The Drosophila phenotype ontology

BACKGROUND: Phenotype ontologies are queryable classifications of phenotypes. They provide a widely-used means for annotating phenotypes in a form that is human-readable, programatically accessible and that can be used to group annotations in biologically meaningful ways. Accurate manual annotation requires clear textual definitions for terms. Accurate grouping and fruitful programatic usage require high-quality formal definitions that can be used to automate classification. The Drosophila phenotype ontology (DPO) has been used to annotate over 159,000 phenotypes in FlyBase to date, but until recently lacked textual or formal definitions. RESULTS: We have composed textual definitions for all DPO terms and formal definitions for 77% of them. Formal definitions reference terms from a range of widely-used ontologies including the Phenotype and Trait Ontology (PATO), the Gene Ontology (GO) and the Cell Ontology (CL). We also describe a generally applicable system, devised for the DPO, for recording and reasoning about the timing of death in populations. As a result of the new formalisations, 85% of classifications in the DPO are now inferred rather than asserted, with much of this classification leveraging the structure of the GO. This work has significantly improved the accuracy and completeness of classification and made further development of the DPO more sustainable. CONCLUSIONS: The DPO provides a set of well-defined terms for annotating Drosophila phenotypes and for grouping and querying the resulting annotation sets in biologically meaningful ways. Such queries have already resulted in successful function predictions from phenotype annotation. Moreover, such formalisations make extended queries possible, including cross-species queries via the external ontologies used in formal definitions. The DPO is openly available under an open source license in both OBO and OWL formats. There is good potential for it to be used more broadly by the Drosophila community, which may ultimately result in its extension to cover a broader range of phenotypes

Anemia among Children Exposed to Polyparasitism in Coastal Kenya

Anemia represents a substantial problem for children living in areas with limited resources and significant parasite burden. We performed a cross-sectional study of 254 Kenyan preschool-and early school-age children in a setting endemic for multiple chronic parasitic infections to explore mechanisms of their anemia. Complete venous blood cell counts revealed a high prevalence of local childhood anemia (79%). Evaluating the potential links between low hemoglobin and socioeconomic factors, nutritional status, hemoglobinopathy, and/or parasite infection, we identified age < 9 years (odds ratio [OR]: 12.0, 95% confidence interval [CI]: 4.4, 33) and the presence of asymptomatic malaria infection (OR: 6.8, 95% CI: 2.1, 22) as the strongest independent correlates of having anemia. A total of 130/155 (84%) of anemic children with iron studies had evidence of iron-deficiency anemia (IDA), 16% had non-IDA; 50/52 of additionally tested anemic children met soluble transferrin-receptor (sTfR) criteria for combined anemia of inflammation (AI) with IDA. Children in the youngest age group had the greatest odds of iron deficiency (OR: 10.0, 95% CI: 3.9, 26). Although older children aged 9-11 years had less anemia, they had more detectable malaria, Schistosoma infection, hookworm, and proportionately more non-IDA. Anemia in this setting appears multifactorial such that chronic inflammation and iron deficiency need to be addressed together as part of integrated management of childhood anemia

Using High Resolution LiDAR Data and a Flux Footprint Parameterization to Scale Evapotranspiration Estimates to Lower Pixel Resolutions

Over the last several decades the hydrologically sensitive Boreal Plains ecoregion of Western Canada has experienced significant warming and drying. To better predict implications of land cover changes on evapotranspiration (ET) and future water resources in this region, high resolution light detection and ranging and energy balance data are used here to spatially parameterize the Penman-Monteith ET model. Within a 5 km × 5 km area of peatland ecosystems, riparian boundaries, and upland mixedwood forests, the influence of land cover heterogeneity on the accuracy of modeled ET is examined at pixel sizes of 1, 10, 25, 250, 500, and 1,000 m, representing resolutions common to popular satellite products (SPOT, Landsat, and MODIS). Modeled ET was compared with tower-based eddy covariance measurements using a weighted flux footprint model. Errors range from 10% to 36% of measured fluxes and results indicate that sensors with small pixel sizes (1 m) offer significantly better accuracy in large heterogeneous flux footprints, while a wider range of pixel sizes (500 m) pixel sizes offered significantly less accuracy, although changes in pixel size within this range offered comparable results

Heat Shock Factor 1 is a Substrate for p38 Mitogen-Activated Protein Kinases

Heat shock factor 1 (HSF1) monitors the structural integrity of the proteome. Phosphorylation at S326 is a hallmark for HSF1 activation, but the identity of the kinase(s) phosphorylating this site has remained elusive. We show here that the dietary agent phenethyl isothiocyanate (PEITC) inhibits heat shock protein 90 (Hsp90), the main negative regulator of HSF1; activates p38 mitogen-activated protein kinase (MAPK); and increases S326 phosphorylation, trimerization, and nuclear translocation of HSF1, and the transcription of a luciferase reporter, as well as the endogenous prototypic HSF1 target Hsp70. In vitro, all members of the p38 MAPK family rapidly and stoichiometrically catalyze the S326 phosphorylation. The use of stable knockdown cell lines and inhibitors indicated that among the p38 MAPKs, p38γ is the principal isoform responsible for the phosphorylation of HSF1 at S326 in cells. A protease-mass spectrometry approach confirmed S326 phosphorylation and unexpectedly revealed that p38 MAPK also catalyzes the phosphorylation of HSF1 at S303/307, previously known repressive posttranslational modifications. Thus, we have identified p38 MAPKs as highly efficient catalysts for the phosphorylation of HSF1. Furthermore, our findings suggest that the magnitude and persistence of activation of p38 MAPK are important determinants of the extent and duration of the heat shock response

Age-Stratified Profiles of Serum IL-6, IL-10, and TNF-α Cytokines Among Kenyan Children with Schistosoma haematobium, Plasmodium falciparum, and Other Chronic Parasitic Co-Infections.

In a study of children having polyparasitic infections in a Schistosoma haematobium-endemic area, we examined the hypothesis that S. haematobium-positive children, compared with S. haematobium-negative children (anti-soluble worm antigen preparation [SWAP] negative and egg negative) have increased systemic production of pro-inflammatory cytokines (interleukin [IL]-6, tumor necrosis factor [TNF]-α) and decreased down-regulatory IL-10. A total of 804 children, 2-19 years of age, were surveyed between July and December 2009 and tested for S. haematobium, Plasmodium falciparum, filariasis, and soil-transmitted helminth infections. Plasma levels of IL-6, TNF-α, and IL-10 were compared for S. haematobium-positive and S. haematobium-negative children, adjusting for malaria, filaria, and hookworm co-infections, and for nutritional status, age group, sex, and geographic location. IL-10 was significantly elevated among children infected with S. haematobium, showing bimodal peaks in 7-8 and 13-14 years age groups. IL-10 was also higher among children who were acutely malnourished, whereas IL-10 levels were lower in the presence of S. haematobium-filaria co-infection. After adjustment for co-factors, IL-6 was significantly elevated among children of 5-6 years and among those with P. falciparum infection. Lower levels of IL-6 were found in malaria-hookworm co-infection. High levels of TNF-α were found in children aged 11-12 years regardless of infection status. In addition, village of residence was a strong predictor of IL-6 and IL-10 plasma levels. In adolescent children infected with S. haematobium, there is an associated elevation in circulating IL-10 that may reduce the risk of later morbidity. Although we did not find a direct link between S. haematobium infection and circulating pro-inflammatory IL-6 and TNF-α levels, future T-cell stimulation studies may provide more conclusive linkages between infection and cytokine responses in settings that are endemic for multiple parasites and multiple co-infections

Hierarchy of lesion processing governs the repair, double-strand break formation and mutability of three-lesion clustered DNA damage

Ionising radiation induces clustered DNA damage sites which pose a severe challenge to the cell’s repair machinery, particularly base excision repair. To date, most studies have focussed on two-lesion clusters. We have designed synthetic oligonucleotides to give a variety of three-lesion clusters containing abasic sites and 8-oxo-7, 8-dihydroguanine to investigate if the hierarchy of lesion processing dictates whether the cluster is cytotoxic or mutagenic. Clusters containing two tandem 8-oxoG lesions opposing an AP site showed retardation of repair of the AP site with nuclear extract and an elevated mutation frequency after transformation into wild-type or mutY Escherichia coli. Clusters containing bistranded AP sites with a vicinal 8-oxoG form DSBs with nuclear extract, as confirmed in vivo by transformation into wild-type E. coli. Using ung1 E. coli, we propose that DSBs arise via lesion processing rather than stalled replication in cycling cells. This study provides evidence that it is not only the prompt formation of DSBs that has implications on cell survival but also the conversion of non-DSB clusters into DSBs during processing and attempted repair. The inaccurate repair of such clusters has biological significance due to the ultimate risk of tumourigenesis or as potential cytotoxic lesions in tumour cells

Yielded to Christ or conformed to this world? Postwar Mennonite responses to labour activism

This is the accepted version of the manuscript.The urbanization of North American Mennonites after the Second World War necessitated a reconsideration of Mennonite religious beliefs. Post-war concerns for social justice led to a greater emphasis on non-violence and agape at the expense of Gelassenheit. The tenor of Mennonite church conference resolutions regarding labour union membership changed; while skepticism remained regarding the wisdom of union involvement, the door was left open for participation in unions. The labour militancy of the 1970s led Manitoba Mennonites to re-examine their engagement with the labour movement, a process that has continued to the present day. Without further research on Mennonite workplaces, it cannot be known exactly how the change in religious emphases has affected Mennonite identity.https://journals.sagepub.com/doi/abs/10.1177/00084298070360020

Parasite clearance dynamics in children hospitalised with severe malaria in the Ho Teaching Hospital, Volta Region, Ghana.

Over 90% of severe malaria (SM) cases occur in African children. Parenteral artesunate is currently the recommended treatment for SM. Studies of parasite clearance in paediatric SM cases are needed for assessment of therapeutic outcomes but are lacking in Africa. Severe malaria patients were recruited in the children's emergency ward at Ho Teaching Hospital, Ghana, in 2018. Blood samples were taken upon admission, every 24 h for 3 days and 1 week after treatment, and DNA extracted. Parasitaemia and parasite densities were performed by microscopy at enrolment and the follow-up days wherever possible. Relative parasite density was measured at each timepoint by duplex qPCR and parameters of parasite clearance estimated. Of 25 evaluable SM patients, clearance of qPCR-detectable parasites occurred within 48 h for 17 patients, but three out of the remaining eight were still qPCR-positive on day 3. Increased time to parasite clearance was seen in children ≥5 years old, those with lower haemoglobin levels and those with a high number of previous malaria diagnoses, but these associations were not statistically significant. We examined parasite clearance dynamics among paediatric cases of SM. Our observations suggest that daily sampling for qPCR estimation of peripheral density is a useful method for assessing treatment response in hospitalised SM cases. The study demonstrated varied parasite clearance response, thus illuminating the complex nature of the mechanism in this important patient group, and further investigations utilizing larger sample sizes are needed to confirm our findings

Forest-linked livelihoods in a globalized world.

Forests have re-taken centre stage in global conversations about sustainability, climate and biodiversity. Here, we use a horizon scanning approach to identify five large-scale trends that are likely to have substantial medium- and long-term effects on forests and forest livelihoods: forest megadisturbances; changing rural demographics; the rise of the middle-class in low- and middle-income countries; increased availability, access and use of digital technologies; and large-scale infrastructure development. These trends represent human and environmental processes that are exceptionally large in geographical extent and magnitude, and difficult to reverse. They are creating new agricultural and urban frontiers, changing existing rural landscapes and practices, opening spaces for novel conservation priorities and facilitating an unprecedented development of monitoring and evaluation platforms that can be used by local communities, civil society organizations, governments and international donors. Understanding these larger-scale dynamics is key to support not only the critical role of forests in meeting livelihood aspirations locally, but also a range of other sustainability challenges more globally. We argue that a better understanding of these trends and the identification of levers for change requires that the research community not only continue to build on case studies that have dominated research efforts so far, but place a greater emphasis on causality and causal mechanisms, and generate a deeper understanding of how local, national and international geographical scales interact.This work was funded by the UK’s Department for International Development (grant number 203516-102) and governed by the University of Michigan’s Institutional Review Board (HUM00092191). JAO acknowledges the 520 support of a European Union FP7 Marie Curie international outgoing fellowship (FORCONEPAL). LVR was funded by the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (Grant agreement No. 853222 FORESTDIET). AJB acknowledges the support of an Australian Research Council Australia Laureate Fellowship (grant number 525 FL160100072). LBF acknowledges support from the European Union Marie Curie global fellowship (CONRICONF). PM was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No 677140 MIDLAND)