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

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.

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

Pathogens ◽

10.3390/pathogens10060671 ◽

2021 ◽

Vol 10 (6) ◽

pp. 671

Author(s):

Ai-Mei Chang ◽

Chen-Chih Chen

Keyword(s):

Gastrointestinal Disease ◽

Sequence Similarity ◽

Domestic Dogs ◽

Gene Sequences ◽

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.

Meiotic Recombination Between Paralogous RBCSB Genes on Sister Chromatids of Arabidopsis thaliana

Genetics ◽

10.1093/genetics/166.2.947 ◽

2004 ◽

Vol 166 (2) ◽

pp. 947-957 ◽

Cited By ~ 1

Author(s):

John G Jelesko ◽

Kristy Carter ◽

Whitney Thompson ◽

Yuki Kinoshita ◽

Wilhelm Gruissem

Keyword(s):

Gene Cluster ◽

Dna Sequences ◽

Meiotic Recombination ◽

Sequence Similarity ◽

Specific Gene ◽

Paralogous Genes ◽

Chimeric Genes ◽

Unequal Recombination ◽

Sister Chromatids

Abstract Paralogous genes organized as a gene cluster can rapidly evolve by recombination between misaligned paralogs during meiosis, leading to duplications, deletions, and novel chimeric genes. To model unequal recombination within a specific gene cluster, we utilized a synthetic RBCSB gene cluster to isolate recombinant chimeric genes resulting from meiotic recombination between paralogous genes on sister chromatids. Several F1 populations hemizygous for the synthRBCSB1 gene cluster gave rise to Luc+ F2 plants at frequencies ranging from 1 to 3 × 10-6. A nonuniform distribution of recombination resolution sites resulted in the biased formation of recombinant RBCS3B/1B::LUC genes with nonchimeric exons. The positioning of approximately half of the mapped resolution sites was effectively modeled by the fractional length of identical DNA sequences. In contrast, the other mapped resolution sites fit an alternative model in which recombination resolution was stimulated by an abrupt transition from a region of relatively high sequence similarity to a region of low sequence similarity. Thus, unequal recombination between paralogous RBCSB genes on sister chromatids created an allelic series of novel chimeric genes that effectively resulted in the diversification rather than the homogenization of the synthRBCSB1 gene cluster.

DNA sequences of RAPD fragments in artiodactyls

Genome ◽

10.1139/g96-057 ◽

1996 ◽

Vol 39 (2) ◽

pp. 456-458 ◽

Cited By ~ 1

Author(s):

Silja Kostia ◽

Jukka Palo ◽

Sirkka-Liisa Varvio

Keyword(s):

Dna Sequences ◽

Sequence Similarity ◽

Receptor Gene ◽

Chromosome 2 ◽

Microsatellite Repeats ◽

Rapd Profile ◽

Inositol 1,4,5 Trisphosphate ◽

Trisphosphate Receptor

A bovine RAPD profile, generated by a 10-mer primer, was analysed by sequencing the major fragments. Three of four different fragments showed homologies to previously characterized mammalian sequences. One was 61–66% identical to LINE sequences and another was 78.5% identical to a human chromosome 2 sequence tagged site. The third fragment was 93.1% identical to the human type 2 inositol 1,4,5-trisphosphate receptor gene. This fragment had counterparts in white-tailed deer and reindeer; fragments of slightly different size in these species showed high sequence similarity and the size differences were due to varying numbers of dinucleotide microsatellite repeats inside the fragment. Key words : RAPD, artiodactyls, sequence similarity, microsatellites, type 2 inositol 1,4,5-trisphosphate receptor.

Cloning, Biochemical Properties, and Distribution of Mycobacterial Haloalkane Dehalogenases

Applied and Environmental Microbiology ◽

10.1128/aem.71.11.6736-6745.2005 ◽

2005 ◽

Vol 71 (11) ◽

pp. 6736-6745 ◽

Cited By ~ 41

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 ◽

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.

Molecular identification ofAustrobilharziaspecies parasitizingCerithidea cingulata(Gastropoda: Potamididae) from Kuwait Bay

Journal of Helminthology ◽

10.1017/s0022149x11000733 ◽

2011 ◽

Vol 86 (4) ◽

pp. 470-478 ◽

Cited By ~ 5

Author(s):

W.Y. Al-Kandari ◽

S.A. Al-Bustan ◽

A.M. Isaac ◽

B.A. George ◽

B.S. Chandy

Keyword(s):

Dna Sequences ◽

Sequence Comparison ◽

Sequence Similarity ◽

Morphological Identification ◽

Data Set ◽

Kuwait Bay ◽

Causative Agents ◽

Avian Schistosomes ◽

Combined Data

AbstractAvian schistosomes belonging to the genusAustrobilharzia(Digenea: Schistosomatidae) are among the causative agents of cercarial dermatitis in humans. In this paper, ribosomal and mitochondrial DNA sequences were used to study schistosome cercariae from Kuwait Bay that have been identified morphologically asAustrobilharziasp. Sequence comparison of the ribosomal DNA (rDNA) 28S and 18S regions of the collected schistosome cercariae with corresponding sequences of other schistosomes in GenBank revealed high sequence similarity. This confirmed the morphological identification of schistosome cercariae from Kuwait Bay as belonging to the genusAustrobilharzia. The finding was further supported by the phylogenetic tree that was constructed based on the combined data set 18S-28S-mitochondrial cytochrome oxidase I (mtCO1) sequences in whichAustrobilharziasp. clustered withA. terrigalensisandA. variglandis. Sequence comparison of theAustrobilharziasp. from Kuwait Bay withA. variglandisandA. terrigalensisbased on mtCO1 showed a variation of 10% and 11%, respectively. Since the sequence variation in the mtCO1 was within the interspecific range among trematodes, it seems that theAustrobilharziaspecies from Kuwait Bay is different from the two species reported in GenBank,A.terrigalensisandA. variglandis.

Viral Hormones: Expanding Dimensions in Endocrinology

Endocrinology ◽

10.1210/en.2019-00271 ◽

2019 ◽

Vol 160 (9) ◽

pp. 2165-2179 ◽

Cited By ~ 7

Author(s):

Qian Huang ◽

C Ronald Kahn ◽

Emrah Altindis

Keyword(s):

Dna Sequences ◽

Sequence Similarity ◽

Endocrine System ◽

Peptide Hormones ◽

Rna Sequences ◽

In Vivo Models ◽

Viral Mimicry

AbstractViruses have developed different mechanisms to manipulate their hosts, including the process of viral mimicry in which viruses express important host proteins. Until recently, examples of viral mimicry were limited to mimics of growth factors and immunomodulatory proteins. Using a comprehensive bioinformatics approach, we have shown that viruses possess the DNA/RNA with potential to encode 16 different peptides with high sequence similarity to human peptide hormones and metabolically important regulatory proteins. We have characterized one of these families, the viral insulin/IGF-1–like peptides (VILPs), which we identified in four members of the Iridoviridae family. VILPs can bind to human insulin and IGF-1 receptors and stimulate classic postreceptor signaling pathways. Moreover, VILPs can stimulate glucose uptake in vitro and in vivo and stimulate DNA synthesis. DNA sequences of some VILP-carrying viruses have been identified in the human enteric virome. In addition to VILPs, sequences with homology to 15 other peptide hormones or cytokines can be identified in viral DNA/RNA sequences, some with a very high identity to hormones. Recent data by others has identified a peptide that resembles and mimics α-melanocyte-stimulating hormone’s anti-inflammatory effects in in vitro and in vivo models. Taken together, these studies reveal novel mechanisms of viral and bacterial pathogenesis in which the microbe can directly target or mimic the host endocrine system. These findings also introduce the concept of a system of microbial hormones that provides new insights into the evolution of peptide hormones, as well as potential new roles of microbial hormones in health and disease.

Phylogenetic analyses and genomic variation of the 2019-nCoV

Journal of Pharmaceutical and Biopharmaceutical Research ◽

10.25082/jpbr.2020.01.004 ◽

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 ◽

Phylogenetic Tree Analysis ◽

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.

Genomic variance of the 2019-nCoV coronavirus

10.1101/2020.02.02.931162 ◽

2020 ◽

Cited By ~ 12

Author(s):

Carmine Ceraolo ◽

Federico M. Giorgi

Keyword(s):

Scientific Community ◽

Sequence Similarity ◽

Genomic Information ◽

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.

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

Plant Methods ◽

10.1186/s13007-021-00712-x ◽

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 ◽

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.

Evolution of Chi motifs in Proteobacteria

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkaa054 ◽

2021 ◽

Author(s):

Angélique Buton ◽

Louis-Marie Bobay

Keyword(s):

Sequence Similarity ◽

Bacterial Species ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

Large Dataset ◽

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.