scholarly journals Molecular Characteristics of Carnivore protoparvovirus 1 with High Sequence Similarity between Wild and Domestic Carnivores in Taiwan

Pathogens ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 671
Author(s):  
Ai-Mei Chang ◽  
Chen-Chih Chen
Keyword(s):  
Gastrointestinal Disease ◽  
Sequence Similarity ◽  
Domestic Dogs ◽  
Molecular Characteristics ◽  
Gene Sequences ◽  
High Sequence Similarity ◽  
Vp2 Gene ◽  
Pcr Screening ◽  
Wild Carnivores ◽  
Domestic Carnivores

Carnivore protoparvovirus 1 (CPPV-1) is a DNA virus causing gastrointestinal disease and immunosuppression in various terrestrial carnivores. Domestic dogs and cats are considered the primary CPPV-1 reservoirs. The habitat overlap of wild carnivores and free-roaming dogs increases the threat of CPPV-1 transmission between them. This study explored the CPPV-1 distribution among wild carnivores in Taiwan through PCR screening and compared the partial capsid protein (VP2) gene sequences from wild and domestic carnivores. In total, 181 samples were collected from 32 masked palm civets (Paguma larvata), 63 Chinese ferret badgers (Melogale moschata), and 86 crab-eating mongooses (Herpestes urva), from 2015 to 2019 were screened for CPPV-1. The average prevalence of CPPV-1 was 17.7% (32/181), with the highest prevalence in masked palm civets (37.5%). In addition, a masked palm civet was coinfected with two CPPV-1 strains. Among the 33 partial VP2 gene sequences, 23 were identical to the sequences amplified from domestic dogs and cats in Asia, and the remaining 10 were identified for the first time. This study supported the circulation of CPPV-1 strains with the same genomic features as domestic carnivores that are also in wild carnivores from the same environment in Taiwan by molecular data. Therefore, further population control and health management of free-roaming domestic carnivores are recommended.

scholarly journals Molecular Characteristics of Carnivore Protoparvovirus 1 With High Sequence Similarity Between Wild and Domestic Carnivores in Taiwan

2021 ◽  
Author(s):  
Ai-Mei Chang ◽  
Chen-Chih Chen
Keyword(s):  
Dna Sequences ◽  
Gastrointestinal Disease ◽  
Sequence Similarity ◽  
Domestic Dogs ◽  
Molecular Characteristics ◽  
High Sequence Similarity ◽  
Vp2 Gene ◽  
Pcr Screening ◽  
Wild Carnivores ◽  
Domestic Carnivores

Carnivore protoparvovirus 1 (CPPV-1) is a DNA virus causing gastrointestinal disease and immunosuppression in various terrestrial carnivores. Domestic dogs and cats are considered the primary CPPV-1 reservoirs. The habitat overlaps of wild carnivores and free-roaming dogs increases the threat of CPPV-1 transmission between them. This study explored the CPPV-1 distribution among wild carnivores through PCR screening and compared the DNA sequences of the partial capsid protein (VP2) between wild and domestic carnivores. In total, 181 samples were screened for the CPPV-1 VP2 gene, including 32 masked palm civets (Paguma larvata), 63 Chinese ferret badgers (Melogale moschata), and 86 crab-eating mongooses (Herpestes urva), from 2015 to 2019 in Taiwan. The average prevalence of CPPV-1 was 17.7% (32/181), with the highest prevalence in masked palm civets (37.5%). In addition, a masked palm civet was coinfected with two CPPV-1 strains. Among the 33 partial VP2 gene sequences, 23 were identical to sequences amplified from domestic dogs and cats in Asia and the remaining 10 were identified for the first time. This study demonstrated that CPPV-1 has circulated between domestic and wild carnivores in rural Taiwan. Therefore, further population control and health management of free-roaming domestic carnivores are recommended.

scholarly journals Cloning, Biochemical Properties, and Distribution of Mycobacterial Haloalkane Dehalogenases

2005 ◽  
Vol 71 (11) ◽  
pp. 6736-6745 ◽  
Author(s):  
Andrea Jesenská ◽  
Martina Pavlová ◽  
Michal Strouhal ◽  
Radka Chaloupková ◽  
Iva Těšínská ◽  
...  
Keyword(s):  
Halogen Bond ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Maximal Activity ◽  
Biochemical Properties ◽  
Open Reading Frames ◽  
Haloalkane Dehalogenase ◽  
Ph Optimum ◽  
High Sequence Similarity ◽  
Pcr Screening

ABSTRACT Haloalkane dehalogenases are enzymes that catalyze the cleavage of the carbon-halogen bond by a hydrolytic mechanism. Genomes of Mycobacterium tuberculosis and M. bovis contain at least two open reading frames coding for the polypeptides showing a high sequence similarity with biochemically characterized haloalkane dehalogenases. We describe here the cloning of the haloalkane dehalogenase genes dmbA and dmbB from M. bovis 5033/66 and demonstrate the dehalogenase activity of their translation products. Both of these genes are widely distributed among species of the M. tuberculosis complex, including M. bovis, M. bovis BCG, M. africanum, M. caprae, M. microti, and M. pinnipedii, as shown by the PCR screening of 48 isolates from various hosts. DmbA and DmbB proteins were heterologously expressed in Escherichia coli and purified to homogeneity. The DmbB protein had to be expressed in a fusion with thioredoxin to obtain a soluble protein sample. The temperature optimum of DmbA and DmbB proteins determined with 1,2-dibromoethane is 45°C. The melting temperature assessed by circular dichroism spectroscopy of DmbA is 47°C and DmbB is 57°C. The pH optimum of DmbA depends on composition of a buffer with maximal activity at 9.0. DmbB had a single pH optimum at pH 6.5. Mycobacteria are currently the only genus known to carry more than one haloalkane dehalogenase gene, although putative haloalkane dehalogenases can be inferred in more then 20 different bacterial species by comparative genomics. The evolution and distribution of haloalkane dehalogenases among mycobacteria is discussed.

scholarly journals Halobiforma lacisalsi sp. nov., isolated from a salt lake in China

2005 ◽  
Vol 55 (5) ◽  
pp. 1949-1952 ◽  
Author(s):  
Xue-Wei Xu ◽  
Min Wu ◽  
Pei-Jin Zhou ◽  
Shuang-Jiang Liu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Salt Lake ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
High Sequence Similarity ◽  
Derivatives Of ◽  
The 16S Rrna Gene

A Gram-negative, motile, neutrophilic and extremely halophilic strain, AJ5T, was isolated from a salt lake in Xinjiang, China, and subjected to polyphasic taxonomic study. The major polar lipids of the isolate were C20C20 and C20C25 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and glycolipid. The DNA G+C content was 64·9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain AJ5T clustered with members of the genus Halobiforma, exhibiting high sequence similarity to the 16S rRNA gene sequences of Halobiforma nitratireducens (96·3 %) and Halobiforma haloterrestris (99·0 %). Comparative analysis of phenotypic characteristics and DNA–DNA hybridization between strain AJ5T and Halobiforma species supported the conclusion that AJ5T represents a novel species within this genus, for which the name Halobiforma lacisalsi sp. nov. is proposed. The type strain is AJ5T (=CGMCC 1.3738T=JCM 12983T).

scholarly journals Phylogenetic analyses and genomic variation of the 2019-nCoV

2020 ◽  
Vol 2 (1) ◽  
pp. 126-130
Author(s):  
Faiz Ul Haq ◽  
◽  
Sidrah Saleem ◽  
Muhammad Imran ◽  
Ayesha Ghazal ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Genomic Variation ◽  
Molecular Characteristics ◽  
Phylogenetic Tree Analysis ◽  
High Sequence Similarity ◽  
Human Environment ◽  
Bat Coronavirus

There is a rising global concern about the SARS CoV-2 as a public health threat. Complete genome sequence have been released by the worldwide scientific community for understanding the molecular characteristics and evolutionary origin of this virus. Aim of the current context is to present phylogenetic relationship and genomic variation of 2019-nCoV. Based on availability of genomic information, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Middle East respiratory syndrome, severe acute respiratory syndrome and Bat coronavirus. The phylogenetic tree analysis suggested that SARS CoV-2 significantly clustered with bat SARS like coronavirus genome, however structural analysis revealed mutation in Spike Glycoprotein and nucleocapsid protein. However our phylogenetic and genomic analysis suggests that bats can be the reservoir for this virus. Lack of forest might be the fact in association of bats with human environment. It is also difficult to study on bats due to absence of proper reagent and availability of few species for research. We confirm high sequence similarity (>99%) among sequenced SARS CoV-2 genomes, and 96% genome identity with the bat coronavirus, confirming the notion of a zoonotic origin of SARS CoV-2.

scholarly journals Citricoccus zhacaiensis sp. nov., isolated from a bioreactor for saline wastewater treatment

2010 ◽  
Vol 60 (3) ◽  
pp. 495-499 ◽  
Author(s):  
Fan-Xu Meng ◽  
Xiao-Chen Yang ◽  
Pei-Song Yu ◽  
Jian-Ming Pan ◽  
Chun-Sheng Wang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
High Sequence Similarity ◽  
Nacl Concentration ◽  
Unknown Lipid ◽  
Citricoccus Zhacaiensis

A Gram-positive, neutrophilic, non-motile and non-spore-forming actinobacterium, strain FS24T, was isolated from a bioreactor treating salt-containing wastewater. This isolate grew in the presence of 0–15 % (w/v) NaCl and at 10-37 °C. The optimum NaCl concentration for growth of FS24T was 5 % (w/v) at 37 °C or 1 % (w/v) at 25 °C. Chemotaxonomic analysis revealed MK-9(H2) as the predominant menaquinone and the major cellular polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, four unknown glycolipids, two unknown phospholipids and an unknown lipid. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The genomic DNA G+C content was 66.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FS24T clustered with members of the genus Citricoccus, exhibiting high sequence similarity to the 16S rRNA gene sequences of the type strains of Citricoccus alkalitolerans (98.9 %) and Citricoccus muralis (98.8 %), respectively. The DNA–DNA relatedness values of strain FS24T to C. alkalitolerans DSM 15665T and C. muralis DSM 14442T were 54 and 39 %, respectively. On the basis of phenotypic and genotypic data, strain FS24T represents a novel species of the genus Citricoccus, for which the name Citricoccus zhacaiensis sp. nov. is proposed. The type strain is FS24T (=CGMCC 1.7064T =JCM 15136T).

scholarly journals Pseudomonas deceptionensis sp. nov., a psychrotolerant bacterium from the Antarctic

2011 ◽  
Vol 61 (10) ◽  
pp. 2401-2405 ◽  
Author(s):  
Ornella Carrión ◽  
David Miñana-Galbis ◽  
Ma Jesús Montes ◽  
Elena Mercadé
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
South Shetland Islands ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Gene Sequences ◽  
High Sequence Similarity ◽  
The Antarctic ◽  
Type Strains

During the taxonomic investigation of cold-adapted bacteria from samples collected in the Antarctic area of the South Shetland Islands, one Gram-reaction-negative, psychrotolerant, aerobic bacterium, designated strain M1T, was isolated from marine sediment collected on Deception Island. The organism was rod-shaped, catalase- and oxidase-positive and motile by means of a polar flagellum. This psychrotolerant strain grew at temperatures ranging from −4 °C to 34 °C. Phylogenetic studies based on 16S rRNA gene sequences confirmed that Antarctic isolate M1T was a member of the genus Pseudomonas and was located in the Pseudomonas fragi cluster. 16S rRNA gene sequence similarity values were >98 % between 13 type strains belonging to the Pseudomonas fluorescens lineage. However, phylogenetic analysis of rpoD gene sequences showed that strain M1T exhibited high sequence similarity only with respect to Pseudomonas psycrophila (97.42 %) and P. fragi (96.40 %) and DNA–DNA hybridization experiments between the Antarctic isolate M1T and the type strains of these two closely related species revealed relatedness values of 58 and 57 %, respectively. Several phenotypic characteristics, together with the results of polar lipid and cellular fatty acid analyses, were used to differentiate strain M1T from related pseudomonads. Based on the evidence of this polyphasic taxonomic study, strain M1T represents a novel species, for which the name Pseudomonas deceptionensis sp. nov. is proposed. The type strain is M1T ( = LMG 25555T  = CECT 7677T).

scholarly journals Genomic variance of the 2019-nCoV coronavirus

2020 ◽  
Author(s):  
Carmine Ceraolo ◽  
Federico M. Giorgi
Keyword(s):  
Scientific Community ◽  
Sequence Similarity ◽  
Molecular Characteristics ◽  
Genomic Information ◽  
High Sequence Similarity ◽  
Sequence Identity ◽  
Genomic Variance ◽  
Global Concern ◽  
Novel Coronavirus ◽  
Bat Coronavirus

AbstractThere is rising global concern for the recently emerged novel Coronavirus (2019-nCov). Full genomic sequences have been released by the worldwide scientific community in the last few weeks in order to understand the evolutionary origin and molecular characteristics of this virus. Taking advantage of all the genomic information currently available, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Bat coronavirus (BCoV) and SARS. We confirm high sequence similarity (>99%) between all sequenced 2019-nCoVs genomes available, with the closest BCoV sequence sharing 96.2% sequence identity, confirming the notion of a zoonotic origin of 2019-nCoV. Despite the low heterogeneity of the 2019-nCoV genomes, we could identify at least two hyper-variable genomic hotspots, one of which is responsible for a Serine/Leucine variation in the viral ORF8-encoded protein. Finally, we perform a full proteomic comparison with other coronaviridae, identifying key aminoacidic differences to be considered for antiviral strategies deriving from previous anti-coronavirus approaches.

Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Middle Lamella ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Citrus Peel ◽  
Human Faeces ◽  
The Family

© 2017 IUMS. A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7% sequence similarity). Strain 14T shared ~99% sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6μm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).

scholarly journals Efficient CRISPR/Cas9 mediated Pooled-sgRNAs assembly accelerates targeting multiple genes related to male sterility in cotton

Plant Methods ◽  
2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Mohamed Ramadan ◽  
Muna Alariqi ◽  
Yizan Ma ◽  
Yanlong Li ◽  
Zhenping Liu ◽  
...  
Keyword(s):  
Genetic Transformation ◽  
Sequence Similarity ◽  
High Specificity ◽  
Transformation Method ◽  
High Sequence Similarity ◽  
Single Experiment ◽  
Next Generation Sequencing Technology ◽  
Cotton Transformation ◽  
Assembly Method ◽  
Multiple Genes

Abstract Background Upland cotton (Gossypium hirsutum), harboring a complex allotetraploid genome, consists of A and D sub-genomes. Every gene has multiple copies with high sequence similarity that makes genetic, genomic and functional analyses extremely challenging. The recent accessibility of CRISPR/Cas9 tool provides the ability to modify targeted locus efficiently in various complicated plant genomes. However, current cotton transformation method targeting one gene requires a complicated, long and laborious regeneration process. Hence, optimizing strategy that targeting multiple genes is of great value in cotton functional genomics and genetic engineering. Results To target multiple genes in a single experiment, 112 plant development-related genes were knocked out via optimized CRISPR/Cas9 system. We optimized the key steps of pooled sgRNAs assembly method by which 116 sgRNAs pooled together into 4 groups (each group consisted of 29 sgRNAs). Each group of sgRNAs was compiled in one PCR reaction which subsequently went through one round of vector construction, transformation, sgRNAs identification and also one round of genetic transformation. Through the genetic transformation mediated Agrobacterium, we successfully generated more than 800 plants. For mutants identification, Next Generation Sequencing technology has been used and results showed that all generated plants were positive and all targeted genes were covered. Interestingly, among all the transgenic plants, 85% harbored a single sgRNA insertion, 9% two insertions, 3% three different sgRNAs insertions, 2.5% mutated sgRNAs. These plants with different targeted sgRNAs exhibited numerous combinations of phenotypes in plant flowering tissues. Conclusion All targeted genes were successfully edited with high specificity. Our pooled sgRNAs assembly offers a simple, fast and efficient method/strategy to target multiple genes in one time and surely accelerated the study of genes function in cotton.

scholarly journals Evolution of Chi motifs in Proteobacteria

2021 ◽  
Author(s):  
Angélique Buton ◽  
Louis-Marie Bobay
Keyword(s):  
Sequence Similarity ◽  
Bacterial Species ◽  
Double Strand Breaks ◽  
Dna Double Strand Breaks ◽  
Large Dataset ◽  
High Sequence Similarity ◽  
Strand Breaks ◽  
E Coli ◽  
Dna Motif ◽  
And Staphylococcus Aureus

Abstract Homologous recombination is a key pathway found in nearly all bacterial taxa. The recombination complex allows bacteria to repair DNA double strand breaks but also promotes adaption through the exchange of DNA between cells. In Proteobacteria, this process is mediated by the RecBCD complex, which relies on the recognition of a DNA motif named Chi to initiate recombination. The Chi motif has been characterized in Escherichia coli and analogous sequences have been found in several other species from diverse families, suggesting that this mode of action is widespread across bacteria. However, the sequences of Chi-like motifs are known for only five bacterial species: E. coli, Haemophilus influenzae, Bacillus subtilis, Lactococcus lactis and Staphylococcus aureus. In this study we detected putative Chi motifs in a large dataset of Proteobacteria and we identified four additional motifs sharing high sequence similarity and similar properties to the Chi motif of E. coli in 85 species of Proteobacteria. Most Chi motifs were detected in Enterobacteriaceae and this motif appears well conserved in this family. However, we did not detect Chi motifs for the majority of Proteobacteria, suggesting that different motifs are used in these species. Altogether these results substantially expand our knowledge on the evolution of Chi motifs and on the recombination process in bacteria.

Sign in / Sign up

Export Citation Format

Share Document