scholarly journals Characterization of the Salmonella bacteriophage vB_SenS-Ent1

2012 ◽  
Vol 93 (9) ◽  
pp. 2046-2056 ◽  
Author(s):  
Dann Turner ◽  
Mohammed Hezwani ◽  
Shona Nelson ◽  
Vyv Salisbury ◽  
Darren Reynolds
Keyword(s):  
Nucleotide Sequence Identity ◽  
Burst Size ◽  
Genome Sequences ◽  
Sequence Identity ◽  
The Family ◽  
Contractile Tail ◽  
Transcriptional Units ◽  
High Level ◽  
Icosahedral Head

The bacteriophage vB_SenS-Ent1 (Ent1) is a member of the family Siphoviridae of tailed bacteriophages and infects a broad range of serovars of the enteric pathogen Salmonella enterica. The virion particle is composed of an icosahedral head 64 nm in diameter and a flexible, non-contractile tail of 116 × 8.5 nm possessing terminal fibres. The adsorption rate constant at 37 °C is 6.73 × 10−9 ml min−1. Latent and eclipse periods are 25 and 20 min, respectively, and the burst size is 35 progeny particles per cell after 35 min at 37 °C. Sequencing revealed a circularly permuted, 42 391 bp dsDNA genome containing 58 ORFs organized into four major transcriptional units. Comparisons with the genome sequences of other bacteriophages revealed a high level of nucleotide sequence identity and shared orthologous proteins with the Salmonella phages SETP3, SE2 and KS7 (SS3e) and the Escherichia phages K1G, K1H, K1ind1 and K1ind3.

Cloning and expression of DiT33 from Dirofilaria immitis: a specific and early marker of heartworm infection

Parasitology ◽  
1996 ◽  
Vol 112 (3) ◽  
pp. 331-338 ◽  
Author(s):  
X. Q. Hong ◽  
J. Santiago Mejia ◽  
S. Kumar ◽  
F. B. Perler ◽  
C. K. S. Carlow
Keyword(s):  
Dirofilaria Immitis ◽  
Cloning And Expression ◽  
E Coli ◽  
Spliced Leader ◽  
Isolation And Characterization ◽  
The Family ◽  
Heartworm Infection ◽  
High Level ◽  
Control And Management

SUMMARYDirofilaria immitis is an important filarial parasite of dogs and cats, and a useful model for human filariasis. Current diagnostic tests for heartworm infection in animals rely on the presence of fecund female worms (usually found 6·5 months post-infection or later) and therefore fail to detect pre-patent infections. Putative pepsin inhibitors from 2 filarial parasites of humans namely Onchocerca volvulus (Ov33, Oc3.6, OvDSB) and Brugia malayi (Bm33), have been shown to be useful in diagnosis of onchocerciasis and lymphatic filariasis, respectively. Previous studies have suggested that a homologue exists in D. immitis (DiT33), which may have potential in diagnosis of heartworm infection. In this study, the isolation and characterization of a cDNA clone encoding DiT33 is described.‡ This cDNA contains 12 bases of the nematode-specific 22 nucleotide spliced leader sequence and encodes a 26·4 kDa-protein with a high level of similarity (87–89%) to other filarial members of the family. DJT33 was over-expressed in E. coli as a fusion with the maltose-binding protein and serological analysis was performed using a panel of clinically defined dog sera. The findings of this study indicate that DiT33 is a promising antigen for the early detection of D. immitis and may be a valuable tool in the control and management of heartworm infection.

scholarly journals Characterization of a new picornavirus isolated from the freshwater fish Lepomis macrochirus

2014 ◽  
Vol 95 (3) ◽  
pp. 601-613 ◽  
Author(s):  
Marisa Barbknecht ◽  
Sol Sepsenwol ◽  
Eric Leis ◽  
Maren Tuttle-Lau ◽  
Mark Gaikowski ◽  
...  
Keyword(s):  
Freshwater Fish ◽  
New Genus ◽  
Lepomis Macrochirus ◽  
Leader Peptide ◽  
Fish Kill ◽  
Sequence Identity ◽  
Phylogenetic Cluster ◽  
The Family ◽  
Sport Fish

The freshwater fish Lepomis macrochirus (bluegill) is common to North American waters, and important both ecologically and as a sport fish. In 2001 an unknown virus was isolated from bluegills following a bluegill fish kill. This virus was identified as a picornavirus [termed bluegill picornavirus (BGPV)] and a diagnostic reverse transcriptase PCR was developed. A survey of bluegills in Wisconsin waters showed the presence of BGPV in 5 of 17 waters sampled, suggesting the virus is widespread in bluegill populations. Experimental infections of bluegills confirmed that BGPV can cause morbidity and mortality in bluegills. Molecular characterization of BGPV revealed several distinct genome characteristics, the most unusual of which is the presence of a short poly(C) tract in the 3′ UTR. Additionally, the genome encodes a polyprotein lacking a leader peptide and a VP0 maturation cleavage site, and is predicted to encode two distinct 2A proteins. Sequence comparison showed that the virus is most closely related to a phylogenetic cluster of picornaviruses that includes the genera Aquamavirus, Avihepatovirus and Parechovirus. However, it is distinct enough, for example sharing only about 38 % sequence identity to the parechoviruses in the 3D region, that it may represent a new genus in the family Picornaviridae.

scholarly journals Rediscovery and genomic characterization of bovine astroviruses

2011 ◽  
Vol 92 (8) ◽  
pp. 1888-1898 ◽  
Author(s):  
Herman Tse ◽  
Wan-Mui Chan ◽  
Hoi-Wah Tsoi ◽  
Rachel Y. Y. Fan ◽  
Candy C. Y. Lau ◽  
...  
Keyword(s):  
Roe Deer ◽  
Mammalian Species ◽  
Capreolus Capreolus ◽  
Genetic Distances ◽  
Genome Sequences ◽  
Sea Lions ◽  
The Family ◽  
Genomic Characterization ◽  
Similar Organization

The genus Mamastrovirus belongs to the family Astroviridae and consists of at least six members infecting different mammalian hosts, including humans, cattle and pigs. In recent years, novel astroviruses have been identified in other mammalian species like roe deer, bats and sea lions. While the bovine astrovirus was one of the earliest astroviruses to have been studied, no further research has been performed recently and its genome sequence remains uncharacterized. In this report, we describe the detection and genomic characterization of astroviruses in bovine faecal specimens obtained in Hong Kong. Five of 209 specimens were found to be positive for astrovirus by RT-PCR. Two of the positive specimens were found to contain sequences from two different astrovirus strains. Complete genome sequences of approximately 6.3 kb in length were obtained for four strains, which showed similar organization of the genome compared to other astroviruses. Phylogenetic analysis confirmed their identities as members of the genus Mamastrovirus, and showed them to be most closely related to the Capreolus capreolus astrovirus. Based on the pairwise genetic distances among their full-length ORF2 sequences, these bovine astroviruses may be assigned into at least three different genotype species. Sequence analysis revealed evidence of potential recombination in ORF2. In summary, we report the first genome sequences of bovine astroviruses and clearly establish the species status of the virus. Additionally, our study is among the first to report co-infection by different astrovirus genotypes in the same host, which is an essential step for recombination to occur.

scholarly journals Three of a Kind: Genetically Similar Tsukamurella Phages TIN2, TIN3, and TIN4

2015 ◽  
Vol 81 (19) ◽  
pp. 6767-6772 ◽  
Author(s):  
Zoe A. Dyson ◽  
Joseph Tucci ◽  
Robert J. Seviour ◽  
Steve Petrovski
Keyword(s):  
Genome Sequencing ◽  
Nucleotide Sequence Identity ◽  
Genome Architecture ◽  
Genome Sequences ◽  
Sludge Treatment ◽  
Content Type ◽  
Sequence Identity ◽  
Enrichment Techniques ◽  
Replication Module ◽  
Highly Virulent

ABSTRACTThreeTsukamurellaphages, TIN2, TIN3, and TIN4, were isolated from activated sludge treatment plants located in Victoria, Australia, using conventional enrichment techniques. Illumina and 454 whole-genome sequencing of theseSiphoviridaeviruses revealed that they had similar genome sequences, ranging in size between 76,268 bp and 76,964 bp. All three phages shared 74% nucleotide sequence identity to the previously describedGordoniaphage GTE7. Genome sequencing suggested that phage TIN3 had suffered a mutation in one of its lysis genes compared to the sequence of phage TIN4, to which it is genetically very similar. Mass spectroscopy data showed the unusual presence of a virion structural gene in the DNA replication module of phage TIN4, disrupting the characteristic modular genome architecture ofSiphoviridaephages. All three phages appeared highly virulent on strains ofTsukamurella inchonensisandTsukamurella paurometabola.

scholarly journals IND-6, a Highly Divergent IND-Type Metallo-β-Lactamase from Chryseobacterium indologenes Strain 597 Isolated in Burkina Faso

2009 ◽  
Vol 53 (10) ◽  
pp. 4320-4326 ◽  
Author(s):  
Boukaré Zeba ◽  
Filomena De Luca ◽  
Alain Dubus ◽  
Michael Delmarcelle ◽  
Jacques Simporé ◽  
...  
Keyword(s):  
Burkina Faso ◽  
Posttranslational Modification ◽  
Human Pathogens ◽  
Turnover Rates ◽  
Chryseobacterium Indologenes ◽  
Sequence Identity ◽  
New Variant ◽  
The Family ◽  
Identification And Characterization

ABSTRACT The genus Chryseobacterium and other genera belonging to the family Flavobacteriaceae include organisms that can behave as human pathogens and are known to cause different kinds of infections. Several species of Flavobacteriaceae, including Chryseobacterium indologenes, are naturally resistant to β-lactam antibiotics (including carbapenems), due to the production of a resident metallo-β-lactamase. Although C. indologenes presently constitutes a limited clinical threat, the incidence of infections caused by this organism is increasing in some settings, where isolates that exhibit multidrug resistance phenotypes (including resistance to aminoglycosides and quinolones) have been detected. Here, we report the identification and characterization of a new IND-type variant from a C. indologenes isolate from Burkina Faso that is resistant to β-lactams and aminoglycosides. The levels of sequence identity of the new variant to other IND-type metallo-β-lactamases range between 72 and 90% (for IND-4 and IND-5, respectively). The purified enzyme exhibited N-terminal heterogeneity and a posttranslational modification consisting of the presence of a pyroglutamate residue at the N terminus. IND-6 shows a broad substrate profile, with overall higher turnover rates than IND-5 and higher activities than IND-2 and IND-5 against ceftazidime and cefepime.

scholarly journals Terasakiispira papahanaumokuakeensis gen. nov., sp. nov., a gammaproteobacterium from Pearl and Hermes Atoll, Northwestern Hawaiian Islands

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3609-3617 ◽  
Author(s):  
Vanessa K. Zepeda ◽  
Hans-Jürgen Busse ◽  
Jan Golke ◽  
Jimmy H. W. Saw ◽  
Maqsudul Alam ◽  
...  
Keyword(s):  
Nucleotide Sequence Identity ◽  
Type Strain ◽  
Type Species ◽  
New Genus ◽  
Hawaiian Islands ◽  
Rrna Gene ◽  
Sequence Identity ◽  
The Family ◽  
Northwestern Hawaiian Islands ◽  
Hydrolysis Of

A Gram-negative, helical bacterium designated PH27AT was cultivated from an anchialine pool on Pearl and Hermes Atoll, Northwestern Hawaiian Islands. The obligately halophilic strain was motile by bipolar tufts of flagella and grew optimally at pH 7, and microaerobically or aerobically. Closest neighbours based on 16S rRNA gene nucleotide sequence identity are Marinospirillum celere v1c_Sn-redT (93.31 %) and M. alkaliphilum Z4T (92.10 %) in the family Oceanospirillaceae, class Gammaproteobacteria. PH27AT is distinguished phenotypically from members of the genus Marinospirillum by its hydrolysis of gelatin, the absence of growth in media containing ≤ 1 % (w/v) NaCl and the ranges of temperature (12–40 °C) and pH (5–8) for growth. The major compound ubiquinone Q-9 distinguishes the quinone system of strain PH27AT from those in members of the genus Marinospirillum and other members of the Oceanospirillaceae, in which the major quinone is Q-8. Major polar lipids in PH27AT were phosphatidylethanolamine and phosphatidylglycerol, with moderate amounts of diphosphatidylglycerol and phosphatidylserine. Spermidine and cadaverine dominated the polyamine pattern; large proportions of cadaverine have not been reported in members of the genus Marinospirillum. Genotypic and chemotaxonomic data show that PH27AT does not belong in the genus Marinospirillum or other genera of the family Oceanospirillaceae or the Halomonadaceae. We propose a new genus, Terasakiispira gen. nov., be created to accommodate Terasakiispira papahanaumokuakeensis gen. nov., sp. nov. as the type species, with PH27AT ( = ATCC BAA-995T = DSM 16455T = DSM 23961T) as the type strain.

scholarly journals Isolation and Characterization of a Bacteriophage Infecting Pseudomonas Aeruginosa and Its Application as a Potential Decontaminating Agent

2021 ◽  
Author(s):  
Sonika Sharma ◽  
Sibnarayan Datta ◽  
Soumya Chatterjee ◽  
Moumita Dutta ◽  
Jhuma Samanta ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Burst Size ◽  
Gc Content ◽  
Alginate Beads ◽  
Open Reading Frames ◽  
Isolation And Characterization ◽  
The Family ◽  
Infected Cells

Abstract To treat antibiotic resistance bacteria, bacteriophage (also called 'phage') application has recently drawn considerable attention from researchers globally. Bacteria like Pseudomonas aeruginosa are known to be associated with nosocomial infections especially in patients with compromised immune systems. In the present work, phage against P. aeruginosa (named 'DRLP1') was isolated from wastewater, enriched and characterized. Morphologically DRLP1 belongs to the family Myoviridae with a high lytic ability. DRLP1 has a burst size of approximately 100 PFU/infected cells, a rapid adsorption time when supplemented with MgCl2, and has viability in a wide temperature range and pH. Genomic sequencing and bioinformatics analysis showed that the phage genome is linear double-stranded, 66,243 bp in length and have a GC content of 54.9%. the genome encodes 93 phage related ORFs open reading frames (ORFs). Phage stability in lyophilized state, adsorption study on sodium alginate beads, and in-vitro pathogen reduction assays were also investigated. Study carried out with artificially contaminated fomites suggests that this phage has the potential for application as a biological decontaminant agent against P. aeruginosa in different conditions.

scholarly journals Psychroserpens mesophilus sp. nov., a mesophilic marine bacterium belonging to the family Flavobacteriaceae isolated from a young biofilm

2006 ◽  
Vol 56 (5) ◽  
pp. 1055-1058 ◽  
Author(s):  
Kae Kyoung Kwon ◽  
Soon Jae Lee ◽  
Jae Hyun Park ◽  
Tae-Young Ahn ◽  
Hong Kum Lee
Keyword(s):  
Marine Bacterium ◽  
Methyl Esters ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
The Family ◽  
Major Respiratory Quinone ◽  
Dominant Fatty Acid ◽  
High Level ◽  
Taxonomic Characterization

A number of marine bacteria isolated from young biofilms were characterized as belonging to the family Flavobacteriaceae. The taxonomic characterization of strain KOPRI 13649T, which was isolated from an acrylic surface at the seashore at Gangneung, Korea, is reported here. The nearly complete 16S rRNA gene sequence of strain KOPRI 13649T was determined and was found to have a high level of similarity with that of Psychroserpens burtonensis (95.0–95.6 %). In addition, phylogenetic analysis and comparison with closely related strains confirmed that the strain represented a novel member of the genus Psychroserpens. The major respiratory quinone of strain KOPRI 13649T was MK-6 and the DNA G+C content was 29.8 mol%. The dominant fatty acid methyl esters were i-15 : 0, a-15 : 0, i-16 : 0, i-15 : 1ω10, 16 : 1ω7 and 15 : 0. Growth was observed at 10–34 °C (optimum 30 °C), at pH 6–9 (optimum 6.5–8.0) and with 0.5–4 % NaCl (optimum 1 %). On the basis of the polyphasic taxonomic evidence presented, strain KOPRI 13649T (=KCCM 42261T=JCM 13413T) should be classified as the type strain of a novel species in the genus Psychroserpens, for which the name Psychroserpens mesophilus sp. nov. is proposed.

scholarly journals Gene Mapping and Phylogenetic Analysis of the Complete Genome from 30 Single-Stranded RNA Male-Specific Coliphages (Family Leviviridae)

2009 ◽  
Vol 83 (21) ◽  
pp. 11233-11243 ◽  
Author(s):  
Stephanie D. Friedman ◽  
Fred J. Genthner ◽  
Jennifer Gentry ◽  
Mark D. Sobsey ◽  
Jan Vinjé
Keyword(s):  
Complete Genome ◽  
Catalytic Domain ◽  
Phylogenetic Analyses ◽  
Detailed Knowledge ◽  
Genome Sequences ◽  
Virus Family ◽  
Sequence Identity ◽  
The Family ◽  
The Individual ◽  
Male Specific

ABSTRACT Male-specific single-stranded RNA (FRNA) coliphages belong to the family Leviviridae. They are classified into two genera (Levivirus and Allolevivirus), which can be subdivided into four genogroups (genogroups I and II in Levivirus and genogroups III and IV in Allolevivirus). Relatively few strains have been completely characterized, and hence, a detailed knowledge of this virus family is lacking. In this study, we sequenced and characterized the complete genomes of 19 FRNA strains (10 Levivirus strains and 9 Allolevivirus strains) and compared them to the 11 complete genome sequences available in GenBank. Nucleotide similarities among strains of Levivirus genogroups I and II were 75% to 99% and 83 to 94%, respectively, whereas similarities among strains of Allolevivirus genogroups III and IV ranged from 70 to 96% and 75 to 95%, respectively. Although genogroup I strain fr and genogroup III strains MX1 and M11 share only 70 to 78% sequence identity with strains in their respective genogroups, phylogenetic analyses of the complete genome and the individual genes suggest that strain fr should be grouped in Levivirus genogroup I and that the MX1 and M11 strains belong in Allolevivirus genogroup III. Strains within each genus share >50% sequence identity, whereas between the two genera, strains have <40% nucleotide sequence identity. Overall, amino acid composition, nucleotide similarities, and replicase catalytic domain location contributed to phylogenetic assignments. A conserved eight-nucleotide signature at the 3′ end of the genome distinguishes leviviruses (5′ ACCACCCA 3′) from alloleviviruses (5′ TCCTCCCA 3′).

scholarly journals Morphological and molecular characterization of Gordionus alpestris (Nematomorpha) from the North-West Caucasus, Russia

2013 ◽  
Vol 50 (1) ◽  
pp. 67-72 ◽  
Author(s):  
S. Spiridonov ◽  
V. Schmatko
Keyword(s):  
Molecular Characterization ◽  
North West ◽  
The North ◽  
The Family ◽  
Pcr Products ◽  
High Level ◽  
Morphological And Molecular Characterization

AbstractDuring the survey of Pachyiulus krivolutskyi Golovatch, 1977 (Diplopoda) near Nickel’ in Adygei Republic (Russia) in the summer 2009 the infestation of these millipeds with nematomorphs of the species Gordionus alpestris was revealed. The morphology of naturally emerging nematomorphs was studied in SEM. The partial sequences of 18S (883 bp) and 28S (393 bp) rDNA PCR-products were obtained and analyzed. An unexpectedly high level of differences between Gordionus alpestris found in diplopods of North-West Caucasus and other molecularly studied representatives of the family Chordodidae was observed.

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