scholarly journals The characterization of two novel neotropical primate papillomaviruses supports the ancient within-species diversity model

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Mirela D’arc ◽  
Filipe R R Moreira ◽  
Cecilia A Dias ◽  
Antonizete R Souza ◽  
Héctor N Seuánez ◽  
...  
Keyword(s):  
Species Diversity ◽  
Open Reading Frames ◽  
Saimiri Sciureus ◽  
Base Pairs ◽  
Pathogenic Potential ◽  
Double Stranded Dna ◽  
Anal Swab ◽  
Icosahedral Viruses ◽  
Phylogenetic Identification ◽  
First Time

Abstract Papillomaviruses (PVs) are non-enveloped icosahedral viruses with a circular double-stranded DNA genome of ∼8,000 base pairs (bp). More than 200 different PV types have been identified to date in humans, which are distributed in five genera, with several strains associated with cancer development. Although widely distributed in vertebrates, Neotropical Primates (NP) PV infection was described for the first time only in 2016. Currently, four complete genomes of NP PVs have been characterized, three from Saimiri sciureus (SscPV1 to SscPV3) and one from Alouatta guariba (AgPV1). In this work, we describe two novel PV strains infecting Callithrix penicillata (provisionally named CpenPV1 and CpenPV2), using anal swab samples from animals residing at the Brasilia Primatology Center and next generation sequencing. The genomes of CpenPV1 (7,288 bp; 41.5% guanine-cytosine content - GC) and CpenPV2 (7,250 bp; 40.7% GC) contain the characteristic open reading frames (ORFs) for the early (E6, E7, E1, E2, and E4) and late (L2 and L1) PV genes. The L1 ORFs, commonly used for phylogenetic identification, share 76 per cent similarity with each other and differ 32 per cent from any other known PV, indicating that these new strains meet the criteria for defining novel species. PV genes phylogenetic variance was analyzed and different degrees of saturation revealed similar levels of topological heterogeneity, ruling out saturation as primary etiological factor for this phenomenon. Interestingly, the two CpenPV strains form a monophyletic clade within the Gammapapillomavirus genus (provisionally named gammapapillomavirus 32). Unlike for other NP PV strains, which grouped into a new sister genus of Alphapapillomavirus, this is the first report of NP PV strains grouping into a genus previously considered to exclusively comprise Old World Primates (OWP) PVs, including human PVs. These findings confirm the existence of a common ancestor for Gammapapillomavirus already infecting primates before the split of OWP and NP at ∼40 million years ago. Finally, our findings are consistent with an ancient within-species diversity model and emphasize the importance of increasing sampling to help understanding the PV-primate codivergence dynamics and pathogenic potential.

scholarly journals DIAGNOSTIC BACTERIOPHAGE V32 AS A TOOL FOR THE RAPID IDENTIFICATION OF ESCHERICHIA COLI SEROGROUP O157

2019 ◽  
Vol 64 (1) ◽  
pp. 57-64
Author(s):  
E. A. Svetoch ◽  
N. V. Volozhantsev ◽  
V. V. Verevkin ◽  
V. P. Myakinina ◽  
A. V. Aleshkin ◽  
...  
Keyword(s):  
High Specificity ◽  
Rapid Identification ◽  
Open Reading Frames ◽  
Farm Animals ◽  
Base Pairs ◽  
Special Equipment ◽  
Simple Method ◽  
E Coli ◽  
Double Stranded Dna ◽  
Myoviridae Family

Bacteriophage V32, a representative of bacterial viruses of the Myoviridae family Ounavirinae subfamily, is proposed for search and identification of E. coli O157 serogroup, including Shiga-toxin producing E. coli O157:H7 (STEC O157:H7), among cultures of enterobacteria from the primary seeding of the material studied. Phage genome containes a linear double-stranded DNA of 87875 base pairs with G/C-content of 38.9% and includes 132 open reading frames (ORF). In the genome, there are no determinants of antibiotic resistance, virulence genes of STEC and other well-known pathogroups of E. coli. It has been established that phage V32 has lytic activity against all studied cultures of E. coli O157 serogroup (n=183) isolated from people and farm animals in various regions of the Russian Federation, as well as in Japan and Italy. At the same time, the phage lyses only 6 of 182 strains (3.3%) of E. coli not belonging to the O157 serogroup and is not active against strains of other enterobacteria. That is, the phage has a high specificity. The use of bacteriophage V32 as a diagnostic tool is a highly efficient, fast, cheap and simple method for identifying E. coli serogroup O157, including the serotype E. coli O157: H7, in any bacteriological laboratory without special equipment and special training of performers.

scholarly journals Comparison of Enterococcus faecalis Biofilm Removal Efficiency among Bacteriophage PBEF129, Its Endolysin, and Cefotaxime

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 426
Author(s):  
Hyun Keun Oh ◽  
Yoon Jung Hwang ◽  
Hye-Won Hong ◽  
Heejoon Myung
Keyword(s):  
Enterococcus Faecalis ◽  
Gc Content ◽  
Bacterial Biofilm ◽  
Open Reading Frames ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Biofilm Removal ◽  
Query Coverage ◽  
Encoding Genes

Enterococcus faecalis is a Gram-positive pathogen which colonizes human intestinal surfaces, forming biofilms, and demonstrates a high resistance to many antibiotics. Especially, antibiotics are less effective for eradicating biofilms and better alternatives are needed. In this study, we have isolated and characterized a bacteriophage, PBEF129, infecting E. faecalis. PBEF129 infected a variety of strains of E. faecalis, including those exhibiting antibiotic resistance. Its genome is a linear double-stranded DNA, 144,230 base pairs in length. Its GC content is 35.9%. The closest genomic DNA sequence was found in Enterococcus phage vB_EfaM_Ef2.3, with a sequence identity of 99.06% over 95% query coverage. Furthermore, 75 open reading frames (ORFs) were functionally annotated and five tRNA-encoding genes were found. ORF 6 was annotated as a phage endolysin having an L-acetylmuramoyl-l-alanine amidase activity. We purified the enzyme as a recombinant protein and confirmed its enzymatic activity. The endolysin’s host range was observed to be wider than its parent phage PBEF129. When applied to bacterial biofilm on the surface of in vitro cultured human intestinal cells, it demonstrated a removal efficacy of the same degree as cefotaxime, but much lower than its parent bacteriophage.

scholarly journals Genomic Analysis of Lytic Phage V09 that Targets Pathogenic Vibrio Parahaemolyticus

2021 ◽  
Author(s):  
Peien Ni ◽  
Xiaoling Lei ◽  
Yujie Yin ◽  
Adelaide Almeida ◽  
Dapeng Wang
Keyword(s):  
Vibrio Parahaemolyticus ◽  
Pathogenic Bacteria ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Lytic Phage ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Pathogenic Vibrio ◽  
Foodborne Pathogenic Bacteria ◽  
Reading Frames

Abstract Phage therapy is a promising approach to control foodborne pathogenic bacteria. In this study, a lytic phage against Vibrio parahaemolyticus, designated Vibrio phage V09, was isolated from surface water in Shanghai, China and its genomic DNA was sequenced. The data demonstrated that phage V09 is a double-stranded DNA phage. Its genome consists of 243,881 base pairs (42.6% guanine-cytosine content) encoding 377 open reading frames and with 27 tRNAs detected. According to phylogenetic analysis, phage V09 can be considered a member of the subfamily Tevenvirinae and family Myoviridae.

Supplement to biota of agaricoid basidiomycetes of Oksky Biosphere Reserve

2008 ◽  
Vol 42 ◽  
pp. 123-129
Author(s):  
E. F. Malysheva ◽  
L. F. Volosnova
Keyword(s):  
Species Diversity ◽  
Biosphere Reserve ◽  
Botanical Institute ◽  
Komarov Botanical Institute ◽  
First Time

New data on species diversity of agaricoid fungi of Oksky Biosphere Reserve are given. The checklist of 41 species with indication of their localities and herbarium numbers (of the Herbarium of the Komarov Botanical Institute, LE) is provided. Three species (Conocybe gigasperma, Entoloma occultopigmentatum, E. scabiosum) are recorded for the first time in Russia.

scholarly journals Remarkable Species Diversity of the Leafhopper Genus Xestocephalus (Hemiptera: Cicadellidae: Aphrodinae) in Thailand

Insects ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 514
Author(s):  
Zonglei Liang ◽  
Christopher H. Dietrich ◽  
Wu Dai
Keyword(s):  
New Species ◽  
Species Diversity ◽  
Single Species ◽  
Comparative Morphology ◽  
Malaise Trap ◽  
Field Sampling ◽  
Tropical Regions ◽  
Trap Field ◽  
The World ◽  
First Time

Xestocephalus Van Duzee is among the most common and widespread genera of Cicadellidae in the temperate and tropical regions of the world. In the present study, 205 specimens of the genus Xestocephalus were collected in Thailand, whereas only a single species of the genus was recorded previously using Malaise trap field sampling, studied by comparative morphology. Seventeen species were recognized, including twelve new species: X. binarius sp. nov., X. chrysanthemum sp. nov., X. cowboyocreus sp. nov., X. densprint sp. nov., X. dimiprocessus sp. nov., X. exproiecturus sp. nov., X. gracilus sp. nov., X. limpidissimus sp. nov., X. malleus sp. nov., X. nonattribus sp. nov., X. recipinams sp. nov., and X. tenusis Liang sp. nov. Four species were recorded in Thailand for the first time: Xestocephalus abyssinicus Heller and Linnavuori, Xestocephalus asper Linnavuori, Xestocephalus ishidae Matsumura, and Xestocephalus toroensis Matsumura. Detailed morphological descriptions of all 17 species are given; photographs of external habitus and male genitalia of the species from Thailand are provided. A checklist of species of the genus is also given, and a key to all Thailand Xestocephalus species is also provided.

scholarly journals Temporal and Spatial Dynamics of Dark Septate Endophytes in the Roots of Lycium ruthenicum in the Desert Region of Northwest China

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 648
Author(s):  
Li Han ◽  
Jingxin Shi ◽  
Chao He ◽  
Xueli He
Keyword(s):  
Species Diversity ◽  
Spatial Dynamics ◽  
Northwest China ◽  
Dark Septate Endophytes ◽  
Desert Ecosystems ◽  
Lycium Ruthenicum ◽  
Different Seasons ◽  
Application Potential ◽  
First Time ◽  
Hydrolyzable Nitrogen

With the intensification of desertification in northwest China, drought has become a serious environmental problem restricting plant growth and ecological restoration. Recently, dark septate endophytes (DSEs) have attracted more attention because of their ability to improve plants’ resistance to drought. Here, we investigated DSE colonization and species diversity in roots of Lycium ruthenicum collected from Anxi and Minqin, in northwest China, during July, September, and December 2019. This study aimed to evaluate the influence of seasonality and sampling sites on DSEs. In different seasons, DSE colonization varied with the phenology of L. ruthenicum. At different sites, DSE colonization significantly differed. Four isolates were reported in desert ecosystems for the first time. The results showed microsclerotial colonization was directly affected by changing seasons, while hyphal colonization and species diversity were directly affected by sampling sites. The soil organic carbon, pH, alkaline phosphatase, and alkali-hydrolyzable nitrogen were the main predictors of DSE colonization and species diversity. We conclude that DSE colonization and diversity showed significant spatial–temporal heterogeneity and were closely related to soil factors. This research provides a basis for the further understanding of the ecological functions of DSEs and their application potential for vegetative restoration and agricultural cultivation in drylands.

scholarly journals Characterization of a Novel Thermobifida fusca Bacteriophage P318

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1042
Author(s):  
Cheepudom ◽  
Lin ◽  
Lee ◽  
Meng
Keyword(s):  
Plant Cell Wall ◽  
Hydrolytic Enzymes ◽  
Thermobifida Fusca ◽  
Genome Replication ◽  
Putative Orfs ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Virion Morphogenesis ◽  
Genome Information

Thermobifida fusca is of biotechnological interest due to its ability to produce an array of plant cell wall hydrolytic enzymes. Nonetheless, only one T. fusca bacteriophage with genome information has been reported to date. This study was aimed at discovering more relevant bacteriophages to expand the existing knowledge of phage diversity for this host species. With this end in view, a thermostable T. fusca bacteriophage P318, which belongs to the Siphoviridae family, was isolated and characterized. P318 has a double-stranded DNA genome of 48,045 base pairs with 3′-extended COS ends, on which 52 putative ORFs are organized into clusters responsible for the order of genome replication, virion morphogenesis, and the regulation of the lytic/lysogenic cycle. In comparison with T. fusca and the previously discovered bacteriophage P1312, P318 has a much lower G+C content in its genome except at the region encompassing ORF42, which produced a protein with unknown function. P1312 and P318 share very few similarities in their genomes except for the regions encompassing ORF42 of P318 and ORF51 of P1312 that are homologous. Thus, acquisition of ORF42 by lateral gene transfer might be an important step in the evolution of P318.

Species diversity and abundance of Dacus (Diptera: Tephritidae) in five ecosystems of Penang, West Malaysia

1982 ◽  
Vol 72 (4) ◽  
pp. 709-716 ◽  
Author(s):  
Tan Keng-Hong ◽  
Lee Soo-Lam
Keyword(s):  
Species Diversity ◽  
Capsicum Annuum ◽  
Fruits And Vegetables ◽  
Methyl Eugenol ◽  
Dacus Dorsalis ◽  
The Difference ◽  
Vegetable Farm ◽  
First Time

AbstractDacus dorsalis Hend. infested eleven, D. cucurbitae Coq. five and D. umbrosus F. two of the eighteen common fruits and vegetables grown in Penang, West Malaysia. D. tau (Wlk.) infested bacang (Mangifera foetida), D. caudatus F. chilli (Capsicum annuum) and D. frauenfeldi Schin. water guava (Eugenia javanica), together with D. dorsalis. Pomelo (Citrus grandis) was found infested for the first time by D. cucurbitae. No flies were trapped using Capilure and trimedlure as baits. Cue-lure attracted D. caudatus, D. cucurbitae, D. frauenfeldi, D. occipitalis (Bez.) and D. tau. Methyl eugenol attracted D. dorsalis and D. umbrosus. Dorsalure was less attractive to D. caudatus and D. dorsalis than cue-lure and methyl eugenol, respectively, but it was equally attractive to D. frauenfeldi as cue-lure. Using traps baited with cue-lure or methyl eugenol in five ecosystems, the highest numbers of males of D. dorsalis, D. umbrosus, D. frauenfeldi and D. caudatus trapped were from a village, on a vegetable farm for D. cucurbitae, and D. occipitalis was only caught in a forest. Analysis showed that for each species of Dacus the difference between ecosystems was highly significant. The few examples caught in grassland were probably migrants.

scholarly journals Hoogsteen Base Pairs Increase the Susceptibility of Double-Stranded DNA to Cytotoxic Damage

2021 ◽  
Vol 120 (3) ◽  
pp. 9a
Author(s):  
Akanksha Manghrani ◽  
Yu Xu ◽  
Emily Cannistraci ◽  
Hashim M. Al-Hashimi
Keyword(s):  
Base Pairs ◽  
Double Stranded Dna

scholarly journals Adding toYersinia enterocoliticaGene Pool Diversity: Two Cryptic Plasmids from a Biotype 1A Isolate

2009 ◽  
Vol 2009 ◽  
pp. 1-10 ◽  
Author(s):  
Daniela Lepka ◽  
Tobias Kerrinnes ◽  
Evelyn Skiebe ◽  
Birgitt Hahn ◽  
Angelika Fruth ◽  
...  
Keyword(s):  
Hypothetical Protein ◽  
Replication Initiation ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Eukaryotic Cells ◽  
Base Pairs ◽  
Significant Similarity ◽  
Replication Initiation Protein ◽  
Cryptic Plasmids ◽  
Reading Frames

We report the nucleotide sequence of two novel cryptic plasmids (4357 and 14 662 base pairs) carried by aYersinia enterocoliticabiotype 1A strain isolated from pork. As distinguished from most biotype 1A strains, this isolate, designated 07-04449, exhibited adherence to eukaryotic cells. The smaller plasmid pYe4449-1 carries five attributable open reading frames (ORFs) encoding the first CcdA/CcdB-like antitoxin/toxin system described for aYersiniaplasmid, a RepA-like replication initiation protein, and mobilizing factors MobA and MobC. The deduced amino acid sequences showed highest similarity to proteins described inSalmonella(CcdA/B),Klebsiella(RepA), andPlesiomonas(MobA/C) indicating genomic fluidity among members of theEnterobacteriaceae. One additional ORF with unknown function, termed ORF5, was identified with an ancestry distinct from the rest of the plasmid. While the C+G content of ORF5 is 38.3%, the rest of pYe4449-1 shows a C+G content of 55.7%. The C+G content of the larger plasmid pYe4449-2 (54.9%) was similar to that of pYe4449-1 (53.7%) and differed from that of theY. enterocoliticagenome (47.3%). Of the 14 ORFs identified on pYe4449-2, only six ORFs showed significant similarity to database entries. For three of these ORFs likely functions could be ascribed: a TnpR-like resolvase and a phage replication protein, localized each on a low C+G island, and DNA primase TraC. Two ORFs of pYe4449-2, ORF3 and ORF7, seem to encode secretable proteins. Epitope-tagging of ORF3 revealed protein expression at4°Cbut not at or above27°Csuggesting adaptation to a habitat outside swine. The hypothetical protein encoded by ORF7 is the member of a novel repeat protein family sharing theDxxGN(x)nDxxGNmotif. Our findings illustrate the exceptional gene pool diversity within the speciesY. enterocoliticadriven by horizontal gene transfer events.

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