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https://www.readbyqxmd.com/read/28926006/developing-a-framework-to-assess-the-costeffectiveness-of-compare-a-global-platform-for-the-exchange-of-sequence-based-pathogen-data
#1
F Alleweldt, S Kara, A Osinski, P Van Baal, K Kellerborg, F M Aarestrup, M Koopmans
Analysing the genomic data of pathogens with the help of next-generation sequencing (NGS) is an increasingly important part of disease outbreak investigations and helps guide responses. While this technology has already been successfully employed to elucidate and control disease outbreaks, wider implementation of NGS also depends on its cost-effectiveness. COMPARE - short for 'Collaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks' - is a major project, funded by the European Union, to develop a global platform for sharing and analysing NGS data and thereby improve the rapid identification, containment and mitigation of emerging infectious diseases and foodborne outbreaks...
April 2017: Revue Scientifique et Technique
https://www.readbyqxmd.com/read/28924501/identification-and-analysis-of-cyp450-genes-from-transcriptome-of-lonicera-japonica-and-expression-analysis-of-chlorogenic-acid-biosynthesis-related-cyp450s
#2
Xiwu Qi, Xu Yu, Daohua Xu, Hailing Fang, Ke Dong, Weilin Li, Chengyuan Liang
BACKGROUND: Lonicera japonica is an important medicinal plant that has been widely used in traditional Chinese medicine for thousands of years. The pharmacological activities of L. japonica are mainly due to its rich natural active ingredients, most of which are secondary metabolites. CYP450s are a large, complex, and widespread superfamily of proteins that participate in many endogenous and exogenous metabolic reactions, especially secondary metabolism. Here, we identified CYP450s in L...
2017: PeerJ
https://www.readbyqxmd.com/read/28923600/fungal-strains-isolation-identification-and-application-for-the-recovery-of-zn-ii-ions
#3
Kiran Aftab, Kalsoom Akhtar, Abida Kausar, Shazia Khaliq, Numrah Nisar, Huma Umbreen, Munawar Iqbal
Fungal biomass proves to be highly efficient for the treatment of wastewater as well as recovery of metal ions from wastewater. Present investigation was aimed to evaluate the efficiency of indigenous fungal isolates for the sequestration of Zn(II) ions aqueous solution. Among twenty five fungal isolates, Aspergillus oryzae SV/09 (AO SV/09), Aspergillus flavus NA9 (AF NA9) and Paecilomyces formosus DTO 63f4 (PF DTO-63f4) were identified by gene sequencing of ITS regions of the ribosomal DNA (rDNA). The AO SV/09, AF NA9 and PF DTO-63f4 showed promising efficiency for the biosorption of Zn(II) ions...
September 4, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28923557/a-molecular-approach-towards-taxonomic-identification-of-elasmobranch-species-from-maltese-fisheries-landings
#4
Adriana Vella, Noel Vella, Sarah Schembri
The mitochondrial genome, through the application of DNA barcoding, provides a powerful tool for identifying species even when specimens are either incomplete or belong to species that exhibit cryptic diversity. In fisheries management accurate identification of whole or part of the specimens landed is a fundamental requirement for the conservation of species affected directly or indirectly by the fisheries activities. In this study cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 2 (ND2) sequences were used to genetically distinguish 36 elasmobranch species collected from Maltese (Central Mediterranean) commercial fisheries landings...
September 8, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28922848/aggressive-behavior-in-silent-subtype-iii-pituitary-adenomas-may-depend-on-suppression-of-local-immune-response-a-whole-transcriptome-analysis
#5
Timothy E Richardson, Zhong-Jian Shen, Mohammed Kanchwala, Chao Xing, Alexander Filatenkov, Ping Shang, Samuel Barnett, Zahidur Abedin, James S Malter, Jack M Raisanen, Dennis K Burns, Charles L White, Kimmo J Hatanpaa
Silent subtype III pituitary adenomas (SS-3) are clinically nonfunctional adenomas that are more aggressive in terms of invasion and risk of recurrence than their conventional null cell counterparts. We previously showed that these tumors can be distinguished by immunohistochemistry based on the identification of a markedly enlarged and fragmented Golgi apparatus. To understand the molecular correlates of differential aggressiveness, we performed whole transcriptome sequencing (RNAseq) on 4 SS-3 and 4 conventional null cell adenomas...
October 1, 2017: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/28922761/rapid-mapping-and-cloning-of-the-virescent-1-gene-in-cotton-by-bulked-segregant-analysis-next-generation-sequencing-and-virus-induced-gene-silencing-strategies
#6
Jiankun Zhu, Jiedan Chen, Fengkai Gao, Chenyu Xu, Huaitong Wu, Kun Chen, Zhanfeng Si, Hu Yan, Tianzhen Zhang
Map-based gene cloning is a vital strategy for the identification of the quantitative trait loci or genes underlying important agronomic traits. The conventional map-based cloning method is powerful but generally time-consuming and labor-intensive. In this context, we introduce an improved bulked segregant analysis method in combination with a virus-induced gene silencing (VIGS) strategy for rapid and reliable gene mapping, identification and functional verification. This method was applied to a multiple recessive marker line of upland cotton, Texas 582 (T582), and identified unique genomic positions harboring mutant loci, showing the reliability and efficacy of this method...
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28919697/16s-ribosomal-rna-sequencing-and-molecular-serotyping-of-avibacterium-paragallinarum-isolated-from-indian-field-conditions
#7
Vihang Vithalrao Patil, Debendranath Mishra, Dilip Vithalrao Mane
AIM: This study was aimed at identifying Indian field isolates of Avibacterium paragallinarum on both molecular as well as serological levels that cause infectious coryza in chickens. MATERIALS AND METHODS: Species-specific polymerase chain reaction (HPG-2 PCR), and 16S ribosomal RNA (rRNA) sequencing were employed for molecular identification. Whereas, multiplex PCR technique was used for serological identification of Indian field isolates of A. paragallinarum...
August 2017: Veterinary World
https://www.readbyqxmd.com/read/28919163/multiplex-pcr-and-ngs-based-identification-of-mrna-splicing-variants-analysis-of-brca1-splicing-pattern-as-a-model
#8
Jan Hojny, Petra Zemankova, Filip Lhota, Jan Sevcik, Viktor Stranecky, Hana Hartmannova, Katerina Hodanova, Ondrej Mestak, David Pavlista, Marketa Janatova, Jana Soukupova, Michal Vocka, Zdenek Kleibl, Petra Kleiblova
Alternative pre-mRNA splicing increases transcriptome plasticity by forming naturally-occurring alternative splicing variants (ASVs). Alterations of splicing processes, caused by DNA mutations, result in aberrant splicing and the formation of aberrant mRNA isoforms. Analyses of hereditary cancer predisposition genes reveal many DNA variants with unknown clinical significance (VUS) that potentially affect pre-mRNA splicing. Therefore, a comprehensive description of ASVs is an essential prerequisite for the interpretation of germline VUS in high-risk individuals...
September 14, 2017: Gene
https://www.readbyqxmd.com/read/28919002/x-linked-adrenoleukodystrophy-in-a-chimpanzee-due-to-an-abcd1-mutation-reported-in-multiple-unrelated-humans
#9
Julian Curiel, Steven Jeffrey Steinberg, Sarah Bright, Ann Snowden, Ann B Moser, Florian Eichler, Holly A Dubbs, Joseph G Hacia, John J Ely, Jocelyn Bezner, Alisa Gean, Adeline Vanderver
BACKGROUND: X-linked adrenoleukodystrophy (X-ALD) is a genetic disorder leading to the accumulation of very long chain fatty acids (VLCFA) due to a mutation in the ABCD1 gene. ABCD1 mutations lead to a variety of phenotypes, including cerebral X-ALD and adrenomyeloneuropathy (AMN) in affected males and 80% of carrier females. There is no definite genotype-phenotype correlation with intrafamilial variability. Cerebral X-ALD typically presents in childhood, but can also present in juveniles and adults...
September 1, 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/28918154/hot-topic-geographical-distribution-and-strain-diversity-of-lactobacillus-wasatchensis-isolated-from-cheese-with-unwanted-gas-formation
#10
Michele Culumber, Donald J McMahon, Fatih Ortakci, Lauren Montierth, Beatriz Villalba, Jeffery R Broadbent, Craig J Oberg
Lactobacillus wasatchensis, an obligate heterofermentative nonstarter lactic acid bacteria (NSLAB) implicated in causing gas defects in aged cheeses, was originally isolated from an aged Cheddar produced in Logan, Utah. To determine the geographical distribution of this organism, we isolated slow-growing NSLAB from cheeses collected in different regions of the United States, Australia, New Zealand, and Ireland. Seven of the cheeses showed significant gas defects and 12 did not. Nonstarter lactic acid bacteria were isolated from these cheeses on de Man, Rogosa, and Sharpe medium supplemented with ribose, a preferred substrate for Lb...
September 13, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28916458/molecular-identification-of-waterborn-free-living-amoebae-acanthamoeba-naegleria-and-vermamoeba-isolated-from-municipal-drinking-water-and-environmental-sources-north-half-of-iran
#11
Ehsan Javanmard, Maryam Niyyati, Jacob Lorenzo-Morales, Zohreh Lasjerdi, Hamed Behniafar, Hamed Mirjalili
The present study tested 80 samples of municipal, geothermal and recreational water samples for the occurrence of waterborn free living amoebae (FLA) including Acanthamoeba, Balamuthia mandrillaris, Vahlkampfiids and Vermamoeba in Semnan province, North half of Iran. Four sets of primers including JDP1,2 primers, ITS1,2 primers (Vahlkampfiids), 16S rRNABal primers (Balamuthia mandrillaris) and NA1,2 primers (Vermamoeba) were used to confirm the morphological identification. From the 80 water samples tested in the present study, 16 (20%) were positive for the outgrowth of free living amoebae based on the morphological page key...
September 12, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28916376/transcriptome-profiling-of-the-plutella-xylostella-lepidoptera-plutellidae-ovary-reveals-genes-involved-in-oogenesis
#12
Lu Peng, Lei Wang, Yi-Fan Yang, Ming-Min Zou, Wei-Yi He, Yue Wang, Qing Wang, Liette Vasseur, Min-Sheng You
BACKGROUND: As a specialized organ, the insect ovary performs valuable functions by ensuring fecundity and population survival. Oogenesis is the complex physiological process resulting in the production of mature eggs, which are involved in epigenetic programming, germ cell behavior, cell cycle regulation, etc. Identification of the genes involved in ovary development and oogenesis is critical to better understand the reproductive biology and screening the potential molecular targets in Plutella xylostella, a worldwide destructive pest of economically major crops...
September 12, 2017: Gene
https://www.readbyqxmd.com/read/28915783/prediction-of-agreement-and-phonetic-overlap-shape-sublexical-identification
#13
Andrea E Martin, Philip J Monahan, Arthur G Samuel
The mapping between the physical speech signal and our internal representations is rarely straightforward. When faced with uncertainty, higher-order information is used to parse the signal and because of this, the lexicon and some aspects of sentential context have been shown to modulate the identification of ambiguous phonetic segments. Here, using a phoneme identification task (i.e., participants judged whether they heard [o] or [a] at the end of an adjective in a noun-adjective sequence), we asked whether grammatical gender cues influence phonetic identification and if this influence is shaped by the phonetic properties of the agreeing elements...
September 2017: Language and Speech
https://www.readbyqxmd.com/read/28914452/comparative-evaluation-of-mcp-gene-in-worldwide-strains-of-megalocytivirus-iridoviridae-family-for-early-diagnostic-marker
#14
A Mishra, G-H Nam, J-A Gim, H-E Lee, A Jo, D Yoon, S Oh, S Kim, A Kim, D-H Kim, Y C Kim, H D Jeong, H-J Cha, Y H Choi, H-S Kim
Members of the Iridoviridae family have been considered as aetiological agents of iridovirus diseases, causing fish mortalities and economic losses all over the world. Virus identification based on candidate gene sequencing is faster, more accurate and more reliable than other traditional phenotype methodologies. Iridoviridae viruses are covered by a protein shell (capsid) encoded by the important candidate gene, major capsid protein (MCP). In this study, we investigated the potential of the MCP gene for use in the diagnosis and identification of infections caused Megalocytivirus of the Iridoviridae family...
September 15, 2017: Journal of Fish Diseases
https://www.readbyqxmd.com/read/28913865/transcriptome-characterization-of-hpg-axis-from-chinese-sea-perch-lateolabrax-maculatus
#15
Z P Wang, D Wang, C L Wang, W J Xie, Y F Zhu, X W Chen
Here the transcriptome and differential gene expression in the adult brain and gonads of the Chinese sea perch Lateolabrax maculatus were reported. A total of 78 256 909 clean reads were generated from the adult brain, ovary and testis by using the Illumina HiSeq2000 platform and assembled into 274 909 contigs. A total of 31 683 unigenes were annotated based on sequence similarity and 20 702 unigenes were found to exhibit 8237 gene ontology terms and 3888 signal pathways. Transcripts of 26 623 unigenes were present in all of the tissues, whereas pairwise comparisons revealed that 671/367, 496/315 and 1668/580 unigenes were up-down regulated by at least two-fold between the brain and ovary, ovary and testis and brain and testis, respectively...
September 14, 2017: Journal of Fish Biology
https://www.readbyqxmd.com/read/28912831/genome-sequencing-and-transcriptome-analysis-of-trichoderma-reesei-qm9978-strain-reveals-a-distal-chromosome-translocation-to-be-responsible-for-loss-of-vib1-expression-and-loss-of-cellulase-induction
#16
Christa Ivanova, Jonas Ramoni, Thiziri Aouam, Alexa Frischmann, Bernhard Seiboth, Scott E Baker, Stéphane Le Crom, Sophie Lemoine, Antoine Margeot, Frédérique Bidard
BACKGROUND: The hydrolysis of biomass to simple sugars used for the production of biofuels in biorefineries requires the action of cellulolytic enzyme mixtures. During the last 50 years, the ascomycete Trichoderma reesei, the main source of industrial cellulase and hemicellulase cocktails, has been subjected to several rounds of classical mutagenesis with the aim to obtain higher production levels. During these random genetic events, strains unable to produce cellulases were generated...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28912544/development-of-chloroplast-genome-resources-for-peanut-arachis-hypogaea-l-and-other-species-of-arachis
#17
Dongmei Yin, Yun Wang, Xingguo Zhang, Xingli Ma, Xiaoyan He, Jianhang Zhang
Peanut (Arachis hypogaea L.) is an important oilseed and cash crop worldwide. Wild Arachis spp. are potental sources of novel genes for the genetic improvement of cultivated peanut. Understanding the genetic relationships with cultivated peanut is important for the efficient use of wild species in breeding programmes. However, for this genus, only a few genetic resources have been explored so far. In this study, new chloroplast genomic resources have been developed for the genus Arachis based on whole chloroplast genomes from seven species that were sequenced using next-generation sequencing technologies...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28911333/profiling-bacterial-communities-by-minion-sequencing-of-ribosomal-operons
#18
Lee J Kerkhof, Kevin P Dillon, Max M Häggblom, Lora R McGuinness
BACKGROUND: An approach utilizing the long-read capability of the Oxford Nanopore MinION to rapidly sequence bacterial ribosomal operons of complex natural communities was developed. Microbial fingerprinting employs domain-specific forward primers (16S rRNA subunit), reverse primers (23S rRNA subunit), and a high-fidelity Taq polymerase with proofreading capabilities. Amplicons contained both ribosomal subunits for broad-based phylogenetic assignment (~ 3900 bp of sequence), plus the intergenic spacer (ITS) region (~ 300 bp) for potential strain-specific identification...
September 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28911188/diversity-of-ochrobactrum-species-in-food-animals-antibiotic-resistance-phenotypes-and-polymorphisms-in-the-blaoch-gene
#19
Carla Andrea Alonso, Yakubu A Kwabugge, Madubuike U Anyanwu, Carmen Torres, Kennedy F Chah
Twenty-six lactose non-fermenting, oxidase, urease and citrate-positive Gram-negative rods, isolated from broiler chickens, pigs and cattle at slaughter, were subjected to the matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry and 16S rDNA sequencing for identification. Susceptibility to 14 antimicrobials was determined by the disc diffusion method. Ochrobactrum isolates resistant to third-generation cephalosporins were PCR-screened for the presence of the Ochrobactrum anthropi ampC gene (blaOCH)...
September 15, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28910860/isolation-of-probiotic-piliated-lactobacillus-rhamnosus-strains-from-human-faecal-microbiota-using-spaaantiserum-based-colony-immunoblotting
#20
Zhen-Quan Yang, Yu Xue, Mi Zhang, Sheng-Qi Rao, Lu Gao, Yong-Qi Yin, Da-Wei Chen, Xiao-Hui Zhou, Xin-An Jiao
Piliated Lactobacillus rhamnosus (pLR) strains possess higher adherent capacity than non-piliated strains. The objective of this study was to isolate and characterise probiotic pLR strains in human faecal samples. To this end, mouse polyclonal antiserum (anti-SpaA) against the recombinant pilus protein (SpaA) of L. rhamnosus strain GG (LGG) was prepared and tested for its reactivity and specificity. With the anti-SpaA, a method combining the de Man Rogosa and Sharpe (MRS) agar plating separation and colony immunoblotting (CIB) was developed to isolate pLR from 124 human faecal samples...
September 15, 2017: Journal of Microbiology and Biotechnology
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