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genotypic sequence

Nicola L D Overton, Axel A Brakhage, Andreas Thywißen, David W Denning, Paul Bowyer
Allergic bronchopulmonary aspergillosis (ABPA) in asthma is a severe, life-affecting disease that potentially affects over 4.8 million people globally. In the UK, ABPA is predominantly caused by the fungus Aspergillus fumigatus. Phagocytosis is important in clearance of this fungus, and Early Endosome Antigen 1 (EEA1) has been demonstrated to be involved in phagocytosis of fungi. We sought to investigate the role of EEA1 mutations and phagocytosis in ABPA. We used exome sequencing to identify variants in EEA1 associated with ABPA...
2018: PloS One
Xiang Jiao, Wen Liu, Hovsep Mahdessian, Patrick Bryant, Jenny Ringdahl, Maria Timofeeva, Susan M Farrington, Malcolm Dunlop, Annika Lindblom
Genome-wide association studies (GWAS) have identified dozens of common genetic variants associated with risk of colorectal cancer (CRC). However, the majority of CRC heritability remains unclear. In order to discover low-frequency, high-risk CRC susceptibility variants in Swedish population, we genotyped 1 515 CRC patients enriched for familial cases, and 12 108 controls. Case/control association analysis suggested eight novel variants associated with CRC risk (OR 2.0-17.6, p-value < 2.0E-07), comprised of seven coding variants in genes RAB11FIP5, POTEA, COL27A1, MUC5B, PSMA8, MYH7B, and PABPC1L as well as one variant downstream of NEU1 gene...
2018: PloS One
Jane Hawkey, David B Ascher, Louise M Judd, Ryan R Wick, Xenia Kostoulias, Heather Cleland, Denis W Spelman, Alex Padiglione, Anton Y Peleg, Kathryn E Holt
Acinetobacter baumannii is a common causative agent of hospital-acquired infections and a leading cause of infection in burns patients. Carbapenem-resistant A. baumannii is considered a major public-health threat and has been identified by the World Health Organization as the top priority organism requiring new antimicrobials. The most common mechanism for carbapenem resistance in A. baumannii is via horizontal acquisition of carbapenemase genes. In this study, we sampled 20 A. baumannii isolates from a patient with extensive burns, and characterized the evolution of carbapenem resistance over a 45 day period via Illumina and Oxford Nanopore sequencing...
March 16, 2018: Microbial Genomics
Jingang Zhang, Xinrui Li, Yuanyuan Su, Min Sun, Junbang Wang, Yunhua Hao
The association between cutaneous adverse drug reactions (cADRs) caused by antiepileptic drugs (AEDs) and human leukocyte antigen-A ( HLA-A ) and HLA-B genes in Chinese Han population in Shanghai was investigated. Through the case-control study, 30 child patients with AED-induced cADRs (cADRs group), 60 AED-tolerant child patients (AED-tolerant group) and 60 normal children not taking AEDs (normal group) were collected. The HLA-B*15:02 and HLA-A*31:01 genotypes were detected using the polymerase chain reaction-sequence-specific oligonucleotide (PCR-SSO) probe method, and the correlation of HLA-B*15:02 and HLA-A*31:01 genes with the incidence of cADRs was analyzed...
April 2018: Experimental and Therapeutic Medicine
Xianhua Wang, Aiguo Ma, Xiuxia Han, Aishan Litifu, Feng Xue
Seven single-nucleotide polymorphism (SNP) sites located in ASAP1 gene have been found associated with tuberculosis (TB) susceptibility by genome-wide association studies in Russia. The case-control study was carried out to test whether these seven SNPs were associated with susceptibility to TB in a Chinese Xinjiang Muslim population. The seven SNPs were genotyped in a case-control design that included 780 Xinjiang Muslim subjects (400 TB patients and 380 controls). Multiplex PCR and direct sequencing were used to detect ASAP1 gene polymorphisms...
April 2018: Experimental and Therapeutic Medicine
Yun-Yan Zhang, En Shi, Zhao-Ping Yang, Qi-Fang Geng, Ying-Xiong Qiu, Zhong-Sheng Wang
Parrotia subaequalis is an endangered palaeoendemic tree from disjunct montane sites in eastern China. Due to the lack of effective genomic resources, the genetic diversity and population structure of this endangered species are not clearly understood. In this study, we conducted paired-end shotgun sequencing (2 × 125 bp) of genomic DNA for two individuals of P. subaequalis on the Illumina HiSeq platform. Based on the resulting sequences, we have successfully assembled the complete chloroplast genome of P...
2018: Frontiers in Plant Science
Ardashel Latsuzbaia, Marc Arbyn, Sankhadeep Dutta, Marc Fischer, Tarik Gheit, Jessica Tapp, Massimo Tommasino, Steven Weyers, Joël Mossong
A novel human papillomavirus genotype was detected in a cervical swab specimen by next-generation sequencing after rolling circular amplification. It was fully cloned and characterized. The L1 open reading frame showed 77% nucleotide similarity with the closest genotype, HPV101, belonging to the gamma-6 species.
March 15, 2018: Genome Announcements
Khaled R Alkharsah, Suriya Rehman, Fatimah Alkhamis, Amani Alnimr, Asim Diab, Amein K Al-Ali
BACKGROUND: Methicillin resistant Staphylococcus aureus (MRSA) constitutes a major global health concern causing hospital and community acquired infections. A wide diversity of MRSA genotypes are circulating in geographically related regions. Therefore understanding the molecular epidemiology of MRSA is fundamental to design control and clearance measures. METHODS: A total of 106 MRSA isolates from infection (51) and carrier colonization sites (55) are characterized genetically based on SCCmec and MLST genotyping methods in addition to detection of PVL, TSST-1 and enterotoxins...
March 15, 2018: Annals of Clinical Microbiology and Antimicrobials
María-Dolores Rey, Graham Moore, Azahara C Martín
Karyotypes of three accessions of <i>Hordeum chilense</i> (H1, H16 and H7), <i>Hordeum vulgare</i> and <i>Triticum aestivum</i> were characterized by physical mapping of several repetitive sequences. A total of fourteen repetitive sequences were used as probes for fluorescence in situ hybridization (FISH) with the aim of identifying inter- and intra-species polymorphisms. The (AG)12 and 4P6 probes only produced hybridization signals in wheat, the BAC7 probe only hybridized to the centromeric region of <i>H...
March 15, 2018: Genome Génome / Conseil National de Recherches Canada
Christopher J Lambert, Briana C Freshner, Arlen Chung, Tamara J Stevenson, D Miranda Bowles, Raheel Samuel, Bruce K Gale, Joshua L Bonkowsky
Zebrafish are a valuable model organism in biomedical research. Their rapid development, ability to model human diseases, utility for testing genetic variants identified from next-generation sequencing, amenity to CRISPR mutagenesis, and potential for therapeutic compound screening, has led to their wide-spread adoption in diverse fields of study. However, their power for large-scale screens is limited by the absence of automated genotyping tools for live animals. This constrains potential drug screen options, limits analysis of embryonic and larval phenotypes, and requires raising additional animals to adulthood to ensure obtaining an animal of the desired genotype...
2018: PloS One
Sunirmal Sheet, Kuntal Ghosh, Satabdi Acharya, Kwang-Pyo Kim, Yang Soo Lee
Apart from being fed to silkworms in sericulture, the ecologically important Mulberry plant has been used for traditional medicine in Asian countries as well as in manufacturing wine, food, and beverages. Germplasm analysis among Mulberry cultivars originating from South Korea is crucial in the plant breeding program for cultivar development. Hence, the genetic deviations and relations among 8 Morus alba plants, and one Morus lhou plant, of different cultivars collected from South Korea were investigated using 10 random amplified polymorphic DNA (RAPD) and 10 inter-simple sequence repeat (ISSR) markers in the present study...
March 15, 2018: Plants (Basel, Switzerland)
Ruwan Weerakkody, David Ross, David A Parry, Bulat Ziganshin, Jana Vandrovcova, Piyush Gampawar, Abdulshakur Abdullah, Jennifer Biggs, Julia Dumfarth, Yousef Ibrahim, Colin Bicknell, Mark Field, John Elefteriades, Nick Cheshire, Timothy J Aitman
PurposeThoracic aortic aneurysm/aortic dissection (TAAD) is a disorder with highly variable age of onset and phenotype. We sought to determine the prevalence of pathogenic variants in TAAD-associated genes in a mixed cohort of sporadic and familial TAAD patients and identify relevant genotype-phenotype relationships.MethodsWe used a targeted polymerase chain reaction and next-generation sequencing-based panel for genetic analysis of 15 TAAD-associated genes in 1,025 unrelated TAAD cases.ResultsWe identified 49 pathogenic or likely pathogenic (P/LP) variants in 47 cases (4...
March 15, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Makoto Chiba, Takanori Itabashi, Koujiro Hirai, Mitsuo Sakamoto, Moriya Ohkuma, Taichiro Ishige, Shinji Kawasaki
A strain (Hime 5-1T ) of lactic acid bacterium was isolated from the gut of the grasshopper Metrioptera engelhardti from a mountainous area of Nagano Prefecture, Japan. Strain Hime 5-1T had a low 16S rRNA gene sequence similarity to known lactic acid bacteria, with the closest recognized relatives being Lactobacillus tucceti (96.7 %), Lactobacillus furfuricola (96.5 %), Lactobacillus versmoldensis (96.3 %) and Lactobacillus nodensis (96.1 %). Comparative analyses of the rpoA and pheS gene sequences indicated that Hime 5-1T is not closely related to other Lactobacillus species...
March 15, 2018: International Journal of Systematic and Evolutionary Microbiology
Hathairat Rachniyom, Atsuko Matsumoto, Yuki Inahashi, Akira Take, Yoko Takahashi, Arinthip Thamchaipenet
A novel actinomycete strain, designated GKU 128T , isolated from the roots of an Indian oak tree [Barringtonia acutangula (L.) Gaertn.] at Khao Khitchakut district, Chantaburi province, Thailand, was characterized by using a polyphasic approach. The strain formed a branched substrate and aerial mycelia which differentiated into straight to flexuous chains of smooth-ornamented spores. Analysis of the cell wall revealed the presence of meso-diaminopimelic acid and N-acetylmuramic acid in the peptidoglycan. The whole-cell sugars were glucose, madurose, mannose, rhamnose and ribose...
March 15, 2018: International Journal of Systematic and Evolutionary Microbiology
Hui Yu, Xinxin You, Jia Li, Xinhui Zhang, Shuai Zhang, Shoujia Jiang, Xueqiang Lin, Hao-Ran Lin, Zining Meng, Qiong Shi
The orange-spotted grouper, Epinephelus coioides, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a genome-wide association study (GWAS) on a natural population of 198 individuals aiming to screen the whole genome of orange-spotted grouper for identification of growth-related loci by restrictionsite associated DNA sequencing...
March 12, 2018: Science China. Life Sciences
Raziyeh Kasaei, David Carmena, Ali Jelowdar, Molouk Beiromvand
Giardia duodenalis is an intestinal flagellated protozoan that infects humans and several animal species. Giardiasis causing more than 200 million symptomatic infections globally is one of the most common causes of diarrhea in developing countries. Based on molecular studies mainly targeting the small-subunit (SSU) rRNA gene locus of the parasite, eight assemblages (A to H) have been identified in humans and other animal species. The aim of the current study was to evaluate the frequency and molecular diversity of G...
March 14, 2018: Parasitology Research
Xian Qi, Xiaofei An, Yongjun Jiao, Huiyan Yu, Ke Xu, Lunbiao Cui, Shenjiao Wang, Fei Deng, Xiang Huo, Haodi Huang, Qigang Dai, Changjun Bao
Five epidemic waves of human infection with influenza A (H7N9) virus have emerged in China since spring 2013. We previously described the epidemiological characterization of the fifth wave in Jiangsu province. In this study, 41 H7N9 viruses from patients and live-poultry markets were isolated and sequenced to further elucidate the genetic features of viruses of the fifth wave in Jiangsu province. Phylogenetic analysis revealed substantial genetic diversity in the internal genes, and 18 genotypes were identified from the 41 H7N9 virus strains...
March 14, 2018: Archives of Virology
Bangari Haldipur, Prudhvi Lal Bhukya, Vidya Arankalle, Kavita Lole
Molecular mechanisms of liver pathology and clinical disease in HEV infection remain unclear. MicroRNAs are known to modulate viral pathogenesis either by directly altering viral gene expression or by enhancing cellular antiviral responses. Given the importance of microRNA-122 (miR-122) in liver pathobiology, we investigated possible role of miR-122 in HEV infection. In silico predictions using genotype 1, 2, 3 and 4 HEV sequences showed that majority of genomes (203/222) harbor at least one miR-122/miR-122* target site...
March 14, 2018: Journal of Virology
Hannah Y P Phoon, Hazilawati Hussin, Baizurah Mohd Hussain, Shu Yong Lim, Jia Jie Woon, Yi Xian Er, Kwai Lin Thong
OBJECTIVES: Hospital environments are potential reservoirs of bacteria associated with nosocomial infections. Here, we determined the distribution of cultivable environmental bacteria of clinical importance from a Malaysian tertiary hospital and to investigate their resistotypes and genotypes. METHODS: Swab and fluid samples (n=358) from healthcare workers' hands, frequently touched surfaces, medical equipment, patients' immediate surroundings, ward sinks and toilets and solutions or fluids of 12 selected wards were collected...
March 11, 2018: Journal of Global Antimicrobial Resistance
Guo-Jin Ou, Pin-Can Su, Hao Yu, Xin Ji, Fan Liu, Sheng-Lan Wang, Yu-Jie Kong, Ling Li, Jue Wang, Zhong Liu, Willy Albert Flegel
BACKGROUND: Human neutrophil antigen 3 (HNA-3) is encoded by the SLC44A2 gene. Antibodies against HNAs can cause severe, often fatal, transfusion reactions, known as transfusion-related acute lung injury, and neonatal neutropenia. We explored the 2 common HNA-3 variants in 9 ethnic populations residing in Sichuan and Yunnan provinces of China as compared to the Han population. METHODS: We genotyped for SLC44A2 (rs2288904) by polymerase chain reaction sequence-based typing among blood donors, for a total of 2206 individuals in Yunnan and 376 in Sichuan...
March 14, 2018: Journal of Translational Medicine
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