The PfEMP1 family of surface proteins is central for Plasmodium falciparum virulence and must retain the ability to bind to host receptors while also diversifying to aid immune evasion. The ...interaction between CIDRα1 domains of PfEMP1 and endothelial protein C receptor (EPCR) is associated with severe childhood malaria. We combine crystal structures of CIDRα1:EPCR complexes with analysis of 885 CIDRα1 sequences, showing that the EPCR-binding surfaces of CIDRα1 domains are conserved in shape and bonding potential, despite dramatic sequence diversity. Additionally, these domains mimic features of the natural EPCR ligand and can block this ligand interaction. Using peptides corresponding to the EPCR-binding region, antibodies can be purified from individuals in malaria-endemic regions that block EPCR binding of diverse CIDRα1 variants. This highlights the extent to which such a surface protein family can diversify while maintaining ligand-binding capacity and identifies features that should be mimicked in immunogens to prevent EPCR binding.
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•EPCR binding is retained by PfEMP1 CIDRα1 domains despite huge sequence variation•Diverse CIDRα1 domains retain structural and chemical features to bind to EPCR•CIDRα1 domains mimic features of a natural ligand of EPCR and block its binding•Patient sera contain neutralizing antibodies that prevent parasite binding to EPCR
PfEMP1 proteins of Plasmodium must retain binding to host receptor EPCR while diversifying for immune evasion. Using structural studies, Lau et al. show that EPCR-binding surfaces of PfEMP1 are conserved in shape and bonding potential, despite sequence diversity, and identify features that should be mimicked in immunogens preventing EPCR binding.
We examined the hypothesis that ecological niche models (ENMs) more accurately predict species distributions when they incorporate information on population genetic structure, and concomitantly, ...local adaptation. Local adaptation is common in species that span a range of environmental gradients (e.g., soils and climate). Moreover, common garden studies have demonstrated a covariance between neutral markers and functional traits associated with a species’ ability to adapt to environmental change. We therefore predicted that genetically distinct populations would respond differently to climate change, resulting in predicted distributions with little overlap. To test whether genetic information improves our ability to predict a species’ niche space, we created genetically informed ecological niche models (gENMs) using Populus fremontii (Salicaceae), a widespread tree species in which prior common garden experiments demonstrate strong evidence for local adaptation. Four major findings emerged: (i) gENMs predicted population occurrences with up to 12‐fold greater accuracy than models without genetic information; (ii) tests of niche similarity revealed that three ecotypes, identified on the basis of neutral genetic markers and locally adapted populations, are associated with differences in climate; (iii) our forecasts indicate that ongoing climate change will likely shift these ecotypes further apart in geographic space, resulting in greater niche divergence; (iv) ecotypes that currently exhibit the largest geographic distribution and niche breadth appear to be buffered the most from climate change. As diverse agents of selection shape genetic variability and structure within species, we argue that gENMs will lead to more accurate predictions of species distributions under climate change.
This article presents a study on the quality and execution of research code from publicly-available replication datasets at the Harvard Dataverse repository. Research code is typically created by a ...group of scientists and published together with academic papers to facilitate research transparency and reproducibility. For this study, we define ten questions to address aspects impacting research reproducibility and reuse. First, we retrieve and analyze more than 2000 replication datasets with over 9000 unique R files published from 2010 to 2020. Second, we execute the code in a clean runtime environment to assess its ease of reuse. Common coding errors were identified, and some of them were solved with automatic code cleaning to aid code execution. We find that 74% of R files failed to complete without error in the initial execution, while 56% failed when code cleaning was applied, showing that many errors can be prevented with good coding practices. We also analyze the replication datasets from journals' collections and discuss the impact of the journal policy strictness on the code re-execution rate. Finally, based on our results, we propose a set of recommendations for code dissemination aimed at researchers, journals, and repositories.
Indicator species (IS) are used to monitor environmental changes, assess the efficacy of management, and provide warning signals for impending ecological shifts. Though widely adopted in recent years ...by ecologists, conservation biologists, and environmental practitioners, the use of IS has been criticized for several reasons, notably the lack of justification behind the choice of any given indicator. In this review, we assess how ecologists have selected, used, and evaluated the performance of the indicator species. We reviewed all articles published in Ecological Indicators (EI) between January 2001 and December 2014, focusing on the number of indicators used (one or more); common taxa employed; terminology, application, and rationale behind selection criteria; and performance assessment methods. Over the last 14 years, 1914 scientific papers were published in EI, describing studies conducted in 53 countries on six continents; of these, 817 (43%) used biological organisms as indicators. Terms used to describe organisms in IS research included “ecological index”, “environmental index”, “indicator species”, “bioindicator”, and “biomonitor,” but these and other terms often were not clearly defined. Twenty percent of IS publications used only a single species as an indicator; the remainder used groups of species as indicators. Nearly 50% of the taxa used as indicators were animals, 70% of which were invertebrates. The most common applications behind the use of IS were to: monitor ecosystem or environmental health and integrity (42%); assess habitat restoration (18%); and assess effects of pollution and contamination (18%). Indicators were chosen most frequently based on previously cited research (40%), local abundance (5%), ecological significance and/or conservation status (13%), or a combination of two or more of these reasons (25%). Surprisingly, 17% of the reviewed papers cited no clear justification for their choice of indicator. The vast majority (99%) of publications used statistical methods to assess the performance of the selected indicators. This review not only improves our understanding of the current uses and applications of IS, but will also inform practitioners about how to better select and evaluate ecological indicators when conducting future IS research.
Circumcision is associated with significant reductions in HIV, HSV-2 and HPV infections among men and significant reductions in bacterial vaginosis among their female partners.
We assessed the penile ...(coronal sulci) microbiota in 12 HIV-negative Ugandan men before and after circumcision. Microbiota were characterized using sequence-tagged 16S rRNA gene pyrosequencing targeting the V3-V4 hypervariable regions. Taxonomic classification was performed using the RDP Naïve Bayesian Classifier. Among the 42 unique bacterial families identified, Pseudomonadaceae and Oxalobactericeae were the most abundant irrespective of circumcision status. Circumcision was associated with a significant change in the overall microbiota (PerMANOVA p = 0.007) and with a significant decrease in putative anaerobic bacterial families (Wilcoxon Signed-Rank test p = 0.014). Specifically, two families-Clostridiales Family XI (p = 0.006) and Prevotellaceae (p = 0.006)-were uniquely abundant before circumcision. Within these families we identified a number of anaerobic genera previously associated with bacterial vaginosis including: Anaerococcus spp., Finegoldia spp., Peptoniphilus spp., and Prevotella spp.
The anoxic microenvironment of the subpreputial space may support pro-inflammatory anaerobes that can activate Langerhans cells to present HIV to CD4 cells in draining lymph nodes. Thus, the reduction in putative anaerobic bacteria after circumcision may play a role in protection from HIV and other sexually transmitted diseases.
enaR: An r package for Ecosystem Network Analysis Borrett, Stuart R.; Lau, Matthew K.; Dray, Stephane
Methods in ecology and evolution,
November 2014, 2014-11-00, 20141101, Volume:
5, Issue:
11
Journal Article
Peer reviewed
Open access
Summary
Network analysis is a useful approach for investigating complex and relational data in many fields including ecology, molecular and evolutionary biology.
Here, we introduce enaR , an r ...package for Ecosystem Network Analysis (ENA). ENA is an analytical tool set rooted in ecosystem ecology with over 30 years of development that examines the structure and dynamics of matter and energy movement between discrete ecological compartments (e.g. a food web).
In addition to describing the primary functionality of the package, we highlight several features including a library of 100 empirical ecosystem models, the ability to analyse and compare multiple models simultaneously, and connections to other ecological network analysis tools in r.
We examined the hypothesis that genetics-based interactions between strongly interacting foundation species, the tree Populus angustifolia and the aphid Pemphigus betae, affect arthropod community ...diversity, stability and species interaction networks of which little is known. In a 2-year experimental manipulation of the tree and its aphid herbivore four major findings emerged: (i) the interactions of these two species determined the composition of an arthropod community of 139 species; (ii) both tree genotype and aphid presence significantly predicted community diversity; (iii) the presence of aphids on genetically susceptible trees increased the stability of arthropod communities across years; and (iv) the experimental removal of aphids affected community network structure (network degree, modularity and tree genotype contribution to modularity). These findings demonstrate that the interactions of foundation species are genetically based, which in turn significantly contributes to community diversity, stability and species interaction networks. These experiments provide an important step in understanding the evolution of Darwin's ‘entangled bank’, a metaphor that characterizes the complexity and interconnectedness of communities in the wild.
Cerebral malaria is a deadly outcome of infection by Plasmodium falciparum, occurring when parasite-infected erythrocytes accumulate in the brain. These erythrocytes display parasite proteins of the ...PfEMP1 family that bind various endothelial receptors. Despite the importance of cerebral malaria, a binding phenotype linked to its symptoms has not been identified. Here, we used structural biology to determine how a group of PfEMP1 proteins interacts with intercellular adhesion molecule 1 (ICAM-1), allowing us to predict binders from a specific sequence motif alone. Analysis of multiple Plasmodium falciparum genomes showed that ICAM-1-binding PfEMP1s also interact with endothelial protein C receptor (EPCR), allowing infected erythrocytes to synergistically bind both receptors. Expression of these PfEMP1s, predicted to bind both ICAM-1 and EPCR, is associated with increased risk of developing cerebral malaria. This study therefore reveals an important PfEMP1-binding phenotype that could be targeted as part of a strategy to prevent cerebral malaria.
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•Structural basis for P. falciparum PfEMP1 binding to endothelial receptor ICAM-1defined•A sequence motif derived from structure predicts group A PfEMP1 binding to ICAM-1•These ICAM-1-binding PfEMP1s also all bind to endothelial protein C receptor (EPCR)•Expression of dual ICAM-1- and EPCR-binding PfEMP1 is associated with cerebral malaria
Plasmodium falciparum-infected erythrocytes display PfEMP1 proteins that bind various endothelial receptors, including ICAM-1. Lennartz et al. structurally characterize PfEMP1 binding to ICAM-1, allowing them to identify a PfEMP1 family that simultaneously binds to both ICAM-1 and EPCR. Dual-binding PfEMP1s display stronger endothelial adhesion and are associated with cerebral malaria.
Network ecology provides a systems basis for approaching ecological questions, such as factors that influence biological diversity, the role of particular species or particular traits in structuring ...ecosystems, and long‐term ecological dynamics (e.g., stability). Whereas the introduction of network theory has enabled ecologists to quantify not only the degree, but also the architecture of ecological complexity, these advances have come at the cost of introducing new challenges, including new theoretical concepts and metrics, and increased data complexity and computational intensity. Synthesizing recent developments in the network ecology literature, we point to several potential solutions to these issues: integrating network metrics and their terminology across sub‐disciplines; benchmarking new network algorithms and models to increase mechanistic understanding; and improving tools for sharing ecological network research, in particular “model” data provenance, to increase the reproducibility of network models and analyses. We propose that applying these solutions will aid in synthesizing ecological sub‐disciplines and allied fields by improving the accessibility of network methods and models.
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