PacBio assembly of a Plasmodium knowlesi genome sequence with Hi-C correction and manual annotation of the SICAvar gene family.

Plasmodium knowlesi has risen in importance as a zoonotic parasite that has been causing regular episodes of malaria throughout South East Asia. The P. knowlesi genome sequence generated in 2008 highlighted and confirmed many similarities and differences in Plasmodium species, including a global view of several multigene families, such as the large SICAvar multigene family encoding the variant antigens known as the schizont-infected cell agglutination proteins. However, repetitive DNA sequences are the bane of any genome project, and this and other Plasmodium genome projects have not been immune to the gaps, rearrangements and other pitfalls created by these genomic features. Today, long-read PacBio and chromatin conformation technologies are overcoming such obstacles. Here, based on the use of these technologies, we present a highly refined de novo P. knowlesi genome sequence of the Pk1(A+) clone. This sequence and annotation, referred to as the 'MaHPIC Pk genome sequence', includes manual annotation of the SICAvar gene family with 136 full-length members categorized as type I or II. This sequence provides a framework that will permit a better understanding of the SICAvar repertoire, selective pressures acting on this gene family and mechanisms of antigenic variation in this species and other pathogens

Magnetic manipulation of superparamagnetic colloids in droplet-based optical devices

Magnetically assembled superparamagnetic colloids have been exploited as fluid mixers, swimmers and delivery systems in several microscale applications. The encapsulation of such colloids in droplets may open new opportunities to build magnetically controlled displays and optical components. Here, we study the assembly of superparamagnetic colloids inside droplets under rotating magnetic fields and exploit this phenomenon to create functional optical devices. Colloids are encapsulated in monodisperse droplets produced by microfluidics and magnetically assembled into dynamic two-dimensional clusters. Using an optical microscope equipped with a magnetic control setup, we investigate the effect of the magnetic field strength and rotational frequency on the size, stability and dynamics of 2D colloidal clusters inside droplets. Our results show that cluster size and stability depend on the magnetic forces acting on the structure under the externally imposed field. By rotating the cluster in specific orientations, we illustrate how magnetic fields can be used to control the effective refractive index and the transmission of light through the colloid-laden droplets, thus demonstrating the potential of the encapsulated colloids in optical applications

Measurement of two-halo neutron transfer reaction p(11^{11}Li,9^{9}Li)t at 3AA MeV

The p(\nuc{11}{Li},\nuc{9}{Li})t reaction has been studied for the first time at an incident energy of 3$A$ MeV delivered by the new ISAC-2 facility at TRIUMF. An active target detector MAYA, build at GANIL, was used for the measurement. The differential cross sectionshave been determined for transitions to the \nuc{9}{Li} ground andthe first excited states in a wide range of scattering angles. Multistep transfer calculations using different \nuc{11}{Li} model wave functions, shows that wave functions with strong correlations between the halo neutrons are the most successful in reproducing the observation.Comment: 6 pages, 3 figures, submitted to Physical Review Letter

Measurement of the 18Ne(a,p_0)21Na reaction cross section in the burning energy region for X-ray bursts

The 18Ne(a,p)21Na reaction provides one of the main HCNO-breakout routes into the rp-process in X-ray bursts. The 18Ne(a,p_0)21Na reaction cross section has been determined for the first time in the Gamow energy region for peak temperatures T=2GK by measuring its time-reversal reaction 21Na(p,a)18Ne in inverse kinematics. The astrophysical rate for ground-state to ground-state transitions was found to be a factor of 2 lower than Hauser-Feshbach theoretical predictions. Our reduced rate will affect the physical conditions under which breakout from the HCNO cycles occurs via the 18Ne(a,p)21Na reaction.Comment: 5 pages, 3 figures, accepted for publication on Physical Review Letter

Comparison of the human immune responses to recombinant proteins representing three distinct surface proteins of Plasmodium vivax merozoites

Universidade Federal de São Paulo (UNIFESP), Escola Paulista de Medicina (EPM) Departamento de Microbiologia, Imunologia e ParasitologiaUniversidade Federal do Pará Departamento de PatologiaCenters for Disease Control and Prevention Division of Parasitic DiseasesInstituto Evandro ChagasUniversidade Federal de Minas Gerais Departamento de ParasitologiaUNIFESP, EPM, Depto. de Microbiologia, Imunologia e ParasitologiaSciEL

Disease progression in Plasmodium knowlesi malaria is linked to variation in invasion gene family members.

Emerging pathogens undermine initiatives to control the global health impact of infectious diseases. Zoonotic malaria is no exception. Plasmodium knowlesi, a malaria parasite of Southeast Asian macaques, has entered the human population. P. knowlesi, like Plasmodium falciparum, can reach high parasitaemia in human infections, and the World Health Organization guidelines for severe malaria list hyperparasitaemia among the measures of severe malaria in both infections. Not all patients with P. knowlesi infections develop hyperparasitaemia, and it is important to determine why. Between isolate variability in erythrocyte invasion, efficiency seems key. Here we investigate the idea that particular alleles of two P. knowlesi erythrocyte invasion genes, P. knowlesi normocyte binding protein Pknbpxa and Pknbpxb, influence parasitaemia and human disease progression. Pknbpxa and Pknbpxb reference DNA sequences were generated from five geographically and temporally distinct P. knowlesi patient isolates. Polymorphic regions of each gene (approximately 800 bp) were identified by haplotyping 147 patient isolates at each locus. Parasitaemia in the study cohort was associated with markers of disease severity including liver and renal dysfunction, haemoglobin, platelets and lactate, (r = ≥ 0.34, p =  <0.0001 for all). Seventy-five and 51 Pknbpxa and Pknbpxb haplotypes were resolved in 138 (94%) and 134 (92%) patient isolates respectively. The haplotypes formed twelve Pknbpxa and two Pknbpxb allelic groups. Patients infected with parasites with particular Pknbpxa and Pknbpxb alleles within the groups had significantly higher parasitaemia and other markers of disease severity. Our study strongly suggests that P. knowlesi invasion gene variants contribute to parasite virulence. We focused on two invasion genes, and we anticipate that additional virulent loci will be identified in pathogen genome-wide studies. The multiple sustained entries of this diverse pathogen into the human population must give cause for concern to malaria elimination strategists in the Southeast Asian region

Merozoite surface protein-3α is a reliable marker for population genetic analysis of Plasmodium vivax

BACKGROUND: The knowledge on population structure of the parasite isolates has contributed greatly to understanding the dynamics of the disease transmission for designing and evaluating malaria vaccines as well as for drug applications. msp-1 and msp-3α genes have been used as a genetic marker in population studies of Plasmodium vivax isolates. In this study, msp-3α was compared and assessed with msp-1 marker in order to find whether msp-3α is a reliable genetic marker for P. vivax population studies. METHODS: This comparative study was designed and carried out as the first assessment of diversity in Pvmsp-3α gene by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in the 50 northern and 94 southern P. vivax isolates from Iran, which had been analysed before for msp-1 gene. RESULTS: Three allele size as, Type A (1.8 kb), Type B (1.5 kb) and Type C (1.2 kb) have been detected among both northern and southern isolates based on PCR results. Type C (70%) and Type A (68.7%) were the predominant fragments among northern and southern parasites, respectively. 99 distinct Pvmsp-3α fragments defined by the size were detected in the 94 southern samples by PCR analysis. However, no mixed genotype infections have been detected among northern isolates. Based on restriction pattern from digestion with Hha I and Alu I 12 and 49 distinct allelic variants have been detected among 50 northern and 94 southern isolates. However, based on msp-1 gene, 30 distinct variants identified in all 146-sequenced Iranian P. vivax isolate. CONCLUSION: The results suggested that PCR-RFLP on msp-3α gene is an adequate, applicable and easily used technique for molecular epidemiology studies of P. vivax isolates without the need for further sequencing analysis

Cross section measurements of the 3He(alpha, gamma) 7Be reaction using DRAGON at TRIUMF.

4 pags., 2 figs. -- Nuclear Physics in Astrophysics V 3–8 April 2011, Eilat, IsraelWe present our initial efforts with the DRAGON separator at TRIUMF facility towards obtaining the energy dependence of the astrophysical S-factor for 3He(¿, ¿)7Be reaction in the energy range of Ecm = 2 to 3 MeV that was recommended by the recent evaluations. A comparison between the existing data and our new complementary Madrid data, together with the recent theoretical calculations, is also given in the context of our ongoing work.This work has been supported by the UK STFC