scholarly journals Phylogenomic Network and Comparative Genomics Reveal a Diverged Member of the ϕKZ-Related Group, Marine Vibrio Phage ϕJM-2012

2013 ◽  
Vol 87 (23) ◽  
pp. 12866-12878 ◽  
Author(s):  
Ho Bin Jang ◽  
Fernand F. Fagutao ◽  
Seong Won Nho ◽  
Seong Bin Park ◽  
In Seok Cha ◽  
...  
Keyword(s):  
Structural Changes ◽  
Comparative Genomic ◽  
Tail Fiber ◽  
Phage Group ◽  
Content Type ◽  
Evolutionary Forces ◽  
Related Group ◽  
Highly Correlated ◽  
Conserved Core ◽  
Unique Genes

Bacteriophages are the largest reservoir of genetic diversity. Here we describe the novel phage ϕJM-2012. This natural isolate from marineVibrio cyclitrophicuspossesses very few gene contents relevant to other well-studied marineVibriophages. To better understand its evolutionary history, we built a mathematical model of pairwise relationships among 1,221 phage genomes, in which the genomes (nodes) are linked by edges representing the normalized number of shared orthologous protein families. This weighted network revealed that ϕJM-2012 was connected to only five members of thePseudomonasϕKZ-like phage family in an isolated network, strongly indicating that it belongs to this phage group. However, comparative genomic analyses highlighted an almost complete loss of colinearity with the ϕKZ-related genomes and little conservation of gene order, probably reflecting the action of distinct evolutionary forces on the genome of ϕJM-2012. In this phage, typical conserved core genes, including six RNA polymerase genes, were frequently displaced and the hyperplastic regions were rich in both unique genes and predicted unidirectional promoters with highly correlated orientations. Further, analysis of the ϕJM-2012 genome showed that segments of the conserved N-terminal parts of ϕKZ tail fiber paralogs exhibited evidence of combinatorial assortment, having switched transcriptional orientation, and there was recruitment and/or structural changes among phage endolysins and tail spike protein. Thus, this naturally occurring phage appears to have branched from a common ancestor of the ϕKZ-related groups, showing a distinct genomic architecture and unique genes that most likely reflect adaptation to its chosen host and environment.

scholarly journals Characterization and Comparative Genomic Analysis of a Novel Bacteriophage, SFP10, Simultaneously Inhibiting both Salmonella enterica and Escherichia coli O157:H7

2011 ◽  
Vol 78 (1) ◽  
pp. 58-69 ◽  
Author(s):  
Minjung Park ◽  
Ju-Hoon Lee ◽  
Hakdong Shin ◽  
Minsik Kim ◽  
Jeongjoon Choi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Salmonella Enterica ◽  
Burst Size ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Tail Fiber ◽  
Content Type ◽  
E Coli ◽  
Development Of Resistance

ABSTRACTSalmonella entericaandEscherichia coliO157:H7 are major food-borne pathogens causing serious illness. Phage SFP10, which revealed effective infection of bothS. entericaandE. coliO157:H7, was isolated and characterized. SFP10 contains a 158-kb double-stranded DNA genome belonging to the Vi01 phage-like familyMyoviridae.In vitroadsorption assays showed that the adsorption constant rates to bothSalmonella entericaserovar Typhimurium andE. coliO157:H7 were 2.50 × 10−8ml/min and 1.91 × 10−8ml/min, respectively. One-step growth analysis revealed that SFP10 has a shorter latent period (25 min) and a larger burst size (>200 PFU) than ordinaryMyoviridaephages, suggesting effective host infection and lytic activity. However, differential development of resistance to SFP10 inS.Typhimurium andE. coliO157:H7 was observed; bacteriophage-insensitive mutant (BIM) frequencies of 1.19 × 10−2CFU/ml forS.Typhimurium and 4.58 × 10−5CFU/ml forE. coliO157:H7 were found, indicating that SFP10 should be active and stable for control ofE. coliO157:H7 with minimal emergence of SFP10-resistant pathogens but may not be forS.Typhimurium. Specific mutation ofrfaLinS.Typhimurium andE. coliO157:H7 revealed the O antigen as an SFP10 receptor for both bacteria. Genome sequence analysis of SFP10 and its comparative analysis with homologousSalmonellaVi01 andShigellaphiSboM-AG3 phages revealed that their tail fiber and tail spike genes share low sequence identity, implying that the genes are major host specificity determinants. This is the first report identifying specific infection and inhibition ofSalmonellaTyphimurium andE. coliO157:H7 by a single bacteriophage.

scholarly journals Novel Phage Group Infecting Lactobacillus delbrueckii subsp. lactis, as Revealed by Genomic and Proteomic Analysis of Bacteriophage Ldl1

2014 ◽  
Vol 81 (4) ◽  
pp. 1319-1326 ◽  
Author(s):  
Eoghan Casey ◽  
Jennifer Mahony ◽  
Horst Neve ◽  
Jean-Paul Noben ◽  
Fabio Dal Bello ◽  
...  
Keyword(s):  
Burst Size ◽  
Bacterial Species ◽  
Lactobacillus Delbrueckii ◽  
Comparative Genomic ◽  
Phage Group ◽  
Content Type ◽  
Large Head ◽  
Electron Microscopy Analysis ◽  
Microscopy Analysis

ABSTRACTLdl1 is a virulent phage infecting the dairy starterLactobacillus delbrueckiisubsp.lactisLdlS. Electron microscopy analysis revealed that this phage exhibits a large head and a long tail and bears little resemblance to other characterized phages infectingLactobacillus delbrueckii.In vitropropagation of this phage revealed a latent period of 30 to 40 min and a burst size of 59.9 ± 1.9 phage particles. Comparative genomic and proteomic analyses showed remarkable similarity between the genome of Ldl1 and that ofLactobacillus plantarumphage ATCC 8014-B2. The genomic and proteomic characteristics of Ldl1 demonstrate that this phage does not belong to any of the four previously recognizedL. delbrueckiiphage groups, necessitating the creation of a new group, called group e, thus adding to the knowledge on the diversity of phages targeting strains of this industrially important lactic acid bacterial species.

scholarly journals Genomic Investigation of Lysogen Formation and Host Lysis Systems of the Salmonella Temperate Bacteriophage SPN9CC

2013 ◽  
Vol 80 (1) ◽  
pp. 374-384 ◽  
Author(s):  
Hakdong Shin ◽  
Ju-Hoon Lee ◽  
Hyunjin Yoon ◽  
Dong-Hyun Kang ◽  
Sangryeol Ryu
Keyword(s):  
Host Cell ◽  
Burst Size ◽  
Group Analysis ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Cell Lysis ◽  
Comparative Genomic ◽  
Phage Group ◽  
Content Type ◽  
Lysis Activity

ABSTRACTTo understand phage infection and host cell lysis mechanisms in pathogenicSalmonella, a novelSalmonella entericaserovar Typhimurium-targeting bacteriophage, SPN9CC, belonging to thePodoviridaefamily was isolated and characterized. The phage infectsS. Typhimurium via the O antigen of lipopolysaccharide (LPS) and forms clear plaques with cloudy centers due to lysogen formation. Phylogenetic analysis of phage major capsid proteins revealed that this phage is a member of the lysogen-forming P22-like phage group. However, comparative genomic analysis of SPN9CC with P22-like phages indicated that their lysogeny control regions and host cell lysis gene clusters show very low levels of identity, suggesting that lysogen formation and host cell lysis mechanisms may be diverse among phages in this group. Analysis of the expression of SPN9CC host cell lysis genes encoding holin, endolysin, and Rz/Rz1-like proteins individually or in combinations inS. Typhimurium andEscherichia colihosts revealed that collaboration of these lysis proteins is important for the lysis of both hosts and that holin is a key protein. To further investigate the role of the lysogeny control region in phage SPN9CC, a ΔcImutant (SPN9CCM) of phage SPN9CC was constructed. The mutant does not produce a cloudy center in the plaques, suggesting that this mutant phage is virulent and no longer temperate. Subsequent comparative one-step growth analysis and challenge assays revealed that SPN9CCM has shorter eclipse/latency periods and a larger burst size, as well as higher host cell lysis activity, than SPN9CC. The present work indicates the possibility of engineering temperate phages as promising biocontrol agents similar to virulent phages.

scholarly journals An Evolutionary Link between Natural Transformation and CRISPR Adaptive Immunity

mBio ◽  
2012 ◽  
Vol 3 (5) ◽  
Author(s):  
Peter Jorth ◽  
Marvin Whiteley
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Bacterial Diversity ◽  
Natural Transformation ◽  
Bacterial Species ◽  
Comparative Genomic ◽  
Content Type ◽  
Immune Systems ◽  
Adaptive Immune ◽  
Adaptive Immune Systems

ABSTRACTNatural transformation by competent bacteria is a primary means of horizontal gene transfer; however, evidence that competence drives bacterial diversity and evolution has remained elusive. To test this theory, we used a retrospective comparative genomic approach to analyze the evolutionary history ofAggregatibacter actinomycetemcomitans, a bacterial species with both competent and noncompetent sister strains. Through comparative genomic analyses, we reveal that competence is evolutionarily linked to genomic diversity and speciation. Competence loss occurs frequently during evolution and is followed by the loss of clustered regularly interspaced short palindromic repeats (CRISPRs), bacterial adaptive immune systems that protect against parasitic DNA. Relative to noncompetent strains, competent bacteria have larger genomes containing multiple rearrangements. In contrast, noncompetent bacterial genomes are extremely stable but paradoxically susceptible to infective DNA elements, which contribute to noncompetent strain genetic diversity. Moreover, incomplete noncompetent strain CRISPR immune systems are enriched for self-targeting elements, which suggests that the CRISPRs have been co-opted for bacterial gene regulation, similar to eukaryotic microRNAs derived from the antiviral RNA interference pathway.IMPORTANCEThe human microbiome is rich with thousands of diverse bacterial species. One mechanism driving this diversity is horizontal gene transfer by natural transformation, whereby naturally competent bacteria take up environmental DNA and incorporate new genes into their genomes. Competence is theorized to accelerate evolution; however, attempts to test this theory have proved difficult. Through genetic analyses of the human periodontal pathogenAggregatibacter actinomycetemcomitans, we have discovered an evolutionary connection between competence systems promoting gene acquisition and CRISPRs (clustered regularly interspaced short palindromic repeats), adaptive immune systems that protect bacteria against genetic parasites. We show that competentA. actinomycetemcomitansstrains have numerous redundant CRISPR immune systems, while noncompetent bacteria have lost their CRISPR immune systems because of inactivating mutations. Together, the evolutionary data linking the evolution of competence and CRISPRs reveals unique mechanisms promoting genetic heterogeneity and the rise of new bacterial species, providing insight into complex mechanisms underlying bacterial diversity in the human body.

What's happening to international business?

2014 ◽  
Vol 10 (1/2) ◽  
pp. 51-64 ◽  
Author(s):  
Snejina Michailova ◽  
Janne Tienari
Keyword(s):  
International Business ◽  
Design Methodology ◽  
Structural Changes ◽  
Business Schools ◽  
Academic Discipline ◽  
Academic Community ◽  
Content Type ◽  
Disciplinary Identity ◽  
Management Scholar ◽  
Self Examination

Purpose – This paper aims to outline different views on international business (IB) as an academic discipline and looks into how IB scholars can cope with challenges to their disciplinary identity when stand-alone IB departments are merged with other departments such as management, marketing or strategy in business schools and universities. Design/methodology/approach – The article offers a critical reflection on the development and future of IB as a discipline. The two authors are an IB and a Management scholar, both of whom were engaged in recent departmental mergers at their respective business schools. While the authors do not analyze these particular mergers, their experiences are inevitably interwoven in the views they express. Findings – Mergers of stand-alone IB departments with other departments bring to light the nature of the IB discipline as a contested terrain. The article discusses how these structural changes challenge the disciplinary identity of IB scholars. It contributes, first, to discussions on the development of IB as a discipline and, second, to understanding identities and identification during major organizational change events in academia. Research limitations/implications – The authors suggest that the threat of marginalization of IB in the context of business schools and universities necessitates a move beyond the “big questions” debate to a critical self-examination and reflection on IB as a discipline and as a global scholarly community. Originality/value – The article offers a critical view on current processes and challenges related to IB as a discipline and an academic community.

scholarly journals Antibiotic Resistance Markers in Burkholderia pseudomallei Strain Bp1651 Identified by Genome Sequence Analysis

2017 ◽  
Vol 61 (6) ◽  
Author(s):  
Julia V. Bugrysheva ◽  
David Sue ◽  
Jay E. Gee ◽  
Mindy G. Elrod ◽  
Alex R. Hoffmaster ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Clavulanic Acid ◽  
Burkholderia Pseudomallei ◽  
Efflux Pump ◽  
Point Mutations ◽  
Comparative Genomic ◽  
Content Type ◽  
Reductase Gene ◽  
Amoxicillin Clavulanic Acid ◽  
Imipenem Resistance

ABSTRACT Burkholderia pseudomallei Bp1651 is resistant to several classes of antibiotics that are usually effective for treatment of melioidosis, including tetracyclines, sulfonamides, and β-lactams such as penicillins (amoxicillin-clavulanic acid), cephalosporins (ceftazidime), and carbapenems (imipenem and meropenem). We sequenced, assembled, and annotated the Bp1651 genome and analyzed the sequence using comparative genomic analyses with susceptible strains, keyword searches of the annotation, publicly available antimicrobial resistance prediction tools, and published reports. More than 100 genes in the Bp1651 sequence were identified as potentially contributing to antimicrobial resistance. Most notably, we identified three previously uncharacterized point mutations in penA, which codes for a class A β-lactamase and was previously implicated in resistance to β-lactam antibiotics. The mutations result in amino acid changes T147A, D240G, and V261I. When individually introduced into select agent-excluded B. pseudomallei strain Bp82, D240G was found to contribute to ceftazidime resistance and T147A contributed to amoxicillin-clavulanic acid and imipenem resistance. This study provides the first evidence that mutations in penA may alter susceptibility to carbapenems in B. pseudomallei. Another mutation of interest was a point mutation affecting the dihydrofolate reductase gene folA, which likely explains the trimethoprim resistance of this strain. Bp1651 was susceptible to aminoglycosides likely because of a frameshift in the amrB gene, the transporter subunit of the AmrAB-OprA efflux pump. These findings expand the role of penA to include resistance to carbapenems and may assist in the development of molecular diagnostics that predict antimicrobial resistance and provide guidance for treatment of melioidosis.

scholarly journals Lytic Myophage Abp53 Encodes Several Proteins Similar to Those Encoded by Host Acinetobacter baumannii and Phage phiKO2

2011 ◽  
Vol 77 (19) ◽  
pp. 6755-6762 ◽  
Author(s):  
Chia-Ni Lee ◽  
Tsai-Tien Tseng ◽  
Juey-Wen Lin ◽  
Yung-Chieh Fu ◽  
Shu-Fen Weng ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Burst Size ◽  
Sputum Sample ◽  
Polyacrylamide Gel Electrophoresis ◽  
Multiple Drug ◽  
Lytic Phage ◽  
Tail Fiber ◽  
Drug Resistant ◽  
Content Type ◽  
Multiple Drug Resistant

ABSTRACTAcinetobacter baumanniiis an important Gram-negative opportunistic pathogen causing nosocomial infections. The emergence of multiple-drug-resistantA. baumanniiisolates has increased in recent years. Directed toward phage therapy, a lytic phage ofA. baumannii, designated Abp53, was isolated from a sputum sample in this study. Abp53 has an isometric head and a contractile tail with tail fibers (belonging toMyoviridae), a latent period of about 10 min, and a burst size of approximately 150 PFU per infected cell. Abp53 could completely lyse 27% of theA. baumanniiisolates tested, which were all multiple drug resistant, but not other bacteria. Mg2+enhanced the adsorption and productivity of, and host lysis by, Abp53. Twenty Abp53 virion proteins were visualized in SDS-polyacrylamide gel electrophoresis, with a 47-kDa protein being the predicted major capsid protein. Abp53 has a double-stranded DNA genome of 95 kb. Sequence analyses of a 10-kb region revealed 8 open reading frames. Five of the encoded proteins, including 3 tail components and 2 hypothetical proteins, were similar to proteins encoded byA. baumanniistrain ACICU. ORF1176 (one of the tail components, 1,176 amino acids [aa]), which is also similar to tail protein gp21 ofKlebsiellaphage phiKO2, contained repeated domains similar to those within the ACICU_02717 protein ofA. baumanniiACICU and gp21. These findings suggest a common ancestry and horizontal gene transfer during evolution. As phages can expand the host range by domain duplication in tail fiber proteins, repeated domains in ORF1176 might have a similar significance in Abp53.

Detection of fungal decay by high-energy multiple impact (HEMI) testing

Holzforschung ◽  
2006 ◽  
Vol 60 (2) ◽  
pp. 217-222 ◽  
Author(s):  
Christian Brischke ◽  
Christian Robert Welzbacher ◽  
Andreas Otto Rapp
Keyword(s):  
Structural Changes ◽  
Brown Rot ◽  
High Energy ◽  
White Rot ◽  
Fungal Decay ◽  
Highly Correlated ◽  
Thermally Modified Wood ◽  
Impact Milling ◽  
Multiple Impact ◽  
Steel Balls

Abstract The suitability of a previously described high-energy multiple impact (HEMI) test for the detection of early fungal decay was examined. The HEMI test characterises the treatment severity of thermally modified wood by stressing the treated material by thousands of impacts of pounding steel balls. This method differentiates between heat treatment intensities, which are manifest as structural changes in the wood. Similar changes in wood structure are known for wood decayed by fungi. Pine (Pinus sylvestris L.) decayed by brown rot and beech (Fagus sylvatica L.) decayed by white rot were tested. Mass loss caused by fungal decay and resistance to impact milling (RIM) determined in HEMI tests were found to be highly correlated. Testing of non-degraded pine, beech, and ash (Fraxinus exelsior L.) showed only marginal effects of wood density on RIM. Furthermore, annual ring angles and RIM of spruce (Picea abies Karst.) were not correlated. Accordingly, the detection of RIM reduction in decayed wood is not masked by variations in density and orientation of the annual rings. Previous results showed no adverse effects of weathering on RIM. Thus, the detection of fungal decay with HEMI tests is feasible not only for laboratory purposes, but also for wood in outdoor applications that has already undergone weathering.

scholarly journals Antimicrobial Properties of 8-Hydroxyserrulat-14-en-19-oic Acid for Treatment of Implant-Associated Infections

2012 ◽  
Vol 57 (1) ◽  
pp. 333-342 ◽  
Author(s):  
Justyna Nowakowska ◽  
Hans J. Griesser ◽  
Marcus Textor ◽  
Regine Landmann ◽  
Nina Khanna
Keyword(s):  
Structural Changes ◽  
Treatment Options ◽  
Antimicrobial Properties ◽  
Bactericidal Effect ◽  
Mouse Tissue ◽  
Logarithmic Phase ◽  
Content Type ◽  
Gram Positive Bacteria ◽  
Time Kill

ABSTRACTTreatment options are limited for implant-associated infections (IAI) that are mainly caused by biofilm-forming staphylococci. We report here on the activity of the serrulatane compound 8-hydroxyserrulat-14-en-19-oic acid (EN4), a diterpene isolated from the Australian plantEremophila neglecta. EN4 elicited antimicrobial activity toward various Gram-positive bacteria but not to Gram-negative bacteria. It showed a similar bactericidal effect against logarithmic-phase, stationary-phase, and adherentStaphylococcus epidermidis, as well as against methicillin-susceptible and methicillin-resistantS. aureuswith MICs of 25 to 50 μg/ml and MBCs of 50 to 100 μg/ml. The bactericidal activity of EN4 was similar againstS. epidermidisand its Δicamutant, which is unable to produce polysaccharide intercellular adhesin-mediated biofilm. In time-kill studies, EN4 exhibited a rapid and concentration-dependent killing of staphylococci, reducing bacterial counts by >3 log10CFU/ml within 5 min at concentrations of >50 μg/ml. Investigation of the mode of action of EN4 revealed membranolytic properties and a general inhibition of macromolecular biosynthesis, suggesting a multitarget activity.In vitro-tested cytotoxicity on eukaryotic cells was time and concentration dependent in the range of the MBCs. EN4 was then tested in a mouse tissue cage model, where it showed neither bactericidal nor cytotoxic effects, indicating an inhibition of its activity. Inhibition assays revealed that this was caused by interactions with albumin. Overall, these findings suggest that, upon structural changes, EN4 might be a promising pharmacophore for the development of new antimicrobials to treat IAI.

Driving forces and structural changes of China as a market provider for Korea

2018 ◽  
Vol 22 (3) ◽  
pp. 194-211 ◽  
Author(s):  
Yongqi Feng ◽  
Tianshu Zhang
Keyword(s):  
Steady State ◽  
Driving Force ◽  
Design Methodology ◽  
Structural Changes ◽  
Driving Forces ◽  
Consumption Expenditure ◽  
Input Output ◽  
Content Type ◽  
Fixed Capital Formation ◽  
The Impact

Purpose The purpose of this paper is to provide a better understanding of the driving forces and structural changes of China as a market provider for Korea. This paper gives the answers for the following questions: How do China’s final demands trigger the growth of its imports from Korea? And what’s the impact of China’s final demands on the import in different industries? Design/methodology/approach Based on the Multi-Regional Input-Output model and World Input-Output Table database, this paper constructs the non-competitive imports input-output (IO) table of China to Korea. According to this table, we can calculate the induced imports coefficient and comprehensive induced import coefficients of China’s four final demands for imports from Korea in the 56 industries in China. Findings Among the four driving forces, the strongest one is changes in inventories and valuables. The impact of final consumption expenditure and fixed capital formation is much lower than that of changes in inventories and valuables, but they have a broader impact for the 56 industries. This paper finds out the China’s import induction of the final demands to Korea peaked in 2005 and 2010 and decreased greatly in 2014, so the position of China as market provider for Korea will no longer rise substantially, contrarily it will be in a steady state. Originality/value First, this paper constructs the non-competitive IO table to analyze the market provider issues between two countries and provides practical ways and methods for studies on the issues of imports and market provider. Second, this paper investigates the different roles of four final demands on driving force of China as market provider for Korea and the structural changes of China as a market provider for Korea among 56 industries from 2000 to 2014.

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