scholarly journals Phylogenetic characterization of Isospora jaracimrmani oocysts from a veiled chameleon (family Chamaeleonidae; Chamaeleo calyptratus) reared at a zoo in Ishikawa, Japan

2021 ◽  
Author(s):  
Fitrine EKAWASTI ◽  
Kazuya KITAGAWA ◽  
Hiroshi DOMAE ◽  
April Hari WARDHANA ◽  
Junki NAGASAWA ◽  
...  
Keyword(s):  
Phylogenetic Characterization ◽  
Chamaeleo Calyptratus

DETECTION AND PHYLOGENETIC CHARACTERIZATION OF HEPATITIS E VIRUS GENOTYPE 3 IN A CAPTIVE WILD BOAR IN THAILAND

2012 ◽  
Vol 43 (3) ◽  
pp. 640-644 ◽  
Author(s):  
Anuwat Wiratsudakul ◽  
Ladawan Sariya ◽  
Phirom Prompiram ◽  
Siriporn Tantawet ◽  
Duangkhamol Suraruangchai ◽  
...  
Keyword(s):  
Wild Boar ◽  
Hepatitis E Virus ◽  
Hepatitis E ◽  
Genotype 3 ◽  
Virus Genotype ◽  
Phylogenetic Characterization

Sequencing and phylogenetic characterization of a novel RNA virus in Arma chinensis

2021 ◽  
Vol 65 (03) ◽  
pp. 320-323
Author(s):  
Yonghao Dong ◽  
Pengjun Xu ◽  
Guangwei Ren ◽  
Changchun Feng ◽  
Dongyang Liu ◽  
...  
Keyword(s):  
Rna Virus ◽  
Phylogenetic Characterization

scholarly journals Las degradation in a fluidized bed reactor and phylogenetic characterization of the biofilm

2013 ◽  
Vol 30 (3) ◽  
pp. 521-529 ◽  
Author(s):  
L. L. Oliveira ◽  
R. B. Costa ◽  
I. K. Sakamoto ◽  
I. C. S. Duarte ◽  
E. L. Silva ◽  
...  
Keyword(s):  
Fluidized Bed ◽  
Fluidized Bed Reactor ◽  
Phylogenetic Characterization

scholarly journals Molecular epidemiology of blaCTX-M gene-producing uropathogenic Escherichia coli among Iranian kidney transplant patients: clonal dissemination of CC131 and CC10

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Mehrdad Halaji ◽  
Shahrzad Shahidi ◽  
Behrooz Ataei ◽  
Abdolamir Atapour ◽  
Awat Feizi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Kidney Transplant ◽  
Phylogenetic Group ◽  
Control Group ◽  
M Gene ◽  
Mlst Analysis ◽  
Phylogenetic Characterization ◽  
Transplant Patients ◽  
Kidney Transplant Patients

Abstract Background This study aimed to investigate the phylogenetic characterization and virulence traits of uropathogenic Escherichia coli (UPEC) isolated from kidney transplant patients (KTPs) as well as non-KTPs and analyze the clonal distribution of Extended spectrum β-lactamases (ESBLs)-producing UPEC containing blaCTX-M gene. Methods To this end, we determined virulence marker and the phylogenetic characterization of UPEC in non-KTPs (n = 65) and KTPs (n = 46). The non-KTPs were considered the control group of the study. Also, according to the Achtman scheme, we performed multilocus sequence typing to assess the relationship between twenty-nine of ESBL-producing isolates containing blaCTX-M gene. Results According to the results of PCR assay, the prevalence of virulence factor genes ranged from 0% (cnf and papG III) to 93.7% (fimH). Also, KTP isolates significantly differed from non-KTP isolates only in terms of the prevalence of pap GI elements. Moreover, the most frequent UPEC isolates were in phylogenetic group B2, followed by group D (18.9%), and group A (13.5%). Furthermore, except for phylogenetic group C, there was no significant correlation between phylogenetic distribution in KTPs and non-KTPs. Additionally, MLST analysis of blaCTX-M carrying isolates identified 18 unique sequence types (ST) the most common of which was ST131 (24.1%), followed by ST1193 (10.3%), while fourteen STs were detected only once. Conclusions The results further revealed significant differences between the UPEC isolates from KTPs and non-KTPs regarding the phylogroups C and PAI gene. Based on MLST analysis, we also observed a relatively high diversity in UPEC isolates obtained from KTPs and non-KTPs. Moreover, clonal complex (CC) 131 and ST131 were found to be the most prevalent clones and ST types, respectively. Besides, for the first time, ST8503 were reported in KTPs. These results suggested regular studies on characterization of UPEC isolates among KTPs.

scholarly journals From raw reads to trees: Whole genome SNP phylogenetics across the tree of life

2015 ◽  
Author(s):  
Sanaa Afroz Ahmed ◽  
Chien-Chi Lo ◽  
Po-E Li ◽  
Karen W Davenport ◽  
Patrick S.G. Chain
Keyword(s):  
Ad Hoc ◽  
Phylogenetic Reconstruction ◽  
Clinical Samples ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Complex Samples ◽  
Phylogenetic Characterization ◽  
Genome Wide ◽  
Genome Assemblies

Next-generation sequencing is increasingly being used to examine closely related organisms. However, while genome-wide single nucleotide polymorphisms (SNPs) provide an excellent resource for phylogenetic reconstruction, to date evolutionary analyses have been performed using different ad hoc methods that are not often widely applicable across different projects. To facilitate the construction of robust phylogenies, we have developed a method for genome-wide identification/characterization of SNPs from sequencing reads and genome assemblies. Our phylogenetic and molecular evolutionary (PhaME) analysis software is unique in its ability to take reads and draft/complete genome(s) as input, derive core genome alignments, identify SNPs, construct phylogenies and perform evolutionary analyses. Several examples using genomes and read datasets for bacterial, eukaryotic and viral linages demonstrate the broad and robust functionality of PhaME. Furthermore, the ability to incorporate raw metagenomic reads from clinical samples with suspected infectious agents shows promise for the rapid phylogenetic characterization of pathogens within complex samples.

scholarly journals Trichoptera in Flanders (Belgium): An ecological and phylogenetic characterization of the order

Zoosymposia ◽  
2011 ◽  
Vol 5 (1) ◽  
pp. 108-114
Author(s):  
SOPHIE C. GOMBEER ◽  
DRIES KNAPEN ◽  
LIEVEN BERVOETS
Keyword(s):  
Poor Quality ◽  
Biotic Index ◽  
Specific Information ◽  
Phylogenetic Characterization ◽  
Present Distribution ◽  
Original Report ◽  
Populated Region ◽  
Environment Agency ◽  
The Relationship

Flanders is a very densely populated region in the economic heart of Europe. To monitor the anthropological impact on the biological integrity of the freshwater courses, the Flemish Environment Agency (VMM) uses the Multimetric Macroinvertebrate Index for Flanders (Gabriels et al. 2006) which was recently developed under the influence of the European Water Framework Directive (WFD, EU 2000). This multimetric tool replaces the Belgian Biotic Index (BBI: range 0=dramatically poor quality to 10=very good quality), a monitoring system based on the sensitivities to pollution of the different macroinvertebrate taxa (De Pauw & Vanhooren 1983, De Pauw et al. 1986). Although recently replaced, the BBI has been used for the past 20 years and this extensive monitoring campaign produced a considerable amount of information on the distribution of macroinvertebrate taxa in Flemish freshwater courses. The Trichoptera (caddisflies) constitute one of these taxa. Unfortunately, determinations of caddisflies as part of the BBI monitoring, are accomplished only at the family level. Specific information on the occurrence and ecological preferences at the species level is scarce and outdated. The only comprehensive report documenting the occurrence of Trichoptera in Belgium dates back to 1984 (Stroot 1984) and since then only minor revisions and additions to the original report have been published (Stroot 1985, 1987; Stroot & Neven 1989). Therefore, the objectives of our research are to update the old species records and to elaborate and improve the ecological and phylogenetic knowledge of the Flemish Trichoptera by (a) identifying the caddisfly species that occur in Flanders; (b) determining their present distribution; (c) detecting which environmental variables influence this distribution; (d) studying whether the relationship among these variables and the species assemblages can be used to distinguish among the ecoregions in Flanders, which are based on similarities in climate, geology, geomorphology, (geo)hydrology and soil characteristics (Sevenant et al. 2002) and (e) investigating the phylogenetic relationships among the Flemish Trichoptera and evaluating their accordance with the current taxonomic classification.

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