82 results on '"Eiglmeier K"'
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52. Composition and genetics of malaria vector populations in the Central African Republic.
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Ndiath MO, Eiglmeier K, Olé Sangba ML, Holm I, Kazanji M, and Vernick KD
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- Animals, Anopheles genetics, Central African Republic, Cross-Sectional Studies, Entomology methods, Female, Insecticide Resistance, Mosquito Vectors genetics, Anopheles classification, Anopheles parasitology, Biodiversity, Mosquito Vectors classification, Mosquito Vectors parasitology, Plasmodium falciparum isolation & purification
- Abstract
Background: In many African countries malaria has declined sharply due to a synergy of actions marked by the introduction of vector control strategies, but the disease remains a leading cause of morbidity and mortality in Central African Republic (CAR). An entomological study was initiated with the aim to characterize the malaria vectors in Bangui, the capital of CAR, and determine their vector competence., Methods: A cross-sectional entomological study was conducted in 15 sites of the district of Bangui, the capital of CAR, in September-October 2013 and a second collection was done in four of those sites between November and December 2013. Mosquitoes were collected by human landing catch (HLC) indoors and outdoors and by pyrethrum spray catch of indoor-resting mosquitoes. Mosquitoes were analysed for species and multiple other attributes, including the presence of Plasmodium falciparum circumsporozoite protein or DNA, blood meal source, 2La inversion karyotype, and the L1014F kdr insecticide resistance mutation., Results: Overall, 1292 anophelines were analysed, revealing a predominance of Anopheles gambiae and Anopheles funestus, with a small fraction of Anopheles coluzzii. Molecular typing of the An. gambiae complex species showed that An. gambiae was predominant (95.7 %) as compared to An. coluzzii (2.1 %), and Anopheles arabiensis was not present. In some areas the involvement of secondary vectors, such as Anopheles coustani, expands the risk of infection. By HLC sampling, An. funestus displayed a stronger endophilic preference than mosquitoes from the An. gambiae sister taxa, with a mean indoor-capture rate of 54.3 % and 67.58 % for An. gambiae sister taxa and An. funestus, respectively. Human biting rates were measured overall for each of the species with 28 or 29 bites/person/night, respectively. Both vectors displayed a strong human feeding preference as determined by blood meal source, which was not different between the different sampling sites. An. coustani appears to be highly exophilic, with 92 % of HLC samples captured outdoors. The mean CSP rate in head-thorax sections of all Anopheles was 5.09 %, and was higher in An. gambiae s.l. (7.4 %) than in An. funestus (3.3 %). CSP-positive An. coustani were also detected in outdoor HLC samples. In the mosquitoes of the An. gambiae sister taxa the kdr-w mutant allele was nearly fixed, with 92.3 % resistant homozygotes, and no susceptible homozygotes detected., Conclusions: This study collected data on anopheline populations in CAR, behaviour of vectors and transmission levels. Further studies should investigate the biting behaviour and susceptibility status of the anophelines to different insecticides to allow the establishment of appropriate vector control based on practical entomological knowledge.
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- 2016
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53. Identification and Characterization of Two Novel RNA Viruses from Anopheles gambiae Species Complex Mosquitoes.
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Carissimo G, Eiglmeier K, Reveillaud J, Holm I, Diallo M, Diallo D, Vantaux A, Kim S, Ménard D, Siv S, Belda E, Bischoff E, Antoniewski C, and Vernick KD
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- Animals, Host Specificity, Phylogeny, Anopheles virology, Dicistroviridae isolation & purification, Dicistroviridae physiology, Reoviridae isolation & purification, Reoviridae physiology
- Abstract
Mosquitoes of the Anopheles gambiae complex display strong preference for human bloodmeals and are major malaria vectors in Africa. However, their interaction with viruses or role in arbovirus transmission during epidemics has been little examined, with the exception of O'nyong-nyong virus, closely related to Chikungunya virus. Deep-sequencing has revealed different RNA viruses in natural insect viromes, but none have been previously described in the Anopheles gambiae species complex. Here, we describe two novel insect RNA viruses, a Dicistrovirus and a Cypovirus, found in laboratory colonies of An. gambiae taxa using small-RNA deep sequencing. Sequence analysis was done with Metavisitor, an open-source bioinformatic pipeline for virus discovery and de novo genome assembly. Wild-collected Anopheles from Senegal and Cambodia were positive for the Dicistrovirus and Cypovirus, displaying high sequence identity to the laboratory-derived virus. Thus, the Dicistrovirus (Anopheles C virus, AnCV) and Cypovirus (Anopheles Cypovirus, AnCPV) are components of the natural virome of at least some anopheline species. Their possible influence on mosquito immunity or transmission of other pathogens is unknown. These natural viruses could be developed as models for the study of Anopheles-RNA virus interactions in low security laboratory settings, in an analogous manner to the use of rodent malaria parasites for studies of mosquito anti-parasite immunity.
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- 2016
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54. Genetic Structure of a Local Population of the Anopheles gambiae Complex in Burkina Faso.
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Markianos K, Bischoff E, Mitri C, Guelbeogo WM, Gneme A, Eiglmeier K, Holm I, Sagnon N, Vernick KD, and Riehle MM
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- Animals, Anopheles classification, Burkina Faso epidemiology, Genetics, Population methods, Genotype, Geography, Humans, Insect Vectors classification, Linkage Disequilibrium, Malaria, Falciparum epidemiology, Malaria, Falciparum parasitology, Phylogeny, Population Dynamics, Species Specificity, Anopheles genetics, Genetic Structures, Genome, Insect genetics, Insect Vectors genetics, Polymorphism, Single Nucleotide
- Abstract
Members of the Anopheles gambiae species complex are primary vectors of human malaria in Africa. Population heterogeneities for ecological and behavioral attributes expand and stabilize malaria transmission over space and time, and populations may change in response to vector control, urbanization and other factors. There is a need for approaches to comprehensively describe the structure and characteristics of a sympatric local mosquito population, because incomplete knowledge of vector population composition may hinder control efforts. To this end, we used a genome-wide custom SNP typing array to analyze a population collection from a single geographic region in West Africa. The combination of sample depth (n = 456) and marker density (n = 1536) unambiguously resolved population subgroups, which were also compared for their relative susceptibility to natural genotypes of Plasmodium falciparum malaria. The population subgroups display fluctuating patterns of differentiation or sharing across the genome. Analysis of linkage disequilibrium identified 19 new candidate genes for association with underlying population divergence between sister taxa, A. coluzzii (M-form) and A. gambiae (S-form).
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- 2016
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55. An Evolution-Based Screen for Genetic Differentiation between Anopheles Sister Taxa Enriches for Detection of Functional Immune Factors.
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Mitri C, Bischoff E, Takashima E, Williams M, Eiglmeier K, Pain A, Guelbeogo WM, Gneme A, Brito-Fravallo E, Holm I, Lavazec C, Sagnon N, Baxter RH, Riehle MM, and Vernick KD
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- Animals, Base Sequence, Evolution, Molecular, Genes, Insect immunology, Genetic Variation, Insect Proteins genetics, Insect Proteins immunology, Malaria transmission, Mice, Molecular Sequence Data, Polymerase Chain Reaction, Anopheles genetics, Anopheles immunology, Insect Vectors genetics, Insect Vectors immunology
- Abstract
Nucleotide variation patterns across species are shaped by the processes of natural selection, including exposure to environmental pathogens. We examined patterns of genetic variation in two sister species, Anopheles gambiae and Anopheles coluzzii, both efficient natural vectors of human malaria in West Africa. We used the differentiation signature displayed by a known coordinate selective sweep of immune genes APL1 and TEP1 in A. coluzzii to design a population genetic screen trained on the sweep, classified a panel of 26 potential immune genes for concordance with the signature, and functionally tested their immune phenotypes. The screen results were strongly predictive for genes with protective immune phenotypes: genes meeting the screen criteria were significantly more likely to display a functional phenotype against malaria infection than genes not meeting the criteria (p = 0.0005). Thus, an evolution-based screen can efficiently prioritize candidate genes for labor-intensive downstream functional testing, and safely allow the elimination of genes not meeting the screen criteria. The suite of immune genes with characteristics similar to the APL1-TEP1 selective sweep appears to be more widespread in the A. coluzzii genome than previously recognized. The immune gene differentiation may be a consequence of adaptation of A. coluzzii to new pathogens encountered in its niche expansion during the separation from A. gambiae, although the role, if any of natural selection by Plasmodium is unknown. Application of the screen allowed identification of new functional immune factors, and assignment of new functions to known factors. We describe biochemical binding interactions between immune proteins that underlie functional activity for malaria infection, which highlights the interplay between pathogen specificity and the structure of immune complexes. We also find that most malaria-protective immune factors display phenotypes for either human or rodent malaria, with broad specificity a rarity.
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- 2015
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56. Association mapping by pooled sequencing identifies TOLL 11 as a protective factor against Plasmodium falciparum in Anopheles gambiae.
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Redmond SN, Eiglmeier K, Mitri C, Markianos K, Guelbeogo WM, Gneme A, Isaacs AT, Coulibaly B, Brito-Fravallo E, Maslen G, Mead D, Niare O, Traore SF, Sagnon N, Kwiatkowski D, Riehle MM, and Vernick KD
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- Animals, Anopheles parasitology, Chromosome Mapping, Genome, Insect, Genotype, Host-Parasite Interactions genetics, Humans, Insect Vectors genetics, Malaria, Falciparum parasitology, Malaria, Falciparum transmission, Phenotype, Plasmodium falciparum pathogenicity, Polymorphism, Single Nucleotide, Anopheles genetics, Genome-Wide Association Study, Malaria, Falciparum genetics, Plasmodium falciparum genetics, Toll-Like Receptors genetics
- Abstract
Background: The genome-wide association study (GWAS) techniques that have been used for genetic mapping in other organisms have not been successfully applied to mosquitoes, which have genetic characteristics of high nucleotide diversity, low linkage disequilibrium, and complex population stratification that render population-based GWAS essentially unfeasible at realistic sample size and marker density., Methods: We designed a novel mapping strategy for the mosquito system that combines the power of linkage mapping with the resolution afforded by genetic association. We established founder colonies from West Africa, controlled for diversity, linkage disequilibrium and population stratification. Colonies were challenged by feeding on the infectious stage of the human malaria parasite, Plasmodium falciparum, mosquitoes were phenotyped for parasite load, and DNA pools for phenotypically similar mosquitoes were Illumina sequenced. Phenotype-genotype mapping was carried out in two stages, coarse and fine., Results: In the first mapping stage, pooled sequences were analysed genome-wide for intervals displaying relativereduction in diversity between phenotype pools, and candidate genomic loci were identified for influence upon parasite infection levels. In the second mapping stage, focused genotyping of SNPs from the first mapping stage was carried out in unpooled individual mosquitoes and replicates. The second stage confirmed significant SNPs in a locus encoding two Toll-family proteins. RNAi-mediated gene silencing and infection challenge revealed that TOLL 11 protects mosquitoes against P. falciparum infection., Conclusions: We present an efficient and cost-effective method for genetic mapping using natural variation segregating in defined recent Anopheles founder colonies, and demonstrate its applicability for mapping in a complex non-model genome. This approach is a practical and preferred alternative to population-based GWAS for first-pass mapping of phenotypes in Anopheles. This design should facilitate mapping of other traits involved in physiology, epidemiology, and behaviour.
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- 2015
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57. The kdr-bearing haplotype and susceptibility to Plasmodium falciparum in Anopheles gambiae: genetic correlation and functional testing.
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Mitri C, Markianos K, Guelbeogo WM, Bischoff E, Gneme A, Eiglmeier K, Holm I, Sagnon N, Vernick KD, and Riehle MM
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- Animals, Anopheles immunology, Burkina Faso, Female, Genetic Linkage, Plasmodium falciparum immunology, Anopheles genetics, Anopheles parasitology, Genetic Loci, Haplotypes, Insecticide Resistance, Plasmodium falciparum growth & development, Potassium Channels, Voltage-Gated genetics
- Abstract
Background: Members of the Anopheles gambiae species complex are primary vectors of human malaria in Africa. It is known that a large haplotype shared between An. gambiae and Anopheles coluzzii by introgression carries point mutations of the voltage-gated sodium channel gene para, including the L1014F kdr mutation associated with insensitivity to pyrethroid insecticides. Carriage of L1014F kdr is also correlated with higher susceptibility to infection with Plasmodium falciparum. However, the genetic mechanism and causative gene(s) underlying the parasite susceptibility phenotype are not known., Methods: Mosquitoes from the wild Burkina Faso population were challenged by feeding on natural P. falciparum gametocytes. Oocyst infection phenotypes were determined and were tested for association with SNP genotypes. Candidate genes in the detected locus were prioritized and RNAi-mediated gene silencing was used to functionally test for gene effects on P. falciparum susceptibility., Results: A genetic locus, Pfin6, was identified that influences infection levels of P. falciparum in mosquitoes. The locus segregates as a ~3 Mb haplotype carrying 65 predicted genes including the para gene. The haplotype carrying the kdr allele of para is linked to increased parasite infection prevalence, but many single nucleotide polymorphisms on the haplotype are also equally linked to the infection phenotype. Candidate genes in the haplotype were prioritized and functionally tested. Silencing of para did not influence P. falciparum infection, while silencing of a predicted immune gene, serine protease ClipC9, allowed development of significantly increased parasite numbers., Conclusions: Genetic variation influencing Plasmodium infection in wild Anopheles is linked to a natural ~3 megabase haplotype on chromosome 2L that carries the kdr allele of the para gene. Evidence suggests that para gene function does not directly influence parasite susceptibility, and the association of kdr with infection may be due to tight linkage of kdr with other gene(s) on the haplotype. Further work will be required to determine if ClipC9 influences the outcome of P. falciparum infection in nature, as well as to confirm the absence of a direct influence by para.
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- 2015
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58. Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.
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Jiang X, Peery A, Hall AB, Sharma A, Chen XG, Waterhouse RM, Komissarov A, Riehle MM, Shouche Y, Sharakhova MV, Lawson D, Pakpour N, Arensburger P, Davidson VL, Eiglmeier K, Emrich S, George P, Kennedy RC, Mane SP, Maslen G, Oringanje C, Qi Y, Settlage R, Tojo M, Tubio JM, Unger MF, Wang B, Vernick KD, Ribeiro JM, James AA, Michel K, Riehle MA, Luckhart S, Sharakhov IV, and Tu Z
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- Animals, Anopheles metabolism, Chromosome Mapping, Chromosomes, Insect genetics, Cluster Analysis, Evolution, Molecular, Genome, Insect, Humans, Insect Proteins genetics, Insect Proteins metabolism, Malaria transmission, Phylogeny, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Synteny, Transcriptome, Urban Population, Anopheles genetics, Insect Vectors genetics
- Abstract
Background: Anopheles stephensi is the key vector of malaria throughout the Indian subcontinent and Middle East and an emerging model for molecular and genetic studies of mosquito-parasite interactions. The type form of the species is responsible for the majority of urban malaria transmission across its range., Results: Here, we report the genome sequence and annotation of the Indian strain of the type form of An. stephensi. The 221 Mb genome assembly represents more than 92% of the entire genome and was produced using a combination of 454, Illumina, and PacBio sequencing. Physical mapping assigned 62% of the genome onto chromosomes, enabling chromosome-based analysis. Comparisons between An. stephensi and An. gambiae reveal that the rate of gene order reshuffling on the X chromosome was three times higher than that on the autosomes. An. stephensi has more heterochromatin in pericentric regions but less repetitive DNA in chromosome arms than An. gambiae. We also identify a number of Y-chromosome contigs and BACs. Interspersed repeats constitute 7.1% of the assembled genome while LTR retrotransposons alone comprise more than 49% of the Y contigs. RNA-seq analyses provide new insights into mosquito innate immunity, development, and sexual dimorphism., Conclusions: The genome analysis described in this manuscript provides a resource and platform for fundamental and translational research into a major urban malaria vector. Chromosome-based investigations provide unique perspectives on Anopheles chromosome evolution. RNA-seq analysis and studies of immunity genes offer new insights into mosquito biology and mosquito-parasite interactions.
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- 2014
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59. Equivalent susceptibility of Anopheles gambiae M and S molecular forms and Anopheles arabiensis to Plasmodium falciparum infection in Burkina Faso.
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Gnémé A, Guelbéogo WM, Riehle MM, Sanou A, Traoré A, Zongo S, Eiglmeier K, Kabré GB, Sagnon N, and Vernick KD
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- Animals, Burkina Faso, DNA, Protozoan genetics, DNA, Protozoan isolation & purification, Genotype, Plasmodium falciparum classification, Plasmodium falciparum genetics, Plasmodium falciparum isolation & purification, Anopheles parasitology, Anopheles physiology, Plasmodium falciparum growth & development
- Abstract
Background: The Anopheles gambiae sensu lato (s.l.) species complex in Burkina Faso consists of Anopheles arabiensis, and molecular forms M and S of Anopheles gambiae sensu stricto (s.s.). Previous studies comparing the M and S forms for level of infection with Plasmodium falciparum have yielded conflicting results., Methods: Mosquito larvae were sampled from natural pools, reared to adulthood under controlled conditions, and challenged with natural P. falciparum by experimental feeding with blood from gametocyte carriers. Oocyst infection prevalence and intensity was determined one week after infection. DNA from carcasses was genotyped to identify species and molecular form., Results: In total, 7,400 adult mosquitoes grown from wild-caught larvae were challenged with gametocytes in 29 experimental infections spanning four transmission seasons. The overall infection prevalence averaged 40.7% for A. gambiae M form, 41.4% for A. gambiae S form, and 40.1% for A. arabiensis. There was no significant difference in infection prevalence or intensity between the three population groups. Notably, infection experiments in which the population groups were challenged in parallel on the same infective blood displayed less infection difference between population groups, while infections with less balanced composition of population groups had lower statistical power and displayed apparent differences that fluctuated more often from the null average., Conclusion: The study clearly establishes that, at the study site in Burkina Faso, there is no difference in genetic susceptibility to P. falciparum infection between three sympatric population groups of the A. gambiae s.l. complex. Feeding the mosquito groups on the same infective blood meal greatly increases statistical power. Conversely, comparison of the different mosquito groups between, rather than within, infections yields larger apparent difference between mosquito groups, resulting from lower statistical power and greater noise, and could lead to false-positive results. In making infection comparisons between population groups, it is more accurate to compare the different groups after feeding simultaneously upon the same infective blood.
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- 2013
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60. Evidence for population-specific positive selection on immune genes of Anopheles gambiae.
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Crawford JE, Bischoff E, Garnier T, Gneme A, Eiglmeier K, Holm I, Riehle MM, Guelbeogo WM, Sagnon N, Lazzaro BP, and Vernick KD
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- Animals, Anopheles immunology, Gene Frequency, Genetic Loci, Genetic Variation, Host-Pathogen Interactions, Linkage Disequilibrium, Molecular Sequence Data, Plasmodium falciparum immunology, Anopheles genetics, Genes, Insect, Selection, Genetic
- Abstract
Host-pathogen interactions can be powerful drivers of adaptive evolution, shaping the patterns of molecular variation at the genes involved. In this study, we sequenced alleles from 28 immune-related loci in wild samples of multiple genetic subpopulations of the African malaria mosquito Anopheles gambiae, obtaining unprecedented sample sizes and providing the first opportunity to contrast patterns of molecular evolution at immune-related loci in the recently discovered GOUNDRY population to those of the indoor-resting M and S molecular forms. In contrast to previous studies that focused on immune genes identified in laboratory studies, we centered our analysis on genes that fall within a quantitative trait locus associated with resistance to Plasmodium falciparum in natural populations of A. gambiae. Analyses of haplotypic and genetic diversity at these 28 loci revealed striking differences among populations in levels of genetic diversity and allele frequencies in coding sequence. Putative signals of positive selection were identified at 11 loci, but only one was shared by two subgroups of A. gambiae. Striking patterns of linkage disequilibrium were observed at several loci. We discuss these results with respect to ecological differences among these strata as well as potential implications for disease transmission.
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- 2012
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61. Diverged alleles of the Anopheles gambiae leucine-rich repeat gene APL1A display distinct protective profiles against Plasmodium falciparum.
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Holm I, Lavazec C, Garnier T, Mitri C, Riehle MM, Bischoff E, Brito-Fravallo E, Takashima E, Thiery I, Zettor A, Petres S, Bourgouin C, Vernick KD, and Eiglmeier K
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- Amino Acid Sequence, Animals, Anopheles immunology, Anopheles parasitology, Gene Order, Gene Silencing, Haplotypes, Molecular Sequence Data, Plasmodium falciparum immunology, Protein Transport, Quantitative Trait Loci, Sequence Alignment, Alleles, Anopheles genetics, Genes, Insect
- Abstract
Functional studies have demonstrated a role for the Anopheles gambiae APL1A gene in resistance against the human malaria parasite, Plasmodium falciparum. Here, we exhaustively characterize the structure of the APL1 locus and show that three structurally different APL1A alleles segregate in the Ngousso colony. Genetic association combined with RNAi-mediated gene silencing revealed that APL1A alleles display distinct protective profiles against P. falciparum. One APL1A allele is sufficient to explain the protective phenotype of APL1A observed in silencing experiments. Epitope-tagged APL1A isoforms expressed in an in vitro hemocyte-like cell system showed that under assay conditions, the most protective APL1A isoform (APL1A(2)) localizes within large cytoplasmic vesicles, is not constitutively secreted, and forms only one protein complex, while a less protective isoform (APL1A(1)) is constitutively secreted in at least two protein complexes. The tested alleles are identical to natural variants in the wild A. gambiae population, suggesting that APL1A genetic variation could be a factor underlying natural heterogeneity of vector susceptibility to P. falciparum.
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- 2012
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62. A cryptic subgroup of Anopheles gambiae is highly susceptible to human malaria parasites.
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Riehle MM, Guelbeogo WM, Gneme A, Eiglmeier K, Holm I, Bischoff E, Garnier T, Snyder GM, Li X, Markianos K, Sagnon N, and Vernick KD
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- Animals, Anopheles classification, Anopheles physiology, Bayes Theorem, Burkina Faso epidemiology, Genotype, Host-Parasite Interactions, Housing, Humans, Hybridization, Genetic, Insect Vectors physiology, Larva genetics, Larva parasitology, Larva physiology, Malaria, Falciparum epidemiology, Malaria, Falciparum prevention & control, Malaria, Falciparum transmission, Microsatellite Repeats, Mosquito Control, Polymorphism, Single Nucleotide, Population Dynamics, Anopheles genetics, Anopheles parasitology, Insect Vectors genetics, Insect Vectors parasitology, Plasmodium falciparum physiology
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Population subgroups of the African malaria vector Anopheles gambiae have not been comprehensively characterized owing to the lack of unbiased sampling methods. In the arid savanna zone of West Africa, where potential oviposition sites are scarce, widespread collection from larval pools in the peridomestic human habitat yielded a comprehensive genetic survey of local A. gambiae population subgroups, independent of adult resting behavior and ecological preference. A previously unknown subgroup of exophilic A. gambiae is sympatric with the known endophilic A. gambiae in this region. The exophilic subgroup is abundant, lacks differentiation into M and S molecular forms, and is highly susceptible to infection with wild Plasmodium falciparum. These findings might have implications for the epidemiology of malaria transmission and control.
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- 2011
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63. Genome sequence of Aedes aegypti, a major arbovirus vector.
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Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, Debruyn B, Decaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, Labutti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CF, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JM, Vanzee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, and Severson DW
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- Aedes metabolism, Animals, Anopheles genetics, Anopheles metabolism, Arboviruses, Base Sequence, DNA Transposable Elements, Dengue prevention & control, Dengue transmission, Drosophila melanogaster genetics, Female, Genes, Insect, Humans, Insect Proteins genetics, Insect Vectors metabolism, Male, Membrane Transport Proteins genetics, Molecular Sequence Data, Multigene Family, Protein Structure, Tertiary genetics, Sequence Analysis, DNA, Sex Characteristics, Sex Determination Processes, Species Specificity, Synteny, Transcription, Genetic, Yellow Fever prevention & control, Yellow Fever transmission, Aedes genetics, Genome, Insect, Insect Vectors genetics
- Abstract
We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of approximately 4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of approximately 2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.
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- 2007
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64. Genome plasticity of BCG and impact on vaccine efficacy.
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Brosch R, Gordon SV, Garnier T, Eiglmeier K, Frigui W, Valenti P, Dos Santos S, Duthoy S, Lacroix C, Garcia-Pelayo C, Inwald JK, Golby P, Garcia JN, Hewinson RG, Behr MA, Quail MA, Churcher C, Barrell BG, Parkhill J, and Cole ST
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- Evolution, Molecular, Genome, Genomics, Humans, Models, Genetic, Molecular Sequence Data, Mycobacterium bovis genetics, Phenotype, Phylogeny, RNA, Messenger metabolism, Tuberculosis immunology, Tuberculosis Vaccines genetics, BCG Vaccine genetics, Genome, Bacterial, Mycobacterium bovis immunology, Tuberculosis microbiology, Tuberculosis prevention & control
- Abstract
To understand the evolution, attenuation, and variable protective efficacy of bacillus Calmette-Guérin (BCG) vaccines, Mycobacterium bovis BCG Pasteur 1173P2 has been subjected to comparative genome and transcriptome analysis. The 4,374,522-bp genome contains 3,954 protein-coding genes, 58 of which are present in two copies as a result of two independent tandem duplications, DU1 and DU2. DU1 is restricted to BCG Pasteur, although four forms of DU2 exist; DU2-I is confined to early BCG vaccines, like BCG Japan, whereas DU2-III and DU2-IV occur in the late vaccines. The glycerol-3-phosphate dehydrogenase gene, glpD2, is one of only three genes common to all four DU2 variants, implying that BCG requires higher levels of this enzyme to grow on glycerol. Further amplification of the DU2 region is ongoing, even within vaccine preparations used to immunize humans. An evolutionary scheme for BCG vaccines was established by analyzing DU2 and other markers. Lesions in genes encoding sigma-factors and pleiotropic transcriptional regulators, like PhoR and Crp, were also uncovered in various BCG strains; together with gene amplification, these affect gene expression levels, immunogenicity, and, possibly, protection against tuberculosis. Furthermore, the combined findings suggest that early BCG vaccines may even be superior to the later ones that are more widely used.
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- 2007
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65. Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms.
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Li J, Riehle MM, Zhang Y, Xu J, Oduol F, Gomez SM, Eiglmeier K, Ueberheide BM, Shabanowitz J, Hunt DF, Ribeiro JM, and Vernick KD
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- Algorithms, Animals, DNA, Complementary genetics, Frameshift Mutation, Genetic Vectors, Genome, Humans, Malaria transmission, Models, Genetic, Predictive Value of Tests, Proteome, Reverse Transcriptase Polymerase Chain Reaction, Anopheles genetics
- Abstract
Background: Complete genome annotation is a necessary tool as Anopheles gambiae researchers probe the biology of this potent malaria vector., Results: We reannotate the A. gambiae genome by synthesizing comparative and ab initio sets of predicted coding sequences (CDSs) into a single set using an exon-gene-union algorithm followed by an open-reading-frame-selection algorithm. The reannotation predicts 20,970 CDSs supported by at least two lines of evidence, and it lowers the proportion of CDSs lacking start and/or stop codons to only approximately 4%. The reannotated CDS set includes a set of 4,681 novel CDSs not represented in the Ensembl annotation but with EST support, and another set of 4,031 Ensembl-supported genes that undergo major structural and, therefore, probably functional changes in the reannotated set. The quality and accuracy of the reannotation was assessed by comparison with end sequences from 20,249 full-length cDNA clones, and evaluation of mass spectrometry peptide hit rates from an A. gambiae shotgun proteomic dataset confirms that the reannotated CDSs offer a high quality protein database for proteomics. We provide a functional proteomics annotation, ReAnoXcel, obtained by analysis of the new CDSs through the AnoXcel pipeline, which allows functional comparisons of the CDS sets within the same bioinformatic platform. CDS data are available for download., Conclusion: Comprehensive A. gambiae genome reannotation is achieved through a combination of comparative and ab initio gene prediction algorithms.
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- 2006
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66. Comparative analysis of BAC and whole genome shotgun sequences from an Anopheles gambiae region related to Plasmodium encapsulation.
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Eiglmeier K, Wincker P, Cattolico L, Anthouard V, Holm I, Eckenberg R, Quesneville H, Jaillon O, Collins FH, Weissenbach J, Brey PT, and Roth CW
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- Amino Acid Sequence, Animals, Base Sequence, Genome, Insect Vectors, Malaria prevention & control, Molecular Sequence Data, Phenotype, Anopheles genetics, Chromosomes, Artificial, Bacterial genetics, Malaria transmission, Plasmodium pathogenicity, Sequence Analysis, DNA
- Abstract
The only natural mechanism of malaria transmission in sub-Saharan Africa is the mosquito, generally Anopheles gambiae. Blocking malaria parasite transmission by stopping the development of Plasmodium in the insect vector would provide a useful alternative to the current methods of malaria control. Toward this end, it is important to understand the molecular basis of the malaria parasite refractory phenotype in An. gambiae mosquito strains. We have selected and sequenced six bacterial artificial chromosome (BAC) clones from the Pen-1 region that is the major quantitative trait locus involved in Plasmodium encapsulation. The sequence and the annotation of five overlapping BAC clones plus one adjacent, but not contiguous clone, totaling 585kb of genomic sequence from the centromeric end of the Pen-1 region of the PEST strain were compared to that of the genome sequence of the same strain produced by the whole genome shotgun technique. This project identified 23 putative mosquito genes plus putative copies of the retrotransposable elements BEL12 and TRANSIBN1_AG in the six BAC clones. Nineteen of the predicted genes are most similar to their Drosophila melanogaster homologs while one is more closely related to vertebrate genes. Comparison of these new BAC sequences plus previously published BAC sequences to the cognate region of the assembled genome sequence identified three retrotransposons present in one sequence version but not the other. One of these elements, Indy, has not been previously described. These observations provide evidence for the recent active transposition of these elements and demonstrate the plasticity of the Anopheles genome. The BAC sequences strongly support the public whole genome shotgun assembly and automatic annotation while also demonstrating the benefit of complementary genome sequences and of human curation. Importantly, the data demonstrate the differences in the genome sequence of an individual mosquito compared to that of a hypothetical, average genome sequence generated by whole genome shotgun assembly.
- Published
- 2005
- Full Text
- View/download PDF
67. Pilot Anopheles gambiae full-length cDNA study: sequencing and initial characterization of 35,575 clones.
- Author
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Gomez SM, Eiglmeier K, Segurens B, Dehoux P, Couloux A, Scarpelli C, Wincker P, Weissenbach J, Brey PT, and Roth CW
- Subjects
- Animals, Base Composition genetics, Open Reading Frames genetics, Peptidoglycan chemistry, Phylogeny, Pilot Projects, Protein Structure, Tertiary, Sequence Alignment, Anopheles genetics, Cloning, Molecular, DNA, Complementary genetics, Genes, Insect genetics, Sequence Analysis, DNA
- Abstract
We describe the preliminary analysis of over 35,000 clones from a full-length enriched cDNA library from the malaria mosquito vector Anopheles gambiae. The clones define nearly 3,700 genes, of which around 2,600 significantly improve current gene definitions. An additional 17% of the genes were not previously annotated, suggesting that an equal percentage may be missing from the current Anopheles genome annotation.
- Published
- 2005
- Full Text
- View/download PDF
68. Assessing the Drosophila melanogaster and Anopheles gambiae genome annotations using genome-wide sequence comparisons.
- Author
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Jaillon O, Dossat C, Eckenberg R, Eiglmeier K, Segurens B, Aury JM, Roth CW, Scarpelli C, Brey PT, Weissenbach J, and Wincker P
- Subjects
- Animals, Conserved Sequence genetics, Evolution, Molecular, Genes, Insect genetics, Sequence Analysis, DNA methods, Sequence Homology, Nucleic Acid, Anopheles genetics, Computational Biology methods, Drosophila melanogaster genetics, Genome
- Abstract
We performed genome-wide sequence comparisons at the protein coding level between the genome sequences of Drosophila melanogaster and Anopheles gambiae. Such comparisons detect evolutionarily conserved regions (ecores) that can be used for a qualitative and quantitative evaluation of the available annotations of both genomes. They also provide novel candidate features for annotation. The percentage of ecores mapping outside annotations in the A. gambiae genome is about fourfold higher than in D. melanogaster. The A. gambiae genome assembly also contains a high proportion of duplicated ecores, possibly resulting from artefactual sequence duplications in the genome assembly. The occurrence of 4063 ecores in the D. melanogaster genome outside annotations suggests that some genes are not yet or only partially annotated. The present work illustrates the power of comparative genomics approaches towards an exhaustive and accurate establishment of gene models and gene catalogues in insect genomes.
- Published
- 2003
- Full Text
- View/download PDF
69. The complete genome sequence of Mycobacterium bovis.
- Author
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Garnier T, Eiglmeier K, Camus JC, Medina N, Mansoor H, Pryor M, Duthoy S, Grondin S, Lacroix C, Monsempe C, Simon S, Harris B, Atkin R, Doggett J, Mayes R, Keating L, Wheeler PR, Parkhill J, Barrell BG, Cole ST, Gordon SV, and Hewinson RG
- Subjects
- Models, Biological, Models, Genetic, Molecular Sequence Data, Mycobacterium bovis genetics, Mycobacterium tuberculosis genetics, Sequence Analysis, DNA, Species Specificity, Genome, Bacterial
- Abstract
Mycobacterium bovis is the causative agent of tuberculosis in a range of animal species and man, with worldwide annual losses to agriculture of $3 billion. The human burden of tuberculosis caused by the bovine tubercle bacillus is still largely unknown. M. bovis was also the progenitor for the M. bovis bacillus Calmette-Guérin vaccine strain, the most widely used human vaccine. Here we describe the 4,345,492-bp genome sequence of M. bovis AF2122/97 and its comparison with the genomes of Mycobacterium tuberculosis and Mycobacterium leprae. Strikingly, the genome sequence of M. bovis is >99.95% identical to that of M. tuberculosis, but deletion of genetic information has led to a reduced genome size. Comparison with M. leprae reveals a number of common gene losses, suggesting the removal of functional redundancy. Cell wall components and secreted proteins show the greatest variation, indicating their potential role in host-bacillus interactions or immune evasion. Furthermore, there are no genes unique to M. bovis, implying that differential gene expression may be the key to the host tropisms of human and bovine bacilli. The genome sequence therefore offers major insight on the evolution, host preference, and pathobiology of M. bovis.
- Published
- 2003
- Full Text
- View/download PDF
70. Bacterial artificial chromosome-based comparative genomic analysis identifies Mycobacterium microti as a natural ESAT-6 deletion mutant.
- Author
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Brodin P, Eiglmeier K, Marmiesse M, Billault A, Garnier T, Niemann S, Cole ST, and Brosch R
- Subjects
- Animals, Bacterial Proteins genetics, Base Sequence, DNA, Bacterial genetics, Gene Deletion, Genetic Variation, Humans, Molecular Sequence Data, Mycobacterium immunology, Mycobacterium pathogenicity, Mycobacterium bovis genetics, Mycobacterium tuberculosis genetics, Species Specificity, Type C Phospholipases genetics, Virulence genetics, Virulence immunology, Antigens, Bacterial genetics, Chromosomes, Artificial, Bacterial genetics, Genome, Bacterial, Mycobacterium classification, Mycobacterium genetics
- Abstract
Mycobacterium microti is a member of the Mycobacterium tuberculosis complex that causes tuberculosis in voles. Most strains of M. microti are harmless for humans, and some have been successfully used as live tuberculosis vaccines. In an attempt to identify putative virulence factors of the tubercle bacilli, genes that are absent from the avirulent M. microti but present in human pathogen M. tuberculosis or Mycobacterium bovis were searched for. A minimal set of 50 bacterial artificial chromosome (BAC) clones that covers almost all of the genome of M. microti OV254 was constructed, and individual BACs were compared to the corresponding BACs from M. bovis AF2122/97 and M. tuberculosis H37Rv. Comparison of pulsed-field gel-separated DNA digests of BAC clones led to the identification of 10 regions of difference (RD) between M. microti OV254 and M. tuberculosis. A 14-kb chromosomal region (RD1(mic)) that partly overlaps the RD1 deletion in the BCG vaccine strain was missing from the genomes of all nine tested M. microti strains. This region covers 13 genes, Rv3864 to Rv3876, in M. tuberculosis, including those encoding the potent ESAT-6 and CFP-10 antigens. In contrast, RD5(mic), a region that contains three phospholipase C genes (plcA to -C), was missing from only the vole isolates and was present in M. microti strains isolated from humans. Apart from RD1(mic) and RD5(mic) other M. microti-specific deleted regions have been identified (MiD1 to MiD3). Deletion of MiD1 has removed parts of the direct repeat region in M. microti and thus contributes to the characteristic spoligotype of M. microti strains.
- Published
- 2002
- Full Text
- View/download PDF
71. Royal Society of Tropical Medicine and Hygiene Meeting at Manson House, London, 18th January 2001. Pathogen genomes and human health. Mycobacterial genomics.
- Author
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Gordon SV, Brosch R, Eiglmeier K, Garnier T, Hewinson RG, and Cole ST
- Subjects
- Bacterial Proteins genetics, DNA, Bacterial genetics, Humans, Mycobacterium leprae metabolism, Mycobacterium tuberculosis metabolism, Tuberculosis genetics, Genome, Bacterial, Mycobacterium leprae genetics, Mycobacterium tuberculosis genetics
- Abstract
The small size of their genomes made bacterial ideal model organisms for the emerging field of genomics. Elucidating the genome sequences of mycobacteria was particularly attractive owing to the difficulties inherent in their manipulation. The slow growth rate, clumping, and requirement for category III containment make manipulation of Mycobacterium tuberculosis-complex strains laborious. M. leprae presents even greater problems as it has resisted all attempts at axenic culture. Availability of genome sequence data promised to accelerate our knowledge of the fundamental biology of these organisms, and to offer clues to the basis for their virulence, tropism and persistence in the host. This article will focus on what the genome sequences of M. tuberculosis and M. leprae have taught us about these pathogens, and how comparative genomics has exposed some of the fundamental differences between the species.
- Published
- 2002
- Full Text
- View/download PDF
72. The decaying genome of Mycobacterium leprae.
- Author
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Eiglmeier K, Parkhill J, Honoré N, Garnier T, Tekaia F, Telenti A, Klatser P, James KD, Thomson NR, Wheeler PR, Churcher C, Harris D, Mungall K, Barrell BG, and Cole ST
- Subjects
- Evolution, Molecular, Humans, Genes, Bacterial genetics, Genome, Bacterial, Leprosy microbiology, Mycobacterium leprae genetics
- Abstract
Everything that we need to know about Mycobacterium leprae, a close relative of the tubercle bacillus, is encrypted in its genome. Inspection of the 3.27 Mb genome sequence of an armadillo-derived Indian isolate of the leprosy bacillus identified 1,605 genes encoding proteins and 50 genes for stable RNA species. Comparison with the genome sequence of Mycobacterium tuberculosis revealed an extreme case of reductive evolution, since less than half of the genome contains functional genes while inactivated or pseudogenes are highly abundant. The level of gene duplication was approximately 34% and, on classification of the proteins into families, the largest functional groups were found to be involved in the metabolism and modification of fatty acids and polyketides, transport of metabolites, cell envelope synthesis and gene regulation. Reductive evolution, gene decay and genome downsizing have eliminated entire metabolic pathways, together with their regulatory circuits and accessory functions, particularly those involved in catabolism. This may explain the unusually long generation time and account for our inability to culture the leprosy bacillus.
- Published
- 2001
73. The integrated genome map of Mycobacterium leprae.
- Author
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Eiglmeier K, Simon S, Garnier T, and Cole ST
- Subjects
- Animals, Base Sequence, Humans, Molecular Sequence Data, Chromosome Mapping, Genome, Bacterial, Leprosy microbiology, Mycobacterium leprae genetics
- Abstract
The integrated map of the Mycobacterium leprae genome unveiled for the first time the genomic organization of this obligate intracellular parasite. Selected cosmid clones, isolated from a genomic library created in the cosmid vector Lorist6, were identified as representing nearly the complete genome and were subsequently used in the M. leprae genome sequencing project. Now a new version of the integrated map of M. leprae can be presented, combining the mapping results from the Lorist6 cosmids with data obtained from a second genomic library constructed in an Escherichia coli-mycobacterium shuttle cosmid, pYUB18. More than 98% of the M. leprae genome is now covered by overlapping large insert genomic clones representing a renewable source of well defined DNA segments and a powerful tool for functional genomics.
- Published
- 2001
74. Preliminary analysis of the genome sequence of Mycobacterium leprae.
- Author
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Cole ST, Honore N, and Eiglmeier K
- Subjects
- Gene Expression, Humans, Sensitivity and Specificity, Sequence Analysis, Genes, Bacterial physiology, Genome, Mycobacterium leprae genetics
- Published
- 2000
- Full Text
- View/download PDF
75. Comparative genomics of the mycobacteria.
- Author
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Brosch R, Gordon SV, Pym A, Eiglmeier K, Garnier T, and Cole ST
- Subjects
- Humans, Mycobacterium classification, Mycobacterium leprae classification, Mycobacterium leprae genetics, Mycobacterium tuberculosis classification, Genome, Bacterial, Genomics methods, Mycobacterium genetics, Mycobacterium tuberculosis genetics, Tuberculosis microbiology
- Abstract
The genus mycobacteria includes two important human pathogens Mycobacterium tuberculosis and Mycobacterium lepra. The former is reputed to have the highest annual global mortality of all pathogens. Their slow growth, virulence for humans and particular physiology makes these organisms extremely difficult to work with. However the rapid development of mycobacterial genomics following the completion of the Mycobacterium tuberculosis genome sequence provides the basis for a powerful new approach for the understanding of these organisms. Five further genome sequencing projects of closely related mycobacterial species with differing host range, virulence for humans and physiology are underway. A comparative genomic analysis of these species has the potential to define the genetic basis of these phenotypes which will be invaluable for the development of urgently needed new vaccines and drugs. This minireview summarises the different techniques that have been employed to compare these genomes and gives an overview of the wealth of data that has already been generated by mycobacterial comparative genomics.
- Published
- 2000
- Full Text
- View/download PDF
76. Comparative genomics of the leprosy and tubercle bacilli.
- Author
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Brosch R, Gordon SV, Eiglmeier K, Garnier T, and Cole ST
- Subjects
- Animals, Chromosome Mapping, Humans, Mice, Mycobacterium leprae pathogenicity, Mycobacterium tuberculosis pathogenicity, Sequence Analysis, DNA, Genome, Bacterial, Genomics, Mycobacterium leprae genetics, Mycobacterium tuberculosis genetics
- Abstract
To achieve the quantum leap in understanding required to overcome two major human diseases, leprosy and tuberculosis, systematic and comparative genome analysis has been undertaken. New insight into the biology of their causative agents has been obtained and the principle findings are reported here.
- Published
- 2000
- Full Text
- View/download PDF
77. Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays.
- Author
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Gordon SV, Brosch R, Billault A, Garnier T, Eiglmeier K, and Cole ST
- Subjects
- Chromosome Mapping, Gene Deletion, Genetic Techniques, Genetic Variation, Chromosomes, Bacterial, Genome, Bacterial, Mycobacterium bovis genetics, Mycobacterium tuberculosis genetics
- Abstract
Whole-genome comparisons of the tubercle bacilli were undertaken using ordered bacterial artificial chromosome (BAC) libraries of Mycobacterium tuberculosis and the vaccine strain, Mycobacterium bovis BCG-Pasteur, together with the complete genome sequence of M. tuberculosis H37Rv. Restriction-digested BAC arrays of M. tuberculosis H37Rv were used in hybridization experiments with radiolabelled M. bovis BCG genomic DNA to reveal the presence of 10 deletions (RD1-RD10) relative to M. tuberculosis. Seven of these regions, RD4-RD10, were also found to be deleted from M. bovis, with the three M. bovis BCG-specific deletions being identical to the RD1-RD3 loci described previously. The distribution of RD4-RD10 in Mycobacterium africanum resembles that of M. tuberculosis more closely than that of M. bovis, whereas an intermediate arrangement was found in Mycobacterium microti, suggesting that the corresponding genes may affect host range and virulence of the various tubercle bacilli. Among the known products encoded by these loci are a copy of the proposed mycobacterial invasin Mce, three phospholipases, several PE, PPE and ESAT-6 proteins, epoxide hydrolase and an insertion sequence. In a complementary approach, direct comparison of BACs uncovered a third class of deletions consisting of two M. tuberculosis H37Rv loci, RvD1 and RvD2, deleted from the genome relative to M. bovis BCG and M. bovis. These deletions affect a further seven genes, including a fourth phospholipase, plcD. In summary, the insertions and deletions described here have important implications for our understanding of the evolution of the tubercle complex.
- Published
- 1999
- Full Text
- View/download PDF
78. On the catalase-peroxidase gene, katG, of Mycobacterium leprae and the implications for treatment of leprosy with isoniazid.
- Author
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Eiglmeier K, Fsihi H, Heym B, and Cole ST
- Subjects
- Cloning, Molecular, Cosmids, Genes, Bacterial genetics, Leprosy drug therapy, Molecular Sequence Data, Mycobacterium leprae drug effects, Mycobacterium leprae enzymology, Pseudogenes genetics, Sequence Homology, Amino Acid, Antitubercular Agents pharmacology, Bacterial Proteins, Isoniazid pharmacology, Leprosy microbiology, Mycobacterium leprae genetics, Peroxidases genetics
- Abstract
The toxicity of the potent tuberculocidal agent, isoniazid, is mediated by the heme-containing enzyme, catalase-peroxidase, encoded by the katG gene. Although isoniazid has been used for the treatment of leprosy, it is shown here that the katG gene of Mycobacterium leprae is a pseudogene, which has probably been inactivated by multiple mutations. Inactive genes were detected by the polymerase chain reaction in several isolates of M. leprae, of different geographical origins, and attempts to complement an isoniazid-resistant strain of Mycobacterium smegmatis with the katG pseudogene were unsuccessful. Isoniazid is thus likely to be of no therapeutic benefit to leprosy patients.
- Published
- 1997
- Full Text
- View/download PDF
79. Gene arrangement and organization in a approximately 76 kb fragment encompassing the oriC region of the chromosome of Mycobacterium leprae.
- Author
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Fsihi H, De Rossi E, Salazar L, Cantoni R, Labò M, Riccardi G, Takiff HE, Eiglmeier K, Bergh S, and Cole ST
- Subjects
- Amino Acid Sequence, Bacterial Proteins genetics, Cell Division genetics, Cell Wall metabolism, Chromosome Mapping, Cloning, Molecular, Cosmids, DNA Replication genetics, DNA, Bacterial genetics, DNA, Bacterial metabolism, DNA-Binding Proteins genetics, Evolution, Molecular, Molecular Sequence Data, Multigene Family, Mycobacterium leprae metabolism, Open Reading Frames, Protein Biosynthesis, Protein Kinases genetics, Pseudogenes, Replication Origin, Sequence Homology, Amino Acid, Chromosomes, Bacterial genetics, Genes, Bacterial, Mycobacterium leprae genetics
- Abstract
A continuous 75627 bp segment of the Mycobacterium leprae chromosome spanning the oriC region was sequenced. The gene order at this locus was similar to that found in the replication origin region of many other prokaryotes, particularly Mycobacterium tuberculosis and Streptomyces coelicolor. As in the case of several Gram-positive bacteria, essential genes involved in basic cellular functions, such as DNA or RNA metabolism (dnaA, dnaB, dnaN, gyrB, gyrA, pcnB, recF, rnpA, ssb), cell wall synthesis (ponA, pbpA) and probably cell division (gidB, rodA) were found. Strikingly, the gidA gene was absent from this part of the genome and there was no rRNA operon near oriC. The gyrA gene harbours an intein coding sequence indicating that protein splicing is required to produce the mature A subunit of DNA gyrase. Among the many other noteworthy features were ORFs encoding putative serine/threonine protein kinases and a protein phosphatase, three tRNA genes, one M. leprae-specific repetitive element and a glnQ pseudogene.
- Published
- 1996
- Full Text
- View/download PDF
80. Characterization of the gene encoding the immunodominant 35 kDa protein of Mycobacterium leprae.
- Author
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Winter N, Triccas JA, Rivoire B, Pessolani MC, Eiglmeier K, Lim EM, Hunter SW, Brennan PJ, and Britton WJ
- Subjects
- Amino Acid Sequence, Antibodies, Monoclonal, Antigens, Bacterial biosynthesis, Antigens, Bacterial isolation & purification, Bacterial Proteins biosynthesis, Bacterial Proteins isolation & purification, Base Sequence, Cosmids, DNA Primers, Gene Expression Regulation, Bacterial, Gene Library, Humans, Leprosy immunology, Molecular Sequence Data, Molecular Weight, Mycobacterium genetics, Mycobacterium metabolism, Polymerase Chain Reaction, Promoter Regions, Genetic, Recombinant Proteins biosynthesis, Restriction Mapping, Sequence Homology, Amino Acid, T-Lymphocytes immunology, Antigens, Bacterial genetics, Bacterial Proteins genetics, Genes, Bacterial, Genes, Dominant, Mycobacterium leprae genetics
- Abstract
Analysis of the interaction between the host immune system and the intracellular parasite Mycobacterium leprae has identified a 35 kDa protein as a dominant antigen. The native 35 kDa protein was purified from the membrane fraction of M. leprae and termed MMPI (major membrane protein I). As the purified protein was not amenable to N-terminal sequencing, partial proteolysis was used to establish the sequences of 21 peptides. A fragment of the 35 kDa protein-encoding gene was amplified by the polymerase chain reaction from M. leprae chromosomal DNA with oligonucleotide primers derived from internal peptide sequences and the whole gene was subsequently isolated from a M. leprae cosmid library. The nucleotide sequence of the gene revealed an open reading frame of 307 amino acids containing most of the peptide sequences derived from the native 35 kDa protein. The calculated subunit mass was 33.7 kDa, but the native protein exists as a multimer of 950 kDa. Database searches revealed no identity between the 35 kDa antigen and known protein sequences. The gene was expressed in Mycobacterium smegmatis under the control of its own promoter or at a higher level using an 'up-regulated' promoter derived from Mycobacterium fortuitum. The gene product reacted with monoclonal antibodies raised to the native protein. Using the bacterial alkaline phosphatase reporter system, we observed that the 35 kDa protein was unable to be exported across the membrane of recombinant M. smegmatis. The 35 kDa protein-encoding gene is absent from members of the Mycobacterium tuberculosis complex, but homologous sequences were detected in Mycobacterium avium, Mycobacterium haemophilum and M. smegmatis. The availability of the recombinant 35 kDa protein will permit dissection of both antibody- and T-cell-mediated immune responses in leprosy patients.
- Published
- 1995
- Full Text
- View/download PDF
81. Nucleotide sequence of the first cosmid from the Mycobacterium leprae genome project: structure and function of the Rif-Str regions.
- Author
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Honoré N, Bergh S, Chanteau S, Doucet-Populaire F, Eiglmeier K, Garnier T, Georges C, Launois P, Limpaiboon T, and Newton S
- Subjects
- Bacterial Proteins genetics, Base Sequence, Codon, Gene Library, Genes, Bacterial, Molecular Sequence Data, Open Reading Frames, Regulatory Sequences, Nucleic Acid, Cosmids, Genome, Bacterial, Mycobacterium leprae genetics
- Abstract
The nucleotide sequence of cosmid B1790, carrying the Rif-Str regions of the Mycobacterium leprae chromosome, has been determined. Twelve open reading frames were identified in the 36716bp sequence, representing 40% of the coding capacity. Five ribosomal proteins, two elongation factors and the beta and beta' subunits of RNA polymerase have been characterized and two novel genes were found. One of these encodes a member of the so-called ABC family of ATP-binding proteins while the other appears to encode an enzyme involved in repairing genomic lesions caused by free radicals. This finding may well be significant as M. leprae, an intracellular pathogen, lives within macrophages.
- Published
- 1993
- Full Text
- View/download PDF
82. Characterization of two genes, glpQ and ugpQ, encoding glycerophosphoryl diester phosphodiesterases of Escherichia coli.
- Author
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Tommassen J, Eiglmeier K, Cole ST, Overduin P, Larson TJ, and Boos W
- Subjects
- Amino Acid Sequence, Base Sequence, Cloning, Molecular, DNA, Bacterial, Escherichia coli enzymology, Molecular Sequence Data, Open Reading Frames, Phosphoric Diester Hydrolases metabolism, Restriction Mapping, Sequence Alignment, Escherichia coli genetics, Genes, Bacterial, Phosphoric Diester Hydrolases genetics
- Abstract
The nucleotide sequences of the glpQ and ugpQ genes of Escherichia coli, which both encode glycerophosphoryl diester phosphodiesterases, were determined. The glpQ gene encodes a periplasmic enzyme of 333 amino acids, produced initially with a 25 residue long signal sequence, while ugpQ codes for a cytoplasmic protein of 247 amino acids. Despite differences in size and cellular location, significant similarity in the primary structures of the two enzymes was found suggesting a common evolutionary origin. The 3' end of the ugpQ gene overlaps an open reading frame that is transcribed in the opposite direction. This open reading frame encodes a polypeptide with an unusual composition, i.e., 46 of the 146 amino acids are Gln or Asn. This polypeptide and the UgpQ protein were identified in an in vitro transcription/translation system as proteins with apparent molecular weights of 19.5 and 27 kDa, respectively.
- Published
- 1991
- Full Text
- View/download PDF
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