Showing papers by "Roger Frutos published in 2016"

Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions.

Abstract: Babesia microti, a tick-transmitted, intraerythrocytic protozoan parasite circulating mainly among small mammals, is the primary cause of human babesiosis. While most cases are transmitted by Ixodes ticks, the disease may also be transmitted through blood transfusion and perinatally. A comprehensive analysis of genome composition, genetic diversity, and gene expression profiling of seven B. microti isolates revealed that genetic variation in isolates from the Northeast United States is almost exclusively associated with genes encoding the surface proteome and secretome of the parasite. Furthermore, we found that polymorphism is restricted to a small number of genes, which are highly expressed during infection. In order to identify pathogen-encoded factors involved in host-parasite interactions, we screened a proteome array comprised of 174 B. microti proteins, including several predicted members of the parasite secretome. Using this immuno-proteomic approach we identified several novel antigens that trigger strong host immune responses during the onset of infection. The genomic and immunological data presented herein provide the first insights into the determinants of B. microti interaction with its mammalian hosts and their relevance for understanding the selective pressures acting on parasite evolution.

Fate of insecticidal Bacillus thuringiensis Cry protein in soil: differences between purified toxin and biopesticide formulation

Abstract: BACKGROUND Bacillus thuringiensis produces insecticidal proteins known as Cry, and its efficiency and absence of side effects make it the most widely used biopesticide. There is little information on the role of soils in the fate of Cry proteins from commercial biopesticide formulations, unlike toxins from genetically modified crops, which have been intensively studied in recent years. The persistence of Cry in soil was followed under field and laboratory conditions. RESULTS Sunlight accelerated loss of detectable Cry under laboratory conditions, but little effect of shade was observed under field conditions. The half-life of biopesticide proteins in soil under natural conditions was about 1 week. Strong temperature effects were observed, but they differed for biopesticide and purified protein, indicating different limiting steps. CONCLUSION For the biopesticide, the observed decline in detectable protein was due to biological factors, possibly including the germination of B. thuringiensis spores, and was favoured by higher temperature. In contrast, for purified proteins, the decline in detectable protein was slower at low temperature, probably because the conformational changes of the soil-adsorbed protein, which cause fixation and hence reduced extraction efficiency, are temperature dependent. (Resume d'auteur)

Plasmodium falciparum parasite population structure and gene flow associated to anti-malarial drugs resistance in Cambodia.

Abstract: Western Cambodia is recognized as the epicentre of emergence of Plasmodium falciparum multi-drug resistance. The emergence of artemisinin resistance has been observed in this area since 2008–2009 and molecular signatures associated to artemisinin resistance have been characterized in k13 gene. At present, one of the major threats faced, is the possible spread of Asian artemisinin resistant parasites over the world threatening millions of people and jeopardizing malaria elimination programme efforts. To anticipate the diffusion of artemisinin resistance, the identification of the P. falciparum population structure and the gene flow among the parasite population in Cambodia are essential. To this end, a mid-throughput PCR-LDR-FMA approach based on LUMINEX technology was developed to screen for genetic barcode in 533 blood samples collected in 2010–2011 from 16 health centres in malaria endemics areas in Cambodia. Based on successful typing of 282 samples, subpopulations were characterized along the borders of the country. Each 11-loci barcode provides evidence supporting allele distribution gradient related to subpopulations and gene flow. The 11-loci barcode successfully identifies recently emerging parasite subpopulations in western Cambodia that are associated with the C580Y dominant allele for artemisinin resistance in k13 gene. A subpopulation was identified in northern Cambodia that was associated to artemisinin (R539T resistant allele of k13 gene) and mefloquine resistance. The gene flow between these subpopulations might have driven the spread of artemisinin resistance over Cambodia.

Subtelomere organization in the genome of the microsporidian Encephalitozoon cuniculi: patterns of repeated sequences and physicochemical signatures

Abstract: The microsporidian Encephalitozoon cuniculi is an obligate intracellular eukaryotic pathogen with a small nuclear genome (2.9 Mbp) consisting of 11 chromosomes. Although each chromosome end is known to contain a single rDNA unit, the incomplete assembly of subtelomeric regions following sequencing of the genome identified only 3 of the 22 expected rDNA units. While chromosome end assembly remains a difficult process in most eukaryotic genomes, it is of significant importance for pathogens because these regions encode factors important for virulence and host evasion. Here we report the first complete assembly of E. cuniculi chromosome ends, and describe a novel mosaic structure of segmental duplications (EXT repeats) in these regions. EXT repeats range in size between 3.5 and 23.8 kbp and contain four multigene families encoding membrane associated proteins. Twenty-one recombination sites were identified in the sub-terminal region of E. cuniculi chromosomes. Our analysis suggests that these sites contribute to the diversity of chromosome ends organization through Double Strand Break repair mechanisms. The region containing EXT repeats at chromosome extremities can be differentiated based on gene composition, GC content, recombination sites density and chromosome landscape. Together this study provides the complete structure of the chromosome ends of E. cuniculi GB-M1, and identifies important factors, which could play a major role in parasite diversity and host-parasite interactions. Comparison with other eukaryotic genomes suggests that terminal regions could be distinguished precisely based on gene content, genetic instability and base composition biais. The diversity of processes assciated with chromosome extremities and their biological consequences, as they are presented in the present study, emphasize the fact that great effort will be necessary in the future to characterize more carefully these regions during whole genome sequencing efforts.

Comparison of the affinity and extraction yield of trace amounts of three Cry proteins from Bacillus thuringiensis in contrasting types of soil

Abstract: The use of insecticidal proteins known as Cry or Bt, either as biopesticides used in agriculture or as vector control or originating from commercial genetically modified crops (GM), is increasing rapidly. The fate of these proteins in the environment depends strongly on their adsorption on the organo–mineral complexes of soil. Environmental monitoring requires the quantification of the proteins and this entails their chemical extraction from soil. Three Cry proteins, Cry1Ac, Cry1C and Cry2A, present in commercial biopesticide formulations or synthesized by GM plants or both were studied. The adsorption of trace amounts of Cry proteins on over 40 types of soil with contrasting properties was measured in dilute suspension. After a short incubation the extraction yield was measured with a previously tested alkaline solution that contained surfactant and another protein. Each of the proteins had a strong affinity for soil. No soil property was observed to determine either the affinity for soil or the extraction yield. There was no simple relation between the affinity (assessed from the distribution coefficient, Kd) and the extraction yield, although there was a significant inverse relation (P < 0.05) for two of the proteins, Cry1Ac and Cry2A. The proteins differ in both their affinity for soil and their extraction yields. We conclude that these insecticidal proteins will be largely immobile in soil, but that routine environmental monitoring can give only semi-quantitative values for protein in soil. (Resume d'auteur)

Additional file 2: Table S1. of Subtelomere organization in the genome of the microsporidian Encephalitozoon cuniculi: patterns of repeated sequences and physicochemical signatures

Abstract: BackgroundThe microsporidian Encephalitozoon cuniculi is an obligate intracellular eukaryotic pathogen with a small nuclear genome (2.9 Mbp) consisting of 11 chromosomes. Although each chromosome end is known to contain a single rDNA unit, the incomplete assembly of subtelomeric regions following sequencing of the genome identified only 3 of the 22 expected rDNA units. While chromosome end assembly remains a difficult process in most eukaryotic genomes, it is of significant importance for pathogens because these regions encode factors important for virulence and host evasion.ResultsHere we report the first complete assembly of E. cuniculi chromosome ends, and describe a novel mosaic structure of segmental duplications (EXT repeats) in these regions. EXT repeats range in size between 3.5 and 23.8 kbp and contain four multigene families encoding membrane associated proteins. Twenty-one recombination sites were identified in the sub-terminal region of E. cuniculi chromosomes. Our analysis suggests that these sites contribute to the diversity of chromosome ends organization through Double Strand Break repair mechanisms. The region containing EXT repeats at chromosome extremities can be differentiated based on gene composition, GC content, recombination sites density and chromosome landscape.ConclusionTogether this study provides the complete structure of the chromosome ends of E. cuniculi GB-M1, and identifies important factors, which could play a major role in parasite diversity and host-parasite interactions. Comparison with other eukaryotic genomes suggests that terminal regions could be distinguished precisely based on gene content, genetic instability and base composition biais. The diversity of processes assciated with chromosome extremities and their biological consequences, as they are presented in the present study, emphasize the fact that great effort will be necessary in the future to characterize more carefully these regions during whole genome sequencing efforts.