A large new Streptococcus bacteriophage

1975 ◽  
Vol 21 (4) ◽  
pp. 571-574 ◽  
Author(s):  
Hans-W. Ackermann ◽  
Teresa Caprioli ◽  
Shanti S. Kasatiya
Keyword(s):  
Double Stranded Dna ◽  
Contractile Tail ◽  
Group D

Phage VD13 possesses a large, elongated head and a long, non-contractile tail. It is active on group D streptococci and contains double-stranded DNA. The phage produces several rare kinds of head malformations, notably polymorphic mottled structures and giant heads which probably contain DNA.

scholarly journals Genomic Organization and Molecular Characterization of Clostridium difficile Bacteriophage ΦCD119

2006 ◽  
Vol 188 (7) ◽  
pp. 2568-2577 ◽  
Author(s):  
Revathi Govind ◽  
Joe A. Fralick ◽  
Rial D. Rolfe
Keyword(s):  
Clostridium Difficile ◽  
Dna Sequence ◽  
Integration Site ◽  
Attachment Site ◽  
Noncoding Region ◽  
Open Reading Frames ◽  
Restriction Enzyme Digestion ◽  
Putative Gene ◽  
Double Stranded Dna ◽  
Contractile Tail

ABSTRACT In this study, we have isolated a temperate phage (ΦCD119) from a pathogenic Clostridium difficile strain and sequenced and annotated its genome. This virus has an icosahedral capsid and a contractile tail covered by a sheath and contains a double-stranded DNA genome. It belongs to the Myoviridae family of the tailed phages and the order Caudovirales. The genome was circularly permuted, with no physical ends detected by sequencing or restriction enzyme digestion analysis, and lacked a cos site. The DNA sequence of this phage consists of 53,325 bp, which carries 79 putative open reading frames (ORFs). A function could be assigned to 23 putative gene products, based upon bioinformatic analyses. The ΦCD119 genome is organized in a modular format, which includes modules for lysogeny, DNA replication, DNA packaging, structural proteins, and host cell lysis. The ΦCD119 attachment site attP lies in a noncoding region close to the putative integrase (int) gene. We have identified the phage integration site on the C. difficile chromosome (attB) located in a noncoding region just upstream of gene gltP, which encodes a carrier protein for glutamate and aspartate. This genetic analysis represents the first complete DNA sequence and annotation of a C. difficile phage.

scholarly journals Isolation and Sequencing of a Temperate Transducing Phage for Pasteurella multocida

2006 ◽  
Vol 72 (5) ◽  
pp. 3154-3160 ◽  
Author(s):  
Susana Campoy ◽  
Jes�s Aranda ◽  
Gerard �lvarez ◽  
Jordi Barb� ◽  
Montserrat Llagostera
Keyword(s):  
Pasteurella Multocida ◽  
Genetic Manipulation ◽  
Attachment Site ◽  
Gene Encoding ◽  
Double Stranded Dna ◽  
Pathogenic Genes ◽  
The Family ◽  
Typical Morphology ◽  
Contractile Tail ◽  
Generalized Transduction

ABSTRACT A temperate bacteriophage (F108) has been isolated through mitomycin C induction of a Pasteurella multocida serogroup A strain. F108 has a typical morphology of the family Myoviridae, presenting a hexagonal head and a long contractile tail. F108 is able to infect all P. multocida serogroup A strains tested but not those belonging to other serotypes. Bacteriophage F108, the first P. multocida phage sequenced so far, presents a 30,505-bp double-stranded DNA genome with cohesive ends (CTTCCTCCCC cos site). The F108 genome shows the highest homology with those of Haemophilus influenzae HP1 and HP2 phages. Furthermore, an F108 prophage attachment site in the P. multocida chromosome has been established to be inside a gene encoding tRNALeu. By using several chromosomal markers that are spread along the P. multocida chromosome, it has been demonstrated that F108 is able to perform generalized transduction. This fact, together with the absence of pathogenic genes in the F108 genome, makes this bacteriophage a valuable tool for P. multocida genetic manipulation.

scholarly journals Isolation and characterisation of Vibrio alginolyticus lytic bacteriophage φVa-1 from brackishwater clam Meritrix meritrix in India

2017 ◽  
Vol 64 (3) ◽  
Author(s):  
E. C. Abhilash ◽  
S. V. Alavandi
Keyword(s):  
Hexagonal Structure ◽  
Vibrio Alginolyticus ◽  
Lytic Bacteriophage ◽  
Electron Microscopic ◽  
Tryptone Soya Agar ◽  
Double Stranded Dna ◽  
Transmission Electron ◽  
The Family ◽  
Contractile Tail ◽  
Overlay Technique

The Gram negative bacterium Vibrio alginolyticus is generally found in marine and brackishwater systems. A lytic bacteriophage capable of specifically infecting V. alginolyticus was isolated from the brackishwater clam (Meretrix meretrix) using agar overlay technique. The phage produced plaques 3 mm in dia, which increased to 5 mm overnight on tryptone soya agar (TSA) plates and the optimum temperature and pH was found to be 32°C and 7.5 respectively. The phage was designated as φVa-1 and nucleic acid characterisation confirmed that the phage has double stranded DNA. Transmission electron microscopic observations revealed that the bacteriophage had hexagonal structure with a long contractile tail andthe phage was found to belong to the family Myoviridae.

Characterization of bacteriophage CP1, an organic solvent sensitive phage associated with Pseudomonas cepacia

1978 ◽  
Vol 24 (11) ◽  
pp. 1404-1412 ◽  
Author(s):  
R. L. Cihlar ◽  
T. G. Lessie ◽  
S. C. Holt
Keyword(s):  
Organic Solvent ◽  
High Titer ◽  
Apparent Molecular Weight ◽  
Pseudomonas Cepacia ◽  
Host Restriction ◽  
Sedimentation Behavior ◽  
Double Stranded Dna ◽  
Tail Sheath ◽  
Total Particle ◽  
Contractile Tail

Pseudomonas cepacia strain 249 has been found to harbor an organic solvent sensitive phage, CP1, which is active on other P. cepacia strains. The efficiency of plating of CP1 was dependent upon the strain on which it was propagated and the strain used as indicator, implying the operation of host restriction and modification systems in certain of the strains. Strain 383 which was used routinely for propagation of CP1 appears to lack such systems. To obtain high-titer lysates it was important to add EDTA to the infected cultures at the onset of lysis to block attachment of phage particles to cell debris. CP1 possesses a distinct head (55 nm in diameter) and a broad contractile tail (15 × 145 nm). Fluorescent staining of phage preparations with acridine orange indicated that CP1 contains double-stranded DNA. CP1 particles contained about 5 × 10−17 g each of protein and DNA for a total particle weight of 10−16 g. The apparent molecular weight of CP1 DNA estimated from its sedimentation behavior and the particle content of DNA was about 3 × 107. Thermal-denaturation studies indicated that the G + C content of CP1 DNA (65%) was lower than that of DNA of its P. cepacia host (71% G + C). The mechanism of inactivation of CP1 by chloroform appears to be related to tail contraction caused by this agent. An atypical reverse contraction of the tail sheath was noted in about 45% of the inactivated particles. No phospholipid was detected in purified preparations of CP1 (<4 × 10−19 g/PFU). The results suggest that inactivation of CP1 by organic solvents involves alteration of a component (presumably a protein) of the phage tail.

scholarly journals Architecture of the flexible tail tube of bacteriophage SPP1

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Maximilian Zinke ◽  
Katrin A. A. Sachowsky ◽  
Carl Öster ◽  
Sophie Zinn-Justin ◽  
Raimond Ravelli ◽  
...  
Keyword(s):  
Hybrid Structure ◽  
Dna Virus ◽  
Flexible Tail ◽  
Double Stranded Dna ◽  
Density Maps ◽  
Relaxation Measurements ◽  
Contractile Tail ◽  
Density Map ◽  
Phage Spp1 ◽  
Structural Restraints

AbstractBacteriophage SPP1 is a double-stranded DNA virus of the Siphoviridae family that infects the bacterium Bacillus subtilis. This family of phages features a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, we present the atomic structure of the tail tube of phage SPP1. Our hybrid structure is based on the integration of structural restraints from solid-state nuclear magnetic resonance (NMR) and a density map from cryo-EM. We show that the tail tube protein gp17.1 organizes into hexameric rings that are stacked by flexible linker domains and, thus, form a hollow flexible tube with a negatively charged lumen suitable for the transport of DNA. Additionally, we assess the dynamics of the system by combining relaxation measurements with variances in density maps.

scholarly journals Characterization of the Genome of the Dairy Lactobacillus helveticus Bacteriophage ΦAQ113

2013 ◽  
Vol 79 (15) ◽  
pp. 4712-4718 ◽  
Author(s):  
Miriam Zago ◽  
Erika Scaltriti ◽  
Lia Rossetti ◽  
Alessandro Guffanti ◽  
Angelarita Armiento ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Consensus Sequence ◽  
Genome Structure ◽  
Lactobacillus Helveticus ◽  
Open Reading Frames ◽  
Content Type ◽  
Double Stranded Dna ◽  
A Genome ◽  
Health Promoting ◽  
Contractile Tail

ABSTRACTThe complete genomic sequence of the dairyLactobacillus helveticusbacteriophage ΦAQ113 was determined. Phage ΦAQ113 is aMyoviridaebacteriophage with an isometric capsid and a contractile tail. The final assembled consensus sequence revealed a linear, circularly permuted, double-stranded DNA genome with a size of 36,566 bp and a G+C content of 37%. Fifty-six open reading frames (ORFs) were predicted, and a putative function was assigned to approximately 90% of them. The ΦAQ113 genome shows functionally related genes clustered together in a genome structure composed of modules for DNA replication/regulation, DNA packaging, head and tail morphogenesis, cell lysis, and lysogeny. The identification of genes involved in the establishment of lysogeny indicates that it may have originated as a temperate phage, even if it was isolated from natural cheese whey starters as a virulent phage, because it is able to propagate in a sensitive host strain. Additionally, we discovered that the ΦAQ113 phage genome is closely related toLactobacillus gasseriphage KC5a andLactobacillus johnsoniiphage Lj771 genomes. The phylogenetic similarities betweenL. helveticusphage ΦAQ113 and two phages that belong to gut species confirm a possible common ancestral origin and support the increasing consideration ofL. helveticusas a health-promoting organism.

Discrimination of monomer from multimer DNA disk-shaped toruses by freezeetch TEM

1984 ◽  
Vol 42 ◽  
pp. 210-211
Author(s):  
George C. Ruben ◽  
Kenneth A. Marx
Keyword(s):  
Biochemical Data ◽  
Dna Structures ◽  
Ice Surface ◽  
Double Stranded Dna ◽  
Data Support ◽  
Dna Organization ◽  
Trivalent Cations

In vitro collapse of DNA by trivalent cations like spermidine produces torus (donut) shaped DNA structures thought to have a DNA organization similar to certain double stranded DNA bacteriophage and viruses. This has prompted our studies of these structures using freeze-etch low Pt-C metal (9Å) replica TEM. With a variety of DNAs the TEM and biochemical data support a circumferential DNA winding model for hydrated DNA torus organization. Since toruses are almost invariably oriented nearly horizontal to the ice surface one of the most accessible parameters of a torus population is annulus (ring) thickness. We have tabulated this parameter for populations of both nicked, circular (Fig. 1: n=63) and linear (n=40: data not shown) ϕX-174 DNA toruses. In both cases, as can be noted in Fig. 1, there appears to be a compact grouping of toruses possessing smaller dimensions separated from a dispersed population possessing considerably larger dimensions.

Synchrony of Digestion of SV40 DNA by Exonuclease III Determined by EM

1975 ◽  
Vol 33 ◽  
pp. 674-675
Author(s):  
Ray Wu ◽  
G. Ruben ◽  
B. Siegel ◽  
P. Spielman ◽  
E. Jay
Keyword(s):  
Dark Field ◽  
Uranyl Acetate ◽  
Enzyme Digestion ◽  
Dna Molecules ◽  
Exonuclease Iii ◽  
Aluminum Films ◽  
Double Stranded Dna ◽  
Before And After ◽  
Exo Iii ◽  
Sv40 Dna

A method for determining long nucleotide sequences of double-stranded DNA is being developed. It involves (a) the synchronous digestion of the DNA from the 3' ends with EL coli exonuclease III (Exo III) followed by (b) resynthesis with labeled nucleotides and DNA polymerase. A crucial factor in the success of this method is the degree to which the enzyme digestion proceeds synchronously under proper conditions of incubation (step a). Dark field EM is used to obtain accurate measurements on the lengths and distribution of the DNA molecules before and after digestion with Exo III, while gel electrophoresis is used in parallel to obtain a mean length for these molecules. It is the measurements on a large enough sample of individual molecules by EM that provides the information on how synchronously the digestion proceeds. For length measurements, the DNA molecules were picked up on 20-30 Å thick carbon-aluminum films, using the aqueous Kleinschmidt technique and stained with 7.5 x 10-5M uranyl acetate in 90% ethanol for 3 minutes.

Torus Circumference and Thickness Parameters From a Linear DNA Size Series Suggest How Toruses Self-Assemble

1985 ◽  
Vol 43 ◽  
pp. 522-523
Author(s):  
George C. Ruben ◽  
Kenneth A. Marx
Keyword(s):  
Tertiary Structure ◽  
Dna Complexes ◽  
Tertiary Structures ◽  
Self Assembling ◽  
Double Stranded Dna ◽  
Calf Thymus ◽  
Dna Organization ◽  
Condensed Dna ◽  
Dna Size

Certain double stranded DNA bacteriophage and viruses are thought to have their DNA organized into large torus shaped structures. Morphologically, these poorly understood biological DNA tertiary structures resemble spermidine-condensed DNA complexes formed in vitro in the total absence of other macromolecules normally synthesized by the pathogens for the purpose of their own DNA packaging. Therefore, we have studied the tertiary structure of these self-assembling torus shaped spermidine- DNA complexes in a series of reports. Using freeze-etch, low Pt-C metal (10-15Å) replicas, we have visualized the microscopic DNA organization of both calf Thymus( CT) and linear 0X-174 RFII DNA toruses. In these structures DNA is circumferentially wound, continuously, around the torus into a semi-crystalline, hexagonal packed array of parallel DNA helix sections.

A New Era of Organ-Preserving Treatment in Pediatric Intraocular Retinoblastoma in Russia: A Multicenter Cohort Study

2018 ◽  
Vol 5 (1) ◽  
pp. 51-69 ◽  
Author(s):  
Тatiana L. Ushakova ◽  
Igor A. Тrofimov ◽  
Оlga V. Gorovtsova ◽  
Аndrey A. Yarovoy ◽  
Svetlana V. Saakyan ◽  
...  
Keyword(s):  
Gamma Knife ◽  
Systemic Chemotherapy ◽  
Focal Therapy ◽  
Primary Treatment ◽  
Local Chemotherapy ◽  
Multicenter Cohort Study ◽  
Cancer Disease ◽  
Tumor Spread ◽  
Group D

Background.Retinoblastoma (RB) is a life threatening cancer disease. A breakthrough in the treatment of children with RB is associated with the improvement of conservative treatment that was administered in at least one of the two tumor-affected eyes in most bilateral cases, that was chemotherapy both systemic and local (selective intra-arterial and intravitreal) in most cases combined with laser therapy, cryotherapy, or brachytherapy. The development of such techniques as local chemotherapy is focused on preservation of visual functions, reducing the number of enucleations and radiotherapy (RT) course. The success of the healing of RB is closely associated with a multidisciplinary approach to diagnosis and treatment, as well as specialized longterm follow-up clinical examination.Objective.eye and vision preservation against large intraocular tumors with different growth types and localization without the course of remote radiation therapy was the main purpose.Methods.In the period from September 2012 to January 2016, the study enrolled 45 patients with RB when at least one eye had intraocular tumor spread corresponding to the group C or D. According to the ABC international classification, patients have a relatively good prognosis for organ-preserving treatment. 4 of 18 children with bilateral RB had undergone primary enucleation of worse eye the worst eye, group E; 49 (77.8%) of the 63 affected eyes had features for groups C and D. In this study, no patient received local chemotherapy initially, only after prior systemic chemotherapy. Selective intra-arterial chemotherapy (SIAC) was applied to 41 patients (45 eyes; mean course number was 2), and 32 patients (34 eyes) had undergone intravitreal chemo therapy (IViC) (mean course number was 2). Focal therapy and local chemotherapy were the main methods of treatment for progression (new lesions on the retina) in 8 (16.3%) of 49 eyes with tumors of group C (n=1) and D (n=7); the relapse in 14 of 49 (new lesions on the retina) in eyes with tumors of group C (n=5) and D (n=6) and (new lesions on the retina and the vitreous) in eyes with tumors of group D (n=3) (28.5%), and stabilization of disease n=23 (46.9%). We should note that 2 patients underwent repeated course of in case of systemic chemotherapy, 1 patient — a Gamma Knife procedure due to registered disease stabilization, progression or relapse.Results.10 (20.4%) of 49 eyes saved due to the combined chemotherapy. In 45 patients diseasefree survival rate was 56.1±8.9 % (with mean follow-up period 26.9±2.5 months). 1 of 45 patients died from leukemia. 44 of 45 patients are alive without metastasis. The mean follow-up was 20 months (3 to 43 months). Eye salvage rate in group C — 14 (93.3%) of 15, in group D — 31 (91.2%) of 34.Conclusion.These methods: second line of systemic chemotherapy, RT, and a Gamma Knife procedure should be considered as a failure of primary treatment. Our study demonstrated a high efficacy of local chemotherapy with promissing techniques of conservation therapy, which safety increases due to experience.

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