• Communications for Statistical Applications and Methods
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• v.12 no.1
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• pp.139-147
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• 2005

It is interesting to locate homogeneous segments within a DNA sequence. Suppose that the DNA sequence has segments within which the observations follow the same residue frequency distribution, and between which observations have different distributions. In this setting, change points correspond to the end points of these segments. This article explores the use of a binary segmentation procedure in detecting the change points in the DNA sequence. The change points are determined using a sequence of nested hypothesis tests of whether a change point exists. At each test, we compare no change-point model with a single change-point model by using the Bayesian information criterion. Thus, the method circumvents the computational complexity one would normally face in problems with an unknown number of change points. We illustrate the procedure by analyzing the genome of the bacteriophage lambda.

• Korean Journal of Microbiology
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• v.32 no.3
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• pp.198-201
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• 1994

The nucleotide sequence of the cohesive end site (cos) of Lactobacillus casei phage J1 genome was determined. Comparison between the nucleotide sequences of the circular cos and the left end of the linear J1 DNA showed that the nicking sites of the terminase were as follows: 5'- GGTCGGCC$\downarrow$ -3' 3'- $\uparrow$CCAGCCGG -5' The cohesive single-stranded ends of J1 were found to be 3'-protruding and composed of 8 nucleotides. The mol% G + C of the cohesive ends was 87.5. The cos site shows dyad symmetry from -33 to + 25 bp if the 5' terminal nucleotide of the left end of the linear J1 DNA is numbered +1. No homology was found among the cos sites of phages reported so far.

• Journal of Microbiology and Biotechnology
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• v.9 no.4
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• pp.457-463
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• 1999

The physical map of bacteriophage $\PhiFC1$ DNA was constructed with the restriction endonucleases SalI, BamHI, EcoRI, XbaI, and AvaI. The 40.5-kb DNA restriction map is shown to be circularly permuted representing the headful packaging mechanism of the phage. The DNA restriction fragments containing the packaging initiation site(pac) was localized on the restriction map and the nucleotide sequences of the region were analyzed. Four open reading frames (ORFs), following one another with the same orientation, were found at the region. The 2nd ORF (ORF-ts) has significant amino acid sequence homologies to the previously known terminase small subunits of other bacteriophages. The putative terminase small subunit gene has a presumptive NTP-hydrolysis motif and a helix-turn-helix motif. The cleavage site for the first round of packaging was found to be located at the coding sequence of the putative terminase small subunit gene. The fourth ORF, even if partially sequenced, has a good amino acid sequence homology to the portal vertex proteins of other bacteriophages representing the evolutionarily conserved arrangements of genes near the pac site of this bacteriophage, $\PhiFC1$.

• Journal of Microbiology and Biotechnology
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• v.29 no.5
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• pp.696-703
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• 2019

Cronobacter sakazakii is an opportunistic pathogen causing serious infections in neonates. In this study, a bacteriophage ${\Phi}CS01$, which infects C. sakazakii, was isolated from swine feces and its morphology, growth parameters, and genomic analysis were investigated. Transmission electron microscopy revealed that ${\Phi}CS01$ has a spherical head and is 65.74 nm in diameter with a 98.75 nm contracted tail, suggesting that it belongs to the family Myoviridae. The major viral proteins are approximately 71 kDa and 64 kDa in size. The latent period of ${\Phi}CS01$ was shown to be 60 min, and the burst size was 90.7 pfu (plaque-forming units)/infected cell. Bacteriophage ${\Phi}CS01$ was stable at $4-60^{\circ}C$ for 1 h and lost infectivity after 1 h of heating at $70^{\circ}C$. Infectivity remained unaffected at pH 4-9 for 2 h, while the bacteriophage was inactivated at pH <3 or >10. The double-stranded ${\Phi}CS01$ DNA genome consists of 48,195 base pairs, with 75 predicted open reading frames. Phylogenetic analysis is closely related to that of the previously reported C. sakazakii phage ESP2949-1. The newly isolated ${\Phi}CS01$ shows infectivity in the host bacterium C. sakazakii, indicating that it may be a promising alternative to antibacterial agents for the removal of C. sakazakii from powdered infant formulas.

• Journal of Microbiology and Biotechnology
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• v.17 no.2
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• pp.262-270
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• 2007

Of the twelve lytic bacteriophages recovered from five different fermenting cucumber tanks that were inoculated with Pediococcus sp. LA0281, a lytic phage, ${\phi}ps05$, was characterized in the present study. The plaques were mostly clear and round-shaped on the lawn of starter strain, indicating lytic phage. Overall appearance indicated that it belongs to the Siphoviridae family or Bradley's group B1, with a small isometric head and a flexible noncontractile tail with swollen base plate. The average size was found to be 51.2 nm in head diameter and 11.6 nm wide ${\times}$ 129.6 nm long for the tail. The single-step growth kinetics curve showed that the eclipse and the latent period were 29 min and 34 min, respectively, and an average burst size was calculated to be 12 particles per infective center. The optimum proliferating temperature ($35^{\circ}C$) was slightly lower than that of cell growth ($35\;to\;40^{\circ}C$). The structural proteins revealed by SDS-PAGE consisted of one main protein of 33 kDa and three minor proteins of 85, 58, and 52 kDa. The phage genome was a linear double-stranded DNA without cohesive ends. Based on the single and double digestion patterns obtained by EcoRI, HindIII, and SalI, the physical map was constructed. The overall size of the phage genome was estimated to be 24.1 kb. The present report describes the presence of a lytic phage active against a commercial starter culture Pediococcus sp. LA0281 in cucumber fermentation, and a preliminary study characterizes the phage on bacterial successions in the process of starter-added cucumber fermentation.

• The Plant Pathology Journal
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• v.32 no.6
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• pp.584-588
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• 2016

Several Bacillus species were isolated from rice field soils, and 16S rRNA gene sequence analysis showed that Bacillus cereus was the most abundant. A strain named BC1 showed antifungal activity against Rhizoctonia solani. Bacteriophages infecting strain BC1 were isolated from the same soil sample. The isolated phage PK16 had an icosahedral head of $100{\pm}5nm$ and tail of $200{\pm}5nm$, indicating that it belonged to the family Myoviridae. Analysis of the complete linear dsDNA genome revealed a 158,127-bp genome with G + C content of 39.9% comprising 235 open reading frames as well as 19 tRNA genes (including 1 pseudogene). Blastp analysis showed that the proteins encoded by the PK16 genome had the closest hits to proteins of seven different bacteriophages. A neighbor-joining phylogenetic tree based on the major capsid protein showed a robust clustering of phage PK16 with phage JBP901 and BCP8-2 isolated from Korean fermented food.

• Food Science of Animal Resources
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• v.40 no.5
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• pp.746-757
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• 2020

Enterotoxigenic Escherichia coli (ETEC) is the major pathogenic E. coli that causes diarrhea and edema in post-weaning piglets. In this study, we describe the morphology and characteristics of ØCJ19, a bacteriophage that infects ETEC, and performed genetic analysis. Phage ØCJ19 belongs to the family Myoviridae. One-step growth curve showed a latent phase of 5 min and burst size of approximately 20 phage particles/infected cell. Phage infectivity was stable for 2 h between 4℃ and 55℃, and the phage was stable between pH 3 and 11. Genetic analysis revealed that phage ØCJ19 has a total of 49,567 bases and 79 open reading frames (ORFs). The full genomic sequence of phage ØCJ19 showed the most similarity to an Escherichia phage, vB_EcoS_ESCO41. There were no genes encoding lysogeny, toxins, virulence factors, or antibiotic resistance in this phage, suggesting that this phage can be used safely as a biological agent to control ETEC. Comparative genomic analysis in terms of the tail fiber proteins could provide genetic insight into host recognition and the relationship with other coliphages. These results showed the possibility to improve food safety by applying phage ØCJ19 to foods of animal origin contaminated with ETEC and suggests that it could be the basis for establishing a safety management system in the animal husbandry.

• Journal of Microbiology and Biotechnology
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• v.22 no.12
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• pp.1613-1620
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• 2012

Bacterial wilt caused by Ralstonia solanacearum is a devastating disease of many economically important crops. Since there is no promising control strategy for bacterial wilt, phage therapy could be adopted using virulent phages. We used phage PE204 as a model lytic bacteriophage to investigate its biocontrol potential for bacterial wilt on tomato plants. The phage PE204 has a short-tailed icosahedral structure and double-stranded DNA genome similar to that of the members of Podoviridae. PE204 is stable under a wide range of temperature and pH, and is also stable in the presence of the surfactant Silwet L-77. An artificial soil microcosm (ASM) to study phage stability in soil was adopted to investigate phage viability under a controlled system. Whereas phage showed less stability under elevated temperature in the ASM, the presence of host bacteria helped to maintain a stable phage population. Simultaneous treatment of phage PE204 at $10^8$ PFU/ml with R. solanacearum on tomato rhizosphere completely inhibited bacterial wilt occurrence, and amendment of Silwet L-77 at 0.1% to the phage suspension did not impair the disease control activity of PE204. The biocontrol activities of phage PE204 application onto tomato rhizosphere before or after R. solanacearum inoculation were also investigated. Whereas pretreatment with the phage was not effective in the control of bacterial wilt, post-treatment of PE204 delayed bacterial wilt development. Our results suggested that appropriate application of lytic phages to the plant root system with a surfactant such as Silwet L-77 could be used to control the bacterial wilt of crops.

• Korean Journal of Microbiology
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• v.49 no.1
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• pp.99-104
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• 2013

Bacteriophage P2 sir mutants are inefficient helpers for their satellite bacteriophage P4. The term, "P2 sir-associated helper inefficiency" has been used to define this phenomenon and it has been suggested that the DNA sequence difference between the cos region of P2 and that of P4 is responsible. To test this hypothesis, P4 derivative phage, P4 sid71 cosP2, containing the cos region of P2 and sid71 allele was constructed through several in vitro DNA manipulation steps. Its burst size was determined using a one-step growth experiment. The results showed that the substitution of the cos region of P2 for the cos region of P4 in P4 sid71 cosP2 overcame "P2 sir-associated helper inefficiency". P4 sid71 cosP2 stock phages prepared with P2 wild type helper and P2 sir helper were analyzed using a CsCl buoyant equilibrium density gradient experiment. The results revealed that the phage particles containing three copies of the P4 genome were the predominant particles in both cases.

• Korean Journal of Microbiology
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• v.34 no.4
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• pp.236-242
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• 1998

While bacteriophage P2-P4 system is very useful experimental tool for the study of viral capsid assembly, there is no useful plasmid vector for the DNA manipulation in bacteriophage P2-P4 system. In this study, a new vector plasmid, P4 ash8 (sid71) kmr, was constructed by swapping the non-essential region of P4 DNA for kanamycin resistance(kmr) gene cassette of plasmid pUC4-K. P4 ash8 sid71 was starting material for the construction, since it tends to be maintained as a plasmid in the absence of the helper phage. The total size of this chimera was designed to be packaged into P4 or P2 size heads with induction by P2 infection. The conversion of plasmid P4 ash8 (sid71) kmr to bacteriophage was proved by burst size determination experiment and CsCl buoyant equilibrium density gradient experiment. Integrase destructed P4 derivative, P4 ash8 sid71 kmr intS, was able to be constructed easily by in vitro DNA manipulation of P4 ash8 sid71 kmr. The plasmid stability experiment with P4 ash8 sid71 kmr if/tS showed that the integrase of P4 affects the stable maintenance of plasmid P4 state.