Sequence Analysis of the Cas2 Gene in Riemerella anatipestifer

2013 ◽  
Vol 647 ◽  
pp. 570-576 ◽  
Author(s):  
Yang He ◽  
An Chun Cheng ◽  
Ming Shu Wang ◽  
De Kang Zhu ◽  
Xiao Jia Wang ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Phylogenetic Tree ◽  
Sequence Alignment ◽  
Homology Search ◽  
Rare Codon ◽  
Composition Analysis ◽  
Capnocytophaga Canimorsus ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Riemerella Anatipestifer

Objective: By analyzing the Cas2gene of Riemerella anatipestifer (RA), the aim was to acquire more useful information as a guide of further study. Methods: Using bioinformatics method, sequence analysis of RA Cas2 gene was performed with some databases and software, including homology search, sequence alignment, phylogenetic tree analysis, composition analysis and physicochemical property analysis. Results: Homology search suggested that Cas2 protein sequence of R. anatipestifer showed high similarity to those of strains within Bergeyella zoohelcum and Capnocytophaga canimorsus, consistent with the result of multiple sequence alignment and phylogenetic tree analysis. The rare codon analysis revealed that there was no rare codon string in RA Cas2 gene. Conclusion: Cas2 gene of R. anatipestifer was evolutionally closely related to those strains of Bergeyella zoohelcum and Capnocytophaga canimorsus, and can be over-expressed in E.coli without considering the impact of rare codons on translation.

Sequence Analysis of the Cas1 Gene in Riemerella anatipestifer

2013 ◽  
Vol 641-642 ◽  
pp. 797-802 ◽  
Author(s):  
Yang He ◽  
An Chun Cheng ◽  
Ming Shu Wang ◽  
De Kang Zhu ◽  
Xiao Jia Wang ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Phylogenetic Tree ◽  
Sequence Alignment ◽  
Homology Search ◽  
Rare Codon ◽  
Composition Analysis ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Riemerella Anatipestifer ◽  
The Impact

Objective: The aim was to analyze Riemerella anatipestifer (RA) Cas1 gene and acquire more useful information for guiding the further study of the gene. Methods: Using bioinformatics method, sequence analysis of RA Cas1 gene was carried out with some databases and software. Results: Composition analysis of RA Cas1 gene, and homology search, sequence alignment, phylogenetic tree analysis and physicochemical property analysis of RA Cas1 protein were performed. Homology search revealed that Cas1 protein sequence of R. anatipestifer showed high similarity to those of strains within the Genus Capnocytophaga and Chryseobacterium, in accordance with the result of multiple sequence alignment and phylogenetic tree analysis. The rare codon analysis showed that there was little rare codon string in RA Cas1 gene. Conclusion: Cas1 gene of R. anatipestifer was evolutionally closely related to those of the Genus Capnocytophaga and Chryseobacterium, and can be over-expressed in E.coli without considering the impact of rare codons on translation.

scholarly journals TLR6 Gene Polymorphism, Sequence Analysis, and Phylogenetic Tree in Susscrofa

2017 ◽  
Vol 12 (4) ◽  
Author(s):  
Nandani Kumari ◽  
L. B. Singh
Keyword(s):  
Sequence Analysis ◽  
Gene Polymorphism ◽  
Phylogenetic Tree ◽  
Gene Evolution ◽  
Toll Like Receptors ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Evolutionary Pattern ◽  
Polymorphic Pattern ◽  
Polymorphic Analysis

TLRs (Toll like receptors) gene have a very important role in early defense against invading pathogens, still we do not have sufficient literature available about them specially TLR6 gene in swine. The current study deals with the characteristic polymorphic, sequencing and evolutionary pattern of TLR6 gene in swine. SSCP based amplification and polymorphic pattern of TLR6 gene, with the eight primers showed different polymorphism. Further, the evolutionary pattern of TLR6 gene was studied through phylogenetic tree analysis. Conclusively, the current comparative phylogenetic and polymorphic analysis of vertebrate TLR6 gene in swine provided informative insights into the process of gene evolution.

scholarly journals Analysis and Sequence Alignment of Peste des Petits Ruminants Virus ChinaSX2020

2021 ◽  
Vol 8 (11) ◽  
pp. 285
Author(s):  
Lingxia Li ◽  
Jinyan Wu ◽  
Xiaoan Cao ◽  
Jijun He ◽  
Xiangtao Liu ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Sequence Alignment ◽  
Specific Antibody ◽  
Immunofluorescence Assay ◽  
Peste Des Petits Ruminants ◽  
Genome Length ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
A Genome ◽  
Lineage Iv

The peste des petits ruminants virus (PPRV) mainly infects goats and sheep and causes a highly contagious disease, PPR. Recently, a PPRV strain named ChinaSX2020 was isolated and confirmed following an indirect immunofluorescence assay and PCR using PPRV-specific antibody and primers, respectively. A sequencing of the ChinaSX2020 strain showed a genome length of 15,954 nucleotides. A phylogenetic tree analysis showed that the ChinaSX2020 genome was classified into lineage IV of the PRRV genotypes. The genome of the ChinaSX2020 strain was found to be closely related to PPRVs isolated in China between 2013 and 2014. These findings revealed that not a variety of PRRVs but similar PPRVs were continuously spreading and causing sporadic outbreaks in China.

scholarly journals Phylogenetic Analysis of Kobuvirus and Astrovirus From Korean Wild Boars: 2016-2018

2021 ◽  
Author(s):  
Jihye Shin ◽  
SeEun Choe ◽  
Bang-Hun Hyun ◽  
Dong-Jun An
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Porcine Kobuvirus ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Wild Boars ◽  
Porcine Astrovirus ◽  
The One

Abstract The prevalence of porcine kobuvirus (PKoV) and porcine astrovirus (PAstV) in 845 Korean wild boars (KWB) during 2016-2018 were 28.0% and 10.6%, respectively, and co-infection of two viruses showed 5.1%. Phylogenetic tree analysis also revealed that 236 PKoVs from KWB were divided to diverse lineages within Aichivirus C group but the one strain (WKoV16CN-8627) was included the same cluster with bovine kobuvirus (Achivirus B). Eighty-nine PAstVs from KWB was belonged predominantly to lineage PAstV4 and only one strain (WAst17JN-10931) included novel to lineage PAstV2. Two viruses are epidemic more in young (≤ 12 months) than in old pigs (> 12 months).

scholarly journals Multiple Sequence Alignment Reveals Diversity among Eight African Bush Mango (Irvingia gabonensis Aubry-Lecomte ex O’Rorke) Cultivars

2021 ◽  
pp. 91-96
Author(s):  
U. G. Adebo ◽  
J. O. Matthew
Keyword(s):  
Sequence Analysis ◽  
Phylogenetic Tree ◽  
Genetic Resources ◽  
Data Base ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Multiple Sequence ◽  
Bush Mango ◽  
Irvingia Gabonensis ◽  
Cluster 2

Multiple sequence analysis is one of the most widely used model in estimating similarity among genotypes. In a bid to access useful information for the utilization of bush mango genetic resources, nucleotide sequences of eight bush mango (Irvingia gabonensis) cultivars were sourced for and retrieved form NCBI data base, and evaluated for diversity and similarity using computational biology approach. The highest alignment score (26.18), depicting the highest similarity, was between two pairs of sequence combinations; BM07:BM58 and BM12:BM69 respectively, while the least score (19.43) was between BM01: BM13. The phylogenetic tree broadly divided the cultivars into four distinct groups; BM07, BM58 (cluster one), BM01 (cluster 2), BM15, BM13 and BM35 (cluster 3), and BM12, BM69 (cluster 4), while the sequences obtained from the analysis revealed only few fully conserved regions, with the single nucleotides A, and T, which were consistent throughout the evolution. Results obtained from this study indicate that the bush mango cultivars are divergent and can be useful genetic resources for bush mango improvement through breeding.

scholarly journals Orthology prediction at scalable resolution by phylogenetic tree analysis

2007 ◽  
Vol 8 (1) ◽  
pp. 83 ◽  
Author(s):  
René TJM van der Heijden ◽  
Berend Snel ◽  
Vera van Noort ◽  
Martijn A Huynen
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Orthology Prediction

scholarly journals Phylogenetic Tree Analysis of the Cold-Hot Nature of Traditional Chinese Marine Medicine for Possible Anticancer Activity

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Xianjun Fu ◽  
Xuxia Song ◽  
Xuebo Li ◽  
Kah Keng Wong ◽  
Jiaoyang Li ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Anticancer Activity ◽  
Anticancer Drugs ◽  
Association Rules ◽  
Marine Organisms ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Genus 2 ◽  
Cluster Pattern ◽  
Chinese Marine

Traditional Chinese Marine Medicine (TCMM) represents one of the medicinal resources for research and development of novel anticancer drugs. In this study, to investigate the presence of anticancer activity (AA) displayed by cold or hot nature of TCMM, we analyzed the association relationship and the distribution regularity of TCMMs with different nature (613 TCMMs originated from 1,091 species of marine organisms) via association rules mining and phylogenetic tree analysis. The screened association rules were collected from three taxonomy groups: (1) Bacteria superkingdom, Phaeophyceae class, Fucales order, Sargassaceae family, andSargassumgenus; (2) Viridiplantae kingdom, Streptophyta phylum, Malpighiales class, and Rhizophoraceae family; (3) Holothuroidea class, Aspidochirotida order, andHolothuriagenus. Our analyses showed that TCMMs with closer taxonomic relationship were more likely to possess anticancer bioactivity. We found that the cluster pattern of marine organisms with reported AA tended to cluster with cold nature TCMMs. Moreover, TCMMs with salty-cold nature demonstrated properties for softening hard mass and removing stasis to treat cancers, and species within Metazoa or Viridiplantae kingdom of cold nature were more likely to contain AA properties. We propose that TCMMs from these marine groups may enable focused bioprospecting for discovery of novel anticancer drugs derived from marine bioresources.

scholarly journals Prevalence of Human Norovirus by Genotype in Contaminated Groundwater in Korea Over the Last Decade (2007-2016)

2017 ◽  
Author(s):  
Siwon Lee ◽  
Sang-Jung Park ◽  
Ji-Hye Kim ◽  
Wonseok Lee ◽  
Hyen-Mi Chung
Keyword(s):  
Phylogenetic Tree ◽  
Republic Of Korea ◽  
Contaminated Groundwater ◽  
Human Norovirus ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Groundwater Samples ◽  
Reference Sequences ◽  
Groundwater Wells

This study investigated the presence of human Norovirus (HuNoV) by genotype in 1,486 groundwater samples, collected from 843 groundwater wells suspected of contamination during 2007-2016, in Republic of Korea. We identified and genotyped 186 HuNoV sequences in 178 HuNoV-positive samples using the RIVM-NoroNet norovirus genotyping tool (NGT) and phylogenetic tree analysis based on RIVM-NoroNet reference sequences. HuNoV GII was more prevalent than GI. The major genotypes detected were HuNoV GII.4 (43.0%), GII.22 (15.6%), GI.5 (10.2%) and GI.1 (8.6%); 14 genotypes accounted for < 5.0%. Increasing HuNoV GII.17 has displayed a worldwide trend, including in Europe and Asia since 2010, and it was the dominant HuNoV genotype during 2013-2014 in Korea. However, HuNoV GII.4 was the major genotype detected in groundwater in Korea in 2015-2016, and it is becoming increasingly prevalent similar to HuNoV GII.17.

scholarly journals Molecular identification and genotyping of Atopobium vaginae, 16s rRNA gene from Bacterial Vaginosis miscarriage women in AL-Hillah city

2013 ◽  
Vol 11 (01) ◽  
pp. 74-82
Author(s):  
Ilham A. Bunyan ◽  
Asmaa K. Gatea ◽  
Alaa K. Hameed
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Tree ◽  
Rrna Gene ◽  
City Hospital ◽  
Phylogenetic Tree Analysis ◽  
Tree Analysis ◽  
Columbia Blood Agar ◽  
The 16S Rrna Gene ◽  
Atopobium Vaginae

This study was aimed to determine the Atopobium vaginae associated BV in vaginosis women and women with miscarriage. Also other aim, the DNA sequencing was performed for phylogenetic tree analysis of 16SrRNA gene in local Atopobium vaginae isolates in comparison with NCBI-Genbank global Atopobium vaginae isolates and finally submission of the present isolates in NCBI-Genbank database. One hundred fifty (150) high vaginal swabs were collected from women with vaginosis(Seventy five samples were taken from married vaginosis women without miscarriage and Seventy five samples from vaginosis women with miscarriage) from Babylon city hospital and private clinics. The age of patient (15– 45) years. The sample was collected by disposable swabs, genomic DNA was extracted from these swabs. 16s rRNA gene detection by polymerase chain reaction technique . Atopobium vaginae was isolated on Columbia blood agar supplemented with antibiotic for the first time in Iraq, the study confirmed that 9 (12.00%) and 5(6.66%) of Atopobium vaginae out of 150 swabs isolated from miscarriage and non-miscarriage vaginosis women respectively. According to the detection of the 16S rRNA gene, the study revealed that 69(92.00%)and 47(62.66%)of Atopobium vaginae out of 150 swabs obtained from miscarriage and non-miscarriage vaginosis women respectively. BLAST analysis showed that the 16S rRNA gene shared more than 98- 99% sequence compatibility with the sequences of Atopobium vaginae. Furthermore, the phylogenetic tree analysis of the 16S rRNA gene indicated that local Atopobium vaginae (NO.1 and NO. 2 ) isolates shared higher homology with other Atopobium vaginae isolates available in the GenBank. The homology of the nucleotides was between (99.17% and 98.75%) respectively.

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