Predicting Functional and Regulatory Divergence of a Drug Resistance Transporter Gene in the Human Malaria Parasite

Background: The paradigm of resistance evolution to chemotherapeutic agents is that a key coding mutation in a specific gene drives resistance to a particular drug. In the case of resistance to the anti-malarial drug chloroquine (CQ), a specific mutation in the transporter pfcrt is associated with resistance. Here, we apply a series of analytical steps to gene expression data from our lab and leverage 3 independent datasets to identify pfcrt-interacting genes. Resulting networks provide insights into pfcrt’s biological functions and regulation, as well as the divergent phenotypic effects of its allelic variants in different genetic backgrounds. Results: To identify pfcrt-interacting genes, we analyze pfcrt co-expression networks in 2 phenotypic states - CQ-resistant (CQR) and CQ-sensitive (CQS) recombinant progeny clones - using a computational approach that prioritizes gene interactions into functional and regulatory relationships. For both phenotypic states, pfcrt co-expressed gene sets are associated with hemoglobin metabolism, consistent with CQ’s expected mode of action. To predict the drivers of co-expression divergence, we integrate topological relationships in the co-expression networks with available high confidence protein-protein interaction data. This analysis identifies 3 transcriptional regulators from the ApiAP2 family and histone acetylation as potential mediators of these divergences. We validate the predicted divergences in DNA mismatch repair and histone acetylation by measuring the effects of small molecule inhibitors in recombinant progeny clones combined with quantitative trait locus (QTL) mapping. Conclusions: This work demonstrates the utility of differential co-expression viewed in a network framework to uncover functional and regulatory divergence in phenotypically distinct parasites. pfcrt-associated co-expression in the CQ resistant progeny highlights CQR-specific gene relationships and possible targeted intervention strategies. The approaches outlined here can be readily generalized to other parasite populations and drug resistances

Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum.

The malaria parasite Plasmodium falciparum has a great capacity for evolutionary adaptation to evade host immunity and develop drug resistance. Current understanding of parasite evolution is impeded by the fact that a large fraction of the genome is either highly repetitive or highly variable and thus difficult to analyze using short-read sequencing technologies. Here, we describe a resource of deep sequencing data on parents and progeny from genetic crosses, which has enabled us to perform the first genome-wide, integrated analysis of SNP, indel and complex polymorphisms, using Mendelian error rates as an indicator of genotypic accuracy. These data reveal that indels are exceptionally abundant, being more common than SNPs and thus the dominant mode of polymorphism within the core genome. We use the high density of SNP and indel markers to analyze patterns of meiotic recombination, confirming a high rate of crossover events and providing the first estimates for the rate of non-crossover events and the length of conversion tracts. We observe several instances of meiotic recombination within copy number variants associated with drug resistance, demonstrating a mechanism whereby fitness costs associated with resistance mutations could be compensated and greater phenotypic plasticity could be acquired

High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

<p>Abstract</p> <p>Background</p> <p>Knowledge of the origins, distribution, and inheritance of variation in the malaria parasite (<it>Plasmodium falciparum</it>) genome is crucial for understanding its evolution; however the 81% (A+T) genome poses challenges to high-throughput sequencing technologies. We explore the viability of the Roche 454 Genome Sequencer FLX (GS FLX) high throughput sequencing technology for both whole genome sequencing and fine-resolution characterization of genetic exchange in malaria parasites.</p> <p>Results</p> <p>We present a scheme to survey recombination in the haploid stage genomes of two sibling parasite clones, using whole genome pyrosequencing that includes a sliding window approach to predict recombination breakpoints. Whole genome shotgun (WGS) sequencing generated approximately 2 million reads, with an average read length of approximately 300 bp. <it>De novo </it>assembly using a combination of WGS and 3 kb paired end libraries resulted in contigs ≤ 34 kb. More than 8,000 of the 24,599 SNP markers identified between parents were genotyped in the progeny, resulting in a marker density of approximately 1 marker/3.3 kb and allowing for the detection of previously unrecognized crossovers (COs) and many non crossover (NCO) gene conversions throughout the genome.</p> <p>Conclusions</p> <p>By sequencing the 23 Mb genomes of two haploid progeny clones derived from a genetic cross at more than 30× coverage, we captured high resolution information on COs, NCOs and genetic variation within the progeny genomes. This study is the first to resequence progeny clones to examine fine structure of COs and NCOs in malaria parasites.</p

The landscape of inherited and de novo copy number variants in a plasmodium falciparum genetic cross

<p>Abstract</p> <p>Background</p> <p>Copy number is a major source of genome variation with important evolutionary implications. Consequently, it is essential to determine copy number variant (CNV) behavior, distributions and frequencies across genomes to understand their origins in both evolutionary and generational time frames. We use comparative genomic hybridization (CGH) microarray and the resolution provided by a segregating population of cloned progeny lines of the malaria parasite, <it>Plasmodium falciparum</it>, to identify and analyze the inheritance of 170 genome-wide CNVs.</p> <p>Results</p> <p>We describe CNVs in progeny clones derived from both Mendelian (i.e. inherited) and non-Mendelian mechanisms. Forty-five CNVs were present in the parent lines and segregated in the progeny population. Furthermore, extensive variation that did not conform to strict Mendelian inheritance patterns was observed. 124 CNVs were called in one or more progeny but in neither parent: we observed CNVs in more than one progeny clone that were not identified in either parent, located more frequently in the telomeric-subtelomeric regions of chromosomes and singleton <it>de novo </it>CNVs distributed evenly throughout the genome. Linkage analysis of CNVs revealed dynamic copy number fluctuations and suggested mechanisms that could have generated them. Five of 12 previously identified expression quantitative trait loci (eQTL) hotspots coincide with CNVs, demonstrating the potential for broad influence of CNV on the transcriptional program and phenotypic variation.</p> <p>Conclusions</p> <p>CNVs are a significant source of segregating and <it>de novo </it>genome variation involving hundreds of genes. Examination of progeny genome segments provides a framework to assess the extent and possible origins of CNVs. This segregating genetic system reveals the breadth, distribution and dynamics of CNVs in a surprisingly plastic parasite genome, providing a new perspective on the sources of diversity in parasite populations.</p

A Molecular Key for the Identification of Blow Flies in Southeastern Nebraska

Immature blow flies (Calliphoridae) are typically the first colonizers of cadavers. Identification of the early instars using traditional, morphology-based keys is difficult because of their small size, similarity, and simplicity in external morphology. Information derived from molecular genetic data would augment the accurate identification of immature flies. Nine species of blow flies commonly found in southeastern Nebraska were used to examine the utility of molecular-based keys. Polymerase chain reaction–restriction fragment length polymorphisms (PCR–RFLP) were investigated with 10 common, inexpensive, restriction enzymes from an amplicon of approximately 1500 bp spanning the mitochondrial cytochrome oxidase I gene. A simple molecular taxonomic key, comprising RFLP from the restriction enzymes HinfI and DraI, enabled the differentiation of all species used. Further development of PCR–RFLP, including more extensive and intensive examination of blow flies, would benefit forensic laboratories in the accurate identification of evidence consisting of immature blow flies

Efficient photocatalysis of Cu doped TiO2/g-C3N4 for the photodegradation of methylene blue

The release of dyes into normal water reservoirs has become a tremendous environmental problem and the development of methods to remove such dyes is essential. A novel photocatalyst was fabricated in which Cu doped to TiO2 was coupled with g-C3N4 (Cu-TiO2/g-C3N4) in different weight percentages as 10, 30 and 50%, hydrothermally. Pure TiO2 consisted of both Anatase and Rutile phases where slight lattice distortions were observed in the Cu-doped TiO2 as evidenced by the XRD and Raman analysis. Cu was present at 1.7% by weight respective to TiO2 according to the XRF analysis. Spherical and irregularly shaped aggregated Cu-doped TiO2 nanoparticles in the range of 15–55 nm were heterogeneously distributed on the g-C3N4 matrix as observed by TEM and SEM. The band gap of TiO2 (3.0 eV) was reduced to 2.67 upon doping with Cu. The band gap of g-C3N4 was found to be 2.81 eV and that of Cu-TiO2/g-C3N4 in different weight percentages were in the range of 2.82 to 2.88 eV. Synthesized photocatalysts were tested on the ability to degrade methylene blue under UV and Visible light. Cu-TiO2/50% g-C3N4 showed the highest rate constant (4.4 × 10-3 min−1) which is 5 and 9.8 times greater than TiO2 and g-C3N4, respectively. The rate constant decreased with the introduction of EDTA and Isopropyl alcohol as they scavenge holes and hydroxyl radicals, respectively. The photocatalytic activity of all the nanomaterials increased with the increasing concentration of persulfate due to the increasing concentration of SO4●- and OH● produced. Synthesized nanomaterials effectively adsorb methylene blue under dark conditions following the pseudo-second-order kinetics suggesting that methylene blue molecules were chemisorbed to the adsorbents. The adsorption rate constant resulting in the best-performing photocatalyst was 0.122 g mg−1 min−1. Hence, it is evident that Cu-TiO2/g-C3N4 can effectively degrade methylene blue

MMWR. Recommendations and reports : Morbidity and mortality weekly report. Recommendations and reports / Centers for Disease Control

This revision of the General Recommendations on Immunization updates the 1989 statement. Changes in the immunization schedule for infants and children include recommendations that the third dose of oral polio vaccine be administered routinely at 6 months of age rather than at age 15 months and that measles-mumps-rubella vaccine be administered routinely to all children at 12-15 months of age. Other updated or new sections include a) a listing of vaccines and other immunobiologics available in the United States by type and recommended routes, advice on the proper storage and handling of immunobiologics, a section on the recommended routes for administration of vaccines, and discussion of the use of jet injectors; b) revisions in the guidelines for spacing administration of immune globulin preparations and live virus vaccines, a discussion of vaccine interactions and recommendations for the simultaneous administration of multiple vaccines, a section on the interchangeability of vaccines from different manufacturers, and a discussion of hypersensitivity to vaccine components; c) a discussion of vaccination during pregnancy, a section on breast-feeding and vaccination, recommendations for the vaccination of premature infants, and updated schedules for immunizing infants and children (including recommendations for the use of Haemophilus influenzae type b conjugate vaccines); d) sections on the immunization of hemophiliacs and immunocompromised persons; e) discussion of the Standards for Pediatric Immunization Practices (including a new table of contraindications and precautions to vaccination), information on the National Vaccine Injury Compensation Program, the Vaccine Adverse Events Reporting System, and Vaccine Information Pamphlets; and f) guidelines for vaccinating persons without documentation of immunization, a section on vaccinations received outside the United States, and a section on reporting of vaccine-preventable diseases. These recommendations are based on information available before publishing and are not comprehensive for each vaccine. The most recent Advisory Committee on Immunization Practices (ACIP) recommendations for each specific vaccine should be consulted for more details.INFECTIOUS DISEASEPrevention and controlSUPERSEDEDACI