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https://www.readbyqxmd.com/read/28813463/genetic-diversity-of-bemisia-tabaci-species-colonizing-cassava-in-central-african-republic-characterized-by-analysis-of-cytochrome-c-oxidase-subunit-i
#1
Brice Kette Tocko-Marabena, Semballa Silla, Christophe Simiand, Innocent Zinga, James Legg, Bernard Reynaud, Helene Delatte
After 2007, upsurges of whiteflies on cassava plants and high incidences of cassava diseases were observed in Central African Republic. This recent upsurge in the abundance of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) was directly linked to serious damage to cassava crops resulting from spread of whitefly-borne cassava mosaic geminiviruses (CMGs). There is currently very little information describing whitefly populations on cassava and associated crops in Central African Republic. The current study aimed to address this gap, and to determine whether the increasing damage associated with B...
2017: PloS One
https://www.readbyqxmd.com/read/28813459/%C3%AE-2-microglobulin-gene-duplication-in-cetartiodactyla-remains-intact-only-in-pigs-and-possibly-confers-selective-advantage-to-the-species
#2
Thong Minh Le, Quy Van Chanh Le, Dung Minh Truong, Hye-Jeong Lee, Min-Kyeung Choi, Hyesun Cho, Hak-Jae Chung, Jin-Hoi Kim, Jeong-Tae Do, Hyuk Song, Chankyu Park
Several β2-microglobulin (B2M) -bound protein complexes undertake key roles in various immune system pathways, including the neonatal Fc receptor (FcRn), cluster of differentiation 1 (CD1) protein, non-classical major histocompatibility complex (MHC), and well-known MHC class I molecules. Therefore, the duplication of B2M may lead to an increase in the biological competence of organisms to the environment. Based on the pig genome assembly SSC10.2, a segmental duplication of ~45.5 kb, encoding the entire B2M protein, was identified in pig chromosome 1...
2017: PloS One
https://www.readbyqxmd.com/read/28812996/reliable-detection-of-herpes-simplex-virus-sequence-variation-by-high-throughput-resequencing
#3
Alison M Morse, Kaitlyn R Calabro, Justin M Fear, David C Bloom, Lauren M McIntyre
High-throughput sequencing (HTS) has resulted in data for a number of herpes simplex virus (HSV) laboratory strains and clinical isolates. The knowledge of these sequences has been critical for investigating viral pathogenicity. However, the assembly of complete herpesviral genomes, including HSV, is complicated due to the existence of large repeat regions and arrays of smaller reiterated sequences that are commonly found in these genomes. In addition, the inherent genetic variation in populations of isolates for viruses and other microorganisms presents an additional challenge to many existing HTS sequence assembly pipelines...
August 16, 2017: Viruses
https://www.readbyqxmd.com/read/28811664/structure-based-cross-docking-analysis-of-antibody-antigen-interactions
#4
Krishna Praneeth Kilambi, Jeffrey J Gray
Antibody-antigen interactions are critical to our immune response, and understanding the structure-based biophysical determinants for their binding specificity and affinity is of fundamental importance. We present a computational structure-based cross-docking study to test the identification of native antibody-antigen interaction pairs among cognate and non-cognate complexes. We picked a dataset of 17 antibody-antigen complexes of which 11 have both bound and unbound structures available, and we generated a representative ensemble of cognate and non-cognate complexes...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811564/computational-identification-of-y-linked-markers-and-genes-in-the-grass-carp-genome-by-using-a-pool-and-sequence-method
#5
Aidi Zhang, Rong Huang, Liangming Chen, Lv Xiong, Libo He, Yongming Li, Lanjie Liao, Zuoyan Zhu, Yaping Wang
The molecular analysis of sex in vertebrates is important, as it has the potential to provide vital information for theoretical and applied research alike. Teleost fish are the ancient vertebrates that present a broad sex chromosome system but lack differentiated sex chromosomes in most species. Hence understanding the sex in fish would not only illuminate the sex determination evolution in vertebrates but also shed light on fish farming. In the present study, we used grass carp as a teleost fish model, studied the Y chromosome by using a pool-and-sequence strategy in combination with fragment-ratio method...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811103/identification-and-phylogenetic-position-of-naegleria-spp-from-geothermal-springs-in-italy
#6
M Montalbano Di Filippo, A Novelletto, D Di Cave, F Berrilli
Naegleria spp. are free-living amoebae belonging to the family Vahlkampfiidae, in the class Heterolobosea. Among the recognized species, Naegleria fowleri causes primary amoebic meningoencephalitis (PAM), while two other species, Naegleria australiensis and Naegleria italica, have been reported as pathogenic in experimental animals. Due to the thermotolerance properties of some species, geothermal water sources including hot springs represent suitable habitats for their proliferation. The main aim of this study was a year-round sampling in two geothermal springs in Central Italy, to investigate the presence of Naegleria spp...
August 12, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28810867/new-inducible-promoter-for-gene-expression-and-synthetic-biology-in-yarrowia-lipolytica
#7
Marion Trassaert, Marie Vandermies, Fréderic Carly, Olivia Denies, Stéphane Thomas, Patrick Fickers, Jean-Marc Nicaud
BACKGROUND: The oleaginous yeast Yarrowia lipolytica is increasingly used as alternative cell factory for the production of recombinant proteins. At present, several promoters with different strengths have been developed based either on the constitutive pTEF promoter or on oleic acid inducible promoters such as pPOX2 and pLIP2. Although these promoters are highly efficient, there is still a lack of versatile inducible promoters for gene expression in Y. lipolytica. RESULTS: We have isolated and characterized the promoter of the EYK1 gene coding for an erythrulose kinase...
August 15, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28810827/validation-of-%C3%AE-lactam-minimum-inhibitory-concentration-predictions-for-pneumococcal-isolates-with-newly-encountered-penicillin-binding-protein-pbp-sequences
#8
Yuan Li, Benjamin J Metcalf, Sopio Chochua, Zhongya Li, Robert E Gertz, Hollis Walker, Paulina A Hawkins, Theresa Tran, Lesley McGee, Bernard W Beall
BACKGROUND: Genomic sequence-based deduction of antibiotic minimum inhibitory concentration (MIC) has great potential to enhance the speed and sensitivity of antimicrobial susceptibility testing. We previously developed a penicillin-binding protein (PBP) typing system and two methods (Random Forest (RF) and Mode MIC (MM)) that accurately predicted β-lactam MICs for pneumococcal isolates carrying a characterized PBP sequence type (phenotypic β-lactam MICs known for at least one isolate of this PBP type)...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28810700/a-single-mini-barcode-test-to-screen-for-australian-mammalian-predators-from-environmental-samples
#9
Elodie Modave, Anna J MacDonald, Stephen D Sarre
Identification of species from trace samples is now possible through the comparison of diagnostic DNA fragments against reference DNA sequence databases. DNA detection of animals from non-invasive samples, such as predator faeces (scats) that contain traces of DNA from their species of origin, has proved to be a valuable tool for the management of elusive wildlife. However, application of this approach can be limited by the availability of appropriate genetic markers. Scat DNA is often degraded, meaning that longer DNA sequences, including standard DNA barcoding markers, are difficult to recover...
August 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28810610/microbial-investigations-in-throat-swab-and-tracheal-aspirate-specimens-are-beneficial-to-predict-the-corresponding-endotracheal-tube-biofilm-flora-among-intubated-neonates-with-ventilator-associated-pneumonia
#10
Yun Pan, Lizhong Du, Qing Ai, Sijie Song, Xiaoli Tang, Danping Zhu, Jialin Yu
Ventilator-associated pneumonia (VAP) is a common nosocomial infection in neonatal intensive care units with high morbidity and mortality. Bacterial biofilm in the endotracheal tube (ET) provides a notable and persistent source of pathogens that may cause VAP, and thus is important for VAP detection. However, during intubation microbial investigations in ET, samples are unavailable due to the infeasibility of collecting ET samples during intubation of neonates. It is therefore of great importance to find alternative sources of samples that can help identify the ET biofilm flora...
August 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28810257/karyotypes-and-distribution-of-tandem-repeat-sequences-in-brassica-nigra-determined-by-fluorescence-in-situ-hybridization
#11
Gui-Xiang Wang, Qun-Yan He, Jiri Macas, Petr Novák, Pavel Neumann, De-Xuan Meng, Hong Zhao, Ning Guo, Shuo Han, Mei Zong, Wei-Wei Jin, Fan Liu
Whole-genome shotgun reads were analyzed to determine the repeat sequence composition in the genome of black mustard, Brassica nigra (L.) Koch. The analysis showed that satellite DNA sequences are very abundant in the black mustard genome. The distribution pattern of 7 new tandem repeats (BnSAT13, BnSAT28, BnSAT68, BnSAT76, BnSAT114, BnSAT180, and BnSAT200) on black mustard chromosomes was visualized using fluorescence in situ hybridization (FISH). The FISH signals of BnSAT13 and BnSAT76 provided useful cytogenetic markers; their position and fluorescence intensity allowed for unambiguous identification of all 8 somatic metaphase chromosomes...
August 16, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28809864/predicting-response-to-radical-chemo-radiotherapy-with-circulating-hpv-dna-locally-advanced-head-and-neck-squamous-carcinoma
#12
Jen Y Lee, Isaac Garcia-Murillas, Rosalind J Cutts, David Gonzalez De Castro, Lorna Grove, Tara Hurley, Fuqiang Wang, Christopher Nutting, Katie Newbold, Kevin Harrington, Nicholas Turner, Shreerang Bhide
BACKGROUND: Following chemo-radiotherapy (CCRT) for human papilloma virus positive (HPV+) locally advanced head and neck cancer, patients frequently undergo unnecessary neck dissection (ND) and/or repeated biopsies for abnormal PET-CT, which causes significant morbidity. We assessed the role of circulating HPV DNA in identifying 'true' residual disease. METHODS: We prospectively recruited test (n=55) and validation (n=33) cohorts. HPV status was confirmed by E7 RT-PCR...
August 15, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28809016/application-of-a-cage-method-to-an-avian-development-study
#13
Ruslan Deviatiiarov, Marina Lizio, Oleg Gusev
Cap analysis of gene expression (CAGE) is a convenient approach for genome-wide identification of promoter regions at single base-pair resolution level and accurate expression estimation of the corresponding transcripts. Depending on the initial biomaterial amount and sequencing technology, different computational pipelines for data processing are available, as well as variations of the CAGE protocol that improve sensitivity and accuracy. Therefore, this chapter elucidates the key steps of sample preparation, sequencing, and data analysis via an example of a promoter expression estimation study in chicken development...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28808963/extraction-and-qpcr-based-detection-of-mirnas-from-cultured-pbmcs-of-bubaline-origin
#14
Chandra S Mukhopadhyay, Ramneek Verma, Jasdeep Singh
MicroRNAs are small noncoding but functionally important RNA molecules that are involved in regulating diverse cellular, metabolic, and immune processes. Their small size necessitates modification in traditional acid phenol-chloroform based RNA isolation procedures to get highly enriched fraction of small RNA that includes miRNAs and siRNAs . Further, of the different methods available, real-time PCR is a powerful tool for precise and specific detection and quantification of miRNA. Moreover, real-time PCR is used to validate the screening or expression of miRNAs that are discovered during high-throughput sequencing, or microarray analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28808767/identification-and-expression-analysis-of-micrornas-during-ovule-development-in-rice-oryza-sativa-by-deep-sequencing
#15
Ya Wu, Liyu Yang, Meiling Yu, Jianbo Wang
MicroRNA (miRNA) expression profiles during rice ovule development revealed the possible miRNA-mediated regulation between ovule sporophytic tissue and female gametophyte and the involvement of miRNAs in programmed cell death. MiRNAs are 20-24-nucleotide small RNAs that play key roles in the regulation of many growth and developmental processes in plants. Rice ovule development comprises a series of biological events, which are regulated by complex molecular mechanisms. To gain insight into miRNA-mediated regulation of rice ovule development, Illumina sequencing was used to examine the expression of miRNAs from the megaspore mother cell meiosis stage to the fertilized ovule stage...
August 14, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28808654/genome-wide-identification-and-transcriptional-expression-analysis-of-cucumber-superoxide-dismutase-sod-family-in-response-to-various-abiotic-stresses
#16
Yong Zhou, Lifang Hu, Hao Wu, Lunwei Jiang, Shiqiang Liu
Superoxide dismutase (SOD) proteins are widely present in the plant kingdom and play important roles in different biological processes. However, little is known about the SOD genes in cucumber. In this study, night SOD genes were identified from cucumber (Cucumis sativus) using bioinformatics-based methods, including 5 Cu/ZnSODs, 3 FeSODs, and 1 MnSOD. Gene structure and motif analysis indicated that most of the SOD genes have relatively conserved exon/intron arrangement and motif composition. Phylogenetic analyses with SODs from cucumber and several other species revealed that these SOD proteins can be traced back to two ancestral SODs before the divergence of monocot and dicot plants...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28808380/identification-and-analysis-of-jasmonate-pathway-genes-in-coffea-canephora-robusta-coffee-by-in-silico-approach
#17
Kosaraju Bharathi, H L Sreenath
BACKGROUND: Coffea canephora is the commonly cultivated coffee species in the world along with Coffea arabica. Different pests and pathogens affect the production and quality of the coffee. Jasmonic acid (JA) is a plant hormone which plays an important role in plants growth, development, and defense mechanisms, particularly against insect pests. The key enzymes involved in the production of JA are lipoxygenase, allene oxide synthase, allene oxide cyclase, and 12-oxo-phytodienoic reductase...
July 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/28808256/spoton-high-accuracy-identification-of-protein-protein-interface-hot-spots
#18
Irina S Moreira, Panagiotis I Koukos, Rita Melo, Jose G Almeida, Antonio J Preto, Joerg Schaarschmidt, Mikael Trellet, Zeynep H Gümüş, Joaquim Costa, Alexandre M J J Bonvin
We present SpotOn, a web server to identify and classify interfacial residues as Hot-Spots (HS) and Null-Spots (NS). SpotON implements a robust algorithm with a demonstrated accuracy of 0.95 and sensitivity of 0.98 on an independent test set. The predictor was developed using an ensemble machine learning approach with up-sampling of the minor class. It was trained on 53 complexes using various features, based on both protein 3D structure and sequence. The SpotOn web interface is freely available at: http://milou...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28808237/coding-and-small-non-coding-transcriptional-landscape-of-tuberous-sclerosis-complex-cortical-tubers-implications-for-pathophysiology-and-treatment
#19
James D Mills, Anand M Iyer, Jackelien van Scheppingen, Anika Bongaarts, Jasper J Anink, Bart Janssen, Till S Zimmer, Wim G Spliet, Peter C van Rijen, Floor E Jansen, Martha Feucht, Johannes A Hainfellner, Pavel Krsek, Josef Zamecnik, Katarzyna Kotulska, Sergiusz Jozwiak, Anna Jansen, Lieven Lagae, Paolo Curatolo, David J Kwiatkowski, R Jeroen Pasterkamp, Ketharini Senthilkumar, Lars von Oerthel, Marco F Hoekman, Jan A Gorter, Peter B Crino, Angelika Mühlebner, Brendon P Scicluna, Eleonora Aronica
Tuberous Sclerosis Complex (TSC) is a rare genetic disorder that results from a mutation in the TSC1 or TSC2 genes leading to constitutive activation of the mechanistic target of rapamycin complex 1 (mTORC1). TSC is associated with autism, intellectual disability and severe epilepsy. Cortical tubers are believed to represent the neuropathological substrates of these disabling manifestations in TSC. In the presented study we used high-throughput RNA sequencing in combination with systems-based computational approaches to investigate the complexity of the TSC molecular network...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28807536/effectiveness-of-household-lockable-pesticide-storage-to-reduce-pesticide-self-poisoning-in-rural-asia-a-community-based-cluster-randomised-controlled-trial
#20
Melissa Pearson, Chris Metcalfe, Shaluka Jayamanne, David Gunnell, Manjula Weerasinghe, Ravi Pieris, Chamil Priyadarshana, Duleeka W Knipe, Keith Hawton, Andrew H Dawson, Palitha Bandara, Dhammika deSilva, Indika Gawarammana, Michael Eddleston, Flemming Konradsen
BACKGROUND: Agricultural pesticide self-poisoning is a major public health problem in rural Asia. The use of safer household pesticide storage has been promoted to prevent deaths, but there is no evidence of effectiveness. We aimed to test the effectiveness of lockable household containers for prevention of pesticide self-poisoning. METHODS: We did a community-based, cluster-randomised controlled trial in a rural area of North Central Province, Sri Lanka. Clusters of households were randomly assigned (1:1), with a sequence computer-generated by a minimisation process, to intervention or usual practice (control) groups...
August 11, 2017: Lancet
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