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  • 1
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    Antagonistic coevolution accelerates molecular evolution (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-02-26
    Description: The Red Queen hypothesis proposes that coevolution of interacting species (such as hosts and parasites) should drive molecular evolution through continual natural selection for adaptation and counter-adaptation. Although the divergence observed at some host-resistance and parasite-infectivity genes is consistent with this, the long time periods typically required to study coevolution have so far prevented any direct empirical test. Here we show, using experimental populations of the bacterium Pseudomonas fluorescens SBW25 and its viral parasite, phage Phi2 (refs 10, 11), that the rate of molecular evolution in the phage was far higher when both bacterium and phage coevolved with each other than when phage evolved against a constant host genotype. Coevolution also resulted in far greater genetic divergence between replicate populations, which was correlated with the range of hosts that coevolved phage were able to infect. Consistent with this, the most rapidly evolving phage genes under coevolution were those involved in host infection. These results demonstrate, at both the genomic and phenotypic level, that antagonistic coevolution is a cause of rapid and divergent evolution, and is likely to be a major driver of evolutionary change within species.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717453/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717453/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Paterson, Steve -- Vogwill, Tom -- Buckling, Angus -- Benmayor, Rebecca -- Spiers, Andrew J -- Thomson, Nicholas R -- Quail, Mike -- Smith, Frances -- Walker, Danielle -- Libberton, Ben -- Fenton, Andrew -- Hall, Neil -- Brockhurst, Michael A -- 079643/Wellcome Trust/United Kingdom -- 098051/Wellcome Trust/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2010 Mar 11;464(7286):275-8. doi: 10.1038/nature08798. Epub 2010 Feb 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20182425" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophages/genetics/*physiology ; *Biological Evolution ; *Evolution, Molecular ; Genetic Variation ; Molecular Sequence Data ; Phenotype ; Pseudomonas fluorescens/*genetics/*virology ; Selection, Genetic/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Genomics. Genome project standards in a new era of sequencing (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-10-10
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3854948/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3854948/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chain, P S G -- Grafham, D V -- Fulton, R S -- Fitzgerald, M G -- Hostetler, J -- Muzny, D -- Ali, J -- Birren, B -- Bruce, D C -- Buhay, C -- Cole, J R -- Ding, Y -- Dugan, S -- Field, D -- Garrity, G M -- Gibbs, R -- Graves, T -- Han, C S -- Harrison, S H -- Highlander, S -- Hugenholtz, P -- Khouri, H M -- Kodira, C D -- Kolker, E -- Kyrpides, N C -- Lang, D -- Lapidus, A -- Malfatti, S A -- Markowitz, V -- Metha, T -- Nelson, K E -- Parkhill, J -- Pitluck, S -- Qin, X -- Read, T D -- Schmutz, J -- Sozhamannan, S -- Sterk, P -- Strausberg, R L -- Sutton, G -- Thomson, N R -- Tiedje, J M -- Weinstock, G -- Wollam, A -- Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium -- Detter, J C -- U54 HG004968/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2009 Oct 9;326(5950):236-7. doi: 10.1126/science.1180614.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA. pchain@lanl.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19815760" target="_blank"〉PubMed〈/a〉
    Keywords: Computational Biology ; Databases, Nucleic Acid/*standards ; *Genome ; Genomics/*standards ; Sequence Analysis, DNA/*standards
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-09-14
    Description: The global epidemic of multidrug-resistant Salmonella Typhimurium DT104 provides an important example, both in terms of the agent and its resistance, of a widely disseminated zoonotic pathogen. Here, with an unprecedented national collection of isolates collected contemporaneously from humans and animals and including a sample of internationally derived isolates, we have used whole-genome sequencing to dissect the phylogenetic associations of the bacterium and its antimicrobial resistance genes through the course of an epidemic. Contrary to current tenets supporting a single homogeneous epidemic, we demonstrate that the bacterium and its resistance genes were largely maintained within animal and human populations separately and that there was limited transmission, in either direction. We also show considerable variation in the resistance profiles, in contrast to the largely stable bacterial core genome, which emphasizes the critical importance of integrated genotypic data sets in understanding the ecology of bacterial zoonoses and antimicrobial resistance.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012302/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012302/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mather, A E -- Reid, S W J -- Maskell, D J -- Parkhill, J -- Fookes, M C -- Harris, S R -- Brown, D J -- Coia, J E -- Mulvey, M R -- Gilmour, M W -- Petrovska, L -- de Pinna, E -- Kuroda, M -- Akiba, M -- Izumiya, H -- Connor, T R -- Suchard, M A -- Lemey, P -- Mellor, D J -- Haydon, D T -- Thomson, N R -- 098051/Wellcome Trust/United Kingdom -- 260864/European Research Council/International -- AI107034/AI/NIAID NIH HHS/ -- HG006139/HG/NHGRI NIH HHS/ -- R01 AI107034/AI/NIAID NIH HHS/ -- R01 GM086887/GM/NIGMS NIH HHS/ -- R01 HG006139/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2013 Sep 27;341(6153):1514-7. doi: 10.1126/science.1240578. Epub 2013 Sep 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24030491" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Drug Resistance, Multiple, Bacterial/*genetics ; Epidemics ; Genome, Bacterial ; *Host-Pathogen Interactions ; Humans ; Molecular Sequence Data ; Phylogeny ; Salmonella Infections/epidemiology/*microbiology ; Salmonella Infections, Animal/epidemiology/*microbiology ; Salmonella typhimurium/*classification/drug effects/genetics ; Zoonoses/*microbiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Evidence for several waves of global transmission in the seventh cholera pandemic (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-08-26
    Description: Vibrio cholerae is a globally important pathogen that is endemic in many areas of the world and causes 3-5 million reported cases of cholera every year. Historically, there have been seven acknowledged cholera pandemics; recent outbreaks in Zimbabwe and Haiti are included in the seventh and ongoing pandemic. Only isolates in serogroup O1 (consisting of two biotypes known as 'classical' and 'El Tor') and the derivative O139 can cause epidemic cholera. It is believed that the first six cholera pandemics were caused by the classical biotype, but El Tor has subsequently spread globally and replaced the classical biotype in the current pandemic. Detailed molecular epidemiological mapping of cholera has been compromised by a reliance on sub-genomic regions such as mobile elements to infer relationships, making El Tor isolates associated with the seventh pandemic seem superficially diverse. To understand the underlying phylogeny of the lineage responsible for the current pandemic, we identified high-resolution markers (single nucleotide polymorphisms; SNPs) in 154 whole-genome sequences of globally and temporally representative V. cholerae isolates. Using this phylogeny, we show here that the seventh pandemic has spread from the Bay of Bengal in at least three independent but overlapping waves with a common ancestor in the 1950s, and identify several transcontinental transmission events. Additionally, we show how the acquisition of the SXT family of antibiotic resistance elements has shaped pandemic spread, and show that this family was first acquired at least ten years before its discovery in V. cholerae.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736323/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736323/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mutreja, Ankur -- Kim, Dong Wook -- Thomson, Nicholas R -- Connor, Thomas R -- Lee, Je Hee -- Kariuki, Samuel -- Croucher, Nicholas J -- Choi, Seon Young -- Harris, Simon R -- Lebens, Michael -- Niyogi, Swapan Kumar -- Kim, Eun Jin -- Ramamurthy, T -- Chun, Jongsik -- Wood, James L N -- Clemens, John D -- Czerkinsky, Cecil -- Nair, G Balakrish -- Holmgren, Jan -- Parkhill, Julian -- Dougan, Gordon -- 076962/Wellcome Trust/United Kingdom -- 076964/Wellcome Trust/United Kingdom -- England -- Nature. 2011 Aug 24;477(7365):462-5. doi: 10.1038/nature10392.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21866102" target="_blank"〉PubMed〈/a〉
    Keywords: Cholera/*epidemiology/microbiology/*transmission ; Genome, Bacterial/genetics ; Haiti/epidemiology ; Humans ; Likelihood Functions ; Molecular Epidemiology ; Pandemics/*statistics & numerical data ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Vibrio cholerae/classification/*genetics/*isolation & purification ; Zimbabwe/epidemiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures (2017)
    BioMed Central
    Details
    Publication Date: 2017-05-06
    Description: Chlamydia abortus (formerly Chlamydophila abortus) is an economically important livestock pathogen, causing ovine enzootic abortion (OEA), and can also cause zoonotic infections in hum...
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 6
    Electronic Resource
    Electronic Resource
    Ducted whistler-mode signals received at two widely spaced locations (1996)
    Springer
    Annales geophysicae 14 (1996), S. 619-627 
    Details
    ISSN: 0992-7689
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract Whistler-mode signals from a single VLF transmitter that have propagated in the same duct, have been observed simultaneously at Faraday, Antarctica (65°S, 64°W) and Dunedin, New Zealand (46°S, 171°E). The signals received have group-delay times that differ in the order of 10 ms, which can be explained by the differences in southern-hemisphere sub-ionospheric propagation time from duct exit region to receiver for the two sites. This difference has been used to determine the location of the duct exit region, with confirmation provided by arrival-bearing information from both sites. The whistler-mode signals typically occur one or two days after geomagnetic activity, with Kp\geq5. The sub-ionospheric-propagation model, LWPC, is used to estimate the whistler-mode power radiated from the duct exit region. These results are then combined with estimated loss values for ionospheric and ducted transmission to investigate the role of wave-particle amplification or absorption. On at least half of the events studied, plasmaspheric amplification of the signals appears to be needed to explain the observed whistler-mode signal strengths.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s00585-996-0619-0
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  • 7
    Electronic Resource
    Electronic Resource
    Evidence of more efficient whistler-mode transmission during periods of increased magnetic activity (1997)
    Springer
    Annales geophysicae 15 (1997), S. 999-1004 
    Details
    ISSN: 0992-7689
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences , Physics
    Notes: Abstract In a previous study it was reported that whistler- mode signals received at Faraday, Antarctica (65°S,64°W) and Dunedin, New Zealand (46°S, 171°E) with entry regions in Pacific longitudes (typically from the VLF transmitter NLK, Seattle, USA) showed an increase in transmission of wave energy as magnetic activity increased. However, signals with entry regions in Atlantic longitudes (typically from the NSS transmitter, Annapolis, USA) did not appear to show such a relationship. This paper reports the results of a study of the same two longitude ranges but with the opposite transmitter providing additional whistler-mode signal information, with L-values in the range 1.8–2.6. Transmissions from NLK once again indicate a relationship between the transmission of wave energy and magnetic activity even though the signals were propagating in Atlantic longitudes, not Pacific. Any trend in NSS events observed at Dunedin was obscured by a limited range of magnetic activity, and duct exit regions so close to the receiver that small-scale excitation effects appeared to be occurring. However, by combining data from both longitudes, i.e Pacific and Atlantic, and using only ducts with exit regions that were 〉 500 km from the receiver, NSS events were found to show the same trend as NLK events. No significant longitude-dependent or transmitter-dependent variations in duct efficiency could be detected. Duct efficiency increases by a factor of about 30 with Kp = 2–8 and this result is discussed in terms of changes in wave-particle interactions and duct size.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s00585-997-0999-9
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  • 8
    Electronic Resource
    Electronic Resource
    The Rap and Hor proteins of Erwinia, Serratia and Yersinia: a novel subgroup in a growing superfamily of proteins regulating diverse physiological processes in bacterial pathogens (1997)
    Oxford, UK : Blackwell Science Ltd
    Molecular microbiology 26 (1997), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: The enteric bacterium Serratia marcescens is an opportunistic human pathogen. The strain ATCC39006 makes the red pigment, prodigiosin (Pig), and the β-lactam antibiotic carbapenem (Car). Mutants were isolated that were concomitantly defective for Pig and Car production. These mutants were found to have a mutation in the rap gene (regulation of antibiotic and pigment). Sequence analysis of the rap gene revealed a predicted protein product showing strong homology to SlyA, originally thought to be a haemolytic virulence determinant in Salmonella typhimurium. Homologues of rap were detected in several bacterial genera, including Salmonella, Yersinia, Enterobacter, and species of the plant pathogen, Erwinia. The Erwinia horEr (homologue of rap) and the Yersinia horYe genes were also found to be very similar to rap and slyA. Marker exchange mutagenesis of horEr revealed that it encoded a regulatory protein controlling the production of antibiotic and exoenzyme virulence determinants in the phytopathogen, Erwinia carotovora subspecies carotovora. We have shown that these new homologues of SlyA form a highly conserved subgroup of a growing superfamily of bacterial regulatory proteins controlling diverse physiological processes in human, animal and plant pathogens.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.1997.5981976.x
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  • 9
    Electronic Resource
    Electronic Resource
    Alaska to New Zealand whistler-mode transmission at 6.8 kHz (1974)
    [s.l.] : Nature Publishing Group
    Nature 248 (1974), S. 493-493 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] We report here one result of an experiment for which we set up a transportable v.l.f. transmitter in Alaska and a receiving station in New Zealand located so as to be approximately geomagnetically conjugate. Since the Otago group already had v.l.f. receiving facilities at Dunedin, New Zealand, the ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/248493a0
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  • 10
    Electronic Resource
    Electronic Resource
    Massive gene decay in the leprosy bacillus (2001)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 409 (2001), S. 1007-1011 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Leprosy, a chronic human neurological disease, results from infection with the obligate intracellular pathogen Mycobacterium leprae, a close relative of the tubercle bacillus. Mycobacterium leprae has the longest doubling time of all known bacteria and has thwarted every effort at culture in the ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/35059006
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