Flexible and cost-effective genomic surveillance of P. falciparum malaria with targeted nanopore sequencing

Genomic surveillance of Plasmodium falciparum malaria can provide policy-relevant information about antimalarial drug resistance, diagnostic test failure, and the evolution of vaccine targets. Yet the large and low complexity genome of P. falciparum complicates the development of genomic methods, while resource constraints in malaria endemic regions can limit their deployment. Here, we demonstrate an approach for targeted nanopore sequencing of P. falciparum from dried blood spots (DBS) that enables cost-effective genomic surveillance of malaria in low-resource settings. We release software that facilitates flexible design of amplicon sequencing panels and use this software to design two target panels for P. falciparum. The panels generate 3-4 kbp reads for eight and sixteen targets respectively, covering key drug-resistance associated genes, diagnostic test antigens, polymorphic markers and the vaccine target csp. We validate our approach on mock and field samples, demonstrating robust sequencing coverage, accurate variant calls within coding sequences, the ability to explore P. falciparum within-sample diversity and to detect deletions underlying rapid diagnostic test failure.

Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples

We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network.  It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented.  For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations.  We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent.  We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines.  Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.

Elucidating relationships between P.falciparum prevalence and measures of genetic diversity with a combined genetic-epidemiological model of malaria

There is an abundance of malaria genetic data being collected from the field, yet using these data to understand the drivers of regional epidemiology remains a challenge. A key issue is the lack of models that relate parasite genetic diversity to epidemiological parameters. Classical models in population genetics characterize changes in genetic diversity in relation to demographic parameters, but fail to account for the unique features of the malaria life cycle. In contrast, epidemiological models, such as the Ross-Macdonald model, capture malaria transmission dynamics but do not consider genetics. Here, we have developed an integrated model encompassing both parasite evolution and regional epidemiology. We achieve this by combining the Ross-Macdonald model with an intra-host continuous-time Moran model, thus explicitly representing the evolution of individual parasite genomes in a traditional epidemiological framework. Implemented as a stochastic simulation, we use the model to explore relationships between measures of parasite genetic diversity and parasite prevalence, a widely-used metric of transmission intensity. First, we explore how varying parasite prevalence influences genetic diversity at equilibrium. We find that multiple genetic diversity statistics are correlated with prevalence, but the strength of the relationships depends on whether variation in prevalence is driven by host- or vector-related factors. Next, we assess the responsiveness of a variety of statistics to malaria control interventions, finding that those related to mixed infections respond quickly (∼months) whereas other statistics, such as nucleotide diversity, may take decades to respond. These findings provide insights into the opportunities and challenges associated with using genetic data to monitor malaria epidemiology.

The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria

Individual malaria infections can carry multiple strains of Plasmodium falciparum with varying levels of relatedness. Yet, how local epidemiology affects the properties of such mixed infections remains unclear. Here, we develop an enhanced method for strain deconvolution from genome sequencing data, which estimates the number of strains, their proportions, identity-by-descent (IBD) profiles and individual haplotypes. Applying it to the Pf3k data set, we find that the rate of mixed infection varies from 29% to 63% across countries and that 51% of mixed infections involve more than two strains. Furthermore, we estimate that 47% of symptomatic dual infections contain sibling strains likely to have been co-transmitted from a single mosquito, and find evidence of mixed infections propagated over successive infection cycles. Finally, leveraging data from the Malaria Atlas Project, we find that prevalence correlates within Africa, but not Asia, with both the rate of mixed infection and the level of IBD.

MECP2e1 isoform mutation affects the form and function of neurons derived from Rett syndrome patient iPS cells

MECP2 mutations cause the X-linked neurodevelopmental disorder Rett Syndrome (RTT) by consistently altering the protein encoded by the MECP2e1 alternative transcript. While mutations that simultaneously affect both MECP2e1 and MECP2e2 isoforms have been widely studied, the consequence of MECP2e1 deficiency on human neurons remains unknown. Here we report the first isoform-specific patient induced pluripotent stem cell (iPSC) model of RTT. RTTe1 patient iPS cell-derived neurons retain an inactive X-chromosome and express only the mutant allele. Single-cell mRNA analysis demonstrated they have a molecular signature of cortical neurons. Mutant neurons exhibited a decrease in soma size, reduced dendritic complexity and decreased cell capacitance, consistent with impaired neuronal maturation. The soma size phenotype was rescued cell-autonomously by MECP2e1 transduction in a level-dependent manner but not by MECP2e2 gene transfer. Importantly, MECP2e1 mutant neurons showed a dysfunction in action potential generation, voltage-gated Na(+) currents, and miniature excitatory synaptic current frequency and amplitude. We conclude that MECP2e1 mutation affects soma size, information encoding properties and synaptic connectivity in human neurons that are defective in RTT.

Rapid, accurate phase quantification of multiphase calcium phosphate materials using Rietveld refinement

Rietveld refinement has been employed to estimate the crystalline phase compositions of multiphase calcium phosphate mixtures containing calcium hydroxyapatite [Ca5(PO4)3OH], and alpha and beta tricalcium phosphate [Ca3(PO4)2]. Two methods were employed using fixed structural models for all three phases and refining the zero offset, scale factors, lattice parameters and one peak breadth parameter using either a constant background (method A) or a background with two refined parameters (method B). Analysis of a matrix of quantitative standards across a broad spectrum of phase compositions indicates that method A results in small systematic deviations of the Rietveld phase compositions (< 1 wt%) from the nominal values, but the systematic deviations are eliminated by refining the background (method B). The methods require approximately 10 min to complete, and are suitable for quality control of calcium phosphate production (and potentially other multiphase systems) when accuracy, precision and time are all significant considerations.

Synthesis and characterization of single-phase silicon-substituted α-tricalcium phosphate

Silicon-substituted calcium phosphate (CaP) powders with a Ca/(P+Si) ratio of 1.50 have been prepared by a wet chemical method, with silicon contents up to 2.16 weight percent (wt%). Sintering for 2 h at 1250 degrees C yields single-phase silicon-substituted alpha tricalcium phosphate (Si-alpha-TCP) for compositions between 0.59 and 1.14 wt% silicon. The sintered powders have been characterized with X-ray fluorescence (XRF) spectrometry, X-ray diffraction (XRD), attenuated total reflection infrared spectroscopy (ATR-IR) and transmission electron microscopy (TEM). Compositions with less than 0.59 wt% silicon result in mixtures of Si-alpha-TCP, beta-TCP, and calcium hydroxyapatite (HA), while compositions with more than 1.14 wt% silicon result in mixtures of Si-alpha-TCP and HA. The lattice parameters of single-phase Si-alpha-TCP prepared with 0.87 wt% silicon are a=12.874(1)A, b = 27.372(2) A, c = 15.225(1) A, and beta = 126.38(1) degrees .

Structure and composition of silicon-stabilized tricalcium phosphate

Silicon stabilized tricalcium phosphate [Si-TCP] is formed within the calcium hydroxyapatite (HA)-tricalcium phosphate (TCP) system when a stoichiometric precipitate of hydroxyapatite is fired at 1,000 degrees in the presence of SiO(2). This paper proposes a composition range and crystallographic structure for Si-TCP. Reitveld XRD powder diffraction, transmission electron microscopy, infrared and proton nuclear magnetic resonance measurements show that crystalline Si-TCP is associated with the displacement of OH from an initial hydroxyapatite structure. The resulting calcium phosphate is modified by the incorporation of silicon into its structure with excess silica contributing to an amorphous component. Si-TCP has a monoclinic structure with a space group P2(1)/a akin to alpha-TCP with estimated lattice constants of a=12.863+/-0.004 A, b=9.119 +/-0.003 A, c=15.232+/-0.004 A, beta=126.3+/-0.1 degrees. It is proposed that Si(4+) substitutes for P(5+)in the TCP lattice with the average chemical composition of Si-TCP set primarily by the mechanisms available for charge compensation. While the formation of OH vacancies in HA initiates the transformation to Si-TCP, two mechanisms of charge compensation in the Si-TCP structure are plausible. If O(2-) vacancies provide charge compensation, the composition of Si-TCP is Ca(3)(P(0.9)Si(0.1)O(3.95))(2) derived for the addition of 0.33 mol SiO(2):mol HA. If excess Ca(2+) compensates, the composition is Ca(3.08)(P(0.92)Si(0.08)O(4))(2) derived for the addition of 0.25 mol SiO(2):mol HA. The reaction occurs most effectively when SiO(2) is added as a colloidal suspension rather than by the in-situ thermal decomposition of a silicon metallorganic compound. The material is a bioceramic of major biological interest because of its osteoconductivity and unique influence on skeletal tissue repair and remodeling.

The fretting corrosion resistance of PVD surface-modified orthopedic implant alloys

The objective of this study was to evaluate the fretting corrosion resistance of both modified and unmodified Ti6Al4V flats fretted against CoCr-alloy spheres in a buffered Hank's solution at 37 degrees C using an original fretting apparatus. A physical vapor deposition (PVD) cathodic arc evaporation technique was used to deposit 3-4 microm thick titanium nitride (TiN), zirconium nitride (ZrN), or amorphous carbon (AC) coatings onto the Ti6Al4V substrates. The fretting behavior of the nitride films (TiN and ZrN) was characterized by the absence of surface damage and the deposition of a Cr-rich oxide transferred from the CoCr-alloy spheres to the modified surfaces. This oxide led to a slight increase in surface roughness. Three of the six multilayered AC coatings tested exhibited extensive fretting damage and generated large, deep, wear scars. Cohesive failure of the AC coating was observed in the low contact stress areas of the fretting scars. The remaining AC-coated specimens experienced only slight polishing wear. The reason for the different behavior within the AC-coated specimens is not clear at the present time. The unmodified Ti6Al4V surfaces experienced severe surface damage consistent with the adhesive galling mechanism to which these alloys are susceptible.

The use of ultrasound to measure breast thickness to select electron energies for breast boost radiotherapy

Ultrasound has been used in 30 patients to measure breast thickness as a means of selecting the most appropriate electron energy for the boost in breast conservation radiotherapy. When compared with electron energies selected on the basis of clinical examination, the target volume was underdosed in 21/30 patients. A major problem in the placement of an electron boost is the demarcation of the target volume.

Comparison of calcium hydroxide and zinc oxide and eugenol pulpectomies in primary teeth of dogs

The purpose of this investigation was to compare calcium hydroxide with zinc oxide and eugenol (ZOE) as root canal obturants in the pulpectomy procedure for irreversibly inflamed primary pulps of dogs. Clinical, radiographic, and histologic comparisons of calcium hydroxide and ZOE root canal filling materials were made in forty-two primary premolars of seven mongrel puppies. When the animals were 6 weeks of age, the pulps of all samples teeth were extirpated and the canals left open to the oral environment. The root canals were assigned to calcium hydroxide, ZOE, and control groups, instrumented, and filled 2 weeks later. The animals were killed 1 day, 1 week, 4 weeks, and 12 weeks after filling. Statistical analysis of all categories for comparison at 4 weeks indicated that calcium hydroxide gave significantly more favorable results than ZOE. Canals treated with calcium hydroxide exhibited less inflammation, less resorption, and more hard-tissue apposition than ZOE-treated and control groups.