Structuring Services and Facilities for Library Instruction

published or submitted for publicatio

Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification

BACKGROUND: Translating genomic technologies into healthcare applications for the malaria parasite Plasmodium falciparum has been limited by the technical and logistical difficulties of obtaining high quality clinical samples from the field. Sampling by dried blood spot (DBS) finger-pricks can be performed safely and efficiently with minimal resource and storage requirements compared with venous blood (VB). Here, the use of selective whole genome amplification (sWGA) to sequence the P. falciparum genome from clinical DBS samples was evaluated, and the results compared with current methods that use leucodepleted VB. METHODS: Parasite DNA with high (>95%) human DNA contamination was selectively amplified by Phi29 polymerase using short oligonucleotide probes of 8-12 mers as primers. These primers were selected on the basis of their differential frequency of binding the desired (P. falciparum DNA) and contaminating (human) genomes. RESULTS: Using sWGA method, clinical samples from 156 malaria patients, including 120 paired samples for head-to-head comparison of DBS and leucodepleted VB were sequenced. Greater than 18-fold enrichment of P. falciparum DNA was achieved from DBS extracts. The parasitaemia threshold to achieve >5× coverage for 50% of the genome was 0.03% (40 parasites per 200 white blood cells). Over 99% SNP concordance between VB and DBS samples was achieved after excluding missing calls. CONCLUSION: The sWGA methods described here provide a reliable and scalable way of generating P. falciparum genome sequence data from DBS samples. The current data indicate that it will be possible to get good quality sequence on most if not all drug resistance loci from the majority of symptomatic malaria patients. This technique overcomes a major limiting factor in P. falciparum genome sequencing from field samples, and paves the way for large-scale epidemiological applications

L1448 IRS2E: A candidate first hydrostatic core

Intermediate between the prestellar and Class 0 protostellar phases, the first core is a quasi-equilibrium hydrostatic object with a short lifetime and an extremely low luminosity. Recent MHD simulations suggest that the first core can even drive a molecular outflow before the formation of the second core (i.e., protostar). Using the Submillimeter Array and the Spitzer Space Telescope, we present high angular resolution observations towards the embedded dense core IRS2E in L1448. We find that source L1448 IRS2E is not visible in the sensitive Spitzer infrared images (at wavelengths from 3.6 to 70 um), and has weak (sub-)millimeter dust continuum emission. Consequently, this source has an extremely low bolometric luminosity (< 0.1 L_sun). Infrared and (sub-)millimeter observations clearly show an outflow emanating from this source; L1448 IRS2E represents thus far the lowest luminosity source known to be driving a molecular outflow. Comparisons with prestellar cores and Class 0 protostars suggest that L1448 IRS2E is more evolved than prestellar cores but less evolved than Class 0 protostars, i.e., at a stage intermediate between prestellar cores and Class 0 protostars. All these results are consistent with the theoretical predictions of the radiative/magneto hydrodynamical simulations, making L1448 IRS2E the most promising candidate of the first hydrostatic core revealed so far.Comment: 20 pages, 4 figures, to be published by Ap

Note and Comment

The Appam Case - On March 6 last the Supreme Court handed down a unanimous decision in the appeals taken in the libel suits filed against the Appam and cargo in the District Court of the United States for the Eastern District of Virginia, affirming the decree of. restitution entered by that court

Prophylactic methylprednisolone to reduce inflammation and improve outcomes from one lung ventilation in children: a randomized clinical trial.

BACKGROUND: One lung ventilation (OLV) results in inflammatory and mechanical injury, leading to intraoperative and postoperative complications in children. No interventions have been studied in children to minimize such injury. OBJECTIVE: We hypothesized that a single 2-mg·kg(-1) dose of methylprednisolone given 45-60 min prior to lung collapse would minimize injury from OLV and improve physiological stability. METHODS: Twenty-eight children scheduled to undergo OLV were randomly assigned to receive 2 mg·kg(-1) methylprednisolone (MP) or normal saline (placebo group) prior to OLV. Anesthetic management was standardized, and data were collected for physiological stability (bronchospasm, respiratory resistance, and compliance). Plasma was assayed for inflammatory markers related to lung injury at timed intervals related to administration of methylprednisolone. RESULTS: Three children in the placebo group experienced clinically significant intraoperative and postoperative respiratory complications. Respiratory resistance was lower (P = 0.04) in the methylprednisolone group. Pro-inflammatory cytokine IL-6 was lower (P = 0.01), and anti-inflammatory cytokine IL-10 was higher (P = 0.001) in the methylprednisolone group. Tryptase, measured before and after OLV, was lower (P = 0.03) in the methylprednisolone group while increased levels of tryptase were seen in placebo group after OLV (did not achieve significance). There were no side effects observed that could be attributed to methylprednisolone in this study. CONCLUSIONS: Methylprednisolone at 2 mg·kg(-1) given as a single dose prior to OLV provides physiological stability to children undergoing OLV. In addition, methylprednisolone results in lower pro-inflammatory markers and higher anti-inflammatory markers in the children\u27s plasma

Electron spin polarization in realistic trajectories around the magnetic node of two counter-propagating, circularly polarized, ultra-intense lasers

It has recently been suggested that two counter-propagating, circularly polarized, ultra-intense lasers can induce a strong electron spin polarization at the magnetic node of the electromagnetic field that they setup (Del Sorbo et al 2017 Phys. Rev. A 96 043407). We confirm these results by considering a more sophisticated description that integrates over realistic trajectories. The electron dynamics is weakly affected by the variation of power radiated due to the spin polarization. The degree of spin polarization differs by approximately 5% if considering electrons initially at rest or already in a circular orbit. The instability of trajectories at the magnetic node induces a spin precession associated with the electron migration that establishes an upper temporal limit to the polarization of the electron population of about one laser period

The genetic risk of acute seizures in African children with falciparum malaria.

PURPOSE: It is unclear why some children with falciparum malaria develop acute seizures and what determines the phenotype of seizures. We sought to determine if polymorphisms of malaria candidate genes are associated with acute seizures. METHODS: Logistic regression was used to investigate genetic associations with malaria-associated seizures (MAS) and complex MAS (repetitive, prolonged, or focal seizures) in four MalariaGEN African sites, namely: Blantyre, Malawi; Kilifi, Kenya; Kumasi, Ghana; and Muheza, Tanzania. The analysis was repeated for five inheritance models (dominant, heterozygous, recessive, additive, and general) and adjusted for potential confounders and multiple testing. KEY FINDINGS: Complex phenotypes of seizures constituted 71% of all admissions with MAS across the sites. MAS were strongly associated with cluster of differentiation-ligand-rs3092945 in females in Kilifi (p = 0.00068) and interleukin (IL)-17 receptor E-rs708567 in the pooled analysis across the sites (p = 0.00709). Complex MAS were strongly associated with epidermal growth factor module-containing mucin-like hormone receptor (EMR)1-rs373533 in Kumasi (p = 0.00033), but none in the pooled analysis. Focal MAS were strongly associated with IL-20 receptor A-rs1555498 in Muheza (p = 0.00016), but none in the pooled analysis. Prolonged MAS were strongly associated with complement receptor 1-rs17047660 in Kilifi (p = 0.00121) and glucose-6-phosphate dehydrogenase-rs1050828 in females in the pooled analysis (p = 0.00155). Repetitive MAS were strongly associated with EMR1-rs373533 in Kumasi (p = 0.00003) and cystic fibrosis transmembrane conductance receptor-rs17140229 in the pooled analysis (p = 0.00543). MAS with coma/cerebral malaria were strongly associated with EMR1-rs373533 in Kumasi (p = 0.00019) and IL10-rs3024500 in the pooled analysis across the sites (p = 0.00064). SIGNIFICANCE: We have identified a number of genetic associations that may explain the risk of seizures in >2,000 cases admitted to hospitals with MAS across four sites in Africa. These associations differed according to phenotype of seizures and site

Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study

Background: Human genetic factors are important determinants of malaria risk. We investigated associations between multiple candidate polymorphisms—many related to the structure or function of red blood cells—and risk for severe Plasmodium falciparum malaria and its specific phenotypes, including cerebral malaria, severe malaria anaemia, and respiratory distress. Methods: We did a case-control study in Kilifi County, Kenya. We recruited as cases children presenting with severe malaria to the high-dependency ward of Kilifi County Hospital. We included as controls infants born in the local community between Aug 1, 2006, and Sept 30, 2010, who were part of a genetics study. We tested for associations between a range of candidate malaria-protective genes and risk for severe malaria and its specific phenotypes. We used a permutation approach to account for multiple comparisons between polymorphisms and severe malaria. We judged p values less than 0·005 significant for the primary analysis of the association between candidate genes and severe malaria. Findings: Between June 11, 1995, and June 12, 2008, 2244 children with severe malaria were recruited to the study, and 3949 infants were included as controls. Overall, 263 (12%) of 2244 children with severe malaria died in hospital, including 196 (16%) of 1233 with cerebral malaria. We investigated 121 polymorphisms in 70 candidate severe malaria-associated genes. We found significant associations between risk for severe malaria overall and polymorphisms in 15 genes or locations, of which most were related to red blood cells: ABO, ATP2B4, ARL14, CD40LG, FREM3, INPP4B, G6PD, HBA (both HBA1 and HBA2), HBB, IL10, LPHN2 (also known as ADGRL2), LOC727982, RPS6KL1, CAND1, and GNAS. Combined, these genetic associations accounted for 5·2% of the variance in risk for developing severe malaria among individuals in the general population. We confirmed established associations between severe malaria and sickle-cell trait (odds ratio [OR] 0·15, 95% CI 0·11–0·20; p=2·61 × 10−58), blood group O (0·74, 0·66–0·82; p=6·26 × 10−8), and –α3·7-thalassaemia (0·83, 0·76–0·90; p=2·06 × 10−6). We also found strong associations between overall risk of severe malaria and polymorphisms in both ATP2B4 (OR 0·76, 95% CI 0·63–0·92; p=0·001) and FREM3 (0·64, 0·53–0·79; p=3·18 × 10−14). The association with FREM3 could be accounted for by linkage disequilibrium with a complex structural mutation within the glycophorin gene region (comprising GYPA, GYPB, and GYPE) that encodes for the rare Dantu blood group antigen. Heterozygosity for Dantu was associated with risk for severe malaria (OR 0·57, 95% CI 0·49–0·68; p=3·22 × 10−11), as was homozygosity (0·26, 0·11–0·62; p=0·002). Interpretation: Both ATP2B4 and the Dantu blood group antigen are associated with the structure and function of red blood cells. ATP2B4 codes for plasma membrane calcium-transporting ATPase 4 (the major calcium pump on red blood cells) and the glycophorins are ligands for parasites to invade red blood cells. Future work should aim at uncovering the mechanisms by which these polymorphisms can result in severe malaria protection and investigate the implications of these associations for wider health. Funding: Wellcome Trust, UK Medical Research Council, European Union, and Foundation for the National Institutes of Health as part of the Bill &amp; Melinda Gates Grand Challenges in Global Health Initiative

The enigmatic core L1451-mm: a first hydrostatic core? or a hidden VeLLO?

We present the detection of a dust continuum source at 3-mm (CARMA) and 1.3-mm (SMA), and 12CO(2-1) emission (SMA) towards the L1451-mm dense core. These detections suggest a compact object and an outflow where no point source at mid-infrared wavelengths is detected using Spitzer. An upper limit for the dense core bolometric luminosity of 0.05 Lsun is obtained. By modeling the broadband SED and the continuum interferometric visibilities simultaneously, we confirm that a central source of heating is needed to explain the observations. This modeling also shows that the data can be well fitted by a dense core with a YSO and disk, or by a dense core with a central First Hydrostatic Core (FHSC). Unfortunately, we are not able to decide between these two models, which produce similar fits. We also detect 12CO(2-1) emission with red- and blue-shifted emission suggesting the presence of a slow and poorly collimated outflow, in opposition to what is usually found towards young stellar objects but in agreement with prediction from simulations of a FHSC. This presents the best candidate, so far, for a FHSC, an object that has been identified in simulations of collapsing dense cores. Whatever the true nature of the central object in L1451-mm, this core presents an excellent laboratory to study the earliest phases of low-mass star formation.Comment: 15 pages, 9 figures, emulateapj. Accepted by Ap