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0000-0001-5783-5269
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Centre National de la Recherche Scientifique
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Publisher: Elsevier BV
Date: 06-2008
DOI: 10.1016/J.VIROL.2008.01.049
Abstract: Simian immunodeficiency viruses (SIVs) are found in an extensive number of African primates, and humans continue to be exposed to these viruses by hunting and handling of primate bushmeat. The purpose of our study was to examine to what extent Piliocolobus badius subspecies are infected with SIV in order to better characterize SIVwrc in general and to gain further insight into the impact of geographic barriers and subspeciation on the evolution of SIVwrc. We analysed sixteen faecal s les and two tissue s les of the P. b. temminckii subspecies collected in the Abuko Nature Reserve (The Gambia, West Africa). SIV infection could only be identified in one tissue s le, and phylogenetic tree analyses of partial pol and env sequences showed that the new SIVwrcPbt virus is closely related to SIVwrcPbb strains from P. b. badius in the Taï forest (Côte d'Ivoire), thus suggesting that geographically separated subspecies are infected with a closely related virus. Molecular characterization and phylogenetic analysis of the full-length genome sequence confirmed that SIVwrcPbt is a species-specific SIV lineage, although it is distantly related to the SIVlho and SIVsun lineages across its entire genome. Characterization of additional SIVwrc viruses is needed to understand the ancestral phylogenetic relation to SIVs from l'Hoest and sun-tailed monkeys and whether recombination occurred between ancestors of the SIVwrc and SIVlho/sun lineages.
Publisher: eLife Sciences Publications, Ltd
Date: 28-06-2020
Publisher: Elsevier BV
Date: 1992
DOI: 10.1016/0303-2647(92)90016-R
Abstract: Sequences from the 5' end terminal part of 28S ribosomal RNA were obtained and compared for 22 animals belonging to all diploblastic phyla and for a large number of representatives of triploblastic Metazoa and protists. Phylogenetic analyses undertaken using different methods showed deep radiations of phyla such as Ctenophora, Cnidaria and Placozoa but also for groups of Porifera of low taxonomic rank. Short internodes between these radiations suggested an early rapid ersification of diploblasts. A long internal branch preceding the ersification of all triploblasts analyzed could be explained either by a long period with a single ancestor or by the extinction of the earliest triploblastic radiations. Finally some unexpected relationships were revealed among Porifera.
Publisher: Oxford University Press (OUP)
Date: 03-1996
DOI: 10.1093/OXFORDJOURNALS.MOLBEV.A025606
Abstract: We have analyzed what phylogenetic signal can be derived by small subunit rRNA comparison for bacteria of different but closely related genera (enterobacteria) and for different species or strains within a single genus (Escherichia or Salmonella), and finally how similar are the ribosomal operons within a single organism (Escherichia coli). These sequences have been analyzed by neighbor-joining, maximum likelihood, and parsimony. The robustness of each topology was assessed by bootstrap. Sequences were obtained for the seven rrn operons of E. coli strain PK3. These data demonstrated differences located in three highly variable domains. Their nature and localization suggest that since the ergence of E. coli and Salmonella typhimurium, most point mutations that occurred within each gene have been propagated among the gene family by conversions involving short domains, and that homogenization by conversions may not have affected the entire sequence of each gene. We show that the differences that exist between the different operons are ignored when sequences are obtained either after cloning of a single operon or directly from polymerase chain reaction (PCR) products. Direct sequencing of PCR products produces a mean sequence in which mutations present in the most variable domains become hidden. Cloning a single operon results in a sequence that differs from that of the other operons and of the mean sequence by several point mutations. For identification of unknown bacteria at the species level or below, a mean sequence or the sequence of a single nonidentified operon should therefore be avoided. Taking into account the seven operons and therefore mutations that accumulate in the most variable domains would perhaps increase tree resolution. However, if gene conversions that homogenize the rRNA multigene family are rare events, some nodes in phylogenetic trees will reflect these recombination events and these trees may therefore be gene trees rather than organismal trees.
Publisher: Microbiology Society
Date: 04-1995
DOI: 10.1099/00207713-45-2-290
Abstract: We describe a new species on the basis of phenotypic characteristics and the results of an analysis of small-subunit rRNA sequences. Three strains of this organism were isolated from a culture of the toxin-producing dinoflagellate Prorocentrum lima. These bacteria are gram-negative, strictly aerobic, ovoid organisms that are motile by means of one or two subpolar flagella. They grow at temperatures ranging from 10 to 37 degrees C and in the presence of NaCl concentrations ranging from 0.1 to 2 M and have an absolute requirement for sodium ions. They are strictly aerobic with a nonfermentative type of metabolism and are not able to grow anaerobically in presence or absence of nitrate. They do not denitrify. They exhibit oxidase, catalase, gelatinase, esculinase, beta-galactosidase, and (to a lesser extent) amylase activities. The three strains which we examined require thiamine and biotin for growth. They grow only when glucose, trehalose, saccharose, fructose, maltose, pyruvate, malate, citrate, esculin, 2-ketoglutarate, 5-ketogluconate, glutamate, or shikimate is present as a sole carbon source. The three strains have identical small-subunit rRNA sequences. A phylogenetic analysis of these sequences revealed that these bacteria belong to the alpha sub ision of the Proteobacteria and that they form a distinct and robust monophyletic group with Roseobacter denitrificans and Roseobacter litoralis. This result and the general phenotypic characteristics of the organisms place them in the genus Roseobacter, although they do not produce bacteriochlorophyll a, in contrast to previously described Roseobacter species.(ABSTRACT TRUNCATED AT 250 WORDS)
Publisher: American Society for Microbiology
Date: 21-01-2021
DOI: 10.1128/MRA.01326-20
Abstract: We report the complete genome sequence of Bradyrhizobium sp. strain BDV5040, representative of Bradyrhizobium genospecies B, which symbiotically associates with legume hosts belonging to all three Fabaceae subfamilies across the Australian continent. The complete genome sequence provides a genetic reference for this Australian genospecies.
Publisher: American Society for Microbiology
Date: 25-02-2021
DOI: 10.1128/MRA.00042-21
Abstract: We report the complete genome sequence of Bradyrhizobium sp. strain BDV5419, representative of Bradyrhizobium genospecies L, which symbiotically associates with the Australian native legume Hardenbergia violaceae and is expected to represent a novel Bradyrhizobium species. The complete genome sequence provides a genetic reference for this Australian genospecies.
Publisher: Oxford University Press (OUP)
Date: 04-1999
Abstract: The genomes of the spirochaetes Borrelia burgdorferi and Treponema pallidum show strong strand-specific skews in nucleotide composition, with the leading strand in replication being richer in G and T than the lagging strand in both species. This mutation bias results in codon usage and amino acid composition patterns that are significantly different between genes encoded on the two strands, in both species. There are also substantial differences between the species, with T.pallidum having a much higher G+C content than B. burgdorferi. These changes in amino acid and codon compositions represent neutral sequence change that has been caused by strong strand- and species-specific mutation pressures. Genes that have been relocated between the leading and lagging strands since B. burgdorferi and T.pallidum erged from a common ancestor now show codon and amino acid compositions typical of their current locations. There is no evidence that translational selection operates on codon usage in highly expressed genes in these species, and the primary influence on codon usage is whether a gene is transcribed in the same direction as replication, or opposite to it. The dnaA gene in both species has codon usage patterns distinctive of a lagging strand gene, indicating that the origin of replication lies downstream of this gene, possibly within dnaN. Our findings strongly suggest that gene-finding algorithms that ignore variability within the genome may be flawed.
Publisher: Elsevier BV
Date: 02-2008
DOI: 10.1016/J.VIROL.2007.09.037
Abstract: Humans and simian species are infected by deltaretroviruses (HTLV and STLV respectively), which are collectively called primate T-cell lymphotropic viruses (PTLVs). In humans, four types of HTLV have been described (HTLV-1 to -4) with three of them having closely related simian virus analogues named STLV-1, 2 and 3. In this study, our aim was to search for a simian HTLV-4-related virus and to document and characterize further the ersity of STLV infections in wild primate populations. We screened 1297 whole blood s les from 13 different primate species from southern Cameroon. Overall, 93 s les gave HTLV-1, HTLV-2 or dual HTLV-1/-2 INNOLIA profiles, 12 were HTLV positive but untypeable and 14 were indeterminate. Subsequently, we performed generic and specific (STLV-1 to -3) tax-rex PCRs to discriminate the different PTLV types, completed with phylogenetic analysis of 450-bp LTR sequences for STLV-1 and 900 bp pX-LTR sequences for STLV-3. We show for the first time that Lophocebus albigena and Cercopithecus cephus carry both STLV-1 and a ergent STLV-3. We also identified a new STLV-1 lineage in one C. cephus. Finally, we identify relative ergence levels in the tax/rex phylogeny suggesting that additional types of PTLV should be defined, particularly for the highly ergent STLV-1(MarB43) strain that we provisionally name STLV-5.
Publisher: Springer Science and Business Media LLC
Date: 2000
Publisher: Cold Spring Harbor Laboratory
Date: 19-09-2019
DOI: 10.1101/771790
Abstract: Antimicrobial resistance (AMR) is a global threat. A better understanding of how antibiotic use and between ward patient transfers (or connectivity) impact hospital AMR can help optimize antibiotic stewardship and infection control strategies. Here, we used metapopulation ecology to explain variations in infection incidences of 17 ESKAPE pathogen variants in a network of 357 hospital wards. Multivariate models identified the strongest influence of ward-level antibiotic use on more resistant variants, and of connectivity on nosocomial species and carbapenem-resistant variants. Pairwise associations between infection incidence and the consumption of specific antibiotics were significantly stronger when such associations represented a priori AMR selection, suggesting that AMR evolves within the network. Piperacillin-tazobactam consumption was the strongest predictor of the cumulative incidence of infections resistant to empirical sepsis therapy. Our data establish that both antibiotic use and connectivity measurably influence hospital AMR and provide a ranking of key antibiotics by their impact on AMR.
Publisher: Elsevier BV
Date: 05-2008
DOI: 10.1016/J.MEEGID.2007.12.010
Abstract: The complement regulatory protein (CRP) of Trypanosoma cruzi is a surface glycoprotein which confers to the infectious trypomastigote forms a protection against the lytic activity of the host complement. CRP belongs to the large family of the trans-sialidase-like proteins and its sequence is highly similar to those of the flagellar FL-160 and chronic exoantigen proteins, encoded by a multigene family. To further define the gene family encoding the CRP, we investigated the protein ersity among several strains of T. cruzi through the sequencing of trypomastigote transcripts, and used a phylogenetic analysis based on the multiple alignment of these proteins with the top scoring sequences detected by a database sequence homology search. Intrastrain variations in CRP sequences revealed the existence of several copies per strain. The interstrain variability of CRP was consistent with the genetic sub isions of T. cruzi into lineages and discrete typing units. The phylogenetic analysis based on a 227 amino acid alignment of CRP sequences with the 200 putative proteins retrieved from the protein databases (including the sequences from the T. cruzi genome project) revealed that the CRP sequences clustered with the FL-160 proteins into a monophyletic group characterized by the presence of the 12 amino acid mimicry epitope that mimics nervous tissues. The phylogeny did not differentiate between the CRP and the FL-160 proteins. The identification of this group of CRP-like proteins and the high sequence similarity observed within it open up new prospects for the exploration of the localization, structure and function of these proteins and a better understanding of their involvement in key aspects of host-parasite interactions, such as the resistance to the complement. This work provides also information for the T. cruzi genome annotation of the trans-sialidase-like putative proteins.
Publisher: Microbiology Society
Date: 05-2006
Abstract: Rhizobial bacteria almost exclusively nodulate members of the families Fabaceae, Mimosaceae and Caesalpiniaceae, but are found on a single non-legume taxon, Parasponia (Ulmaceae). Based on their host-range, their nitrogen-fixing ability and strain competition experiments, bacterial strains isolated from Parasponia were thought to constitute a separate lineage that would account for their exceptional host affinity. This hypothesis was investigated by focusing on four isolates that are representative of the morphological and cultural types of Parasponia -nodulating bradyrhizobia. Their evolutionary relationships with other rhizobia were analysed using 16S rRNA gene sequences and their nodulation properties were explored using the nodA gene as a proxy for host-range specificity. Phylogenetic analyses of the 16S rRNA and nodA gene sequences revealed that bacterial isolates from Parasponia species are embedded among other bradyrhizobia. They did not cluster together in topologies based on the 16S rRNA or nodA gene sequences, but were scattered among other bradyrhizobia belonging to either the Bradyrhizobium japonicum or the Bradyrhizobium elkanii lineages. These data suggest that the ability of some bradyrhizobia to nodulate species of the genus Parasponia does not represent a historical relationship that predates the relationship between rhizobia and legumes, but is probably a more recent host switch for some rhizobia.
Publisher: Oxford University Press (OUP)
Date: 11-1999
DOI: 10.1093/OXFORDJOURNALS.MOLBEV.A026060
Abstract: The pattern of codon usage in the amitochondriate diplomonad Giardia lamblia has been investigated. Very extensive heterogeneity was evident among a s le of 65 genes. A discrete group of genes featured unusual codon usage due to the amino acid composition of their products: these variant surface proteins (VSPs) are unusually rich in Cys and, to a lesser extent, Gly and Thr. Among the remaining 50 genes, correspondence analysis revealed a single major source of variation in synonymous codon usage. This trend was related to the extent of use of a particular subset of 21 codons which are inferred to be those which are optimal for translation at one end of this trend were genes expected to be expressed at low levels with near random codon usage, while at the other extreme were genes expressed at high levels in which these optimal codons are used almost exclusively. These optimal codons all end in C or G so G + C content at silent sites varies enormously among genes, from values around 40%, expected to reflect the background level of the genome, up to nearly 100%. Although VSP genes are occasionally extremely highly expressed, they do not, in general, have high frequencies of optimal codons, presumably because their high expression is only intermittent. These results indicate that natural selection has been very effective in shaping codon usage in G. lamblia. These analyses focused on sequences from strains placed within G. lamblia "assemblage A" a few sequences from other strains revealed extensive ergence at silent sites, including some ergence in the pattern of codon usage.
Publisher: Microbiology Society
Date: 26-07-2023
Abstract: Bradyrhizobia are particularly abundant in Australia, where they nodulate native legumes growing in the acidic and seasonally dry soils that predominate in these environments. They are essential to Australian ecosystems by helping legumes to compensate for nutrient deficiencies and the low fertility of Australian soils. During a survey of Australian native rhizobial communities in 1994–1995, several Bradyrhizobium genospecies were identified, among which genospecies B appeared to be present in various edaphic and climatic conditions and associate with a large range of leguminous hosts across the whole continent. We took advantage of the recent sequencing of the genome of strain BDV5040 T , representative of Bradyrhizobium genospecies B, to re-evaluate the taxonomic status of this lineage. We further characterized strain BDV5040 T based on morpho-physiological traits and determined its phylogenetic relationships with the type strains of all currently described Bradyrhizobium species using both small subunit (SSU) rRNA gene and complete genome sequences. The digital DNA–DNA hybridization relatedness with any type strain was less than 35 % and both SSU rRNA gene and genome phylogenies confirmed the initial observation that this strain does not belong to any formerly described species within the genus Bradyrhizobium . All data thus support the description of the novel species Bradyrhizobium commune sp. nov. for which the type strain is BDV5040 T (=CFBP 9110 T =LMG 32898 T ), isolated from a nodule of Bossiaea ensata in Ben Boyd National Park in New South Wales, Australia.
Publisher: Oxford University Press (OUP)
Date: 06-2006
DOI: 10.1111/J.1365-2672.2006.02902.X
Abstract: To contribute to the understanding of Cytisus scoparius success at invading and establishing itself in Australia. Root-nodule bacteria isolated from C. scoparius, growing on five different sites and originally introduced to Australia, were compared with isolates from indigenous plants growing in France and isolates from native legumes growing on the same Australian sites as C. scoparius. Small-subunit rDNA from 251 isolates were analysed by PCR-RFLP and representatives from different genospecies were selected for sequencing. Phylogenetic analyses revealed a great ersity of lineages belonging to Bradyrhizobium, with one genospecies being specific for Cytisus both in Australia and in France, Rhizobium and Mesorhizobium and one falling outside the described genera of legume-nodulating bacteria. Principal component analysis showed that the Cytisus Australian rhizobial communities are more similar to each other than to their co-occurring native partners. Early established rhizobial symbionts may have an increased probability to contribute inoculum for the development of further nodules. This is a first report comparing rhizobia nodulating C. scoparius in its native and exotic environments. Cytisus scoparius symbionts were identified outside the Bradyrhizobium genus and a new lineage of legume-nodulating bacteria was identified.
Publisher: Elsevier BV
Date: 12-2006
DOI: 10.1016/J.EXPPARA.2006.04.005
Abstract: The comparisons of 170 sequences of kinetoplast DNA minicircle hypervariable region obtained from 19 stocks of Trypanosoma cruzi and 2 stocks of Trypanosoma cruzi marenkellei showed that only 56% exhibited a significant homology one with other sequences. These sequences could be grouped into homology classes showing no significant sequence similarity with any other homology group. The 44% remaining sequences thus corresponded to unique sequences in our data set. In the DTU I ("Discrete Typing Units") 51% of the sequences were unique. In contrast, in the DTU IId, 87.5% of sequences were distributed into three classes. The results obtained for T. cruzi marinkellei, showed that all sequences were unique, without any similarity between them and T. cruzi sequences. Analysis of palindromes in all sequence sets show high frequency of the EcoRI site. Analysis of repetitive sequences suggested a common ancestral origin of the kDNA. The editing mechanism that occurs in kinetoplastidae is discussed.
Publisher: American Society for Microbiology
Date: 2009
DOI: 10.1128/JVI.01725-08
Abstract: Simian immunodeficiency viruses (SIVs) are found in an extensive number of African primates and humans continue to be exposed to these viruses by hunting and handling of primate bushmeat. Full-length genome sequences were obtained from SIVs derived from two Colobinae species inhabiting the Taï forest, Ivory Coast, each belonging to a different genus: SIVwrc from western red colobus ( Piliocolobus badius badius ) (SIVwrc Pbb -98CI04 and SIVwrc Pbb -97CI14) and SIVolc (SIVolc-97CI12) from olive colobus ( Procolobus verus ). Phylogenetic analysis showed that western red colobus are the natural hosts of SIVwrc, and SIVolc is also a distinct species-specific lineage, although distantly related to the SIVwrc lineage across the entire length of its genome. Overall, both SIVwrc and SIVolc, are also distantly related to the SIVlho/sun lineage across the whole genome. Similar to the group of SIVs (SIVsyk, SIVdeb, SIVden, SIVgsn, SIVmus, and SIVmon) infecting members of the Cercopithecus genus, SIVs derived from western red and olive colobus, L'Hoest and suntailed monkeys, and SIVmnd-1 from mandrills form a second group of viruses that cluster consistently together in phylogenetic trees. Interestingly, the ergent SIVcol lineage, from mantled guerezas ( Colobus guereza ) in Cameroon, is also closely related to SIVwrc, SIVolc, and the SIVlho/sun lineage in the 5′ part of Pol. Overall, these results suggest an ancestral link between these different lentiviruses and highlight once more the complexity of the natural history and evolution of primate lentiviruses.
Publisher: Wiley
Date: 03-2008
Abstract: 2-D DNA display is a simple separation method that provides a fast and economical way of visualizing polymorphism and comparing genomes. The DNA fragments are separated first according to their size by standard gel electrophoresis and then according to their sequence composition using denaturing gradient gel electrophoresis. First developed by Fischer and Lerman (Cell 1979, 16, 191-200), this method has recently been used to distinguish strains within a bacterial species. The genomic restriction fragments are displayed as spots on a 2-D surface. Although most of the relevant physical mechanisms are understood, this technique is mostly empirical and remains essentially qualitative. In view of optimizing this procedure, we combine our understanding of the different physical mechanisms at play to develop a complete numerical model to predict the relative coordinates of the spots as a function of the corresponding DNA sequence and of the experimental conditions. We experimentally validate our model by predicting the outcome of a 2-D display of the lambda phage genome. It thus becomes possible to optimize in silico the experimental parameters, to predict whether specific mutations as well as yet undescribed genetic polymorphisms can be resolved, and to assist in interpreting the experimental data.
Publisher: Elsevier BV
Date: 2008
DOI: 10.1016/J.MEEGID.2007.08.004
Abstract: Numerous African primates are infected with simian immunodeficiency viruses (SIVs). It is now well established that the clade of SIVs infecting west-central African chimpanzees (Pan troglodytes troglodytes) and western gorillas (Gorilla gorilla gorilla) represent the progenitors of human immunodeficiency virus type 1 (HIV-1), whereas HIV-2 results from different cross-species transmissions of SIVsmm from sooty mangabeys (Cercocebus atys atys). We present here the first molecular epidemiological survey of simian immunodeficiency virus (SIVwrc) in wild-living western red colobus monkeys (Piliocolobus badius badius) which are frequently hunted by the human population and represent a favourite prey of western chimpanzees (Pan troglodytes verus). We collected faecal s les (n=88) and we assessed in idual discrimination by microsatellite analyses and visual observation. We tested the inferred 53 adult in iduals belonging to two neighbouring habituated groups for presence of SIVwrc infection by viral RNA (vRNA) detection. We lified viral polymerase (pol) (650 bp) and/or envelope (env) (570 bp) sequences in 14 in iduals, resulting in a minimal prevalence of 26% among the in iduals s led, possibly reaching 50% when considering the relatively low sensitivity of viral RNA detection in faecal s les. With a few exceptions, phylogenetic analysis of pol and env sequences revealed a low degree of intragroup genetic ersity and a general viral clustering related to the social group of origin. However, we found a higher intergroup ersity. Behavioural and demographic data collected previously from these communities indicate that red colobus monkeys live in promiscuous multi-male societies, where females leave their natal group at the sub-adult stage of their lives and where extra-group copulations or male immigration have been rarely observed. The phylogenetic data we obtained seem to reflect these behavioural characteristics. Overall, our results indicate that wild-living red colobus represent a substantial reservoir of SIVwrc. Moreover, because of their frequent association with other monkey species, the predation pressure exerted by chimpanzees (Pan troglodytes verus) and by poachers around and inside the park, simian to simian and simian to human SIVwrc cross-species transmission cannot be excluded.
Publisher: Public Library of Science (PLoS)
Date: 07-03-2007
Publisher: Springer Science and Business Media LLC
Date: 10-2003
DOI: 10.1007/S00239-003-2496-4
Abstract: MgtC is a virulence factor required for intramacrophage survival and growth in low Mg2+ medium in two pathogens that are not phylogenetically related, Salmonella typhimurium and Mycobacterium tuberculosis. In S. typhimurium, mgtC is carried by the SPI-3 pathogenicity island and hybridization studies have suggested that the distribution of mgtC among enterobacteria is limited. In the present study, we searched for the presence of mgtC-like sequences in eubacterial genomes. Analyses of MgtC-like proteins phylogeny and mgtC-like chromosomal context support the hypothesis that mgtC has been acquired by horizontal gene transfer repeatedly throughout bacterial evolution. In addition, the phylogenetic analysis revealed the existence of a subgroup of proteins, that includes the S. typhimurium and M. tuberculosis MgtC proteins, as well as MgtC-related proteins from other pathogens that are able to survive in macrophages, B. melitensis and Y. pestis. We propose that MgtC has a similar function in all these distantly related pathogens, most likely providing the ability to grow in a low Mg2+ environment.
Publisher: Elsevier BV
Date: 11-2007
DOI: 10.1016/J.VIROL.2007.06.018
Abstract: It is now well established that the clade of simian immunodeficiency viruses (SIVs) infecting west central African chimpanzees (Pan troglodytes troglodytes) and western gorillas (Gorilla gorilla gorilla) comprises the progenitors of human immunodeficiency virus type 1 (HIV-1). In this study, we have greatly expanded our previous molecular epidemiological survey of SIVcpz in wild chimpanzees in Cameroon. The new results confirm a wide but uneven distribution of SIVcpzPtt in P. t. troglodytes throughout southern Cameroon and indicate the absence of SIVcpz infection in Pan troglodytes vellerosus. Analyzing 725 fecal s les from 15 field sites, we obtained partial nucleotide sequences from 16 new SIVcpzPtt strains and determined full-length sequences for two of these. Phylogenetic analyses of these new viruses confirmed the previously reported phylogeographic clustering of SIVcpzPtt lineages, with viruses related to the ancestors of HIV-1 groups M and N circulating exclusively in southeastern and south central P. t. troglodytes communities, respectively. Importantly, the SIVcpzPtt strains from the southeastern corner of Cameroon represent a relatively isolated clade indicating a defined geographic origin of the chimpanzee precursor of HIV-1 group M. Since contacts between humans and apes continue, the possibility of ongoing transmissions of SIV from chimpanzees (or gorillas) to humans has to be considered. In this context, our finding of distinct SIVcpzPtt envelope V3 sequence clades suggests that these peptides may be useful for the serological differentiation of SIVcpzPtt and HIV-1 infections, and thus the diagnosis of new cross-species transmissions if they occurred.
Publisher: Oxford University Press (OUP)
Date: 06-1995
Publisher: Microbiology Society
Date: 08-2002
DOI: 10.1099/00221287-148-8-2557
Abstract: Major differences in evolutionary relationships of the 16S rRNA gene and the nitrogenase alpha-subunit gene (nifD) were observed among 38 strains of Bradyrhizobium sp. nodule bacteria from North America, Central America, Asia and Australia. Two lineages were evident in the 16S rRNA phylogeny representing strains related to Bradyrhizobium japonicum (29 isolates) or Bradyrhizobium elkanii (9 isolates). Both clades were distributed across most or all of the geographic regions s led. By contrast, in the nifD tree almost all isolates were placed into one of three groups each exclusively composed of taxa from a single geographic region (North Temperate, Central America or Australia). Isolates that were closely related or identical in gene sequence at one locus often had ergent sequences at the other locus and a partition homogeneity test indicated that the 16S rRNA and nifD phylogenies were significantly incongruent. No evidence for any gene duplication of nifD was found by Southern hybridization analysis on a subset of the strains, so unrecognized paralogy is not likely to be responsible for the discrepancy between 16S rRNA and nifD tree topologies. These results are consistent with a model whereby geographic areas were initially colonized by several erse 16S rRNA lineages, with subsequent horizontal gene transfer of nifD leading to increased nifD sequence homogeneity within each regional population.
Publisher: Microbiology Society
Date: 1995
DOI: 10.1099/00207713-45-1-139
Abstract: The taxonomic status of Pasteurella piscicida (strain NCIMB 2058T [T = type strain] and a strain isolated from the environment) was investigated by performing phylogenetic analyses of small-subunit rRNA sequences, DNA-DNA hybridization analyses, and biochemical characterization analyses. The results of the phylogenetic analyses and the levels of DNA-DNA complementarity demonstrated conclusively that Pasteurella piscicida is extremely closely related to Photobacterium damsela ATCC 33539T. Since the two taxa exhibited a level of DNA-DNA relatedness of 80%, they are members of the same species. The high level of DNA relatedness and the presence of specific morphological and biochemical characteristics support the hypothesis that two subspecies should be recognized. On the basis of its phylogenetic position, we concluded that Pasteurella piscicida should be renamed Photobacterium damsela subsp. piscicida comb. nov.
Publisher: The Royal Society
Date: 29-12-1992
Abstract: The comparatively good fossil record of post-Palaeozoic echinoids allows rates of morphological change to be estimated over the past 260 million years and com pared with rates of molecular evolution. Parsimony analysis of morphological data, based predominantly on skeletal characteristics, and parsimony, distance and maximum likelihood analyses of molecular data, from the first 380 bases from the 5' end of the 28 S rRNA molecule, for 10 species of echinoid produce congruent phylogenies. The m olecular sequence chosen is dem onstrably far from saturation and sister groups have ergence times ranging from about 15 to 260 Ma. Parsimony analysis allows the great majority of molecular and morphological apomorphies to be placed in one of 18 independent geological time intervals, providing a direct measure of rates of evolution for periods in the geological past. Because most molecular fixed point m utations in our sequences cannot be polarized unambiguously by outgroup comparison (making the outgroup states effectively random), distance and parsimony analyses both tend spuriously to root the echinoid tree on the longest internal branch. A topology identical to that derived from morphological data is, however, obtained using Maximum Likelihood and also parsimony analysis where outgroup rooting is restricted to more conserved regions. This is taken as the correct topology for assessing rates of evolution. Overall, both morphological and molecular changes show a m oderately strong correlation with time elapsed, but a weaker correlation with one another. Statistically significant differences in evolutionary rate are found between some, but not all, pair-wise comparisons of sister lineages for both molecular and morphological data. The molecular clock rate for echinaceans is three times faster than that for cidaroids and irregular echinoids. Spearm an’s rank correlation test, which requires only relative m agnitude of changes to be known, suggests that morphological change has a slightly better correlation with time than does molecular change, averaged over all ten species. However, when just echinaceans are considered an extremely good correlation is found between the num ber of molecular changes and time elapsed, whereas morphological change remains poorly correlated. Thus, molecular rates approxim ate to a clocklike model within restricted echinoid elades, but vary significantly between clades. Averaging results over all echinoids produces a correlation that is no better than the correlation between morphological change and time elapsed.
Publisher: JSTOR
Date: 06-1995
DOI: 10.2307/2413706
Publisher: Wiley
Date: 27-10-2009
Abstract: 2-D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, first according to their size and then to their sequence composition. In this article, we present an exhaustive study of the numerical issues associated with a model aimed at predicting the final absolute locations of DNA fragments in 2-D display experiments. We show that simple expressions for the mobility of DNA fragments in both dimensions allow one to reproduce experimental final absolute locations better than experimental uncertainties. However, our simulations also point out that the results of 2-D display experiments are not sufficient to determine the best set of parameters for the modeling of fragments separation in the second dimension and that additional detailed measurements of the mobility of a few sequences are necessary to achieve this goal. We hope that this work will help in establishing simulations as a powerful tool to optimize experimental conditions without having to perform a large number of preliminary experiments and to estimate whether 2-D DNA display is suited to identify a mutation or a genetic difference that is expected to exist between the genomes of closely related organisms.
Publisher: Microbiology Society
Date: 07-1994
DOI: 10.1099/00207713-44-3-416
Abstract: We sequenced nearly complete small-subunit rRNAs of 54 reference strains belonging to the genera Vibrio, Photobacterium, Aeromonas, and Plesiomonas. We then performed a phylogenetic analysis by comparing the sequences which we obtained with all other known sequences for bacteria belonging to the gamma subgroup of the Proteobacteria (thus providing a data base consisting of 70 sequences for the genera investigated), using methods such as neighbor joining, maximum likelihood, and maximum parsimony, as well as bootstrap, to assess the robustness of each topology. Our results confirmed that the family Vibrionaceae should include only Photobacterium and Vibrio species (but not Vibrio marinus) that Aeromonas species deserve family rank and that Plesiomonas shigelloides is linked to the family Enterobacteriaceae. The genera Vibrio, Photobacterium, Aeromonas, and Plesiomonas, together with the family Enterobacteriaceae, the family Pasteurellaceae, and probably the genus Alteromonas, form a robust monophyletic unit within the gamma 3 subgroup of the Proteobacteria.
Publisher: Microbiology Society
Date: 04-2000
DOI: 10.1099/00221287-146-4-851
Abstract: Synonymous codon usage in the complete genome of Helicobacter pylori was investigated. The moderate A+T-richness of the genome (G+C=39 mol%) is reflected in the overall synonymous codon usage but the frequencies of some codons cannot be explained by simple mutational biases. A low level of heterogeneity among genes was observed, but this does not appear to be due to varying mutational bias or translational selection. Some of the heterogeneity was due to amino acid composition variation among the encoded proteins, and some may be attributable to recent acquisition of genes from other species. Since Hel. pylori codon usage is not dominated by biased mutation patterns, the absence of evidence for translationally mediated selection among synonymous codons is striking. This has implications with regard to the life history of this species, and in particular suggests that Hel. pylori strains are not subject to periods of competitive exponential growth. Despite the lack of selected codon usage, base composition immediately after the translation initiation site is skewed, consistent with selection against secondary structure formation in this region.
Publisher: American Society for Microbiology
Date: 2001
DOI: 10.1128/AEM.67.1.396-402.2001
Abstract: The structure of rhizobial communities nodulating Acacia in southeastern Australia from south Queensland to Tasmania was investigated by a molecular approach. A total of 118 isolates from nodule s les from 13 different Acacia species collected at 44 sites were characterized by small-subunit (SSU) ribosomal DNA (rDNA) PCR-restriction fragment length polymorphism analysis. Nine rhizobial genomospecies were identified, and these taxa corresponded to previously described genomospecies (B. Lafay and J. J. Burdon, Appl. Environ. Microbiol. 64:3989–3997, 1998). Eight of these genomospecies belonged to the Bradyrhizobium lineage and accounted for 96.6% of the isolates. The remaining genomospecies corresponded to Rhizobium tropici . For analysis of geographic patterns, results were grouped into five latitudinal regions regardless of host origin. In each region, as observed previously for rhizobial isolates taken from non- Acacia legumes (Lafay and Burdon, Appl. Environ. Microbiol. 64:3989–3997, 1998), rhizobial communities were dominated by one or two genomospecies, the identities of which varied from place to place. Despite this similarity in patterns, the most abundant genomospecies for Acacia isolates differed from the genomospecies found in the non- Acacia -derived rhizobial collection, suggesting that there is a difference in nodulation patterns of the Mimosoideae and the Papilionoideae. Only two genomospecies were both widespread and relatively abundant across the range of sites s led. Genomospecies A was found in all regions except the most northern sites located in Queensland, whereas genomospecies B was not detected in Tasmania. This suggests that genomospecies A might be restricted to the more temperate regions of Australia, whereas in contrast, genomospecies B occurs in different climatic and edaphic conditions across the whole continent. The latter hypothesis is supported by the presence of genomospecies B in southwestern Australia, based on partial SSU rDNA sequence data (N. D. S. Marsudi, A. R. Glenn, and M. J. Dilworth, Soil Biol. Biochem. 31:1229–1238, 1998).
Publisher: Cold Spring Harbor Laboratory
Date: 13-02-2018
DOI: 10.1101/264945
Abstract: Although the bacterial secondary chromosomes/megaplasmids/chromids, first noticed about forty years ago, are commonly held to originate from stabilized plasmids, their true nature and definition are yet to be resolved. On the premise that the integration of a replicon within the cell cycle is key to deciphering its essential nature, we show that the content in genes involved in the replication, partition and segregation of the replicons and in the cell cycle discriminates the bacterial replicons into chromosomes, plasmids, and another class of essential genomic elements that function as chromosomes. These latter do not derive directly from plasmids. Rather, they arise from the fission of a multi-replicon molecule corresponding to the co-integrated and rearranged ancestral chromosome and plasmid. All essential replicons in a distributed genome are thus neochromosomes. Having a distributed genome appears to extend and accelerate the exploration of the bacterial genome evolutionary landscape, producing complex regulation and leading to novel eco-phenotypes and species ersification.
Publisher: Public Library of Science (PLoS)
Date: 15-10-2014
Publisher: eLife Sciences Publications, Ltd
Date: 27-10-2020
DOI: 10.7554/ELIFE.54795
Abstract: Antimicrobial resistance (AMR) is a global threat. A better understanding of how antibiotic use and between-ward patient transfers (or connectivity) impact population-level AMR in hospital networks can help optimize antibiotic stewardship and infection control strategies. Here, we used a metapopulation framework to explain variations in the incidence of infections caused by seven major bacterial species and their drug-resistant variants in a network of 357 hospital wards. We found that ward-level antibiotic consumption volume had a stronger influence on the incidence of the more resistant pathogens, while connectivity had the most influence on hospital-endemic species and carbapenem-resistant pathogens. Piperacillin-tazobactam consumption was the strongest predictor of the cumulative incidence of infections resistant to empirical sepsis therapy. Our data provide evidence that both antibiotic use and connectivity measurably influence hospital AMR. Finally, we provide a ranking of key antibiotics by their estimated population-level impact on AMR that might help inform antimicrobial stewardship strategies.
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Bénédicte Lafay.