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Haile, M.

Publications and source records attributed to Haile, M..

6 recordsLinked to original sources

Neural correlates of novel word-form learning in developmental language disorder

Children with developmental language disorder (DLD) have persistent language learning difficulties and often perform poorly on pseudoword repetition, a task that probes phonological, memory, and speech-motor processes that support vocabulary acquisition. Research on the neural basis of pseudoword repetition in DLD is limited. We used whole-brain functional MRI (fMRI) to examine pseudoword repetition and repetition-based learning in 46 children with DLD (ages 10-15 years) and 71 age-matched children with typical language development. During scanning, children heard and repeated pseudowords paired with visual referents, allowing us to track learning-related changes in neural activity across repetitions. Repeated pseudoword production yielded comparable behavioural learning across groups, with faster productions by later repetitions. Post-scan, form-referent recognition was comparable across groups, whereas pseudoword repetition accuracy was lower in DLD. Pseudoword repetition engaged a distributed neural network, including inferior frontal cortex bilaterally (greater on the left), premotor and sensorimotor cortex, and posterior temporal and occipital regions. Group differences emerged primarily in regions where activity was task negative (i.e., below baseline or deactivated): lateral occipito-parietal cortex (posterior angular gyrus), medial parieto-occipital cortex (retrosplenial), and right posterior cingulate cortex. Learning-related decreases in activity were similar across groups, but region-of-interest analyses showed reduced leftward lateralisation of activity in inferior frontal gyrus in DLD. These findings suggest weaker disengagement of the default mode network during a linguistically demanding task in DLD. Although repetition-based pseudoword learning recruited similar neural mechanisms in both groups, these mechanisms may operate less efficiently in DLD, alongside reduced hemispheric specialisation in inferior frontal cortex. HighlightsO_LISimilar repetition-related neural attenuation across groups during pseudoword learning. C_LIO_LIReduced default-mode network suppression during pseudoword repetition in DLD. C_LIO_LIReduced left-hemisphere specialisation of inferior frontal cortex in DLD. C_LIO_LIRepetition-based learning in DLD supported by less efficient neural networks. C_LI

neuroscience↗

In situ cryoET reveals inhibitor-induced perturbations in Pf80S GTPase interactions

Malaria parasites rely heavily on rapid, high fidelity protein synthesis to infect and replicate in human erythrocytes, making translation an attractive target for new antimalarials. Here, we have determined in situ structures of Pf80S ribosomes in thirteen conformational and compositional states from cryoFIB-milled Plasmodium falciparum-infected human erythrocytes across the stages of asexual intraerythrocytic parasite replication. We observe eight active translation intermediates, enabling us to define the native malarial translation elongation cycle, which surprisingly features a bifurcation at the decoding stage of the cycle that has not previously been described. Examination of perturbations in the distribution of ribosomes among these states in the presence of a malaria-specific translation inhibitor suggests that the inhibitor impedes PfeEF2 and PfeEF1 interactions with the ribosome. We integrated our in situ cryoET data with proteomic and ultrastructural data to arrive at a deeper understanding of malarial translation, which will inform development of new therapies.

biophysics↗

Optimizing bulk segregant analysis of drug resistance using Plasmodium falciparum genetic crosses conducted in humanized mice

BackgroundClassical genetic crosses in malaria parasites involve isolation, genotyping, and phenotyping of multiple progeny parasites, which is time consuming and laborious. Bulk segregant analysis (BSA) offers a powerful and efficient alternative to identify loci underlying complex traits in the human malaria parasite, Plasmodium falciparum. MethodsWe have used BSA, which combines genetic crosses using humanized mice with pooled sequencing of progeny populations to measure changes in allele frequency following selection with antimalarial drugs. We used dihydroartemisinin (DHA) drug selection in two genetic crosses (Mal31xKH004 and NF54xNHP1337). We specifically investigated how synchronization, cryopreservation, and the drug selection regimen of progeny pools impacted the success of BSA experiments. FindingsWe detected a strong and repeatable quantitative trait locus (QTL) at chr13 kelch13 locus in both crosses, but did not detect QTLs at ferredoxin (fd), the apicoplast ribosomal protein S10 (arps10), multidrug resistance protein 2 (mdr2). QTLs were detected using synchronized, but not unsynchronized pools, consistent with the stage-specific action of DHA. We also successfully applied BSA to cryopreserved progeny pools. InterpretationOur results provide proof-of-principal of the utility of BSA for rapid, robust genetic mapping of drug resistance loci. Use of cryopreserved progeny pools expands the utility of BSA because we can conduct experiments using archived progeny pools from previous genetic crosses. BSA provides a powerful approach that complements traditional QTL methods for investigating the genetic architecture of resistance to antimalarials, and to reveal new or accessory loci contributing to artemisinin resistance. FundingNational Institutes of Health (NIH); Wellcome trust. O_TEXTBOXResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSGenetic crosses have been immensely successful for determining the genetic basis of drug resistance in malaria parasites, but require laborious cloning, characterization of drug resistance and genome-wide genotyping of individual progeny. This is a major limitation given that genetic crosses can now be conducted efficiently using humanized mice, rather than chimpanzees. Bulk segregant analysis (BSA) provides an attractive alternative approach because (i) large numbers of uncloned recombinant progeny can be analyzed, increasing statistical power (ii) phenotyping is not required, because we identify QTLs by treatment of progeny bulks, and identifying genome regions that show skews in allele frequency after treatment (iii) genome sequencing of bulk samples provides a rapid, accurate readout of genome-wide allele frequencies. This approach has been effectively leveraged in yeast, rodent malaria and several model organisms. Added value of this studyHere we validate and optimize this approach for P. falciparum genetic crosses, focusing on resistance to dihydroartemisin (DHA) a central component of the first-line antimalarial combination. Mutations in kelch13 are known to confer resistance to DHA, but several additional candidate loci have also been suggested to contribute. Our results confirm involvement of kelch13, but did not identify linkage with other putative candidate loci. We optimized methodology, showing that synchronization is critical, and that BSA can be successfully applied to cryopreserved progeny pools. Implications of all the available evidenceBSA combined with recent advances in rapidly generating genetic crosses provides a powerful approach to investigate the genetic basis of drug resistance in P. falciparum. C_TEXTBOX

genomics↗

Bulk Segregant Approaches to Nutritional Genomics in Plasmodium falciparum

What genes determine growth and nutrient utilization in asexual blood-stage malaria parasites? Competition experiments between a lab-adapted African parasite (NF54), and a recently isolated Asian parasite (NHP4026) reveal contrasting outcomes in different media: NF54 outcompetes NHP4026 in media containing human serum, while NHP4026 outcompetes NF54 in media containing AlbuMAX, a lipid-rich bovine serum formulation. We conducted parasite genetic crosses and compared genome-wide allele frequency changes in progeny populations cultured in media containing serum or AlbuMAX: this bulk segregant analysis (BSA) reveals three quantitative trait loci (QTL) underlying differential growth. The strongest QTL (chromosome 13) contains EBA-140: competition experiments between EBA-140-knockout and isogenic wildtype parasites showed fitness reversals in the two media types, validating this locus as the causative gene. These results (i) demonstrate the effectiveness of BSA for dissecting fitness traits in Plasmodium falciparum, and (ii) reveal an intimate link between red blood cell invasion and nutrient composition of growth media.

genetics↗

Genomics of Ocular Chlamydia trachomatis after 5 years of SAFE interventions for trachoma in Amhara, Ethiopia

BackgroundTo eliminate trachoma as a public health problem, the WHO recommends the SAFE strategy. As part of the SAFE strategy in the Amhara Region, Ethiopia, the Trachoma Control Program distributed over 124 million doses of antibiotic between 2007 and 2015. Despite these interventions, trachoma remained hyperendemic in many districts and a considerable level of Chlamydia trachomatis (Ct) infection was evident. MethodsWe utilised residual material from Abbott m2000 Ct diagnostic tests to sequence 99 ocular Ct samples from Amhara and investigated the role of Ct genomic variation in the continued transmission of Ct following 5 years of SAFE. FindingsSequences were typical of ocular Ct, at the whole-genome level and in tissue tropism-associated genes. There was no evidence of macrolide-resistance in this Ct population. Polymorphism in a region around ompA gene was associated with village-level TF prevalence. Additionally, greater ompA diversity at the district-level was associated with increased Ct infection prevalence. InterpretationWe found no evidence for Ct genomic variation contributing to continued transmission of Ct after treatment, adding to previous evidence that azithromycin does not drive acquisition of macrolide resistance alleles in Ct. Increased Ct infection in villages and in districts with more ompA variants requires longitudinal investigation to understand what impact this may have on treatment success and host immunity. FundingEuropean Commission; Neglected Tropical Disease Support Center; International Trachoma Initiative

genomics↗

Genetic mapping of fitness determinants across the malaria parasite Plasmodium falciparum life cycle

Malaria is transmitted through female Anopheline mosquitoes where gamete fusion and meiosis occurs, and humans where parasites proliferate asexually. We describe a powerful approach to identify the genetic determinants of parasite fitness across both invertebrate and vertebrate life-cycle stages in human malaria parasite Plasmodium falciparum using bulk segregant analysis (BSA). We combined experimental genetic crosses using humanized mice, with selective whole genome amplification and BSA at multiple developmental stages in both mosquito and vertebrate host to examine parasite competition and identify genomic regions under selection. We generated crosses between artemisinin resistant (ART-R, kelch13-C580Y) and ART-sensitive (ART-S, kelch13-WT) parasite clones recently isolated from Southeast Asian patients. We then quantified genome-wide changes in allele frequency in the parasite progeny population from infected midgut and salivary glands of Anopheles stephensi mosquitoes, infected livers, emerging merozoites and aliquots of in vitro cultured progeny parasites at intervals over 30 days. Three striking results emerge: we observed (i) a strong skew (>80%) towards alleles from the ART-R parent in the mosquito stage, that dropped to [~]50% in the blood stage as selfed ART-R parasites were selected against; (ii) highly repeatable skews in allele frequencies across the genome in blood stage parasites; (iii) particularly strong selection (selection coefficient (s) [≤] 0.18/asexual cycle) against alleles from the ART-R parent at loci on chromosome 12 containing MRP2 and chromosome 14 containing ARPS10. This approach robustly identifies selected loci and has strong potential for identifying parasite genes that interact with the mosquito vector or compensatory loci involved in drug resistance.

evolutionary biology↗