Daily rhythms in gene expression of the human parasite Schistosoma mansoni.

BACKGROUND: The consequences of the earth's daily rotation have led to 24-h biological rhythms in most organisms. Even some parasites are known to have daily rhythms, which, when in synchrony with host rhythms, can optimise their fitness. Understanding these rhythms may enable the development of control strategies that take advantage of rhythmic vulnerabilities. Recent work on protozoan parasites has revealed 24-h rhythms in gene expression, drug sensitivity and the presence of an intrinsic circadian clock; however, similar studies on metazoan parasites are lacking. To address this, we investigated if a metazoan parasite has daily molecular oscillations, whether they reveal how these longer-lived organisms can survive host daily cycles over a lifespan of many years and if animal circadian clock genes are present and rhythmic. We addressed these questions using the human blood fluke Schistosoma mansoni that lives in the vasculature for decades and causes the tropical disease schistosomiasis. RESULTS: Using round-the-clock transcriptomics of male and female adult worms collected from experimentally infected mice, we discovered that ~ 2% of its genes followed a daily pattern of expression. Rhythmic processes included a stress response during the host's active phase and a 'peak in metabolic activity' during the host's resting phase. Transcriptional profiles in the female reproductive system were mirrored by daily patterns in egg laying (eggs are the main drivers of the host pathology). Genes cycling with the highest amplitudes include predicted drug targets and a vaccine candidate. These 24-h rhythms may be driven by host rhythms and/or generated by a circadian clock; however, orthologs of core clock genes are missing and secondary clock genes show no 24-h rhythmicity. CONCLUSIONS: There are daily rhythms in the transcriptomes of adult S. mansoni, but they appear less pronounced than in other organisms. The rhythms reveal temporally compartmentalised internal processes and host interactions relevant to within-host survival and between-host transmission. Our findings suggest that if these daily rhythms are generated by an intrinsic circadian clock then the oscillatory mechanism must be distinct from that in other animals. We have shown which transcripts oscillate at this temporal scale and this will benefit the development and delivery of treatments against schistosomiasis.

Study protocol for the multicentre cohorts of Zika virus infection in pregnant women, infants, and acute clinical cases in Latin America and the Caribbean: the ZIKAlliance consortium.

BACKGROUND: The European Commission (EC) Horizon 2020 (H2020)-funded ZIKAlliance Consortium designed a multicentre study including pregnant women (PW), children (CH) and natural history (NH) cohorts. Clinical sites were selected over a wide geographic range within Latin America and the Caribbean, taking into account the dynamic course of the ZIKV epidemic. METHODS: Recruitment to the PW cohort will take place in antenatal care clinics. PW will be enrolled regardless of symptoms and followed over the course of pregnancy, approximately every 4 weeks. PW will be revisited at delivery (or after miscarriage/abortion) to assess birth outcomes, including microcephaly and other congenital abnormalities according to the evolving definition of congenital Zika syndrome (CZS). After birth, children will be followed for 2 years in the CH cohort. Follow-up visits are scheduled at ages 1-3, 4-6, 12, and 24 months to assess neurocognitive and developmental milestones. In addition, a NH cohort for the characterization of symptomatic rash/fever illness was designed, including follow-up to capture persisting health problems. Blood, urine, and other biological materials will be collected, and tested for ZIKV and other relevant arboviral diseases (dengue, chikungunya, yellow fever) using RT-PCR or serological methods. A virtual, decentralized biobank will be created. Reciprocal clinical monitoring has been established between partner sites. Substudies of ZIKV seroprevalence, transmission clustering, disabilities and health economics, viral kinetics, the potential role of antibody enhancement, and co-infections will be linked to the cohort studies. DISCUSSION: Results of these large cohort studies will provide better risk estimates for birth defects and other developmental abnormalities associated with ZIKV infection including possible co-factors for the variability of risk estimates between other countries and regions. Additional outcomes include incidence and transmission estimates of ZIKV during and after pregnancy, characterization of short and long-term clinical course following infection and viral kinetics of ZIKV. STUDY REGISTRATIONS: clinicaltrials.gov NCT03188731 (PW cohort), June 15, 2017; clinicaltrials.gov NCT03393286 (CH cohort), January 8, 2018; clinicaltrials.gov NCT03204409 (NH cohort), July 2, 2017.

Alphavirus Restriction by IFITM Proteins.

Interferon inducible transmembrane proteins (IFITMs) are broad-spectrum antiviral factors. In cell culture the entry of many enveloped viruses, including orthomyxo-, flavi-, and filoviruses, is inhibited by IFITMs, though the mechanism(s) involved remain unclear and may vary between viruses. We demonstrate that Sindbis and Semliki Forest virus (SFV), which both use endocytosis and acid-induced membrane fusion in early endosomes to infect cells, are restricted by the early endosomal IFITM3. The late endosomal IFITM2 is less restrictive and the plasma membrane IFITM1 does not inhibit normal infection by either virus. IFITM3 inhibits release of the SFV capsid into the cytosol, without inhibiting binding, internalization, trafficking to endosomes or low pH-induced conformational changes in the envelope glycoprotein. Infection by SFV fusion at the cell surface was inhibited by IFITM1, but was equally inhibited by IFITM3. Furthermore, an IFITM3 mutant (Y20A) that is localized to the plasma membrane inhibited infection by cell surface fusion more potently than IFITM1. Together, these results indicate that IFITMs, in particular IFITM3, can restrict alphavirus infection by inhibiting viral fusion with cellular membranes. That IFITM3 can restrict SFV infection by fusion at the cell surface equivalently to IFITM1 suggests that IFITM3 has greater antiviral potency against SFV.

Strawberry and Achenes Hydroalcoholic Extracts and Their Digested Fractions Efficiently Counteract the AAPH-Induced Oxidative Damage in HepG2 Cells.

Strawberry fruits are highly appreciated by consumers worldwide due to their bright red color, typical aroma, and juicy texture. While the biological activity of the complete fruit has been widely studied, the potential beneficial effects of the achenes (commonly named seeds) remain unknown. In addition, when raw fruit and achenes are consumed, the digestion process could alter the release and absorption of their phytochemical compounds, compromising their bioactivity. In the present work, we evaluated the protective effects against oxidative damage of nondigested and digested extracts from strawberry fruit and achenes in human hepatocellular carcinoma (HepG2) cells. For that purpose, cells were treated with different concentration of the extracts prior to incubation with the stressor agent, AAPH (2,2'-azobis(2-amidinopropane) dihydrochloride). Subsequently, intracellular accumulation of reactive oxygen species (ROS) and the percentage of live, dead, and apoptotic cells were determined. Our results demonstrated that all the evaluated fractions were able to counteract the AAPH-induced damage, suggesting that the achenes also present biological activity. The positive effects of both the raw fruit and achenes were maintained after the in vitro digestion process.

Strawberry Achenes Are an Important Source of Bioactive Compounds for Human Health.

Strawberries are highly appreciated for their taste, nutritional value and antioxidant compounds, mainly phenolics. Fruit antioxidants derive from achenes and flesh, but achene contribution to the total fruit antioxidant capacity and to the bioaccessibility after intake is still unknown. In this work, the content of total phenolic compounds, flavonoids, anthocyanins and antioxidant capacity (TEAC, FRAP and DPPH) of achenes and flesh were compared in non-digested as well as in gastric and intestinal extracts after in vitro digestion. Results showed that, despite strawberry achenes represent a small fraction of the fruit, their contribution to total fruit antioxidant content was more than 41% and accounted for 81% of antioxidant capacity (TEAC). Achenes have higher quantity and different quality of antioxidants in non-digested and digested extracts. Antioxidant release was higher in the in vitro gastric digested extracts, but digestion conditions did not only affect quantity but quality, resulting in differences in antioxidant capacity and highlighting the importance of simulating physiological-like extraction conditions for assessing fruit antioxidant properties on human health. These results give new insights into the use of strawberry achenes as a source of bioactive compounds to be considered in strawberry breeding programs for improving human health.

Single-cell transcriptomics of the human parasite Schistosoma mansoni first intra-molluscan stage reveals tentative tegumental and stem-cell regulators.

Schistosomiasis is a major Neglected Tropical Disease, caused by the infection with blood flukes in the genus Schistosoma. To complete the life cycle, the parasite undergoes asexual and sexual reproduction within an intermediate snail host and a definitive mammalian host, respectively. The intra-molluscan phase provides a critical amplification step that ensures a successful transmission. However, the cellular and molecular mechanisms underlying the development of the intra-molluscan stages remain poorly understood. Here, single cell suspensions from S. mansoni mother sporocysts were produced and sequenced using the droplet-based 10X Genomics Chromium platform. Six cell clusters comprising two tegument, muscle, neuron, parenchyma and stem/germinal cell clusters were identified and validated by in situ hybridisation. Gene Ontology term analysis predicted key biological processes for each of the clusters, including three stem/germinal sub-clusters. Furthermore, putative transcription factors predicted for stem/germinal and tegument clusters may play key roles during parasite development and interaction with the intermediate host.

Method for Classifying Schizophrenia Patients Based on Machine Learning.

Schizophrenia is a chronic and severe mental disorder that affects individuals in various ways, particularly in their ability to perceive, process, and respond to stimuli. This condition has a significant impact on a considerable number of individuals. Consequently, the study, analysis, and characterization of this pathology are of paramount importance. Electroencephalography (EEG) is frequently utilized in the diagnostic assessment of various brain disorders due to its non-intrusiveness, excellent resolution and ease of placement. However, the manual analysis of electroencephalogram (EEG) recordings can be a complex and time-consuming task for healthcare professionals. Therefore, the automated analysis of EEG recordings can help alleviate the burden on doctors and provide valuable insights to support clinical diagnosis. Many studies are working along these lines. In this research paper, the authors propose a machine learning (ML) method based on the eXtreme Gradient Boosting (XGB) algorithm for analyzing EEG signals. The study compares the performance of the proposed XGB-based approach with four other supervised ML systems. According to the results, the proposed XGB-based method demonstrates superior performance, with an AUC value of 0.94 and an accuracy value of 0.94, surpassing the other compared methods. The implemented system exhibits high accuracy and robustness in accurately classifying schizophrenia patients based on EEG recordings. This method holds the potential to be implemented as a valuable complementary tool for clinical use in hospitals, supporting clinicians in their clinical diagnosis of schizophrenia.

Relation between Strawberry Fruit Redness and Bioactivity: Deciphering the Role of Anthocyanins as Health Promoting Compounds.

The red colour of most berries is often associated to fruit healthiness, since it has been linked to enrichment in anthocyanins (polyphenol with antioxidative properties). However, recent studies suggest that anthocyanins could not be the major contributors to bioactivity leading to uncertainty about their role as important molecules in the generation of health-promoting properties. To shed light on this issue, spectrophotometric and HPLC techniques were used for characterizing the content of phenolic compounds, including anthocyanins, in fruits of red (Fragaria x ananassa, cv. Fortuna) and white strawberry (Fragaria vesca spp. XXVIII) species (distinguishing receptacle from achene). In addition, the effect of these extracts on the reduction of intracellular ROS was tested, as well as on the activity of antioxidant enzymes and the quantification of cell oxidation markers. The results showed that white receptacle extracts (deprived of anthocyanins) were able to protect cells from oxidative damage to a greater extent than red fruits. This could be due per se to their high antioxidant capacity, greater than that shown in red fruits, or to the ability of antioxidants to modulate the activity of antioxidant enzymes, thus questioning the positive effect of anthocyanins on the wholesomeness of strawberry fruits. The results shed light on the relevance of anthocyanins in the prevention of health-associated oxidative damage.

Area of Habitat maps for the world's terrestrial birds and mammals.

Area of Habitat (AOH) is "the habitat available to a species, that is, habitat within its range". It complements a geographic range map for a species by showing potential occupancy and reducing commission errors. AOH maps are produced by subtracting areas considered unsuitable for the species from their range map, using information on each species' associations with habitat and elevation. We present AOH maps for 5,481 terrestrial mammal and 10,651 terrestrial bird species (including 1,816 migratory bird species for which we present separate maps for the resident, breeding and non-breeding areas). Our maps have a resolution of 100 m. On average, AOH covered 66 ± 28% of the range maps for mammals and 64 ± 27% for birds. The AOH maps were validated independently, following a novel two-step methodology: a modelling approach to identify outliers and a species-level approach based on point localities. We used AOH maps to produce global maps of the species richness of mammals, birds, globally threatened mammals and globally threatened birds.

COMBINE: a coalesced mammal database of intrinsic and extrinsic traits.

The use of species' traits in macroecological analyses has gained popularity in the last decade, becoming an important tool to understand global biodiversity patterns. Currently, trait data can be found across a wide variety of data sets included in websites, articles, and books, each one with its own taxonomic classification, set of traits, and data management methodology. Mammals, in particular, are among the most studied taxa, with large sources of trait information readily available. To facilitate the use of these data, we did an extensive review of published mammal trait data sources between 1999 and May 2020 and produced COMBINE: a COalesced Mammal dataBase of INtrinsic and Extrinsic traits. Our aim was to create a taxonomically integrated database of mammal traits that maximized trait number and coverage without compromising data quality. COMBINE contains information on 54 traits for 6,234 extant and recently extinct mammal species, including information on morphology, reproduction, diet, biogeography, life habit, phenology, behavior, home range, and density. Additionally, we calculated other relevant traits such as habitat and altitudinal breadths for all species and dispersal for terrestrial non-volant species. All data are compatible with the taxonomies of the IUCN Red List v. 2020-2 and PHYLACINE v. 1.2. Missing data were adequately flagged and imputed for non-biogeographical traits with 20% or more data available. We obtained full data sets for 21 traits such as female maturity, litter size, maximum longevity, trophic level, and dispersal, providing imputation performance statistics for all. This data set will be especially useful for those interested in including species' traits in large-scale ecological and conservation analyses. There are no copyright or proprietary restrictions; we request citation of this publication and all relevant underlying data sources (found in Data S1: trait_data_sources.csv), upon using these data.

Metabolic reconfiguration of strawberry physiology in response to postharvest practices.

The strawberry fruit is perishable due to its high water content and soft texture, yet exhibits pleasant organoleptic and nutritional profile. Here we conducted a metabolomics-driven analysis followed by linear modelling to dissect the molecular processes in strawberry postharvest. Fruits from five cultivars were harvested and refrigerated during a ten-day period under three different atmospheres: ambient, CO2-enriched and O3-enriched. These analyses revealed that metabolites involved in, (i) organoleptic and nutritional properties; (ii) stress tolerance displayed duration and postharvest treatment-dependent levels. Ozone-enriched atmosphere appears to counteract postharvest negative effects, with fruits exhibiting lower levels of fermentative metabolites when compared to fruits kept in an ambient atmosphere. Furthermore, metabolic reconfiguration towards the synthesis of protective metabolites of those fruits can possibly confer enhanced tolerance to postharvest abiotic stresses. Finally, results from the linear modelling identified metabolites which could be used as biomarkers to assess strawberry quality during its postharvest shelf life.

Single-cell atlas of the first intra-mammalian developmental stage of the human parasite Schistosoma mansoni.

Over 250 million people suffer from schistosomiasis, a tropical disease caused by parasitic flatworms known as schistosomes. Humans become infected by free-swimming, water-borne larvae, which penetrate the skin. The earliest intra-mammalian stage, called the schistosomulum, undergoes a series of developmental transitions. These changes are critical for the parasite to adapt to its new environment as it navigates through host tissues to reach its niche, where it will grow to reproductive maturity. Unravelling the mechanisms that drive intra-mammalian development requires knowledge of the spatial organisation and transcriptional dynamics of different cell types that comprise the schistomulum body. To fill these important knowledge gaps, we perform single-cell RNA sequencing on two-day old schistosomula of Schistosoma mansoni. We identify likely gene expression profiles for muscle, nervous system, tegument, oesophageal gland, parenchymal/primordial gut cells, and stem cells. In addition, we validate cell markers for all these clusters by in situ hybridisation in schistosomula and adult parasites. Taken together, this study provides a comprehensive cell-type atlas for the early intra-mammalian stage of this devastating metazoan parasite.

Early Hypophosphatemia in High-Risk Preterm Infants: Efficacy and Safety of Sodium Glycerophosphate From First Day on Parenteral Nutrition.

BACKGROUND: Early hypophosphatemia is common in premature infants ≤1250 g. The aim of this study was to assess the frequency and severity of hypophosphatemia after sodium glycerophosphate supplementation from first day of life in parenteral nutrition and to address the safety of this practice. METHODS: Prospective cohort study of infants ≤1250 g birth weight born in a tertiary-care level neonatal intensive care unit and supplied with sodium glycerophosphate from the first day of life. Primary outcome was the presence of hypophosphatemia (<4 mg/dL) on the first week. Data were compared with our 2014 prospective subcohort of infants ≤1250 g receiving phosphate after 48 hours of life and morbidity with that of our 2016 retrospective cohort of ≤1250 g. RESULTS: Fifty-four neonates were included. The frequency of hypophosphatemia was 29.6%. Only 1 patient presented hypophosphatemia <2 mg/dL. Mild hypokalemia was found in 8 patients (50%). No cases of hypernatremia were observed. Patients with hypophosphatemia had significantly lower gestational age (27.4 vs 28.8 weeks, P = .032) and lower z-score birth weight (-1.68 vs -0.47; P = .001). When compared with the 2014 subcohort, we found a lower frequency of hypophosphatemia (29.6% vs 69.2%; P = .008) and a lower rate of samples with hypophosphatemia (20.4% vs 51.4%; P = .0002) and critical hypophosphatemia (0.68% vs 11.4%, P = .0005). No differences were found in morbidity or mortality. CONCLUSIONS: Sodium glycerophosphate supplementation in parenteral nutrition from the first day of life significantly decreased the frequency of hypophosphatemia. No adverse events were reported.

[The use of strength and difficulties questionnaire in psychosocial evaluation and attention deficit hyperactivity disorder screening in preterm infants]. / Uso del Strength and Difficulties Questionnaire en prematuros para su evaluación psicosocial y cribado del trastorno por déficit de atención e hiperactividad.

INTRODUCTION: Behavioural disorders and learning disabilities are often recognised in<1,500g or<32 weeks very low birth weight (VLBW) infants. There is very limited data in the Spanish population. OBJECTIVE: To determine the presence of psychosocial disorders in preterm infants at 6 years of age, as assessed by the strength and difficulties (SDQ) questionnaire, in comparison to a reference population. To set a cut-off value to use SDQ as a screening tool for attention deficit hyperactivity disorder (ADHD) in the preterm child. PARTICIPANTS AND METHODS: A prospective observational study was conducted on premature children assessed at 6 years of age using the SDQ. Perinatal variables, neurodevelopment, and diagnosis of ADHD, according to the DSM-5, were collected. RESULTS: A total of 214 children who met all the requirements, were included. When compared with the reference population they had significantly higher scores in emotional symptoms, in peer relationships, and in the total score of the test. The hyperactivity scale and the total test score are good predictors of a diagnosis of ADHD, with an area under the ROC curve of 0.83 (95% CI: 0.76-0.90) for hyperactivity, and 0.87 (95% CI: 0.80-0.93) for the total score. The scores for hyperactivity and the total test, from which the screening for ADHD could be considered positive would be≥6 and≥13 respectively, and a combination of hyperactivity≥5 and total score≥12. CONCLUSIONS: Preterm children are at higher risk of emotional and peer relationship problems than those born full term. The SDQ test could be used for ADHD screening.

Genetic diversity of strawberry germplasm using metabolomic biomarkers.

High-throughput metabolomics technologies can provide the quantification of metabolites levels across various biological processes in different tissues, organs and species, allowing the identification of genes underpinning these complex traits. Information about changes of metabolites during strawberry development and ripening processes is key to aiding the development of new approaches to improve fruit attributes. We used network-based methods and multivariate statistical approaches to characterize and investigate variation in the primary and secondary metabolism of seven domesticated and seven wild strawberry fruit accessions at three different fruit development and ripening stages. Our results demonstrated that Fragaria sub-species can be identified solely based on the gathered metabolic profiles. We also showed that domesticated accessions displayed highly similar metabolic changes due to shared domestication history. Differences between domesticated and wild accessions were detected at the level of metabolite associations which served to rank metabolites whose regulation was mostly altered in the process of domestication. The discovery of comprehensive metabolic variation among strawberry accessions offers opportunities to probe into the genetic basis of variation, providing insights into the pathways to relate metabolic variation with important traits.

Bioaccessibility and potential bioavailability of phenolic compounds from achenes as a new target for strawberry breeding programs.

Strawberry is a major natural source of bioactive compounds. Botanically, strawberry is an aggregate fruit consisting of a fleshy floral receptacle that bears a cluster of real dry fruits (achenes). Existing knowledge on the phenolic composition of achenes and its contribution to that of the whole fruit is limited. Also, the gastric and intestinal bioavailability of phenols is poorly known. In this work, a combination of spectrophotometric and HPLC-DAD methods was used to analyse the phenolic composition of whole fruits and achenes before and after in vitro digestion. Five different phenol families were identified. Also, achenes were found to contribute a sizeable fraction of phenolic acids and hydrolysable tannins in the whole fruit. Because the mere presence of phenolic compounds in a food matrix does not ensure their ready absorption and bioavailability, polyphenol potential bioavailability could be an effective selection criterion for strawberry breeding programs aimed at improving dietary healthiness.

True Blood: dengue virus evolution.

This month's Genome Watch highlights insights into different selection pressures in dengue virus evolution.

Developmental stages of cultivated strawberry flowers in relation to chilling sensitivity.

Environmental factors affecting flower development may limit the yields of fruiting crops worldwide. In temperate regions, chilling temperatures during flower development can compromise fruit production, but their negative effects vary depending on the differing susceptibilities of each developmental stage. The cultivated strawberry (Fragaria× ananassa Duch.) is widely grown worldwide but financial returns are influenced by sudden shifts to chilling temperatures occurring during the cropping cycle. Despite this important limitation, knowledge of F.× ananassa flower development is lacking, in contrast to the diploid wild-type strawberry (F. vesca). In this study we describe steps in floral development of cultivated strawberry and define their vulnerability to chilling temperatures. To achieve this, flower buds from strawberry plants of cv. 'Camarosa' were labelled and monitored from bud initiation until anthesis. Description of morphological and functional changes during flower development was based on histological sections and scanning electron microscopy. To determine the impact of low temperatures at different developmental stages, plants carrying buds of different sizes were chilled at 2 °C for 24 h. Several parameters related to male and female gametophyte development were later evaluated in flowers as they approached anthesis. Fragaria× ananassa flower development was divided into 16 stages according to landmark events. These stages were similar to those documented for F. vesca but three new additional intermediate stages were described. Timing of developmental processes was achieved by correlating developmental staging with specific bud sizes and days before anthesis. Time to reach anthesis from early bud stages was 17-18 days. During this period, we detected four critical periods vulnerable to low temperatures. These were mostly related to male gametophyte development but also to injury to female organs at late developmental stages. These results provide the essential groundwork on floral biology of cultivated strawberry that is a prerequisite for successful comparative studies of cold tolerance among genotypes during flower formation.

Potential Sources of Resistance for Melon to Nonpersistently Aphid-borne Viruses.

Two hundred and sixty-eight Cucumis melo and wild relative accessions were evaluated for resistance to Cucumber mosaic virus (CMV), Papaya ringspot virus strain W (PRSV-W), Watermelon mosaic virus (WMV), and Zucchini yellow mosaic virus (ZYMV). Symptom development and systemic infection based on double antibody sandwich enzyme-linked immunosorbent assays were monitored. Sources of resistance were scarce. However, a number of them were found among the C. melo accessions tested. Thus, the accession C-189 behaved similarly to PI 161375 and showed resistance to "common" CMV strains although it was infected by a "song" type CMV. For WMV, the accessions C-768 and C-425, although infected, exhibited very mild symptoms, and recovery from infection occurred in some occasions in the former. A similar trait was also found in C-105, although in this case symptoms rarely appear and part of the plants are not infected. In addition, C-105 was highly resistant to virus transmission by Aphis gossypii, similarly to PI 161375. Accessions C-885 and C-769 exhibited resistance to PRSV-W, WMV, and ZYMV; therefore they are potential sources of multiple resistance. Resistance traits were also found in wild relatives that could be exploited when interspecific barriers with C. melo can be circumvented.