com/read/28329684/cis-regulatory-circuits-regulating-nek6-kinase-overexpression-in-transformed-b-cells-are-super-enhancer-independent
#9
Yue Huang, Olivia I Koues, Jiang-Yang Zhao, Regina Liu, Sarah C Pyfrom, Jacqueline E Payton, Eugene M Oltz
Alterations in distal regulatory elements that control gene expression underlie many diseases, including cancer. Epigenomic analyses of normal and diseased cells have produced correlative predictions for connections between dysregulated enhancers and target genes involved in pathogenesis. However, with few exceptions, these predicted cis-regulatory circuits remain untested. Here, we dissect cis-regulatory circuits that lead to overexpression of NEK6, a mitosis-associated kinase, in human B cell lymphoma. We find that only a minor subset of predicted enhancers is required for NEK6 expression...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28329005/rethinking-the-influence-of-hydroelectric-development-on-gene-flow-in-a-long-lived-fish-the-lake-sturgeon-acipenser-fulvescens
#10
Craig A McDougall, Amy B Welsh, Thierry Gosselin, W Gary Anderson, Patrick A Nelson
Many hydroelectric dams have been in place for 50 - >100 years, which for most fish species means that enough generations have passed for fragmentation induced divergence to have accumulated. However, for long-lived species such as Lake Sturgeon, Acipenser fulvescens, it should be possible to discriminate between historical population structuring and contemporary gene flow and improve the broader understanding of anthropogenic influence. On the Winnipeg River, Manitoba, two hypotheses were tested: 1) Measureable quantities of former reservoir dwelling Lake Sturgeon now reside downstream of the Slave Falls Generating Station, and 2) genetically differentiated populations of Lake Sturgeon occur upstream and downstream, a result of historical structuring...
2017: PloS One
https://www.readbyqxmd.com/read/28328508/hapiso-an-accurate-method-for-the-haplotype-specific-isoforms-reconstruction-from-long-single-molecule-reads
#11
Serghei Mangul, Harry Taegyun Yang, Farhad Hormozdiari, Alex Dainis, Elizabeth Tseng, Euan A Ashley, Alex Zelikovsky, Eleazar Eskin
Sequencing of RNA provides the possibility to study an individual's transcriptome landscape and determine allelic expression ratios. Single-molecule protocols generate multi-kilobase reads longer than most transcripts allowing sequencing of complete haplotype isoforms. This allows partitioning the reads into two parental haplotypes. While the read length of the single-molecule protocols is long, the relatively high error rate limits the ability to accurately detect the genetic variants and assemble them into the haplotype-specific isoforms...
March 17, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28327996/genome-sequencing-of-the-sweetpotato-whitefly-bemsia-tabaci-med-q
#12
Wen Xie, Chunhai Chen, Zezhong Yang, Litao Guo, Xin Yang, Dan Wang, Ming Chen, Jinqun Huang, Yanan Wen, Yang Zeng, Yating Liu, Jixing Xia, Lixia Tian, Hongying Cui, Qingjun Wu, Shaoli Wang, Baoyun Xu, Xianchun Li, Xinqiu Tan, Murad Ghanim, Baoli Qiu, Huipeng Pan, Dong Chu, Helene Delatte, M N Maruthi, Feng Ge, Xueping Zhou, Xiaowei Wang, Fanghao Wan, Yuzhou Du, Chen Luo, Fengming Yan, Evan L Preisser, Xiaoguo Jiao, Brad S Coates, Jinyang Zhao, Qiang Gao, Jinquan Xia, Ye Yin, Yong Liu, Judith K Brown, Xuguo Joe Zhou, Youjun Zhang
Background: The sweetpotato whitefly Bemisia tabaci is a highly destructive agricultural and ornamental crop pest. It damages host plants through both phloem feeding and vectoring plant pathogens. Introductions of B. tabaci are difficult to quarantine and eradicate because of its high reproductive rates, broad host plant range, and insecticide resistance. Findings: A total of 791 Gb of raw DNA sequence from whole genome shotgun sequencing, and 13 BAC pooling libraries were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries...
March 15, 2017: GigaScience
https://www.readbyqxmd.com/read/28327671/candidate-loci-involved-in-domestication-and-improvement-detected-by-a-published-90k-wheat-snp-array
#13
Lifeng Gao, Guangyao Zhao, Dawei Huang, Jizeng Jia
Selection is one of the most important forces in crop evolution. Common wheat is a major world food crop and a typical allopolyploid with a huge and complex genome. We applied four approaches to detect loci selected in wheat during domestication and improvement. A total of 7,984 candidate loci were detected, accounting for 23.3% of all 34,317 SNPs analysed, a much higher proportion than estimated in previous reports. We constructed a first generation wheat selection map which revealed the following new insights on genome-wide selection: (1) diversifying selection acted by increasing, decreasing or not affecting gene frequencies; (2) the number of loci under selection during domestication was much higher than that during improvement; (3) the contribution to wheat improvement by the D sub-genome was relatively small due to the bottleneck of hexaploidisation and diversity can be expanded by using synthetic wheat and introgression lines; and (4) clustered selection regions occur throughout the wheat genome, including the centromere regions...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327641/sequential-displacement-of-type-vi-secretion-system-effector-genes-leads-to-evolution-of-diverse-immunity-gene-arrays-in-vibrio-cholerae
#14
Paul C Kirchberger, Daniel Unterweger, Daniele Provenzano, Stefan Pukatzki, Yan Boucher
Type VI secretion systems (T6SS) enable bacteria to engage neighboring cells in contact-dependent competition. In Vibrio cholerae, three chromosomal clusters each encode a pair of effector and immunity genes downstream of those encoding the T6SS structural machinery for effector delivery. Different combinations of effector-immunity proteins lead to competition between strains of V. cholerae, which are thought to be protected only from the toxicity of their own effectors. Screening of all publically available V...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327598/global-dna-methylation-analysis-identifies-two-discrete-clusters-of-pheochromocytoma-with-distinct-genomic-and-genetic-alterations
#15
Samuel Backman, Rajani Maharjan, Alberto Falk-Delgado, Joakim Crona, Kenko Cupisti, Peter Stålberg, Per Hellman, Peyman Björklund
Pheochromocytomas and paragangliomas (PPGLs) are rare and frequently heritable neural-crest derived tumours arising from the adrenal medulla or extra-adrenal chromaffin cells respectively. The majority of PPGL tumours are benign and do not recur with distant metastases. However, a sizeable fraction of these tumours secrete vasoactive catecholamines into the circulation causing a variety of symptoms including hypertension, palpitations and diaphoresis. The genetic landscape of PPGL has been well characterized and more than a dozen genes have been described as recurrently mutated...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327152/trim8-restores-p53-tumour-suppressor-function-by-blunting-n-myc-activity-in-chemo-resistant-tumours
#16
Francesca Mastropasqua, Flaviana Marzano, Alessio Valletti, Italia Aiello, Giuseppe Di Tullio, Annalisa Morgano, Sabino Liuni, Elena Ranieri, Luisa Guerrini, Giuseppe Gasparre, Elisabetta Sbisà, Graziano Pesole, Antonio Moschetta, Mariano Francesco Caratozzolo, Apollonia Tullo
BACKGROUND: TRIM8 plays a key role in controlling the p53 molecular switch that sustains the transcriptional activation of cell cycle arrest genes and response to chemotherapeutic drugs. The mechanisms that regulate TRIM8, especially in cancers like clear cell Renal Cell Carcinoma (ccRCC) and colorectal cancer (CRC) where it is low expressed, are still unknown. However, recent studies suggest the potential involvement of some microRNAs belonging to miR-17-92 and its paralogous clusters, which could include TRIM8 in a more complex pathway...
March 21, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28326787/linear-peptides-are-the-major-products-of-a-biosynthetic-pathway-that-encodes-for-cyclic-depsipeptides
#17
Thomas P Wyche, Antonio C Ruzzini, Christine Beemelmanns, Ki Hyun Kim, Jonathan L Klassen, Shugeng Cao, Michael Poulsen, Tim S Bugni, Cameron R Currie, Jon Clardy
Three new dentigerumycin analogues are produced by Streptomyces sp. M41, a bacterium isolated from a South African termite, Macrotermes natalensis. The structures of the complex nonribosomal peptide synthetase-polyketide synthase (NRPS/PKS) hybrid compounds were determined by 1D- and 2D-NMR spectroscopy, high-resolution mass spectrometry, and circular dichroism (CD) spectroscopy. Both cyclic and linear peptides are reported, and the genetic organization of the NRPS modules within the biosynthetic gene cluster accounts for the observed structural diversity...
March 22, 2017: Organic Letters
https://www.readbyqxmd.com/read/28326315/genomewide-expression-and-functional-interactions-of-genes-under-drought-stress-in-maize
#18
Nepolean Thirunavukkarasu, Rinku Sharma, Nidhi Singh, Kaliyugam Shiriga, Sweta Mohan, Swati Mittal, Shikha Mittal, Mallana Gowdra Mallikarjuna, Atmakuri Ramakrishna Rao, Prasanta Kumar Dash, Firoz Hossain, Hari Shanker Gupta
A genomewide transcriptome assay of two subtropical genotypes of maize was used to observe the expression of genes at seedling stage of drought stress. The number of genes expressed differentially was greater in HKI1532 (a drought tolerant genotype) than in PC3 (a drought sensitive genotype), indicating primary differences at the transcriptional level in stress tolerance. The global coexpression networks of the two genotypes differed significantly with respect to the number of modules and the coexpression pattern within the modules...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28326151/chronic-porphyromonas-gingivalis-infection-accelerates-the-occurrence-of-age-related-granules-in-apoe-mice-brains
#19
Sim K Singhrao, Sasanka Chukkapalli, Sophie Poole, Irina Velsko, St John Crean, Lakshmyya Kesavalu
This study explored the origin of age-related granules in the apolipoprotein E gene knockout (ApoE(-/-)) B6 background mice brains following chronic gingival infection with Porphyromonas gingivalis for 24 weeks. Intracerebral localization of P. gingivalis was detected by fluorescence in situ hybridization (FISH) and its protease by immunohistochemistry. The age-related granules were observed by periodic acid-Schiff (PAS), silver impregnation, and immunostaining. FISH showed intracerebral dissemination of P...
2017: Journal of Oral Microbiology
https://www.readbyqxmd.com/read/28326099/disease-risk-assessment-using-a-voronoi-based-network-analysis-of-genes-and-variants-scores
#20
Lin Chen, Gouri Mukerjee, Ruslan Dorfman, Seyed M Moghadas
Much effort has been devoted to assess disease risk based on large-scale protein-protein network and genotype-phenotype associations. However, the challenge of risk prediction for complex diseases remains unaddressed. Here, we propose a framework to quantify the risk based on a Voronoi tessellation network analysis, taking into account the disease association scores of both genes and variants. By integrating ClinVar, SNPnexus, and DISEASES databases, we introduce a gene-variant map that is based on the pairwise disease-associated gene-variant scores...
2017: Frontiers in Genetics
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