Project description:Campylobacter jejuni has become the predominant cause of sheep abortions in the U.S. However, little is know about the genetic diversity among the isolates collected from different time periods. In this study, the genetic diversity of sheep aborion isolates of C. jejuni was investigated by Array-based CGH
Project description:Campylobacter jejuni has become the predominant cause of sheep abortions in the U.S. However, little is know about the genetic diversity among the isolates collected from different time periods. In this study, the genetic diversity of sheep abortion isolates of C. jejuni was investigated by Array-based CGH
Project description:Campylobacter jejuni has become the predominant cause of sheep abortions in the U.S. However, little is know about the genetic diversity among the isolates collected from different time periods. In this study, the genetic diversity of sheep aborion isolates of C. jejuni was investigated by Array-based CGH Each isolate was compared to IA3902, a dye-swap replicate was applied for each isolate
Project description:Campylobacter jejuni has become the predominant cause of sheep abortions in the U.S. However, little is know about the genetic diversity among the isolates collected from different time periods. In this study, the genetic diversity of sheep abortion isolates of C. jejuni was investigated by Array-based CGH Each isolate was compared to IA3902, a dye-swap replicate was applied for each isolate
Project description:The sheep (Ovis aries) plays a major socio-economic role in the world. Copy number variations (CNVs) are increasingly recognized as a key and potent source of genetic variation and phenotypic diversity, but little is known about the extent to which CNVs contribute to genetic variation in Chinese sheep breeds. Analyses of CNVs in the genomes of eight sheep breeds were performed using the sheep SNP50 BeadChip genotyping array. A total of 111 CNV regions (CNVRs) were obtained from 160 Chinese sheep breeds. These CNVRs covered 13.75 Mb of the sheep genome sequence. A total of 22 Go terms and 17 candidate genes were obtained from the functional analysis. Ten CNVRs were selected for validation, of which 7 CNVRs were further experimentally confirmed by quantitative PCR. Four candidate genes were selected to confirm the results of the functional analysis. These results provide a resource for furthering understanding of ruminant biology, and for further improving the genetic quality of sheep breeds.
Project description:Peruvian Native American individuals were genotyped as part of the Peruvian Genome Project (PGP). This data was used to infer population structure, demographic history and natural selection. We addressed question about gene flow across the Andes and Natural Selection in Andes and Amazon
Project description:Plasmodium vivax causes 25-40% of malaria cases worldwide, yet research on this human malaria parasite has been neglected. Nevertheless, the recent publication of the P. vivax reference genome now allows genomics and systems biology approaches to be applied to this pathogen. We show here that whole genome analysis of the parasite can be achieved directly from ex vivo-isolated parasites, without the need for in vitro propagation. A single isolate of P. vivax obtained from a febrile patient with clinical malaria from Peru was subjected to whole genome sequencing (30X coverage). This analysis revealed over 18,261 single nucleotide polymorphisms (SNPs), 6,257 of which were further validated using a tiling microarray. Within core chromosomal genes we find that one SNP per every 985 bases of coding sequence distinguishes this recent Peruvian isolate, designated IQ07, from the reference Sal1 strain obtained in 1970. This full-genome sequence of a P. vivax isolate, the second overall and first of an uncultured patient isolate, shows that the same regions with low numbers of aligned sequencing reads are also highly variable by genomic microarray analysis. Finally, we show that the genes containing the largest ratio of nonsynonymous to synonymous SNPs encode two AP2 transcription factors and the P. vivax multidrug resistance-associated protein (PvMRP1), an ABC transporter shown to be associated with quinoline and antifolate tolerance in P. falciparum. This analysis provides a new data set for comparative analysis with important potential for identifying markers for global parasite diversity and drug resistance mapping studies. Genome DNA from Peruvian P. vivax Isolate IQ07 vs. Reference Sal1
Project description:The present study performed the proteomic and biological activities of Peruvian Crotalus durissus, an endangered species reported to cause neuro and myotoxic symptoms. Due to the severity of its envenomation and to its geographical location, Peruvian Crotalus durissus is considered of public health importance in Peru. Snakebite treatment depends on rapid administration of appropriate antivenom. In this sense, the recognition of Peruvian Crotalus durissus venom (PCdV) by Brazilian and Peruvian antivenoms was tested. The results of this study increase the scarce knowledge about PCdV composition and demonstrate antivenom recognition of PCdV proteins, indicating a possible efficiency of these antivenoms to treat Peruvian Crotalus durissus accidents
Project description:Here we fully characterize the genomes of 14 Plasmodium falciparum patient isolates taken recently from the Iquitos regions using genome-scanning, a microarray-based technique which delineates the majority of single-base changes, indels and copy number variants distinguishing the coding regions of two clones. We show that the parasite population in the Peruvian Amazon is highly structured with a limited number of genotypes and low recombination frequencies. Despite the essentially clonal nature of some isolates, we see high frequencies of mutations in subtelomeric highly variable genes and internal var genes indicating mutations arising during self-mating or mitotic replication. The data also reveal that 1 or 2 meioses separate different isolates showing that P. falciparum clones isolated from different individuals in defined geographical regions could be useful in linkage analyses or quantitative trait locus studies. Through pair-wise comparisons of different isolates we discovered point mutations in the apicoplast genome that are close to known mutations that confer clindamycin resistance in other species but which were hitherto unknown in malaria parasites. Subsequent drug sensitivity testing revealed over 100-fold increase clindamycin EC50 in strains harboring one of these mutations. This evidence of clindamycin resistant parasites in the Amazon suggests a shift should be made in health policy away from quinine+clindamycin therapy for malaria in pregnant women and infants and that the development of new lincosamide antibiotics for malaria should be reconsidered. Genome DNA from Peruvian Isolates vs. Reference 3D7