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Infection, genetics and evolution : journal of mol... 26건

  1. [해외논문]   Global distribution of NA1 genotype of respiratory syncytial virus and its evolutionary dynamics assessed from the past 11 years   SCIE

    Haider, Md Shakir Hussain (Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India ) , Deeba, Farah (Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India ) , Khan, Wajihul Hasan (Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India ) , Naqvi, Irshad H. (Dr. M.A. Ansari Health Centre, Jamia Millia Islamia, New Delhi, India ) , Ali, Sher (Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India ) , Ahmed, Anwar (Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia ) , Broor, Shobha (Department of Microbiology, Faculty of Medicine and Health Science, Shree Guru Gobind Singh Tricentenary University, Gurgaon, Haryana, India ) , Alsenaidy, Hytham A. (College of Medicine, Shaqra University, Shaqra, Saudi Arabia ) , Alsenaidy, Abdulrahman M. (Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia ) , Dohare, Ravins (Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India ) , Parveen, Shama (Centre for Interdisciplinary Research in Basic)
    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases v.60 ,pp. 140 - 150 , 2018 , 1567-1348 ,

    초록

    Abstract Respiratory syncytial virus (RSV) is a potent pathogen having global distribution. The main purpose of this study was to gain an insight into distribution pattern of the NA1 genotype of group A RSV across the globe together with its evolutionary dynamics. We focused on the second hypervariable region of the G protein gene and used the same for Phylogenetic, Bayesian and Network analyses. Eighteen percent of the samples collected from 500 symptomatic pediatric patients with acute respiratory tract infection (ARI) were found to be positive for RSV during 2011–15 from New Delhi, India. Of these, group B RSV was predominant and clustered into two different genotypes (BA and SAB4). Similarly, group A viruses clustered into two genotypes (NA1 and ON1). The data set from the group A viruses included 543 sequences from 23 different countries including 67 strains from India. The local evolutionary dynamics suggested consistent virus population of NA1 genotype in India during 2009 to 2014. The molecular clock analysis suggested that most recent common ancestor of group A and NA1 genotype have emerged in during the years 1953 and 2000, respectively. The global evolutionary rates of group A viruses and NA1 genotype were estimated to be 3.49 × 10 −3 (95% HPD, 2.90–4.17 × 10 −3 ) and 3.56 × 10 −3 (95% HPD, 2.91 × 10 −3 –4.18 × 10 −3 ) substitution/site/year, respectively. Analysis of the NA1 genotype of group A RSV reported during 11 years i.e. from 2004 to 2014 showed its dominance in 21 different countries across the globe reflecting its evolutionary dynamics. The Network analysis showed highly intricate but an inconsistent pattern of haplotypes of NA1 genotype circulating in the world. Present study seems to be first comprehensive attempt on global distribution and evolution of NA1 genotype augmenting the optimism towards the vaccine development. Highlights RSV was detected in 18.6% of the symptomatic patients The tMRCA of RSV-A and NA1 genotype suggested that they emerged in years 1953 and 2000 respectively. Global evolutionary rates of RSV-A and NA1 were 3.49 × 10 −3 and 3.56 × 10 −3 respectively. BSP showed that the effective population size of the Indian NA1 genotype was constant from 2009 to 14. Network analysis showed highly tangled but an inconsistent pattern of haplotypes of NA1 genotype.

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  2. [해외논문]   Characterization of Botrytis cinerea isolates collected on pepper in Southern Turkey by using molecular markers, fungicide resistance genes and virulence assay   SCIE

    Polat, İ (Batı Akdeniz Agricultural Research Institute, Antalya, Turkey ) , lknur (Muğla Sıtkı Koçman University, Faculty of Science, Department of Molecular Biology and Genetics, 48000 Muğla, Turkey ) , Baysal, Ö (Institute of Biosciences and Bioresources (IBBR), National Research Council of Italy (CNR), Palermo, Italy ) , mü (Batı Akdeniz Agricultural Research Institute, Antalya, Turkey ) , r (Batı Akdeniz Agricultural Research Institute, Antalya, Turkey ) , Mercati, Francesco (Batı Akdeniz Agricultural Research Institute, Antalya, Turkey ) , Gü (Mediterranean University of Reggio Calabria, Reggio Calabria, Italy ) , mrü (Institute of Biosciences and Bioresources (IBBR), National Research Council of Italy (CNR), Palermo, Italy) , kcü , , Emine , Sü , lü , , Gö , rkem , Kitapcı, Aytü , l , Araniti, Fabrizio , Carimi, Francesco
    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases v.60 ,pp. 151 - 159 , 2018 , 1567-1348 ,

    초록

    Abstract Botrytis cinerea is a polyphagous fungal pathogen causing gray mold disease. Moreover, it is one of the most destructive infections of small fruit crops such as pepper ( Capsicum annnum L.). C . sativum is a species belonging to the Solanaceae family and Turkey is one of the main producers in the World. In the present work, aiming to obtain information useful for pest management, fifty B . cinerea isolates collected from Turkey and a reference isolate (B05.10) were characterized using molecular markers and fungicide resistance genes. Morphological and molecular (ITS1-ITS4) identification of B . cinerea isolates, the degree of virulence and mating types were determined. Since one or several allelic mutations in the histidine kinase ( Bos1 ) and β - tubulin genes generally confer the resistance to fungicides, the sequences of these target genes were investigated in the selected isolates, which allowed the identification of two different haplotypes. Mating types were also determined by PCR assays using primer specific for MAT1–1 alpha gene (MAT1-1-1) and MAT1–2 HMG (MAT1-2-1) of B . cinerea . Twenty-two out of 50 isolates (44%) were MAT1–2, while 38% were MAT1–1. Interestingly, out of whole studied samples, 9 isolates (18%) were heterokaryotic or mixed colonies. In addition, cluster and population structure analyses identified five main groups and two genetic pools, respectively, underlining a good level of variability in the analysed panel. The results highlighted the presence of remarkable genetic diversity in B . cinerea isolates collected in a crucial economical area for pepper cultivation in Turkey and the data will be beneficial in view of future gray mold disease management. Highlights In the present work, virulence evaluation and molecular markers characterization of fifty B . cinerea isolates from a crucial economical area for pepper cultivation in Turkey were carried out to obtain information for the pest management. Morphological and molecular (ITS1-ITS4) identification of isolates and degrees of virulence were determined in - vitro and in - vivo . Mutations in the histidine kinase ( Bos1 ) and β-tubulin genes were investigated, identifying two different haplotypes in the analysed collection. Mating types were also determined by PCR assay using primers specific for MAT1–1 alpha gene (MAT1-1-1) and MAT1–2 HMG (MAT1-2-1) of B . cinerea . Cluster and PcoA approaches and population structure analysis highlighted five clusters grouped in two main genetic pools, confirming a remarkable genetic diversity in the isolates collected. The present study is the starting point for future gray mold disease management in Turkey.

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  3. [해외논문]   Association of HCV mutated proteins and host SNPs in the development of hepatocellular carcinoma   SCIE

    Suhail, Mohd (King Fahd Medical Research Center, King Abdulaziz University, PO Box 80216, Jeddah 21589, Saudi Arabia ) , Sohrab, Sayed Sartaj (Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, PO Box 80216, Jeddah 21589, Saudi Arabia ) , Qureshi, Abid (Biomedical Informatics Centre, Sher-i-Kashmir Institute of Medical Sciences (SKIMS), Srinagar, J&K, India ) , Tarique, Mohd (Department of Surgery, Sylvester Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, United States ) , Abdel-Hafiz, Hany (Dept of Medicine, University of Colorado Denver, Aurora, CO 80045, United States ) , Al-Ghamdi, Khalid (Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia ) , Qadri, Ishtiaq (Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia)
    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases v.60 ,pp. 160 - 172 , 2018 , 1567-1348 ,

    초록

    Abstract Hepatitis C virus plays a significant role in the development of hepatocellular carcinoma (HCC) globally. The pathogenic mechanisms of hepatocellular carcinoma with HCV infection are generally linked with inflammation, cytokines, fibrosis, cellular signaling pathways, and liver cell proliferation modulating pathways. HCV encoded proteins (Core, NS3, NS4, NS5A) interact with a broad range of hepatocytes derived factors to modulate an array of activities such as cell signaling, DNA repair, transcription and translational regulation, cell propagation, apoptosis, membrane topology. These four viral proteins are also implicated to show a strong conversion potential in tissue culture. Furthermore, Core and NS5A also trigger the accretion of the β-catenin pathway as a common target to contribute viral induced transformation. There is a strong association between HCV variants within Core, NS4, and NS5A and host single nucleotide polymorphisms (SNPs) with the HCC pathogenesis. Identification of such viral mutants and host SNPs is very critical to determine the risk of HCC and response to antiviral therapy. In this review, we highlight the association of key variants, mutated proteins, and host SNPs in development of HCV induced HCC. How such viral mutants may modulate the interaction with cellular host machinery is also discussed. Highlights There is a strong association between HCV variants within Core, NS4 and NS5A and host SNPs with the HCC pathogenesis. Core and NS5A also trigger the accretion of β-catenin pathway as a common target to contribute viral induced transformation. Single-point mutations, Phe 43 and Leu 106, of HCV NS3 protein, impair its interaction with p53. The A28C polymorphism has been suggested to alter the coil structure of amino acids 8–12 into β-sheet.

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  4. [해외논문]   Importance of common TLR2 genetic variants on clinical phenotypes and risk in tuberculosis disease in a Western Chinese population   SCIE

    Zhang, Jingwei (Department of Laboratory Medicine, Chengdu Second People's Hospital, Chengdu 610017, PR China ) , Zhao, Zhenzhen (Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China ) , Zhong, Huiyu (Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China ) , Wu, Lijuan (Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China ) , Zhou, Wenjing (Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China ) , Peng, Wu (Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China ) , Hu, Xuejiao (Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China ) , Song, Jiajia (Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China ) , Liu, Tangyuheng (Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, PR China ) , Wu, Qian (Department of Laboratory Medicine, West China Hospital, Sichuan University, Chen) , Bai, Hao , Zhou, Yi , Chen, Xuerong , Chen, Jie , Lu, Xiaojun , Ying, Binwu
    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases v.60 ,pp. 173 - 180 , 2018 , 1567-1348 ,

    초록

    Abstract Objectives Abundant studies have suggested that TLR2 genetic variants involve in susceptibility to TB infection. We tried to verified the hypothesis that TLR2 genetic loci effect on the susceptibility to TB in the Western Chinese population. Methods A total 1109 individuals (634 TB patients and 475 healthy controls) were genotyped for rs3804099, rs3804100 and rs76112010 by using a custom-by-design 2x48-Plex SNP scan TM Kit. The statistical analysis between candidate 3 SNPs and risk and phenotypes of TB were conducted in this study. Significant SNPs were further interrogated in relation to TB susceptibility to TB infection and clinical phenotypes. Results None of the three genetic loci (rs3804099, rs3804100 and rs76112010) showed statistically significant differences between all TB cases and healthy controls in genotype, allele frequencies and genetic models (all p > 0.05). Statistical comparisons of retreatment TB cases and healthy controls or primary cases revealed that rs3804099 was significantly associated with the increased risk of developing TB in Western Chinese population. For genotypes frequencies, the subgroups of retreatment TB group versus healthy control group analysis and retreatment TB group versus primary TB group analysis results showed the p = 0.041 and p = 0.002 respectively. For recessive model, the subgroup of retreatment TB group versus healthy control group and retreatment TB group versus primary TB group analyses showed the p = 0.028 and P = 0.002 after Bonferroni correction respectively. Furthermore, analysis of the genotypes of rs76112010 in relation to clinical phenotypes of active TB using the dominant model demonstrated that it was strongly correlated with different hematological parameters (Erythrocyte P = 0.043, Hemoglobin P = 0.047, Hematocrit P = 0.027). Conclusion Our study presented the significant associations of rs3804099 with TB susceptibility in the retreatment TB subgroup analysis. Our study proposed that common TLR2 genetic variants may influence TB development and disease phenotypes in Western Chinese population. Highlights The impact of TLR2 on TB predisposition has been identified in West China population. The statistical analysis between candidate 3 SNPs and risk and phenotypes of TB were conducted. rs3804099 and rs3804100 have associations with TB susceptibility in the retreated TB. rs76112010 was strongly correlated with different hematological parameters.

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  5. [해외논문]   The role of TonB-dependent copper receptor in virulence of Acinetobacter baumannii   SCIE

    Abdollahi, Sajad (Department of Biology, Shahed University, Tehran, Iran ) , Rasooli, Iraj (Department of Biology, Shahed University, Tehran, Iran ) , Mousavi Gargari, Seyed Latif (Department of Biology, Shahed University, Tehran, Iran)
    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases v.60 ,pp. 181 - 190 , 2018 , 1567-1348 ,

    초록

    Abstract Acinetobacter baumannii is an opportunistic gram negative pathogen that can adhere to different surfaces and cause different nosocomial infections. To investigate the role of TonB-dependent copper receptor, an outer membrane protein, in virulence of A. baumannii, we deleted this receptor from A. baumannii chromosome. There was a significant decrease in biofilm formation by copper receptor deficient mutant strain. Similarly, the adherence to human epithelial cell and the hydrophobicity were declined. The survival rate of the mutant strain in human sera was reduced while no change was observed in motility of strains. In murine pneumonia model, the bacterial lethal dose 0 (LD 0 ), LD 50 and LD 100 were increased for mutant strain. Moreover, in vivo and in vitro experiments revealed changes in growth rate and dissemination of mutant strain; so that the bacterial load of the mutant was significantly reduced in the spleen and lung. The findings suggest a critical role for TonB-dependent copper receptor in virulence of A. baumannii . Highlights Copper receptor plays crucial role in A. baumannii adherence to epithelial cells. TonB-dependent copper receptor deficient A. baumannii was created. The mutant strain exhibited reduced adherence to human epithelial cells. Biofilm formation and the hydrophobicity were significantly decreased. The lethal dose of ∆copper receptor strain was increased in murine pneumonia model.

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    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  6. [해외논문]   The molecular characteristics of avian influenza viruses (H9N2) derived from air samples in live poultry markets   SCIE

    Wu, Yanheng (Corresponding author at: Zhongshan Center for Disease Control and Prevention, Zhongshan, Guangdong Province, PR China.) , Lin, Jinsi , Yang, Shuhuan , Xie, Ying , Wang, Man , Chen, Xueqin , Zhu, Yayang , Luo, Le , Shi, Wuyang
    Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases v.60 ,pp. 191 - 196 , 2018 , 1567-1348 ,

    초록

    Abstract Objective To study the molecular characteristics of H9N2-subtype avian influenza viruses (AIVs) isolated from air samples collected in live poultry markets (LPMs) and explore their sequence identities with AIVs that caused human infection. Methods Weekly surveillance of H9N2-subtype AIVs in the air of LPMs was conducted from 2015 to 2016. H9-positive samples were isolated from chicken embryos. Whole genome sequences of the isolated AIVs were obtained through high-throughput sequencing. Phylogenetic analysis and key loci variations of the sequences were further analyzed. Results A total of 327 aerosol samples were collected from LPMs. Nine samples were positive for H9-subtype AIVs based on quantitative real-time reverse transcription polymerase chain reaction (qRRT-PCR). According to the whole genome sequence analysis and phylogenetic analysis, except for the A/Environment/Zhongshan/ZS201505/2015 (ZS201505) strain, 8 gene segments of 8 aerosol H9N2 isolates and 2 H9N2 human isolates in 2015 were located in the same clade. Among key loci variations, except for the ZS201505 strain, H9N2-subtype AIVs had no mutations in eight receptor binding sites of hemagglutinin (HA), and stalks of neuraminidase (NA) proteins exhibited a deletion site of three bases. The PA gene of ZS201503 and ZS201602 exhibited an L336M mutation. The N30D and T215A mutations in the M1 gene and amino acid residues L89V in PB2, P42S in NS1 and S31N in M2 were retained in these 9 strains of H9N2 isolates, which could enhance the virus's virulence. Conclusion Live H9N2 AIVs survived in the aerosol of LPMs in Zhongshan City. The aerosol viruses had a close evolutionary relationship with human epidemic strains, indicating that there might be a risk of AIV transmission from polluted aerosols in LPMs to humans. Mutations in H9N2-subtype AIVs isolated from air samples collected from LPMs suggested their pathogenicity was enhanced to infect humans. Highlights 9 strains of avian influenza viruses (H9N2) were isolated from the air samples in live poultry market. Procedure of bioaerosol sampling and the whole genome sequencing and assembly were illustrated in the manuscript. The aerosol H9N2 avian influenza viruses have a close evolutionary relationship with human infected H9N2 strains. Mutations of the aerosol isolates were found that might enhance the virus’s virulence and improve pathogenicity to infect human beings.

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