scholarly journals NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Philip L. Tzou ◽  
Xiaoqiu Huang ◽  
Robert W. Shafer
Keyword(s):  
Amino Acid ◽  
Gene Sequences ◽  
Virus Gene ◽  
Amino Acid Alignment

scholarly journals Analysis of Neurotoxin Cluster Genes in Clostridium botulinum Strains Producing Botulinum Neurotoxin Serotype A Subtypes

2008 ◽  
Vol 74 (9) ◽  
pp. 2778-2786 ◽  
Author(s):  
Mark J. Jacobson ◽  
Guangyun Lin ◽  
Brian Raphael ◽  
Joanne Andreadis ◽  
Eric A. Johnson
Keyword(s):  
Amino Acid ◽  
Clostridium Botulinum ◽  
Botulinum Neurotoxin ◽  
Amino Acid Sequences ◽  
Gene Sequences ◽  
Amino Acid Levels ◽  
Cluster Type ◽  
Botulinum Neurotoxin Serotype A ◽  
Cluster Gene ◽  
Degree Of Similarity

ABSTRACT Neurotoxin cluster gene sequences and arrangements were elucidated for strains of Clostridium botulinum encoding botulinum neurotoxin (BoNT) subtypes A3, A4, and a unique A1-producing strain (HA− Orfx+ A1). These sequences were compared to the known neurotoxin cluster sequences of C. botulinum strains that produce BoNT/A1 and BoNT/A2 and possess either a hemagglutinin (HA) or an Orfx cluster, respectively. The A3 and HA− Orfx+ A1 strains demonstrated a neurotoxin cluster arrangement similar to that found in A2. The A4 strain analyzed possessed two sets of neurotoxin clusters that were similar to what has been found in the A(B) strains: an HA cluster associated with the BoNT/B gene and an Orfx cluster associated with the BoNT/A4 gene. The nucleotide and amino acid sequences of the neurotoxin cluster-specific genes were determined for each neurotoxin cluster and compared among strains. Additionally, the ntnh gene of each strain was compared on both the nucleotide and amino acid levels. The degree of similarity of the sequences of the ntnh genes and corresponding amino acid sequences correlated with the neurotoxin cluster type to which the ntnh gene was assigned.

scholarly journals Prevalence and Genetic Characterization of Two Mitochondrial Gene Sequences of Strobilocercus Fasciolaris in the Livers of Brown Rats (Rattus norvegicus) in Heilongjiang Province in Northeastern China

2020 ◽  
Vol 10 ◽  
Author(s):  
Fengnian Zhao ◽  
Yun Zhou ◽  
Yanchen Wu ◽  
Kexin Zhou ◽  
Aiqin Liu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Intraspecific Variation ◽  
Rattus Norvegicus ◽  
Genetic Characterization ◽  
Northeastern China ◽  
Amino Acid Sequences ◽  
Morphological Observation ◽  
Heilongjiang Province ◽  
Gene Sequences

Rodents constitute the largest and most successful group of mammals worldwide. Brown rats (Rattus norvegicus) are one of the most common rodent species, and they serve as intermediate hosts of Hydatigera taeniaeformis. Although there have been a few studies reporting on the presence of the larval form of H. taeniaeformis (strobilocercus fasciolaris) in brown rats worldwide, little information is available on the genetic characterization of this parasite, with no molecular data from China. Therefore, from April 2014 to March 2016, this study was carried out to understand the prevalence and genetic characters of strobilocercus fasciolaris in brown rats captured in Heilongjiang Province in northeastern China. The livers of brown rats were collected and examined for the presence of cysts. Each cyst was identified based on morphological observation: the larvae with the naked eye and the scolexes under a microscope. The results were confirmed by polymerase chain reaction (PCR) and sequencing of the cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 4 (nad4) genes. At the investigated sites, 11.8% (13/110) of the brown rats were infected with strobilocercus fasciolaris. Based on sequence analysis, there were 10 and six haplotypes regarding the cox1 and the nad4 loci, with 24 and 42 polymorphic sites, respectively (degree of intraspecific variation: 0.3%–4.4% and 0.6%–4.7%, respectively). Twelve nucleotide sequences (six of the 10 at the cox1 locus and all six at the nad4 locus) have not previously been described. Base differences in three of the six novel cox1 gene sequences and five of the six novel nad4 gene sequences caused amino acid changes. Phylogenetic analyses of the cox1 and nad4 gene sequences based on neighbor-joining and Bayesian inference trees indicated that all the strobilocercus fasciolaris isolates belonged to Hydatigera taeniaeformis sensu stricto (s.s.). This is the first report on the genetic characterization of strobilocercus fasciolaris in brown rats in China. The findings of novel cox1 and nad4 nucleotide and amino acid sequences may reflect the region-specific genetic characterization of the parasite. The data will be useful to explore the biological and epidemiological significance of the intraspecific variation within H. taeniaeformis s.s.

scholarly journals octoFLU: Automated Classification for the Evolutionary Origin of Influenza A Virus Gene Sequences Detected in U.S. Swine

2019 ◽  
Vol 8 (32) ◽  
Author(s):  
Jennifer Chang ◽  
Tavis K. Anderson ◽  
Michael A. Zeller ◽  
Phillip C. Gauger ◽  
Amy L. Vincent
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Antigenic Drift ◽  
Evolutionary Origin ◽  
Automated Classification ◽  
Gene Sequences ◽  
Influenza A Viruses ◽  
Query Gene ◽  
Data Set ◽  
Virus Gene

The diversity of the 8 genes of influenza A viruses (IAV) in swine reflects introductions from nonswine hosts and subsequent antigenic drift and shift. Here, we curated a data set and present a pipeline that assigns evolutionary lineage and genetic clade to query gene segments.

scholarly journals In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019

2020 ◽  
Author(s):  
Arshi Siddiqui ◽  
Rashmi Chowdhary ◽  
Harjeet Singh Maan ◽  
Sudhir Kumar Goel ◽  
Nidhi Tripathi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Vaccine Efficacy ◽  
Influenza A ◽  
In Silico Analysis ◽  
Central India ◽  
Gene Sequences ◽  
Ha Gene ◽  
Influenza A H1n1 ◽  
Silico Analysis

Background and Objectives: Influenza A/H1N1pdm09 causes respiratory illness and remains a concern for public health. Since its first emergence in 2009, the virus has been continuously circulating in the form of its genetic variants. Influenza A/ H1N1pdm09 surveillance is essential for uncovering emerging variants of epidemiologic and vaccine efficacy. The present study attempts in silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India during 2009-2019. Materials and Methods: We have investigated the antigenic drift analysis of 96 isolates’ hemagglutinin (HA) gene sequences (59 central Indian and 37 local Indian and 28 global reference HA gene sequences) of Influenza A/H1N1pdm09 viruses from 2009 to 2019. The study includes mutational (Multiple sequence Alignment), phylogenetic (Maximum Likelihood Method), and statistical analysis (Covariance and correlation) of HA sequences submitted in NCBI, IRD and GISAID from central India. Results: Phylogenetic analysis indicated maximum clustering of central Indian HA gene sequences in genogroup 6B. Analysis of amino acid sequence alignment revealed changes in receptor binding site (RBS). The frequency of S220T amino acid substitution was found to be high followed by S202T, K300E A273T, K180Q. The Karl Pearson correlation coefficient (r) and covariance between the number of mutations and the death toll was found +0.246 and +100.3 respectively. Conclusion: The study identifies the continuous genetic variations in the HA gene sequences of circulating Influenza A/ H1N1pdm09 in central India from the year 2009 to 2019. Further suggesting importance of monitoring the gradual evolution of the virus with regards to an increase in virulence, pathogenicity and vaccine efficacy timely.

scholarly journals Rifampin and Rifabutin Resistance Mechanism inHelicobacter pylori

1999 ◽  
Vol 43 (6) ◽  
pp. 1497-1499 ◽  
Author(s):  
Markus Heep ◽  
Daniela Beck ◽  
Ekkehard Bayerdörffer ◽  
Norbert Lehn
Keyword(s):  
Escherichia Coli ◽  
Helicobacter Pylori ◽  
Mycobacterium Tuberculosis ◽  
Amino Acid ◽  
Resistance Mechanism ◽  
Clinical Isolates ◽  
Gene Sequences ◽  
H Pylori

ABSTRACT Eighty-one clinical isolates of Helicobacter pylorishowed no resistance to rifampin (MIC range, 0.032 to 2 μg/ml; MIC at which 50% of isolates are inhibited [MIC50], 0.25 μg/ml). The MIC50 of rifabutin was 0.008 μg/ml (n = 16). All resistant laboratory mutants of H. pylori ATCC 43504 showed amino acid exchanges in codons 524 to 545 or codon 585 of the rpoB gene, corresponding to the gene sequences from Mycobacterium tuberculosis andEscherichia coli.

scholarly journals ERG11 Polymorphism in Voriconazole-Resistant Candida tropicalis: Weak Role of ERG11 Expression, Ergosterol Content, and Membrane Permeability

2020 ◽  
Vol 65 (1) ◽  
pp. e00325-20
Author(s):  
Patricia Navarro-Rodríguez ◽  
Loida López-Fernández ◽  
Adela Martin-Vicente ◽  
Josep Guarro ◽  
Javier Capilla
Keyword(s):  
Amino Acid ◽  
Membrane Permeability ◽  
Candida Tropicalis ◽  
Gene Sequencing ◽  
Missense Mutations ◽  
Sterol Content ◽  
Content Type ◽  
Ergosterol Content ◽  
Amino Acid Alignment

ABSTRACTMutations in ERG11 were detected by gene sequencing and amino acid alignment in 18 Candida tropicalis strains with different degrees of sensitivity to voriconazole (VRC). ERG11 expression, sterol content, and membrane permeability were also evaluated. We report three missense mutations in ERG11 that resulted in resistance to VRC. The transcriptional levels of ERG11 as well as the ergosterol content and membrane permeability demonstrated no correlation to only a slight correlation with the obtained MIC values, but the data did suggest a tendency toward such a correlation.

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