Whole genome sequencing identifies novel mutations in malaria parasites resistant to artesunate (ATN) and to ATN + mefloquine combination

Introduction

The global evolution of resistance to Artemisinin-based Combination Therapies (ACTs) by malaria parasites, will severely undermine our ability to control this devastating disease.

Methods

Here, we have used whole genome sequencing to characterize the genetic variation in the experimentally evolved Plasmodium chabaudi parasite clone AS-ATNMF1, which is resistant to artesunate + mefloquine.

Results and discussion

Five novel single nucleotide polymorphisms (SNPs) were identified, one of which was a previously undescribed E738K mutation in a 26S proteasome subunit that was selected for under artesunate pressure (in AS-ATN) and retained in AS-ATNMF1. The wild type and mutated three-dimensional (3D) structure models and molecular dynamics simulations of the P. falciparum 26S proteasome subunit Rpn2 suggested that the E738K mutation could change the toroidal proteasome/cyclosome domain organization and change the recognition of ubiquitinated proteins. The mutation in the 26S proteasome subunit may therefore contribute to altering oxidation-dependent ubiquitination of the MDR-1 and/or K13 proteins and/or other targets, resulting in changes in protein turnover. In light of the alarming increase in resistance to artemisin derivatives and ACT partner drugs in natural parasite populations, our results shed new light on the biology of resistance and provide information on novel molecular markers of resistance that may be tested (and potentially validated) in the field.

Safety profile and SARS-CoV-2 breakthrough infections among HCWs receiving anti-SARS-CoV-2 and influenza vaccines simultaneously: an Italian observational study

In October/December 2021, World Health Organization and other international agencies recommended the offer of the third dose of anti-SARS-CoV-2 vaccine. In this period, the routine offer of seasonal influenza vaccination was also guaranteed and simultaneous administration of the two vaccines was encouraged. This study aims to evaluate the safety profile and to estimate the incidence of SARS-CoV-2 breakthrough infections in subjects receiving the anti-SARS-CoV-2 and influenza vaccines simultaneously. The study population was represented by healthcare workers (HCWs) of Bari Policlinico General Hospital who received the influenza (Flucelvax Tetra®) and/or anti-SARS-CoV-2 vaccination (BNT162b2 mRNA COVID-19 vaccine, Comirnaty®) either in coadministration or separately in October 2021. Reports of adverse events following immunization (AEFIs) were investigated to study the safety of both vaccines in coadministration and in separate-instance administration. Post-vaccination SARS-CoV-2 breakthrough infection was also studied. 942 HCWs accepted to join our study. 610/942 received both vaccines simultaneously. 25.26 % subjects (238/942) were only vaccinated against SARS-CoV-2, while the remaining 94 HCWs received the influenza vaccination first and subsequently received the anti-SARS-CoV2 booster dose. 717 HCWs reported AEFIs (Reporting Rate 76.1 per 100 subjects). Simultaneous administration of the two vaccines was not related with an increase of the rate of AEFIs compared to the single administration of SARS-CoV-2 vaccine, but the AEFIs' rate was lower among subjects who received only influenza vaccine. Post-vaccination SARS-CoV-2 infections were notified for 41.5 % of enrolled subjects (391/942). Incidence of breakthrough infection and symptomatic disease was not significantly different between the simultaneous administration group and other subjects. Our data suggests that simultaneous administration of a quadrivalent influenza vaccine and an mRNA anti-SARS-CoV-2 vaccine neither affected the safety of said products nor was associated with a higher risk of SARS-CoV-2 breakthrough infection.

The safety of pneumococcal vaccines at the time of sequential schedule: data from surveillance of adverse events following 13-valent conjugated pneumococcal and 23-valent polysaccharidic pneumococcal vaccines in newborns and the elderly, in Puglia (Italy), 2013-2020

Background

Nowadays, two types of anti-pneumococcal vaccine are available: pneumococcal 13-valent conjugate vaccine (PCV13), first licensed in the United States (US) in 2013, and pneumococcal 23-valent polysaccaridic vaccine (PPSV23), first licensed in the US in 1999. These vaccines are recommended in Italy for the immunization of newborns and of the elderly, using a combined sequential schedule for the latter. This report aims to describe the PCV13- and PPSV23-related AEFIs notified in Puglia in 2013-2020, in order to design these products' safety profile in a real-life scenario, three years after the official recommendation about the sequential schedule for people over 60 years of age.

Methods

This is a retrospective observational study. Data were gathered from the list of AEFIs notified following PCV13 and PPSV23 administration in Puglia in 2013-2020. The number of administered vaccine doses was obtained from the regional immunization database. AEFIs were classified according to WHO's algorithm, and causality assessment was carried out in case of serious AEFIs.

Results

From January 2013 to December 2020, 764,183 doses of PCV13 and 40,382 doses of PPSV23 were administered in Puglia. In the same period, 71 PCV13 AEFIs (Reporting Rate: 9.29 x100,000 doses) and 5 PPSV23 AEFIs (Reporting Rate: 12.4 x100,000 doses) were reported. The overall male/female ratio in AEFIs was 0.85. The majority of AEFIs occurred in subjects aged less than 2 (64/76, 84.2%), while 10 out of 76 (13.2%) occurred in patients aged 60 or older. 22 AEFIs were classified as serious and for 12 (54.5%) causality assessment showed a consistent relationship with immunization. The most commonly reported symptoms were fever (Reporting Rate: 4.72 x100,000 doses) and neurological symptoms (Reporting Rate: 3.23 x100,000 doses). Only one death was notified, classified as non-vaccine-related.

Conclusions

The benefit of pneumococcal vaccination appears to be greater than the risk of AEFIs for both PCV13 and PPSV23. In fact, AEFIs occur in less than 0.1‰ of patients and the majority of AEFIs are mild and self-limiting.

Extreme ultraviolet transient gratings: A tool for nanoscale photoacoustics

Collective lattice dynamics determine essential aspects of condensed matter, such as elastic and thermal properties. These exhibit strong dependence on the length-scale, reflecting the marked wavevector dependence of lattice excitations. The extreme ultraviolet transient grating (EUV TG) approach has demonstrated the potential of accessing a wavevector range corresponding to the 10s of nm length-scale, representing a spatial scale of the highest relevance for fundamental physics and forefront technology, previously inaccessible by optical TG and other inelastic scattering methods. In this manuscript we report on the capabilities of this technique in the context of probing thermoelastic properties of matter, both in the bulk and at the surface, as well as discussing future developments and practical considerations.

High-performance Fe(Se,Te) films on chemical CeO2-based buffer layers

The fabrication of a Fe-based coated conductor (CC) becomes possible when Fe(Se,Te) is grown as an epitaxial film on a metallic oriented substrate. Thanks to the material's low structural anisotropy, less strict requirements on the template microstructure allow for the design of a simplified CC architecture with respect to the REBCO multi-layered layout. This design, though, still requires a buffer layer to promote the oriented growth of the superconducting film and avoid diffusion from the metallic template. In this work, Fe(Se,Te) films are grown on chemically-deposited, CeO₂-based buffer layers via pulsed laser deposition, and excellent properties are obtained when a Fe(Se,Te) seed layer is used. Among all the employed characterization techniques, transmission electron microscopy proved essential to determine the actual effect of the seed layer on the final film properties. Also, systematic investigation of the full current transport properties J(θ, H, T) is carried out: Fe(Se,Te) samples are obtained with sharp superconducting transitions around 16 K and critical current densities exceeding 1 MA cm^-2 at 4.2 K in self-field. The in-field and angular behavior of the sample are in line with data from the literature. These results are the demonstration of the feasibility of a Fe-based CC, with all the relative advantages concerning process simplification and cost reduction.

Incidence of SARS-COV-2 infection among swimming athletes: data from real life in Apulia (Italy), July 2020/August 2021

BACKGROUND

As other indoor sports facilities, swimming pools were closed in Italy from March to May 2020 and from October 2020 to July 2021 due to the outbreak of the COVID-19 pandemic; access to these facilities was restricted to athletes of national relevance. This decision was based on "precautionary principles" and without evidence of a high risk of SARS-COV-2 circulation among swimming pools' attendants. The aim of this paper is to describe the pattern of SARS-COV-2 circulation among swimming athletes in Apulia (Southern Italy).

STUDY DESIGN

The study aims to investigate the hypothesis that attending a pool increases the risk of SARS-COV-2 infection. The outcome measure is the incidence of SARS-COV-2 infection among swimming athletes compared with the general population.

METHODS

This is a retrospective cross-sectional study carried out in Apulia, Southern Italy. The study was performed through the analysis of both the database of the Italian Swimming Federation and the SARS-COV-2 infections in Apulia Region, from July 2020 to August 2021.

RESULTS

Among 2,939 federally licensed athletes, 221 had an history of SARS-COV-2 infection from July 2020 to August 2021, with an incidence of 75.2 /1,000. In the general Apulian population, during the same time span, the incidence of SARS-COV-2 infection was 67.3/1,000 and - considering the incidence rate ratio - there is no difference between the two populations (IRR=1.1; 95% CI=0.9-1.3; p>0.05).

CONCLUSIONS

The incidence of SARS-COV-2 infection in Apulian swimmers showed no significant differences with the general population.

metaLINCS: an R package for meta-level analysis of LINCS L1000 drug signatures using stratified connectivity mapping

Summary

Accessing the collection of perturbed gene expression profiles, such as the LINCS L1000 connectivity map, is usually performed at the individual dataset level, followed by a summary performed by counting individual hits for each perturbagen. With the metaLINCS R package, we present an alternative approach that combines rank correlation and gene set enrichment analysis to identify meta-level enrichment at the perturbagen level and, in the case of drugs, at the mechanism of action level. This significantly simplifies the interpretation and highlights overarching themes in the data. We demonstrate the functionality of the package and compare its performance against those of three currently used approaches.

Availability and implementation

metaLINCS is released under GPL3 license. Source code and documentation are freely available on GitHub (https://github.com/bigomics/metaLINCS).

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

Bacterial biofilms on medical masks disposed in the marine environment: a hotspot of biological and functional diversity

The present paper was aimed at investigating the role of disposable medical masks as a substrate for microbial biofilm growth and for the selection of specific microbial traits in highly impacted marine environments. In this view, we have immerged masks in a coastal area affected by a continuous input of artisanal fishery wastes and hydrocarbons pollution caused by intense maritime traffic. Masks maintained one month in the field were colonized by a bacterial community significantly different from that detected in the natural matrices from the same areas (seawater and sediments). The masks served as a viable substrate for the growth and enrichment of phototrophic microorganisms (Oxyphotobacteria), as well as Ruminococcaceae, Gracilibacteria, and Holophageae. In a follow-up investigation, masks previously colonized in the field were transferred in lab-scale microcosms which were supplemented with hydrocarbons and which contained also a piece of a virgin mask. After one month, a shift in the community composition, likely triggered by hydrocarbons addition, was observed in the previously colonized mask, with signatures characteristic of hydrocarbon-degrading microbial groups. Such hydrocarbon-degrading bacteria were also found to colonize the virgin mask. Remarkably, SEM micrographs provided indications of the occurrence of morphological modifications of the surface components of the virgin masks colonized by hydrocarbonoclastic bacteria. Overall, for the first time, we have demonstrated the potential risk for human and animal health determined by the uncorrected disposal of masks which are suitable substrates for pathogens colonization, permanence and spreading. Moreover, we have herein strengthened the knowledge on the role of hydrocarbon-degrading bacteria in the colonization and modification of fossil-based plastics in marine environment.

LUNCH-Lung Ultrasound for early detection of silent and apparent aspiratioN in infants and young CHildren with cerebral palsy and other developmental disabilities: study protocol of a randomized controlled trial

Background

Children with neurological impairment may have dysphagia and/or gastro-esophageal reflux disease (GERD), which predispose to complications affecting the airways, increasing risk for aspiration-induced acute and chronic lung disease, or secondarily malnutrition, further neurodevelopmental disturbances, stressful interactions with their caregivers and chronic pain. Only multidisciplinary clinical feeding evaluation and empirical trials are applied to provide support to the management of feeding difficulties related to dysphagia or GERD, but no standardized feeding or behavioral measure exists at any age to assess aspiration risk and support the indication to perform a videofluoroscopic swallowing study (VFSS) or a fibre-optic endoscopic examination of swallowing (FEES), in particular in newborns and infants with neurological impairments. Lung ultrasound (LUS) has been proposed as a non-invasive, radiation-free tool for the diagnosis of pulmonary conditions in infants, with high sensitivity and specificity.

Methods

A RCT will be conducted in infants aged between 0 and 6 years having, or being at risk for, cerebral palsy, or other neurodevelopmental disease that determines abnormal muscular tone or motor developmental delay assessed by a quantitative scale for infants or if there is the suspicion of GERD or dysphagia based on clinical symptoms. Infants will be allocated in one of 2 groups: 1) LUS-monitored management (LUS-m); 2) Standard care management (SC-m) and after baseline assessment (T0), both groups will undergo an experimental 6-months follow-up. In the first 3 months, infants will be evaluated a minimum of 1 time per month, in-hospital, for a total of 3 LUS-monitored meal evaluations. Primary and secondary endpoint measures will be collected at 3 and 6 months.

Discussion

This paper describes the study protocol consisting of a RCT with two main objectives: (1) to evaluate the benefits of the use of LUS for monitoring silent and apparent aspiration in the management of dysphagia and its impact on pulmonary illness and growth and (2) to investigate the impact of the LUS management on blood sample and bone metabolism, pain and interaction with caregivers.

Trial registration

Trial registration date 02/05/2020; ClinicalTrials.gov Identifier: NCT04253951.

Mn-induced Fermi-surface reconstruction in the SmFeAsO parent compound

The electronic ground state of iron-based materials is unusually sensitive to electronic correlations. Among others, its delicate balance is profoundly affected by the insertion of magnetic impurities in the FeAs layers. Here, we address the effects of Fe-to-Mn substitution in the non-superconducting Sm-1111 pnictide parent compound via a comparative study of SmFe[Formula: see text]Mn[Formula: see text]AsO samples with [Formula: see text] 0.05 and 0.10. Magnetization, Hall effect, and muon-spin spectroscopy data provide a coherent picture, indicating a weakening of the commensurate Fe spin-density-wave (SDW) order, as shown by the lowering of the SDW transition temperature [Formula: see text] with increasing Mn content, and the unexpected appearance of another magnetic order, occurring at [Formula: see text] and 20 K for [Formula: see text] and 0.10, respectively. We attribute the new magnetic transition at [Formula: see text], occurring well inside the SDW phase, to a reorganization of the Fermi surface due to Fe-to-Mn substitutions. These give rise to enhanced magnetic fluctuations along the incommensurate wavevector [Formula: see text], further increased by the RKKY interactions among Mn impurities.

Aggression differentially modulates neural correlates of social intention attribution to benevolent, tickling and taunting laughter: An fMRI study in children and adolescents

Human laughter is a powerful means of communicating social intention, ranging from welcoming and friendly to hostile and ridiculing. To be communicated accurately, the recipient must correctly identify the laugher's underlying social intention. Regular misattribution of the social intention of others has been associated with maladaptive psychosocial development, in particular with aggressive behavior. We investigated the relationship between self-reported aggressive behavior and the neural correlates of social intention attributions to different audiovisual laughter types in 50 healthy children and adolescents (29 female, 10-18 years, M 15.5, SD 2.2) using functional magnetic resonance imaging. Trial-by-trial associations of neural response and behavioral attributions were distinctly modulated by aggression for benevolent versus taunting and tickling laughter. With increasing aggression, hostile misattributions of benevolent laughter were associated with decreased dorsolateral prefrontal and anterior insular cortex activation. In contrast, hostile attributions of taunting and tickling laughter were associated with increased superior frontal, superior temporal, medial prefrontal, supplementary motor, and anterior and mid-cingulate cortex activation. We argue that aggression may be associated with down-regulated emotional saliency of benevolent laughter, whereas up-regulated neural responses to taunting laughter may underlie a heightened sensitivity to hostility or acceptance of taunting behavior in more aggressive individuals.

Preoperative anxiety in patients admitted for brain surgery: A systematic review

Introduction

Up to 80% of patients scheduled for surgery experience preoperative anxiety, which may implicate perioperative psychological and physical discomforts. Several studies focused on this phenomenon in neurosurgical setting, still controversial evidence exists.

Objectives

Our aim is to synthesize this evidence, investigating prevalence, implications and therapy of preoperative anxiety in brain surgery patients.

Methods

We performed a systematic review of literature by searching PubMed, Embase, and Cochrane Library databases. Data were extracted using the PICO framework. PRISMA guidelines were applied, and the risk of bias was assessed using the RoB 2 and ROBINS tools, as was the methodological quality of the included studies, following GRADE criteria; we excluded articles with serious risk of bias and/or low quality.

Results

We included 27 articles, accounting for 2558 patients of twelve different countries. Prevalence of anxiety before brain surgery was up to 89%, reaching higher levels in women. Anxiety concerned mostly anesthesia and surgical outcome. No correlation emerged between level of anxiety and laterality, histological type of tumor or survival rate. Before surgery, anxious patients performed worse in cognitive tasks and had worse subjective evaluation of their cognitive abilities. After surgery, preoperative anxiety was associated with depression, longer hospitalization, increase of physical disability and lower quality of life. Effective approaches to reduce anxiety were acupuncture, music therapy, virtual reality and pharmacological support.

Conclusions

Preoperative anxiety in brain surgery patients is a common experience that should not be underestimated to achieve a better perioperative care through early detection and adequate pharmacological or non-pharmacological management.

Association of CYP2B6 Genetic Variation with Efavirenz and Nevirapine Drug Resistance in HIV-1 Patients from Botswana

Purpose

CYP2B6 liver enzyme metabolizes the two non-nucleoside reverse transcriptase inhibitors Efavirenz (EFV) and Nevirapine (NVP) used in the antiretroviral therapy (ART) regimens for HIV-infected individuals. Polymorphisms of the CYP2B6 gene influence drug levels in plasma and possibly virological outcomes. The aim of this study was to explore the potential impact of CYP2B6 genotype and haplotype variation on the risk of developing EFV/NVP drug resistance mutations (DRMs) in HIV-1 patients receiving EFV-/NVP-containing regimens in Botswana.

Patients and Methods

Participants were a sub-sample of a larger study (Tshepo study) conducted in Gaborone, Botswana, among HIV-infected individuals taking EFV/NVP containing ART. Study samples were retrieved and assigned to cases (with DRMs) and controls (without DRMs). Four single-nucleotide polymorphisms (SNPs) in the CYP2B6 gene (−82T>C; 516G>T; 785A>G; 983T>C) were genotyped, the haplotypes reconstructed, and the metabolic score assigned. The possible association between drug resistance and several independent factors (baseline characteristics and CYP2B6 genotypes) was assessed by Binary Logistic Regression (BLR) analysis. EFV/NVP resistance status and CYP2B6 haplotypes were also analyzed using Z-test, chi-square and Fisher’s exact test statistics.

Results

Two hundred and twenty-seven samples were analysed (40 with DRMs, 187 without DRMs). BLR analysis showed an association between EFV/NVP resistance and CYP2B6 516G allele (OR: 2.26; 95% CI: 1.27–4.01; P=0.005). Moreover, haplotype analysis revealed that the proportion of EFV/NVP-resistant infections was higher among CYP2B6 fast than extensive/slow metabolizers (30.8% vs 16.8%; P=0.035), with the 516G allele more represented in the haplotypes of fast than extensive/slow metabolizers (100.0% vs 53.8%; P<0.001).

Conclusion

We demonstrated that the CYP2B6 516G allele, and even more when combined in fast metabolic haplotypes, is associated with the presence of EFV/NVP resistance, strengthening the need to assess the CYP2B6 genetic profiles in HIV-infected patients in order to improve the virologic outcomes of NNRTI containing ART.

Marine hydrocarbon-degrading bacteria breakdown poly(ethylene terephthalate) (PET)

Pollution of aquatic ecosystems by plastic wastes poses severe environmental and health problems and has prompted scientific investigations on the fate and factors contributing to the modification of plastics in the marine environment. Here, we investigated, by means of microcosm studies, the role of hydrocarbon-degrading bacteria in the degradation of poly(ethylene terephthalate) (PET), the main constituents of plastic bottles, in the marine environment. To this aim, different bacterial consortia, previously acclimated to representative hydrocarbons fractions namely, tetradecane (aliphatic fraction), diesel (mixture of hydrocarbons), and naphthalene/phenantrene (aromatic fraction), were used as inocula of microcosm experiments, in order to identify peculiar specialization in poly(ethylene terephthalate) degradation. Upon formation of a mature biofilm on the surface of poly(ethylene terephthalate) films, the bacterial biodiversity and degradation efficiency of each selected consortium was analyzed. Notably, significant differences on biofilm biodiversity were observed with distinctive hydrocarbons-degraders being enriched on poly(ethylene terephthalate) surface, such as Alcanivorax, Hyphomonas, and Cycloclasticus species. Interestingly, ATR-FTIR analyses, supported by SEM and water contact angle measurements, revealed major alterations of the surface chemistry and morphology of PET films, mainly driven by the bacterial consortia enriched on tetradecane and diesel. Distinctive signatures of microbial activity were the alteration of the FTIR spectra as a consequence of PET chain scission through the hydrolysis of the ester bond, the increased sample hydrophobicity as well as the formation of small cracks and cavities on the surface of the film. In conclusion, our study demonstrates for the first time that hydrocarbons-degrading marine bacteria have the potential to degrade poly(ethylene terephthalate), although their degradative activity could potentially trigger the formation of harmful microplastics in the marine environment.

Mn substitution effect on the local structure of La(Fe1-xMnx)AsO studied by temperature dependent x-ray absorption measurements

The local structure of La(Fe1-xMnx)AsO has been investigated using temperature dependent Fe K-edge extended x-ray absorption fine structure (EXAFS) measurements. The EXAFS data reveal distinct behavior of Fe-As and Fe-Fe atomic displacements with a clear boundary betweenx⩽ 0.02 andx> 0.02. The Fe-As bondlength shows a gradual thermal expansion while the Fe-Fe bond manifests a temperature dependent anomaly at ∼180 K forx> 0.02. It is interesting to find characteristically different nature of Fe-As and Fe-Fe bondlengths shown by the temperature dependent mean square relative displacements. Indeed, the Fe-As bond, stiffer than that of the Fe-Fe, gets softer forx⩽ 0.02 and hardly shows any change forx> 0.02. On the other hand, Fe-Fe bond tends to be stiffer forx⩽ 0.02 followed by a substantial softening forx> 0.02. Such a distinction has been seen also in the As K-edge x-ray absorption near edge structure, probing local geometry around As atom together with the valence electronic structure. The results suggest that local atomic displacements by Mn substitution inducing increased iron local magnetic moment that should be the main reason for its dramatic effect in iron-based superconductors.

Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm

Haemonchus contortus is a globally distributed and economically important gastrointestinal pathogen of small ruminants and has become a key nematode model for studying anthelmintic resistance and other parasite-specific traits among a wider group of parasites including major human pathogens. Here, we report using PacBio long-read and OpGen and 10X Genomics long-molecule methods to generate a highly contiguous 283.4 Mbp chromosome-scale genome assembly including a resolved sex chromosome for the MHco3(ISE).N1 isolate. We show a remarkable pattern of conservation of chromosome content with Caenorhabditis elegans, but almost no conservation of gene order. Short and long-read transcriptome sequencing allowed us to define coordinated transcriptional regulation throughout the parasite's life cycle and refine our understanding of cis- and trans-splicing. Finally, we provide a comprehensive picture of chromosome-wide genetic diversity both within a single isolate and globally. These data provide a high-quality comparison for understanding the evolution and genomics of Caenorhabditis and other nematodes and extend the experimental tractability of this model parasitic nematode in understanding helminth biology, drug discovery and vaccine development, as well as important adaptive traits such as drug resistance.

Photobiomodulation modulates the expression of inflammatory cytokines during the compensatory hypertrophy process in skeletal muscle

Compensatory hypertrophy (CH) occurs due to excessive mechanical load on a muscle, promoting an increase in the size of muscle fibers. In clinical practice, situations such as partial nerve injuries, denervation, and muscle imbalance caused by trauma to muscles and nerves or diseases that promote the loss of nerve conduction can induce CH in muscle fibers. Photobiomodulation (PBM) has demonstrated beneficial effects on muscle tissue during CH. The aim of the present study was to evaluate the effect of PBM on the inflammatory cytokines interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α) as well as type 2 metalloproteinases (MMP-2) during the process of CH due to excessive load on the plantaris muscle in rats. Forty-five Wistar rats weighing 250 g were divided into three groups: control group (n = 10), hypertrophy (H) group (n = 40), and H + PBM group (n = 40). CH was induced through the ablation of synergist muscles of the plantaris muscle. The tendons of the gastrocnemius and soleus muscles were isolated and sectioned to enable the partial removal of each of muscle. The preserved plantaris muscle below the removed muscles was submitted to excessive functional load. PBM was performed with low-level laser (AsGaAl, λ = 780 nm; 40 mW; energy density: 10 J/cm²; 10 s on each point, 8 points; 3.2 J). Animals from each group were euthanized after 7 and 14 days. The plantaris muscles were carefully removed and sent for analysis of the gene and protein expression of IL-6 and TNF-α using qPCR and ELISA, respectively. MMP-2 activity was analyzed using zymography. The results were submitted to statistical analysis (ANOVA + Tukey's test, p < 0.05). The protein expression analysis revealed an increase in IL-6 levels in the H + PBM group compared to the H group and a reduction in the H group compared to the control group. A reduction in TNF-α was found in the H and H + PBM groups compared to the control group at 7 days. The gene expression analysis revealed an increase in IL-6 in the H + PBM group compared to the H group at 14 days as well as an increase in TNF-α in the H + PBM group compared to the H group at 7 days. Increases in MMP-2 were found in the H and H + PBM groups compared to the control group at both 7 and 14 days. Based on findings in the present study, it is concluded that PBM was able to modulate pro-inflammatory cytokines that are essential for the compensatory hypertrophy process. However, it has not shown a modulation effect directly in MMP-2 activity during the same period evaluated.

Microscopic pathways for stress relaxation in repulsive colloidal glasses

Residual stresses are well-known companions of all glassy materials. They affect and, in many cases, even strongly modify important material properties like the mechanical response and the optical transparency. The mechanisms through which stresses affect such properties are, in many cases, still under study, and their full understanding can pave the way to a full exploitation of stress as a primary control parameter. It is, for example, known that stresses promote particle mobility at small length scales, e.g., in colloidal glasses, gels, and metallic glasses, but this connection still remains essentially qualitative. Exploiting a preparation protocol that leads to colloidal glasses with an exceptionally directional built-in stress field, we characterize the stress-induced dynamics and show that it can be visualized as a collection of "flickering," mobile regions with linear sizes of the order of ≈20 particle diameters (≈2 μm here) that move cooperatively, displaying an overall stationary but locally ballistic dynamics.

Omics Playground: a comprehensive self-service platform for visualization, analytics and exploration of Big Omics Data

As the cost of sequencing drops rapidly, the amount of 'omics data increases exponentially, making data visualization and interpretation-'tertiary' analysis a bottleneck. Specialized analytical tools requiring technical expertise are available. However, consolidated and multi-faceted tools that are easy to use for life scientists is highly needed and currently lacking. Here we present Omics Playground, a user-friendly and interactive self-service bioinformatics platform for the in-depth analysis, visualization and interpretation of transcriptomics and proteomics data. It provides a large number of different tools in which special attention has been paid to single cell data. With Omics Playground, life scientists can easily perform complex data analysis and visualization without coding, and significantly reduce the time to discovery.

Profiling microRNAs through development of the parasitic nematode Haemonchus identifies nematode-specific miRNAs that suppress larval development

Parasitic nematodes transition between dramatically different free-living and parasitic stages, with correctly timed development and migration crucial to successful completion of their lifecycle. However little is known of the mechanisms controlling these transitions. microRNAs (miRNAs) negatively regulate gene expression post-transcriptionally and regulate development of diverse organisms. Here we used microarrays to determine the expression profile of miRNAs through development and in gut tissue of the pathogenic nematode Haemonchus contortus. Two miRNAs, mir-228 and mir-235, were enriched in infective L3 larvae, an arrested stage analogous to Caenorhabditis elegans dauer larvae. We hypothesized that these miRNAs may suppress development and maintain arrest. Consistent with this, inhibitors of these miRNAs promoted H. contortus development from L3 to L4 stage, while genetic deletion of C. elegans homologous miRNAs reduced dauer arrest. Epistasis studies with C. elegans daf-2 mutants showed that mir-228 and mir-235 synergise with FOXO transcription factor DAF-16 in the insulin signaling pathway. Target prediction suggests that these miRNAs suppress metabolic and transcription factor activity required for development. Our results provide novel insight into the expression and functions of specific miRNAs in regulating nematode development and identify miRNAs and their target genes as potential therapeutic targets to limit parasite survival within the host.

Structural and magnetic properties of the Yb2Pd2(In1-x Sn x ) system: a synchrotron x-ray and neutron powder diffraction investigation

The structural properties of the Yb₂Pd₂(In_1-x Sn _x ) system were investigated at room temperature by synchrotron x-ray powder diffraction. All the inspected compositions (x  =  0.0, 0.3, 0.4, 0.5, 0.6, 0.8, 0.9) crystallize in the tetragonal space group P4/mbm; the cell parameters exhibit a non-linear dependence on composition, whereas cell volume changes more regularly, with a minimum at x  =  0.8. Samples with Sn content x  =  0.5, 0.6, 0.9 were also analysed by neutron diffraction down to 0.5 K. No evidence for a structural transition can be detected at low temperature, whereas an antiferromagnetic ordering is observed, characterized by a propagation vectors k  =  (0,0,½). Magnetic moments order in the tetragonal ab-plane and the magnetic structure belongs to the Shubnikov magnetic space group P4/mbm.

The confounding effects of high genetic diversity on the determination and interpretation of differential gene expression analysis in the parasitic nematode Haemonchus contortus

Differential expression analysis between parasitic nematode strains is commonly used to implicate candidate genes in anthelmintic resistance or other biological functions. We have tested the hypothesis that the high genetic diversity of an organism such as Haemonchus contortus could complicate such analyses. First, we investigated the extent to which sequence polymorphism affects the reliability of differential expression analysis between the genetically divergent H. contortus strains MHco3(ISE), MHco4(WRS) and MHco10(CAVR). Using triplicates of 20 adult female worms from each population isolated under parallel experimental conditions, we found that high rates of sequence polymorphism in RNAseq reads were associated with lower efficiency read mapping to gene models under default TopHat2 parameters, leading to biased estimates of inter-strain differential expression. We then showed it is possible to largely compensate for this bias by optimising the read mapping single nucleotide polymorphism (SNP) allowance and filtering out genes with particularly high single nucleotide polymorphism rates. Once the sequence polymorphism biases were removed, we then assessed the genuine transcriptional diversity between the strains, finding ≥824 differentially expressed genes across all three pairwise strain comparisons. This high level of inter-strain transcriptional diversity not only suggests substantive inter-strain phenotypic variation but also highlights the difficulty in reliably associating differential expression of specific genes with phenotypic differences. To provide a practical example, we analysed two gene families of potential relevance to ivermectin drug resistance; the ABC transporters and the ligand-gated ion channels (LGICs). Over half of genes identified as differentially expressed using default TopHat2 parameters were shown to be an artifact of sequence polymorphism differences. This work illustrates the need to account for sequence polymorphism in differential expression analysis. It also demonstrates that a large number of genuine transcriptional differences can occur between H. contortus strains and these must be considered before associating the differential expression of specific genes with phenotypic differences between strains.

Upregulated expression of the antioxidant sestrin 2 identified by transcriptomic analysis of Japanese encephalitis virus-infected SH-SY5Y neuroblastoma cells

Japanese encephalitis virus (JEV) exerts a profound burden of viral encephalitis. We have investigated the differentially expressed transcripts in the neuronal transcriptome during JEV infection by RNA sequencing (RNA-Seq) of virus-infected SH-SY5Y human neuroblastoma cells. Gene ontology analysis revealed significant enrichment from two main pathways: endoplasmic reticulum (ER)-nucleus signaling (P value: 5.75E-18; false discovery rate [FDR] 3.11E-15) and the ER unfolded protein response (P value: 7.58E-18; FDR 3.11E-15). qPCR validation showed significant upregulation and differential expression (P < 0.01) of ER stress-signaling transcripts (SESN2, TRIB3, DDIT3, DDIT4, XBP1, and ATF4) at 24 h post-infection for both low (LN) and high (HN) neurovirulence JEV strains. Immunoblot analysis following JEV infection of SH-SY5Y cells showed an increase in levels of SESN2 protein following JEV infection. Similarly, Zika virus (MR766) infection of SH-SY5Y showed a titer-dependent increase in ER stress-signaling transcripts; however, this was absent or diminished for DDIT4 and ATF4, respectively, suggestive of differences in the induction of stress-response transcripts between flaviviruses. Interestingly, SLC7A11 and SLC3A2 mRNA were also both deregulated in JEV-infected SH-SY5Y cells and encode the two constituent subunits of the plasma membrane xCT amino acid antiporter that relieves oxidative stress by export of glutamate and import of cystine. Infection of SH-SY5Y and HEK293T cells by the JEV HN strain Sw/Mie/40/2004 lead to significant upregulation of the SLC7A11 mRNA to levels comparable to DDIT3. Our findings suggest upregulation of antioxidants including SESN2 and, also, the xCT antiporter occurs to counteract the oxidative stress elicited by JEV infection.

Nanoscale transient gratings excited and probed by extreme ultraviolet femtosecond pulses

Advances in developing ultrafast coherent sources operating at extreme ultraviolet (EUV) and x-ray wavelengths allow the extension of nonlinear optical techniques to shorter wavelengths. Here, we describe EUV transient grating spectroscopy, in which two crossed femtosecond EUV pulses produce spatially periodic nanoscale excitations in the sample and their dynamics is probed via diffraction of a third time-delayed EUV pulse. The use of radiation with wavelengths down to 13.3 nm allowed us to produce transient gratings with periods as short as 28 nm and observe thermal and coherent phonon dynamics in crystalline silicon and amorphous silicon nitride. This approach allows measurements of thermal transport on the ~10-nm scale, where the two samples show different heat transport regimes, and can be applied to study other phenomena showing nontrivial behaviors at the nanoscale, such as structural relaxations in complex liquids and ultrafast magnetic dynamics.

Fast recovery of the pristine magnetic and structural phases in superconducting LaFeAsO0.89F0.11 by Mn/Fe substitution

We report an experimental study on the effect of Mn impurities in the optimally doped [Formula: see text] compound. The results show that a very tiny amount of Mn, of the order of 0.1%, is enough to destroy superconductivity and to recover at low temperatures both the magnetic ground state and the orthorhombic structure of the pristine LaFeAsO parent compound. The results are discussed within a model where electron correlations enhance the Ruderman-Kittel-Kasuya-Yosida interaction among impurities.

Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus

BACKGROUND

Infections with helminths cause an enormous disease burden in billions of animals and plants worldwide. Large scale use of anthelmintics has driven the evolution of resistance in a number of species that infect livestock and companion animals, and there are growing concerns regarding the reduced efficacy in some human-infective helminths. Understanding the mechanisms by which resistance evolves is the focus of increasing interest; robust genetic analysis of helminths is challenging, and although many candidate genes have been proposed, the genetic basis of resistance remains poorly resolved.

RESULTS

Here, we present a genome-wide analysis of two genetic crosses between ivermectin resistant and sensitive isolates of the parasitic nematode Haemonchus contortus, an economically important gastrointestinal parasite of small ruminants and a model for anthelmintic research. Whole genome sequencing of parental populations, and key stages throughout the crosses, identified extensive genomic diversity that differentiates populations, but after backcrossing and selection, a single genomic quantitative trait locus (QTL) localised on chromosome V was revealed to be associated with ivermectin resistance. This QTL was common between the two geographically and genetically divergent resistant populations and did not include any leading candidate genes, suggestive of a previously uncharacterised mechanism and/or driver of resistance. Despite limited resolution due to low recombination in this region, population genetic analyses and novel evolutionary models supported strong selection at this QTL, driven by at least partial dominance of the resistant allele, and that large resistance-associated haplotype blocks were enriched in response to selection.

CONCLUSIONS

We have described the genetic architecture and mode of ivermectin selection, revealing a major genomic locus associated with ivermectin resistance, the most conclusive evidence to date in any parasitic nematode. This study highlights a novel genome-wide approach to the analysis of a genetic cross in non-model organisms with extreme genetic diversity, and the importance of a high-quality reference genome in interpreting the signals of selection so identified.

A single test approach for accurate and sensitive detection and taxonomic characterization of Trypanosomes by comprehensive analysis of internal transcribed spacer 1 amplicons

To improve our knowledge on the epidemiological status of African trypanosomiasis, better tools are required to monitor Trypanosome genotypes circulating in both mammalian hosts and tsetse fly vectors. This is important in determining the diversity of Trypanosomes and understanding how environmental factors and control efforts affect Trypanosome evolution. We present a single test approach for molecular detection of different Trypanosome species and subspecies using newly designed primers to amplify the Internal Transcribed Spacer 1 region of ribosomal RNA genes, coupled to Illumina sequencing of the amplicons. The protocol is based on Illumina’s widely used 16s bacterial metagenomic analysis procedure that makes use of multiplex PCR and dual indexing. Results from analysis of wild tsetse flies collected from Zambia and Zimbabwe show that conventional methods for Trypanosome species detection based on band size comparisons on gels is not always able to accurately distinguish between T. vivax and T. godfreyi. Additionally, this approach shows increased sensitivity in the detection of Trypanosomes at species level with the exception of the Trypanozoon subgenus. We identified subspecies of T. congolense, T. simiae, T. vivax, and T. godfreyi without the need for additional tests. Results show T. congolense Kilifi subspecies is more closely related to T. simiae than to other T. congolense subspecies. This agrees with previous studies using satellite DNA and 18s RNA analysis. While current classification does not list any subspecies for T. godfreyi, we observed two distinct clusters for these species. Interestingly, sequences matching T. congolense Tsavo (now classified as T. simiae Tsavo) clusters distinctly from other T. simiae Tsavo sequences suggesting the Nannomonas group is more divergent than currently thought thus the need for better classification criteria. This method presents a simple but comprehensive way of identification of Trypanosome species and subspecies-specific using one PCR assay for molecular epidemiology of trypanosomes.

Tsetse flies are central actors in the transmission of Trypanosomes to vertebrate hosts. Therefore, detection of Trypanosomes in the tsetse flies is important for understanding the epidemiology of African trypanosomiasis as a component of new control or surveillance strategies. We have developed a method that combines multiplex PCR and next-generation sequencing for the detection of different Trypanosome species and subspecies. Similar to the widely used bacterial metagenomic analysis protocol, this method uses a modular, two-step PCR process followed by sequencing of all amplicons in a single run, making sequencing of amplicons more efficient and cost-effective when dealing with large sample sizes. As part of this approach, we designed novel Internal Transcribed Spacer 1 primers optimized for short read sequencing and have slightly better sensitivity than conventional primers. Taxonomic identification of amplicons is based on BLAST searches against the constantly updated NCBI’s nt database. Our approach is more accurate than traditional gel-based analyses which are prone to misidentification of species. It is also able to discriminate between subspecies of T. congolense, T. simiae, T. vivax, and T. godfreyi species. This method has the potential to provide new insights into the epidemiology of different Trypanosome genotypes and the discovery of new ones.

The huge effect of Mn substitution on the structural and magnetic properties of LaFeAsO: the La(Fe,Mn)AsO system

The substitution of Mn for Fe on the sub-lattice in LaFeAsO has a remarkable impact on both structural and magnetic properties; for example, the structural and magnetic transition temperatures decrease of ~20 K in samples with a Mn-content as low as x  =  0.01. Such a dramatic effect results from the high stability of the substituting Mn²⁺ ion (3d ⁵) in its high-spin state, which opposes any variation to its electronic state (configuration), perturbing thereby interactions within the Fe sub-lattice between the Fe ions surrounding the substituent. Several investigations ascertained that the structural transformation in LnFeAsO compounds (Ln: lanthanide) cannot be ascribed to lattice degrees of freedom, but rather to electronic or spin ones. In this context, even an extremely low concentration of Mn²⁺ ions diluted in the Fe sub-lattice produces a reduction of the electronic degree of freedom of the system, thus hindering the structural transformation and the magnetic transition.

Aggression modulates neural correlates of hostile intention attribution to laughter in children

The tendency to interpret nonverbal social signals as hostile in intention is associated with aggressive responding, poor social functioning and mental illness, and can already be observed in childhood. To investigate the neural correlates of such hostile attributions of social intention, we performed a functional magnetic imaging study in 10-18 year old children and adolescents. Fifty healthy participants rated videos of laughter, which they were told to imagine as being directed towards them, as friendly versus hostile in social intention. Hostile intention ratings were associated with neural response in the right temporal voice area (TVA). Moreover, self-reported trait physical aggression modulated this relationship in both the right TVA and bilateral lingual gyrus, with stronger associations between hostile intention ratings and neural activation in children with higher trait physical aggression scores. Functional connectivity results showed decreased connectivity between the right TVA and left dorsolateral prefrontal cortex with increasing trait physical aggression for making hostile social intention attributions. We conclude that children's social intention attributions are more strongly related to activation of early face and voice-processing regions with increasing trait physical aggression.

Suppression of ferromagnetic order by Ag-doping: a neutron scattering investigation on Ce2(Pd1-x Ag x )2In (x = 0.20, 0.50)

The ground state magnetic behaviour of Ce₂(Pd_0.8Ag_0.2)₂In and Ce₂(Pd_0.5Ag_0.5)₂In, found in the ferromagnetic branch of Ce₂Pd₂In, has been investigated by neutron powder diffraction at low temperature. Ce₂(Pd_0.8Ag_0.2)₂In is characterized by a ferromagnetic structure with the Ce moments aligned along the c-axis and values of 0.96(2) µ _B. The compound retains the P4/mbm throughout the magnetic transition, although the magnetic ordering is accompanied by a significant decrease of the lattice strain along [0 0 l], suggesting a magnetostructural contribution. The magnetic behaviour of Ce₂(Pd_0.5Ag_0.5)₂In is very different; this compound exhibits an extremely reduced magnetic scattering contribution in the diffraction pattern, that can be ascribed to a different kind of ferromagnetic ordering, with extremely reduced magnetic moments (~0.1 µ _B) aligned along [0 l 0]. These results point to a competition between different types of magnetic correlations induced by Ag-substitution, giving rise to a magnetically frustrated scenario in Ce₂(Pd_0.5Ag_0.5)₂In.

A New Regimen of Cisplatin, Epirubicin and Methotrexate (PEM-3) as Primary Chemothfrapy for Locally Advanced Bladder Cancer

In this phase II study, 41 patients with locally advanced urothelial bladder cancer (T2-4, NO, MO) were treated with primary chemotherapy (cisplatin, epirubicin, methotrexate: PEM-3). All the patients were assessable for response and toxicity. Clinical monitoring was performed with computerized tomography and cystoscopy. Nineteen clinical complete remissions (46%) and 10 partial remissions (24.5%) were obtained (CR + PR, 70.5%; 95% confidence interval, 57%-85%). Ten patients were considered to have clinically stable disease (24.5%), and 2 patients progressed (5%). Surgery after chemotherapy was performed in 22 cases: in 6 patients (27%) a pathologic complete response was achieved. The pathologic stage was lower than the initial clinical stage in 13 patients (59%). After a median follow-up of 3 years (range, 1-4), the median time to progression was 104 weeks. At this writing, 20 patients, 12 of which were submitted to surgery and 8 were not operated, are disease-free. The 3-year survival rate is 52%. No one had to interrupt the treatment because of toxicity. In conclusion, the PEM-3 regimen is a very active and well-tolerated regimen in locally advanced bladder cancer.

Human cytochrome P450 2B6 genetic variability in Botswana: a case of haplotype diversity and convergent phenotypes

Identification of inter-individual variability for drug metabolism through cytochrome P450 2B6 (CYP2B6) enzyme is important for understanding the differences in clinical responses to malaria and HIV. This study evaluates the distribution of CYP2B6 alleles, haplotypes and inferred metabolic phenotypes among subjects with different ethnicity in Botswana. A total of 570 subjects were analyzed for CYP2B6 polymorphisms at position 516 G > T (rs3745274), 785 A > G (rs2279343) and 983 T > C (rs28399499). Samples were collected in three districts of Botswana where the population belongs to Bantu (Serowe/Palapye and Chobe) and San-related (Ghanzi) ethnicity. The three districts showed different haplotype composition according to the ethnic background but similar metabolic inferred phenotypes, with 59.12%, 34.56%, 2.10% and 4.21% of the subjects having, respectively, an extensive, intermediate, slow and rapid metabolic profile. The results hint at the possibility of a convergent adaptation of detoxifying metabolic phenotypes despite a different haplotype structure due to the different genetic background. The main implication is that, while there is substantial homogeneity of metabolic inferred phenotypes among the country, the response to drugs metabolized via CYP2B6 could be individually associated to an increased risk of treatment failure and toxicity. These are important facts since Botswana is facing malaria elimination and a very high HIV prevalence.

Transcriptomic profiling of nematode parasites surviving vaccine exposure

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Surviving Haemonchus contortus from vaccinated sheep were compared with control worms.

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There is no evidence for changes in expression of genes encoding Barbervax® antigens.

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There was increased expression of other proteases and regulators of lysosome trafficking.

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Surviving worms displayed up-regulated lipid storage and defecation abilities.

Some nematode species are economically important parasites of livestock, while others are important human pathogens causing some of the most important neglected tropical diseases. In both humans and animals, anthelmintic drug administration is the main control strategy, but the emergence of drug-resistant worms has stimulated the development of alternative control approaches. Among these, vaccination is considered to be a sustainable and cost effective strategy. Currently, Barbervax® for the ruminant strongylid Haemonchus contortus is the only registered subunit vaccine for a nematode parasite, although a vaccine for the human hookworm Necator americanus is undergoing clinical trials (HOOKVAC consortium). As both these vaccines comprise a limited number of proteins, there is potential for selection of nematodes with altered sequences or expression of the vaccine antigens. Here we compared the transcriptome of H. contortus populations from sheep vaccinated with Barbervax® with worms from control animals. Barbervax® antigens are native integral membrane proteins isolated from the brush border of the intestinal cells of the adult parasite and many of those are proteases. Our findings provide no evidence for changes in expression of genes encoding Barbervax® antigens in the surviving parasite populations. However, surviving parasites from vaccinated animals showed increased expression of other proteases and regulators of lysosome trafficking, and displayed up-regulated lipid storage and defecation abilities that may have circumvented the effect of the vaccine. Implications for other potential vaccines for human and veterinary nematodes are discussed.

Increased Expression of a MicroRNA Correlates with Anthelmintic Resistance in Parasitic Nematodes

Resistance to anthelmintic drugs is a major problem in the global fight against parasitic nematodes infecting humans and animals. While previous studies have identified mutations in drug target genes in resistant parasites, changes in the expression levels of both targets and transporters have also been reported. The mechanisms underlying these changes in gene expression are unresolved. Here, we take a novel approach to this problem by investigating the role of small regulatory RNAs in drug resistant strains of the important parasite Haemonchus contortus. microRNAs (miRNAs) are small (22 nt) non-coding RNAs that regulate gene expression by binding predominantly to the 3′ UTR of mRNAs. Changes in miRNA expression have been implicated in drug resistance in a variety of tumor cells. In this study, we focused on two geographically distinct ivermectin resistant strains of H. contortus and two lines generated by multiple rounds of backcrossing between susceptible and resistant parents, with ivermectin selection. All four resistant strains showed significantly increased expression of a single miRNA, hco-miR-9551, compared to the susceptible strain. This same miRNA is also upregulated in a multi-drug-resistant strain of the related nematode Teladorsagia circumcincta. hco-miR-9551 is enriched in female worms, is likely to be located on the X chromosome and is restricted to clade V parasitic nematodes. Genes containing predicted binding sites for hco-miR-9551 were identified computationally and refined based on differential expression in a transcriptomic dataset prepared from the same drug resistant and susceptible strains. This analysis identified three putative target mRNAs, one of which, a CHAC domain containing protein, is located in a region of the H. contortus genome introgressed from the resistant parent. hco-miR-9551 was shown to interact with the 3′ UTR of this gene by dual luciferase assay. This study is the first to suggest a role for miRNAs and the genes they regulate in drug resistant parasitic nematodes. miR-9551 also has potential as a biomarker of resistance in different nematode species.

Rapid identification of genes controlling virulence and immunity in malaria parasites

Identifying the genetic determinants of phenotypes that impact disease severity is of fundamental importance for the design of new interventions against malaria. Here we present a rapid genome-wide approach capable of identifying multiple genetic drivers of medically relevant phenotypes within malaria parasites via a single experiment at single gene or allele resolution. In a proof of principle study, we found that a previously undescribed single nucleotide polymorphism in the binding domain of the erythrocyte binding like protein (EBL) conferred a dramatic change in red blood cell invasion in mutant rodent malaria parasites Plasmodium yoelii. In the same experiment, we implicated merozoite surface protein 1 (MSP1) and other polymorphic proteins, as the major targets of strain-specific immunity. Using allelic replacement, we provide functional validation of the substitution in the EBL gene controlling the growth rate in the blood stages of the parasites.

Developing a greater understanding of malaria genetics is a key step in combating the threat posed by the disease. Here we use a novel approach to study two important properties of the parasite; the rate at which parasites grow within a single host, and the means by which parasites are affected by the host immune system. Two malaria strains with different biological properties were crossed in mosquitoes to produce a hybrid population, which was then grown in naïve and vaccinated mice. Parasites with genes conveying increased growth or immune evasion are favoured under natural selection, leaving a signature on the genetic composition of the cross population. We describe a novel mathematical approach to interpret this signature, identifying selected genes within the parasite population. We discover new genetic variants conveying increased within-host growth and resistance to host immunity in a mouse malaria strain. Experimental validation highlights the ability of this rapid experimental process for generating insights into malaria biology.

Experimental Evidence for Static Charge Density Waves in Iron Oxypnictides

In this Letter we report high-resolution synchrotron x-ray powder diffraction and transmission electron microscope analysis of Mn-substituted LaFeAsO samples, demonstrating that a static incommensurate modulated structure develops across the low-temperature orthorhombic phase, whose modulation wave vector depends on the Mn content. The incommensurate structural distortion is likely originating from a charge-density-wave instability, a periodic modulation of the density of conduction electrons associated with a modulation of the atomic positions. Our results add a new component in the physics of Fe-based superconductors, indicating that the density wave ordering is charge driven.

Effect of Direction and Tension of Kinesio Taping Application on Sensorimotor Coordination

The present study investigates whether different directions and tensions of Kinesio(®) Tex tape (KT) application differently influence the precision of sensorimotor synchronization, defined as the ability to coordinate actions with predictable external events. 10 healthy participants performed sets of repetitive wrist flexion-extensions synchronized to a series of paced audio stimuli with an inter-onset interval (IOI) of 500 and 400 ms. KT was applied over the wrist and finger extensor muscles. 2 facilitatory (light and moderate tension) and one inhibitory KT applications were used in different sessions. Standard deviation of the asynchrony (SDasy) and percentage difference of SDasy were calculated and compared across KT and the no-KT control cases. Direction and tension of KT application did not differently influence the ability to coordinate rhythmic movements to an auditory stimulus. However, compared with the no-KT control case, SDasy decreased significantly in all KT cases in both 500- and 400-ms IOI. Independent of direction/tension, the effect of KT on improving sensorimotor synchronization is likely associated with variations in the nature of the neuro-anatomical constraints determining the control of voluntary movement. KT is then proposed to be tested on sensorimotor disorders associated with intense repetitive exercise to check for regaining effective motor control.

New insights into the magnetic properties of LaErO3, (La0.5Er0.5)2O3 and (La0.5Dy0.5)2O3 oxides

Orthorhombic LaErO3 and cubic (La0.5 Ln 0.5)2O3 oxides (Ln: Er, Dy) were examined by neutron powder diffraction between 1.5 K and 15 K in order to investigate their crystallographic and magnetic structures. At 1.5 K both LaErO3 and (La0.5Er0.5)2O3 display a magnetic moments ordering, whereas for (La0.5Dy0.5)2O3 only short range magnetic correlations can be argued, suggesting a possible magnetic moments ordering at lower temperature. LaErO3 is characterized by a magnetic wavevector k  =  (0, 0, 0) and forms an antiferromagnetic G x C y A z -type structure belonging to the [Formula: see text] Shubnikov group with a total magnetic moment of 6.78(3) μ B. The antiferromagnetic structure of (La0.5Er0.5)2O3 is similar to the one typical of Er2O3, with a total magnetic moment of 4.28(2) μ B at both different magnetic sites; it is characterized by k  =  (0, 0, 0) and belongs to the magnetic [Formula: see text] Shubnikov group.

CYP2B6 poor metaboliser alleles involved in efavirenz and nevirapine metabolism: CYP2B6*9 and CYP2B6*18 distribution in HIV-exposed subjects from Dschang, Western Cameroon

The prescription of patients' tailored anti-infectious treatments is the ultimate goal of pharmacogenetics/genomics applied to antimicrobial treatments, providing a basis for personalized medicine. Despite the efforts to screen Africans for alleles underlying defective metabolism for a panel of different drugs, still more research is necessary to clarify the interplay between host genetic variation and treatments' response. HIV is a major infectious disease in sub-Saharan African countries, and the main prescribed anti-HIV combination therapy includes efavirenz (EFV) or nevirapine (NVP). The two drugs are both mainly metabolised by cytochrome P450 2B6 liver enzyme (CYP2B6). Defective variants of CYP2B6 gene, leading to higher drug exposure with subsequent possible side effects and low compliance, are well known. However, little is known about CYP2B6 alleles in Cameroon where only one study was done on this subject. The main objective of the present work is to assess, in a subset of HIV-exposed subjects from Dschang in West Cameroon, the prevalence of two SNPs in the CYP2B6 gene: 516G>T (rs3745274) and 983T>C (rs28399499), both associated to a defective EFV and NVP metabolism. We analyzed 168 DNA samples collected during two cross-sectional surveys performed in Dschang, West Cameroon. In the population studied the observed allele frequencies of 516G>T and 983T>C were 44.35% (95%CI, 36.84-51.86%) and 12.80% (95%CI, 7.75-17.85%), respectively. Moreover, concerning the CYP2B6 expected phenotypes, 28.57% of the population showed a poor metaboliser phenotype, while 27.38% and 44.05% showed an extensive (wild-type) and an intermediate metaboliser phenotype, respectively. Here we found that an important fraction of the subjects is carrying EFV/NVP poor metaboliser alleles. Our findings could help to improve the knowledge about the previewed efficacy of anti-HIV drug therapy in Cameroon. Finally, we designed a new method of detection for the 983T>C genetic variation that can be applied in resource-limited laboratories.

Effect of water on the transport properties of protic and aprotic imidazolium ionic liquids - an analysis of self-diffusivity, conductivity, and proton exchange mechanism

In this paper we report on the transport properties of protic and aprotic ionic liquids of the imidazolium cation (C2C1Im(+) or C2HIm(+)) and the TFSI(-) or TfO(-) anion as a function of added water. We observe that the self-diffusion coefficient of the ionic species increases upon addition of water, and that the cation diffuses faster than the anion in the entire water concentration range investigated. We also observe that the overall increase of anionic and cationic diffusion coefficients is significant for C2HImTfO while it is rather weak for C2C1ImTFSI, the former being more hydrophilic. Moreover, the difference between cationic and anionic self-diffusivity specifically depends on the structure of the ionic liquid's ions. The degree of ion-ion association has been investigated by comparing the molar conductivity obtained by impedance measurements with the molar conductivity calculated from NMR data using the Nernst-Einstein equation. Our data indicate that the ions are partly dissociated (Λimp/ΛNMR in the range 0.45-0.75) but also that the degree of association decreases in the order C2HImTfO > C2HImTFSI ≈ C2C1ImTfO > C2C1ImTFSI. From these results, it seems that water finds different sites of interaction in the protic and aprotic ionic liquids, with a strong preference for hydrogen bonding to the -NH group (when available) and a stronger affinity to the TfO anion as compared to the TFSI. For the protic ionic liquids, the analysis of (1)H NMR chemical shifts (upon addition of H2O and D2O, respectively) indicates a water-cation interaction of hydrogen bonding nature. In addition, we could probe proton exchange between the -NH group and deuterated water for the protic cation, which occurs at a significantly faster rate if associated with the TfO anion as compared to the TFSI.

Computational approaches for the identification and optimization of Src family kinases inhibitors

Src family kinases (SFKs) are a group of non-receptor tyrosine kinases whose activity is involved in the regulation of cellular morphology, motility, proliferation and survival. An aberrant activation and expression of these kinases contribute to the pathogenesis and progression of a broad range of diseases, such as a large number of solid tumors, various hematological malignancies and some neuronal pathologies. The search for SFK inhibitors is therefore a promising research topic in medicinal chemistry. Computational studies such as receptor-based and/or ligand-based virtual screening, docking, and molecular modeling proved to be a powerful tool for identifying new SFKs inhibitors. In this review we report and analyze the main examples of computational approaches that allowed the identification of new SFKs ligands and the optimization of either activity and pharmacokinetic profile of lead compounds.

The cytochrome P450 family in the parasitic nematode Haemonchus contortus

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The Haemonchus contortus genome encodes a large family of cytochrome P450 (CYP) genes.

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Haemonchus contortus lacks the dramatic CYP family expansions seen in Caenorhabditis elegans.

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Haemonchus contortus orthologues of C. elegans CYPs share similar expression profiles.

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The majority of H. contortus CYPs are most highly expressed in larval stages.

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The parasite intestine is a major site of CYP expression.

Haemonchus contortus, a highly pathogenic and economically important parasitic nematode of sheep, is particularly adept at developing resistance to the anthelmintic drugs used in its treatment and control. The basis of anthelmintic resistance is poorly understood for many commonly used drugs with most research being focused on mechanisms involving drug targets or drug efflux. Altered or increased drug metabolism is a possible mechanism that has yet to receive much attention despite the clear role of xenobiotic metabolism in pesticide resistance in insects. The cytochrome P450s (CYPs) are a large family of drug-metabolising enzymes present in almost all living organisms, but for many years thought to be absent from parasitic nematodes. In this paper, we describe the CYP sequences encoded in the H. contortus genome and compare their expression in different parasite life-stages, sexes and tissues. We developed a novel real-time PCR approach based on partially assembled CYP sequences “tags” and confirmed findings in the subsequent draft genome with RNA-seq. Constitutive expression was highest in larval stages for the majority of CYPs, although higher expression was detected in the adult male or female for a small subset of genes. Many CYPs were expressed in the worm intestine. A number of H. contortus genes share high identity with Caenorhabditis elegans CYPs and the similarity in their expression profiles supports their classification as putative orthologues. Notably, H. contortus appears to lack the dramatic CYP subfamily expansions seen in C. elegans and other species, which are typical of CYPs with exogenous roles. However, a small group of H. contortus genes cluster with the C. elegans CYP34 and CYP35 subfamilies and may represent candidate xenobiotic metabolising genes in the parasite.