Haplotype specific-sequencing reveals MBL2 association with asymptomatic Plasmodium falciparum infection

<p>Abstract</p> <p>Background</p> <p>Mannose binding lectin (MBL) has an important role in the activation of the complement system and opsonization of pathogenic microorganisms. Frequent polymorphisms found in the <it>MBL2 </it>gene affect the concentration and functionality of the protein and are associated with enhanced susceptibility to severe malaria in African children. Most <it>MBL2 </it>typing strategies were designed to the analysis of selected variants, the significance of whole haplotypes is poorly known. In this work, a new typing strategy was developed and validated in an association analysis of <it>MBL2 </it>with adult asymptomatic infection.</p> <p>Methods</p> <p><it>MBL2 </it>allele-specific fragments of 144 healthy Gabonese adults were amplified by using haplotype-specific sequencing (HSS), a new strategy that combines sequence-specific PCR and sequence-based typing. The Gabonese were investigated for the presence of <it>Plasmodium falciparum </it>parasitaemia by the amplification of parasite genes, immunochromatographic antigen detection and microscopic analysis. HSS results were also compared with a previously used real-time PCR (RT-PCR) method in 72 Euro-Brazilians.</p> <p>Results</p> <p>Fourteen polymorphisms were identified beside the commonly investigated promoter (<it>H, L</it>; <it>X, Y</it>; <it>P, Q</it>) and exon 1 (<it>A, O</it>; <it>O </it>= <it>B</it>, <it>C </it>or <it>D</it>) variants. The <it>MBL2*LYPA/LYPA </it>genotype was associated with the absence of asymptomatic infection (P = 0.017), whereas the <it>MBL2*LYQC </it>haplotype and <it>YA/YO </it>+ <it>YO/YO </it>genotypes were associated with positive parasite counts in asymptomatic adults (P = 0.033 and 0.018, respectively). The associations were specific to <it>LYPA </it>(identical to the reference sequence Y16577) and <it>LYQC </it>(Y16578) and would not have been revealed by standard genotyping, as there was no association with <it>LYPA </it>and <it>LYQC </it>haplotypes carrying new polymorphisms defined by sequence-based typing. In contrast, HSS and RT-PCR produced very similar results in the less diverse European-derived population.</p> <p>Conclusion</p> <p>In this work, a new typing strategy for a highly polymorphic gene was developed and validated focusing on the asymptomatic status of <it>P. falciparum-</it>infected adults. In populations with high nucleotide diversity, it allowed for the identification of associations with fine-scaled haplotypes that would not have been found using common typing techniques. In this preliminary study, <it>MBL2 </it>haplotypes or SNPs linked to them were found associated with susceptibility to infection and parasitaemia control of asymptomatic adults.</p

A Bayesian non-linear method for feature selection in machine translation quality estimation

We perform a systematic analysis of the effectiveness of features for the problem of predicting the quality of machine translation (MT) at the sentence level. Starting from a comprehensive feature set, we apply a technique based on Gaussian processes, a Bayesian non-linear learning method, to automatically identify features leading to accurate model performance. We consider application to several datasets across different language pairs and text domains, with translations produced by various MT systems and scored for quality according to different evaluation criteria. We show that selecting features with this technique leads to significantly better performance in most datasets, as compared to using the complete feature sets or a state-of-the-art feature selection approach. In addition, we identify a small set of features which seem to perform well across most datasets

Redox proteomics of the inflammatory secretome identifies a common set of redoxins and other glutathionylated proteins released in inflammation, influenza virus infection and oxidative stress

Protein cysteines can form transient disulfides with glutathione (GSH), resulting in the production of glutathionylated proteins, and this process is regarded as a mechanism by which the redox state of the cell can regulate protein function. Most studies on redox regulation of immunity have focused on intracellular proteins. In this study we have used redox proteomics to identify those proteins released in glutathionylated form by macrophages stimulated with lipopolysaccharide (LPS) after pre-loading the cells with biotinylated GSH. Of the several proteins identified in the redox secretome, we have selected a number for validation. Proteomic analysis indicated that LPS stimulated the release of peroxiredoxin (PRDX) 1, PRDX2, vimentin (VIM), profilin1 (PFN1) and thioredoxin 1 (TXN1). For PRDX1 and TXN1, we were able to confirm that the released protein is glutathionylated. PRDX1, PRDX2 and TXN1 were also released by the human pulmonary epithelial cell line, A549, infected with influenza virus. The release of the proteins identified was inhibited by the anti-inflammatory glucocorticoid, dexamethasone (DEX), which also inhibited tumor necrosis factor (TNF)-α release, and by thiol antioxidants (N-butanoyl GSH derivative, GSH-C4, and N-acetylcysteine (NAC), which did not affect TNF-α production. The proteins identified could be useful as biomarkers of oxidative stress associated with inflammation, and further studies will be required to investigate if the extracellular forms of these proteins has immunoregulatory functions

How Do Humans Control Physiological Strain during Strenuous Endurance Exercise?

Background: Methodology/principal Findings: Conclusions/significance: Distance running performance is a viable model of human locomotion.To evaluate the physiologic strain during competitions ranging from 5-100 km, we evaluated heart rate (HR) records of competitive runners (n = 211). We found evidence that: 1) physiologic strain (% of maximum HR (%HRmax)) increased in proportional manner relative to distance completed, and was regulated by variations in running pace; 2) the %HRmax achieved decreased with relative distance; 3) slower runners had similar %HRmax response within a racing distance compared to faster runners, and despite differences in pace, the profile of %HRmax during a race was very similar in runners of differing ability; and 4) in cases where there was a discontinuity in the running performance, there was evidence that physiologic effort was maintained for some time even after the pace had decreased.The overall results suggest that athletes are actively regulating their relative physiologic strain during competition, although there is evidence of poor regulation in the case of competitive failures.2.308 SJR (2008) Q1, 60/1774 Medicine (miscellaneous), 19/144 Biochemistry, genetics and molecular biology (miscellaneous), 15/175 Agricultural and biological sciences (miscellaneous)UE

Resting and Post Bronchial Challenge Testing Carbon Dioxide Partial Pressure in Individuals with and without Asthma

Objective: There is conflicting evidence about resting carbon dioxide levels in asthmatic individuals. We wanted to determine if transcutaneously measured carbon dioxide levels prior and during bronchial provocation testing differ according to asthma status reflecting dysfunctional breathing. Methods: We investigated active firefighters and policemen by means of a validated questionnaire on respiratory symptoms, spirometry, bronchial challenge testing with methacholine (MCT) and measurement of transcutaneous blood carbon dioxide partial pressure (PtcCO 2) at rest prior performing spirometry, one minute and five minutes after termination of MCT. A respiratory physician blinded to the PtcCO2 results assigned a diagnosis of asthma after reviewing the available study data and the files of the workers medical screening program. Results: The study sample consisted of 128 male and 10 female individuals. Fifteen individuals (11%) had physiciandiagnosed asthma. There was no clinically important difference in median PtcCO 2 at rest, one and five minutes after recovery from MCT in asthmatics compared to non-asthmatics (35.6 vs 35.7 mmHg, p = 0.466; 34.7 vs 33.4 mmHg, p = 0.245 and 37.4 vs 36.4 mmHg, p = 0.732). The median drop in PtcCO2 during MCT and the increase after MCT was lower in asthmatics compared to non-asthmatics (0.1 vs 3.2 mmHg, p = 0.014 and 1.9 vs 2.9 mmHg, p = 0.025). Conclusions: PtcCO2 levels at rest prior and during recovery after MCT do not differ in individuals with or without physicia

The effect of ambient temperature on gross-efficiency in cycling

Time-trial performance deteriorates in the heat. This might potentially be the result of a temperature-induced decrease in gross-efficiency (GE). The effect of high ambient temperature on GE during cycling will be studied, with the intent of determining if a heat-induced change in GE could account for the performance decrements in time trial exercise found in literature. Ten well-trained male cyclists performed 20-min cycle ergometer exercise at 60% \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$P_{V{\text{O}}_{{\text{2max}}} }$$\end{document} (power output at which VO2max was attained) in a thermo-neutral climate (N) of 15.6 ± 0.3°C, 20.0 ± 10.3% RH and a hot climate (H) of 35.5 ± 0.5°C, 15.5 ± 3.2% RH. GE was calculated based on VO2 and RER. Skin temperature (Tsk), rectal temperature (Tre) and muscle temperature (Tm) (only in H) were measured. GE was 0.9% lower in H compared to N (19.6 ± 1.1% vs. 20.5 ± 1.4%) (P < 0.05). Tsk (33.4 ± 0.6°C vs. 27.7 ± 0.7°C) and Tre (37.4 ± 0.6°C vs. 37.0 ± 0.6°C) were significantly higher in H. Tm was 38.7 ± 1.1°C in H. GE was lower in heat. Tm was not high enough to make mitochondrial leakage a likely explanation for the observed reduced GE. Neither was the increased Tre. Increased skin blood flow might have had a stealing effect on muscular blood flow, and thus impacted GE. Cycling model simulations showed, that the decrease in GE could account for half of the performance decrement. GE decreased in heat to a degree that could explain at least part of the well-established performance decrements in the heat

Common Data Elements for COVID-19 Neuroimaging: A GCS-NeuroCOVID Proposal

Funder: National Institute of Neurological Disorders and Stroke; doi: http://dx.doi.org/10.13039/100000065Funder: James S. McDonnell Foundation; doi: http://dx.doi.org/10.13039/100000913Funder: National Institute of Health ResearchFunder: United Kingdom Research and InnovationFunder: Addenbrooke’s Charitable Trus

Measurement of Warfarin in the Oral Fluid of Patients Undergoing Anticoagulant Oral Therapy

BACKGROUND: Patients on warfarin therapy undergo invasive and expensive checks for the coagulability of their blood. No information on coagulation levels is currently available between two controls. METHODOLOGY: A method was developed to determine warfarin in oral fluid by HPLC and fluorimetric detection. The chromatographic separation was performed at room temperature on a C-18 reversed-phase column, 65% PBS and 35% methanol mobile phase, flow rate 0.7 mL/min, injection volume 25 µL, excitation wavelength 310 nm, emission wavelength 400 nm. FINDINGS: The method was free from interference and matrix effect, linear in the range 0.2-100 ng/mL, with a detection limit of 0.2 ng/mL. Its coefficient of variation was <3% for intra-day measurements and <5% for inter-day measurements. The average concentration of warfarin in the oral fluid of 50 patients was 2.5±1.6 ng/mL (range 0.8-7.6 ng/mL). Dosage was not correlated to INR (r = -0.03, p = 0.85) but positively correlated to warfarin concentration in the oral fluid (r = 0.39, p = 0.006). The correlation between warfarin concentration and pH in the oral fluid (r = 0.37, p = 0.009) confirmed the importance of pH in regulating the drug transfer from blood. A correlation between warfarin concentration in the oral fluid and INR was only found in samples with pH values ≥7.2 (r = 0.84, p = 0.004). CONCLUSIONS: Warfarin diffuses from blood to oral fluid. The method allows to measure its concentration in this matrix and to analyze correlations with INR and other parameters

The between and within day variation in gross efficiency

Before the influence of divergent factors on gross efficiency (GE) [the ratio of mechanical power output (PO) to metabolic power input (PI)] can be assessed, the variation in GE between days, i.e. the test–retest reliability, and the within day variation needs to be known. Physically active males (n = 18) performed a maximal incremental exercise test to obtain VO2max and PO at VO2max (PVO2max), and three experimental testing days, consisting of seven submaximal exercise bouts evenly distributed over the 24 h of the day. Each submaximal exercise bout consisted of six min cycling at 45, 55 and 65% PVO2max, during which VO2 and RER were measured. GE was determined from the final 3 min of each exercise intensity with: GE = (PO/PI) × 100%. PI was calculated by multiplying VO2 with the oxygen equivalent. GE measured during the individually highest exercise intensity with RER <1.0 did not differ significantly between days (F = 2.70, p = 0.08), which resulted in lower and upper boundaries of the 95% limits of agreement of 19.6 and 20.8%, respectively, around a mean GE of 20.2%. Although there were minor within day variations in GE, differences in GE over the day were not significant (F = 0.16, p = 0.99). The measurement of GE during cycling at intensities approximating VT is apparently very robust, a change in GE of ~0.6% can be reliably detected. Lastly, GE does not display a circadian rhythm so long as the criteria of a steady-state VO2 and RER <1.0 are applied