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https://www.readbyqxmd.com/read/29231761/a-rapid-method-to-identify-salmonella-enterica-serovar-gallinarum-biovar-pullorum-using-a-specific-target-gene-ipaj
#1
Lijuan Xu, Zijian Liu, Yang Li, Chao Yin, Yachen Hu, Xiaolei Xie, Qiuchun Li, Xinan Jiao
Salmonella enterica serovar Gallinarum biovar Pullorum (S. Pullorum) is the pathogen of pullorum disease, which leads to severe economic losses in many developing countries. Traditional methods to identify S. enterica have relied on biochemical reactions and serotyping, which are time-consuming with accurate identification if properly carried out. In this study, we developed a rapid polymerase chain reaction (PCR) method targeting the specific gene ipaJ to detect S. Pullorum. Among the 650 S. Pullorum strains isolated from 1962 to 2016 all over China, 644 strains were identified to harbor ipaJ gene in the plasmid pSPI12 accounting to a detection rate of 99...
December 12, 2017: Avian Pathology: Journal of the W.V.P.A
https://www.readbyqxmd.com/read/29230401/shiga-toxin-producing-escherichia-coli-o157-shedding-dynamics-in-an-australian-beef-herd
#2
Christina Ahlstrom, Petra Muellner, Geraldine Lammers, Meghan Jones, Sophie Octavia, Ruiting Lan, Jane Heller
Shiga toxin-producing Escherichia coli (STEC) O157 is an important foodborne pathogen that can be transmitted to humans both directly and indirectly from the feces of beef cattle, its primary reservoir. Numerous studies have investigated the shedding dynamics of E. coli O157 by beef cattle; however, the spatiotemporal trends of shedding are still not well understood. Molecular tools can increase the resolution through the use of strain typing to explore transmission dynamics within and between herds and identify strain-specific characteristics that may influence pathogenicity and spread...
2017: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/29230357/comparative-analyses-of-putative-toxin-gene-homologs-from-an-old-world-viper-daboia-russelii
#3
Neeraja M Krishnan, Binay Panda
Availability of snake genome sequences has opened up exciting areas of research on comparative genomics and gene diversity. One of the challenges in studying snake genomes is the acquisition of biological material from live animals, especially from the venomous ones, making the process cumbersome and time-consuming. Here, we report comparative sequence analyses of putative toxin gene homologs from Russell's viper (Daboia russelii) using whole-genome sequencing data obtained from shed skin. When compared with the major venom proteins in Russell's viper studied previously, we found 45-100% sequence similarity between the venom proteins and their putative homologs in the skin...
2017: PeerJ
https://www.readbyqxmd.com/read/29230233/whole-genome-sequencing-of-fusarium-fujikuroi-provides-insight-into-the-role-of-secretory-proteins-and-cell-wall-degrading-enzymes-in-causing-bakanae-disease-of-rice
#4
Bishnu M Bashyal, Kirti Rawat, Sapna Sharma, Deepika Kulshreshtha, S Gopala Krishnan, Ashok K Singh, Himanshu Dubey, Amolkumar U Solanke, T R Sharma, Rashmi Aggarwal
Fusarium fujikuroi causing bakanae disease has emerged as one of the major pathogen of rice across the world. The study aims to comparative genomic analysis of Fusarium fujikuroi isolates and identification of the secretary proteins of the fungus involved in rice pathogenesis. In the present study, F. fujikuroi isolate "F250" was sequenced with an assembly size of 42.47 Mb providing coverage of 96.89% on reference IMI58289 genome. A total of 13,603 protein-coding genes were predicted from genome assembly. The average gene density in the F...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29230066/functional-and-evolutionary-analysis-of-korean-bob-tailed-native-dog-using-whole-genome-sequencing-data
#5
Daehwan Lee, Dajeong Lim, Daehong Kwon, Juyeon Kim, Jongin Lee, Mikang Sim, Bong-Hwan Choi, Seog-Gyu Choi, Jaebum Kim
Rapid and cost effective production of large-scale genome data through next-generation sequencing has enabled population-level studies of various organisms to identify their genotypic differences and phenotypic consequences. This is also used to study indigenous animals with historical and economical values, although they are less studied than model organisms. The objective of this study was to perform functional and evolutionary analysis of Korean bob-tailed native dog Donggyeong with distinct tail and agility phenotype using whole-genome sequencing data by using population and comparative genomics approaches...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29229917/whole-genome-sequencing-and-snv-genotyping-of-nebbiolo-vitis-vinifera-l-clones
#6
Giorgio Gambino, Alessandra Dal Molin, Paolo Boccacci, Andrea Minio, Walter Chitarra, Carla Giuseppina Avanzato, Paola Tononi, Irene Perrone, Stefano Raimondi, Anna Schneider, Mario Pezzotti, Franco Mannini, Ivana Gribaudo, Massimo Delledonne
'Nebbiolo' (Vitis vinifera) is among the most ancient and prestigious wine grape varieties characterised by a wide genetic variability exhibited by a high number of clones (vegetatively propagated lines of selected mother plants). However, limited information is available for this cultivar at the molecular and genomic levels. The whole-genomes of three 'Nebbiolo' clones (CVT 71, CVT 185 and CVT 423) were re-sequenced and a de novo transcriptome assembly was produced. Important remarks about the genetic peculiarities of 'Nebbiolo' and its intra-varietal variability useful for clonal identification were reported...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29229813/human-genetic-variation-alters-crispr-cas9-on-and-off-targeting-specificity-at-therapeutically-implicated-loci
#7
Samuel Lessard, Laurent Francioli, Jessica Alfoldi, Jean-Claude Tardif, Patrick T Ellinor, Daniel G MacArthur, Guillaume Lettre, Stuart H Orkin, Matthew C Canver
The CRISPR-Cas9 nuclease system holds enormous potential for therapeutic genome editing of a wide spectrum of diseases. Large efforts have been made to further understanding of on- and off-target activity to assist the design of CRISPR-based therapies with optimized efficacy and safety. However, current efforts have largely focused on the reference genome or the genome of cell lines to evaluate guide RNA (gRNA) efficiency, safety, and toxicity. Here, we examine the effect of human genetic variation on both on- and off-target specificity...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29229660/rationale-and-design-of-geneius-a-prospective-observational-study-on-the-genetic-and-environmental-determinants-of-body-mass-index-evolution-in-canadian-undergraduate-students
#8
Rita E Morassut, Christine Langlois, Akram Alyass, Adeola F Ishola, Fereshteh T Yazdi, Alexandra J Mayhew, Hudson Reddon, James MacKillop, Marie Pigeyre, David Meyre
INTRODUCTION: Obesity is a global epidemic and is a risk factor for developing other comorbidities. Young adulthood is a critical period for body weight change and establishing healthy lifestyle behaviours. The 'Freshman 15' suggests that undergraduate students gain 15 lbs (6.8 kg) during their first year of university, although evidence estimates a more modest weight gain of approximately 3-5 lbs (1.4-2.3 kg). Previous studies have only investigated weight change in the first year and do not study potential risk factors...
December 10, 2017: BMJ Open
https://www.readbyqxmd.com/read/29229636/topical-antibiotic-use-co-selects-for-the-carriage-of-mobile-genetic-elements-conferring-resistance-to-unrelated-antimicrobials-in-staphylococcus-aureus
#9
Glen P Carter, Mark B Schultz, Sarah L Baines, Anders Goncalves da Silva, Helen Heffernan, Audrey Tiong, Peter H Pham, Ian R Monk, Timothy P Stinear, Benjamin P Howden, Deborah A Williamson
Topical antibiotics such as mupirocin and fusidic acid are commonly used in the prevention and treatment of skin infections, particularly those caused by staphylococci. However, widespread use of these agents is associated with increased resistance to these agents, potentially limiting their efficacy. Of particular concern is the observation that resistance to topical antibiotics is often associated with multidrug resistance, suggesting that topical antibiotics may play a role in the emergence of multidrug-resistant (MDR) strains...
December 11, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29229634/genomic-insights-into-colistin-resistant-klebsiella-pneumoniae-from-a-tunisian-teaching-hospital
#10
Nadia Jaidane, Rémy A Bonnin, Wejdene Mansour, Delphine Girlich, Elodie Creton, Garance Colleton, Cherifa Chaouch, Noureddine Boujaafar, Olfa Bouallegue, Thierry Naas
The emergence of colistin-resistant Klebsiella pneumoniae (CoRKp) is a public health concern since this antibiotic has become the last line of treatment for infections caused by multidrug-resistant (MDR) gram-negatives. In this study, we have investigated the molecular basis of colistin-resistance in 13 MDR Kp isolated from 12 patients in a teaching hospital in Sousse, Tunisia. Whole-genome sequencing (WGS) was used to decipher the molecular mechanism of colistin-resistance and to identify the resistome of these CoRKp It revealed a genome of ca...
December 11, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29229569/the-hardy-rubber-tree-genome-provides-insights-into-the-evolution-of-polyisoprene-biosynthesis
#11
Ta-Na Wuyun, Lin Wang, Huimin Liu, Xuewen Wang, Liangsheng Zhang, Jeffrey L Bennetzen, Tiezhu Li, Lirong Yang, Panfeng Liu, Lanying Du, Lu Wang, Mengzhen Huang, Jun Qing, Lili Zhu, Wenquan Bao, Hongguo Li, Qingxin Du, Jingle Zhu, Hong Yang, Shuguang Yang, Hui Liu, Hui Yue, Jiang Hu, Guoliang Yu, Yu Tian, Fan Liang, Jingjing Hu, Depeng Wang, Ruiwen Gao, Dejun Li, Hongyan Du
Eucommia ulmoides is an economically important tree; however, the lack of its genome sequence restricts the theoretical and applied studies. Here we present a high-quality assembly of its ∼1.2 Gb genome (scaffold N50 = 1.88 Mb) with at least 26,723 predicted genes for E. ulmoides, the first sequenced genome of the order Garryales, which we obtained using an integrated strategy combining Illumina sequencing, Pacbio sequencing and Bionano mapping. As a sister taxon to lamiids and campanulids, the E. ulmoides underwent an ancient genome triplication shared by core eudicots but no further whole-genome duplication (WGD) in the last ∼125 million years...
December 8, 2017: Molecular Plant
https://www.readbyqxmd.com/read/29229530/trichoderma-harzianum-mtcc-5179-impacts-the-population-and-functional-dynamics-of-microbial-community-in-the-rhizosphere-of-black-pepper-piper-nigrum-l
#12
Palaniyandi Umadevi, Muthuswamy Anandaraj, Vivek Srivastav, Sailas Benjamin
Employing Illumina Hiseq whole genome metagenome sequencing approach, we studied the impact of Trichoderma harzianum on altering the microbial community and its functional dynamics in the rhizhosphere soil of black pepper (Piper nigrum L.). The metagenomic datasets from the rhizosphere with (treatment) and without (control) T. harzianum inoculation were annotated using dual approach, i.e., stand alone and MG-RAST. The probiotic application of T. harzianum in the rhizhosphere soil of black pepper impacted the population dynamics of rhizosphere bacteria, archae, eukaryote as reflected through the selective recruitment of bacteria [Acidobacteriaceae bacterium (p=1...
November 29, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/29229490/pseudomonas-aeruginosa-intensive-care-unit-outbreak-winnowing-of-transmissions-with-molecular-and-genomic-typing
#13
Benjamin J Parcell, Katarina Oravcova, Miguel Pinheiro, Matthew T G Holden, Gabby Phillips, Jane F Turton, Stephen H Gillespie
BACKGROUND: Pseudomonas aeruginosa healthcare outbreaks can be time consuming and difficult to investigate. Guidance does not specify which typing technique is most practical to base decisions on. AIM: We explore the usefulness of whole genome sequencing (WGS) in the investigation of a Pseudomonas aeruginosa outbreak describing how it compares with pulsed-field gel electrophoresis (PFGE) and variable number tandem repeat (VNTR) analysis. METHODS: Six patient isolates and six environmental samples from an Intensive Care Unit (ICU) positive for P...
December 8, 2017: Journal of Hospital Infection
https://www.readbyqxmd.com/read/29228988/a-vp24-truncated-isolate-of-white-spot-syndrome-virus-is-inefficient-in-per-os-infection
#14
Yali Han, Fang Li, Limei Xu, Feng Yang
White spot syndrome virus (WSSV) is a major pathogen of penaeid shrimp. Here we identified a new WSSV strain, WSSV-CN04, from naturally infected Marsupenaeus japonicus. Whole genomic sequencing results indicate that the WSSV-CN04 genome was 281 054 bp in length, and encoded 157 hypothetic proteins. The genome sequence of WSSV-CN04 was most closely related to the low-virulent strain WSSV-CN03, sharing 97.5% sequence identity. Notably, in WSSV-CN04, the major envelop protein VP24 was not only truncated but also absent in the virions...
December 11, 2017: Veterinary Research
https://www.readbyqxmd.com/read/29228905/evaluation-of-methods-and-marker-systems-in-genomic-selection-of-oil-palm-elaeis-guineensis-jacq
#15
Qi Bin Kwong, Chee Keng Teh, Ai Ling Ong, Fook Tim Chew, Sean Mayes, Harikrishna Kulaveerasingam, Martti Tammi, Suat Hui Yeoh, David Ross Appleton, Jennifer Ann Harikrishna
BACKGROUND: Genomic selection (GS) uses genome-wide markers as an attempt to accelerate genetic gain in breeding programs of both animals and plants. This approach is particularly useful for perennial crops such as oil palm, which have long breeding cycles, and for which the optimal method for GS is still under debate. In this study, we evaluated the effect of different marker systems and modeling methods for implementing GS in an introgressed dura family derived from a Deli dura x Nigerian dura (Deli x Nigerian) with 112 individuals...
December 11, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29227741/new-subclass-b1-metallo-%C3%AE-lactamase-gene-from-a-clinical-pathogenic-myroides-odoratus-strain
#16
Su Xu, Yijian Chen, Zhuyingjie Fu, Ying Li, Guixiu Shi, Xiaogang Xu, Yang Liu, Minggui Wang
Myroides odoratus is a low-virulence opportunistic human pathogen. Infections caused by M. odoratus are not common, but reports are increasing in recent years. The biggest challenge for treatment is its resistance to most antibiotics. In 2015, we isolated a pathogenic multidrug-resistant strain of M. odoratus from a urinary tract infection (UTI) patient's urine sample. To report the experience in managing M. odoratus-related UTI and investigate the genetic mechanism of this carbapenem-resistant strain, we conducted a series of microbiological and molecular studies...
December 11, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/29227476/the-molecular-landscape-of-pediatric-acute-myeloid-leukemia-reveals-recurrent-structural-alterations-and-age-specific-mutational-interactions
#17
Hamid Bolouri, Jason E Farrar, Timothy Triche, Rhonda E Ries, Emilia L Lim, Todd A Alonzo, Yussanne Ma, Richard Moore, Andrew J Mungall, Marco A Marra, Jinghui Zhang, Xiaotu Ma, Yu Liu, Yanling Liu, Jaime M Guidry Auvil, Tanja M Davidsen, Patee Gesuwan, Leandro C Hermida, Bodour Salhia, Stephen Capone, Giridharan Ramsingh, Christian Michel Zwaan, Sanne Noort, Stephen R Piccolo, E Anders Kolb, Alan S Gamis, Malcolm A Smith, Daniela S Gerhard, Soheil Meshinchi
We present the molecular landscape of pediatric acute myeloid leukemia (AML) and characterize nearly 1,000 participants in Children's Oncology Group (COG) AML trials. The COG-National Cancer Institute (NCI) TARGET AML initiative assessed cases by whole-genome, targeted DNA, mRNA and microRNA sequencing and CpG methylation profiling. Validated DNA variants corresponded to diverse, infrequent mutations, with fewer than 40 genes mutated in >2% of cases. In contrast, somatic structural variants, including new gene fusions and focal deletions of MBNL1, ZEB2 and ELF1, were disproportionately prevalent in young individuals as compared to adults...
December 11, 2017: Nature Medicine
https://www.readbyqxmd.com/read/29227468/metagenomic-binning-and-association-of-plasmids-with-bacterial-host-genomes-using-dna-methylation
#18
John Beaulaurier, Shijia Zhu, Gintaras Deikus, Ilaria Mogno, Xue-Song Zhang, Austin Davis-Richardson, Ronald Canepa, Eric W Triplett, Jeremiah J Faith, Robert Sebra, Eric E Schadt, Gang Fang
Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome 'bins'. These methods exploit sequence composition, species abundance, or chromosome organization but cannot fully distinguish closely related species and strains. We present a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing...
December 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29227308/medical-bioinformatics-in-melanoma
#19
Phil F Cheng
PURPOSE OF REVIEW: Bioinformatic insights from next-generation sequencing has been integral in understanding melanoma biology, resistance to treatment and provided new avenues for melanoma treatment. Whole-genome sequencing, whole-exome sequencing and RNA sequencing has redefined the molecular classification of melanoma, revealed distinct genetic aberrations that define clinical subtypes of melanoma and uncovered the diverse heterogeneity that resides in an individual tumor. RECENT FINDINGS: In this review, we will summarize the recent whole-genome study that catalogs the genomic landscape across many melanoma subtypes, the single-cell RNA sequencing studies that interrogates tumor heterogeneity and the personalized vaccine approaches to melanoma treatment...
December 8, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/29226517/natural-selection-beyond-genes-identification-and-analyses-of-evolutionarily-conserved-elements-in-the-genome-of-the-collared-flycatcher-ficedula-albicollis
#20
Rory J Craig, Alexander Suh, Mi Wang, Hans Ellegren
It is becoming increasingly clear that a significant proportion of the functional sequence within eukaryotic genomes is noncoding. However, since the identification of conserved elements (CEs) has been restricted to a limited number of model organisms, the dynamics and evolutionary character of the genomic landscape of conserved, and hence likely functional, sequence is poorly understood in most species. Moreover, identification and analysis of the full suite of functional sequence is particularly important for the understanding of the genetic basis of trait loci identified in genome scans or quantitative trait locus mapping efforts...
December 11, 2017: Molecular Ecology
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