Protein export into malaria parasite-infected erythrocytes: mechanisms and functional consequences.

Phylum Apicomplexa comprises a large group of obligate intracellular parasites of high medical and veterinary importance. These organisms succeed intracellularly by effecting remarkable changes in a broad range of diverse host cells. The transformation of the host erythrocyte is particularly striking in the case of the malaria parasite Plasmodium falciparum. P. falciparum exports hundreds of proteins that mediate a complex cellular renovation marked by changes in the permeability, rigidity, and cytoadherence properties of the host erythrocyte. The past decade has seen enormous progress in understanding the identity and function of these exported effectors, as well as the mechanisms by which they are trafficked into the host cell. Here we review these advances, place them in the context of host manipulation by related apicomplexans, and propose key directions for future research.

Plasmodium Egress Across the Parasite Life Cycle.

Human malaria, caused by infection with Plasmodium parasites, remains one of the most important global public health problems, with the World Health Organization reporting more than 240 million cases and 600,000 deaths annually as of 2020 (World malaria report 2021). Our understanding of the biology of these parasites is critical for development of effective therapeutics and prophylactics, including both antimalarials and vaccines. Plasmodium is a protozoan organism that is intracellular for most of its life cycle. However, to complete its complex life cycle and to allow for both amplification and transmission, the parasite must egress out of the host cell in a highly regulated manner. This review discusses the major pathways and proteins involved in the egress events during the Plasmodium life cycle-merozoite and gametocyte egress out of red blood cells, sporozoite egress out of the oocyst, and merozoite egress out of the hepatocyte. The similarities, as well as the differences, between the various egress pathways of the parasite highlight both novel cell biology and potential therapeutic targets to arrest its life cycle.

Outwitting evolution: fighting drug-resistant TB, malaria, and HIV.

Although caused by vastly different pathogens, the world's three most serious infectious diseases, tuberculosis, malaria, and HIV-1 infection, share the common problem of drug resistance. The pace of drug development has been very slow for tuberculosis and malaria and rapid for HIV-1. But for each disease, resistance to most drugs has appeared quickly after the introduction of the drug. Learning how to manage and prevent resistance is a major medical challenge that requires an understanding of the evolutionary dynamics of each pathogen. This Review summarizes the similarities and differences in the evolution of drug resistance for these three pathogens.

Histidine-rich protein II nanoparticle delivery of heme iron load drives endothelial inflammation in cerebral malaria.

Histidine-rich protein II (HRPII) is secreted by Plasmodium falciparum during the blood stage of malaria infection. High plasma levels of HRPII are associated with cerebral malaria, a severe and highly fatal complication of malaria. HRPII has been shown to induce vascular leakage, the hallmark of cerebral malaria, in blood-brain barrier (BBB) and animal models. We have discovered an important mechanism for BBB disruption that is driven by unique features of HRPII. By characterizing serum from infected patients and HRPII produced by P. falciparum parasites in culture, we found that HRPII exists in large multimeric particles of 14 polypeptides that are richly laden with up to 700 hemes per particle. Heme loading of HRPII is required for efficient binding and internalization via caveolin-mediated endocytosis in hCMEC/D3 cerebral microvascular endothelial cells. Upon acidification of endolysosomes, two-thirds of the hemes are released from acid-labile binding sites and metabolized by heme oxygenase 1, generating ferric iron and reactive oxygen species. Subsequent activation of the NLRP3 inflammasome and IL-1ß secretion resulted in endothelial leakage. Inhibition of these pathways with heme sequestration, iron chelation, or anti-inflammatory drugs protected the integrity of the BBB culture model from HRPII:heme. Increased cerebral vascular permeability was seen after injection of young mice with heme-loaded HRPII (HRPII:heme) but not with heme-depleted HRPII. We propose that during severe malaria infection, HRPII:heme nanoparticles in the bloodstream deliver an overwhelming iron load to endothelial cells to cause vascular inflammation and edema. Disrupting this process is an opportunity for targeted adjunctive therapies to reduce the morbidity and mortality of cerebral malaria.

An essential endoplasmic reticulum-resident N-acetyltransferase ortholog in Plasmodium falciparum.

N-terminal acetylation is a common eukaryotic protein modification that involves the addition of an acetyl group to the N-terminus of a polypeptide. This modification is largely performed by cytosolic N-terminal acetyltransferases (NATs). Most associate with the ribosome, acetylating nascent polypeptides co-translationally. In the malaria parasite Plasmodium falciparum, exported effectors are thought to be translated into the endoplasmic reticulum (ER), processed by the aspartic protease plasmepsin V and then N-acetylated, despite having no clear access to cytosolic NATs. Here, we used inducible gene deletion and post-transcriptional knockdown to investigate the primary ER-resident NAT candidate, Pf3D7_1437000. We found that it localizes to the ER and is required for parasite growth. However, depletion of Pf3D7_1437000 had no effect on protein export or acetylation of the exported proteins HRP2 and HRP3. Despite this, Pf3D7_1437000 depletion impedes parasite development within the host red blood cell and prevents parasites from completing genome replication. Thus, this work provides further proof of N-terminal acetylation of secretory system proteins, a process unique to apicomplexan parasites, but strongly discounts a promising candidate for this post-translational modification.

Malaria parasite translocon structure and mechanism of effector export.

The putative Plasmodium translocon of exported proteins (PTEX) is essential for transport of malarial effector proteins across a parasite-encasing vacuolar membrane into host erythrocytes, but the mechanism of this process remains unknown. Here we show that PTEX is a bona fide translocon by determining structures of the PTEX core complex at near-atomic resolution using cryo-electron microscopy. We isolated the endogenous PTEX core complex containing EXP2, PTEX150 and HSP101 from Plasmodium falciparum in the 'engaged' and 'resetting' states of endogenous cargo translocation using epitope tags inserted using the CRISPR-Cas9 system. In the structures, EXP2 and PTEX150 interdigitate to form a static, funnel-shaped pseudo-seven-fold-symmetric protein-conducting channel spanning the vacuolar membrane. The spiral-shaped AAA+ HSP101 hexamer is tethered above this funnel, and undergoes pronounced compaction that allows three of six tyrosine-bearing pore loops lining the HSP101 channel to dissociate from the cargo, resetting the translocon for the next threading cycle. Our work reveals the mechanism of P. falciparum effector export, and will inform structure-based design of drugs targeting this unique translocon.

COVID-19 pandemic reveals persistent disparities in nitrogen dioxide pollution.

The unequal spatial distribution of ambient nitrogen dioxide ([Formula: see text]), an air pollutant related to traffic, leads to higher exposure for minority and low socioeconomic status communities. We exploit the unprecedented drop in urban activity during the COVID-19 pandemic and use high-resolution, remotely sensed [Formula: see text] observations to investigate disparities in [Formula: see text] levels across different demographic subgroups in the United States. We show that, prior to the pandemic, satellite-observed [Formula: see text] levels in the least White census tracts of the United States were nearly triple the [Formula: see text] levels in the most White tracts. During the pandemic, the largest lockdown-related [Formula: see text] reductions occurred in urban neighborhoods that have 2.0 times more non-White residents and 2.1 times more Hispanic residents than neighborhoods with the smallest reductions. [Formula: see text] reductions were likely driven by the greater density of highways and interstates in these racially and ethnically diverse areas. Although the largest reductions occurred in marginalized areas, the effect of lockdowns on racial, ethnic, and socioeconomic [Formula: see text] disparities was mixed and, for many cities, nonsignificant. For example, the least White tracts still experienced ∼1.5 times higher [Formula: see text] levels during the lockdowns than the most White tracts experienced prior to the pandemic. Future policies aimed at eliminating pollution disparities will need to look beyond reducing emissions from only passenger traffic and also consider other collocated sources of emissions such as heavy-duty vehicles.

Native structure of the RhopH complex, a key determinant of malaria parasite nutrient acquisition.

The RhopH complex is implicated in malaria parasites' ability to invade and create new permeability pathways in host erythrocytes, but its mechanisms remain poorly understood. Here, we enrich the endogenous RhopH complex in a native soluble form, comprising RhopH2, CLAG3.1, and RhopH3, directly from parasite cell lysates and determine its atomic structure using cryo-electron microscopy (cryo-EM), mass spectrometry, and the cryoID program. CLAG3.1 is positioned between RhopH2 and RhopH3, which both share substantial binding interfaces with CLAG3.1 but make minimal contacts with each other. The forces stabilizing individual subunits include 13 intramolecular disulfide bonds. Notably, CLAG3.1 residues 1210 to 1223, previously predicted to constitute a transmembrane helix, are embedded within a helical bundle formed by residues 979 to 1289 near the C terminus of CLAG3.1. Buried in the core of the RhopH complex and largely shielded from solvent, insertion of this putative transmembrane helix into the erythrocyte membrane would likely require a large conformational rearrangement. Given the unusually high disulfide content of the complex, it is possible that such a rearrangement could be initiated by the breakage of allosteric disulfide bonds, potentially triggered by interactions at the erythrocyte membrane. This first direct observation of an exported Plasmodium falciparum transmembrane protein-in a soluble, trafficking state and with atomic details of buried putative membrane-insertion helices-offers insights into the assembly and trafficking of RhopH and other parasite-derived complexes to the erythrocyte membrane. Our study demonstrates the potential the endogenous structural proteomics approach holds for elucidating the molecular mechanisms of hard-to-isolate complexes in their native, functional forms.

Societal shifts due to COVID-19 reveal large-scale complexities and feedbacks between atmospheric chemistry and climate change.

The COVID-19 global pandemic and associated government lockdowns dramatically altered human activity, providing a window into how changes in individual behavior, enacted en masse, impact atmospheric composition. The resulting reductions in anthropogenic activity represent an unprecedented event that yields a glimpse into a future where emissions to the atmosphere are reduced. Furthermore, the abrupt reduction in emissions during the lockdown periods led to clearly observable changes in atmospheric composition, which provide direct insight into feedbacks between the Earth system and human activity. While air pollutants and greenhouse gases share many common anthropogenic sources, there is a sharp difference in the response of their atmospheric concentrations to COVID-19 emissions changes, due in large part to their different lifetimes. Here, we discuss several key takeaways from modeling and observational studies. First, despite dramatic declines in mobility and associated vehicular emissions, the atmospheric growth rates of greenhouse gases were not slowed, in part due to decreased ocean uptake of CO2 and a likely increase in CH4 lifetime from reduced NO x emissions. Second, the response of O3 to decreased NO x emissions showed significant spatial and temporal variability, due to differing chemical regimes around the world. Finally, the overall response of atmospheric composition to emissions changes is heavily modulated by factors including carbon-cycle feedbacks to CH4 and CO2, background pollutant levels, the timing and location of emissions changes, and climate feedbacks on air quality, such as wildfires and the ozone climate penalty.

Concomitant Medial Collateral Ligament Injury Increases the Risk of Revision Anterior Cruciate Ligament Reconstruction.

PURPOSE: To compare rates of revisions between patients with isolated anterior cruciate ligament (ACL) reconstruction and those who had concomitant medial collateral ligament (MCL) injuries managed either operatively or nonoperatively at the time of index anterior cruciate ligament reconstruction (ACLR). METHODS: Using laterality-specific International Classification of Diseases, Tenth Revision (ICD-10) and Current Procedural Terminology (CPT) codes, we queried the PearlDiver-Mariner Database for all patients who underwent ACLR between 2016 and 2020. Patients were included if they were ages 15 or older and had a minimum of 2 years of follow-up after index ACLR. Patients were then divided into cohorts by presence or absence of concomitant MCL injury. The cohort of concomitant MCL injuries was further subdivided into those with MCL injuries managed nonoperatively, with MCL repair, or with MCL reconstruction at the time of index ACLR. Multivariate regression was performed between cohorts to evaluate for factors associated with revision ACLR. RESULTS: We identified 47,306 patients with isolated ACL injuries and 10,846 with concomitant MCL and ACL injuries. In total, 93% of patients with concomitant MCL injuries had their MCL treated nonoperatively; however, the annual proportion of patients being surgically managed for their MCL injury increased by 70% from 2016 to 2020. Concomitant MCL injury patients had greater odds of undergoing revision ACLR compared with patients with isolated ACL injuries (odds ratio 1.50, 95% confidence interval 1.36-1.66, P < .001). Among patients with concomitant MCL injuries, surgically managed patients had a greater risk of revision ACLR compared with nonoperatively managed MCL injuries (odds ratio 1.39, 95% confidence interval 1.01-1.86, P = .034). CONCLUSIONS: Despite an increase in operatively managed concomitant MCL injuries, most concomitant MCL injuries were still managed nonoperatively at the time of ACLR. Patients with concomitant MCL injuries, particularly those managed operatively, at the time of ACLR are at increased risk of requiring revision ACLR compared with those with isolated ACL injuries. LEVEL OF EVIDENCE: Level III, retrospective comparative case series.

Incidence, risk factors, and complications of acromial stress fractures after reverse total shoulder arthroplasty.

BACKGROUND: An acromial stress fracture (ASF) is an uncommon complication after reverse total shoulder arthroplasty (RTSA) that can have severe clinical consequences on shoulder function. Although patient-specific factors have been identified to influence the risk of ASF, it is unclear whether modifying these factors can minimize risk. Moreover, there is limited information on the treatment outcomes of these fractures. Therefore, the purpose of this study was to determine modifiable risk factors for ASFs and the complication and revision rates of conservatively and operatively managed ASFs. METHODS: The PearlDiver database was queried to identify a cohort of patients who underwent RTSA with minimum 2-year follow-up. Current Procedural Terminology and International Classification of Diseases codes were used to compare the demographic characteristics, comorbidities, and medication use of patients with and without ASFs. Surgical complication and revision rates were compared between operatively and conservatively treated fractures. RESULTS: The overall incidence of ASFs was 1.4%. Patient-specific factors that were independently associated with the occurrence of an ASF included osteoporosis, rheumatologic disease, shoulder corticosteroid injection within 3 months before surgery, and chronic oral corticosteroid use. Among patients with osteoporosis, the initiation of physical therapy within 6 weeks after surgery also increased the risk of ASF. Patients who underwent surgical treatment of ASFs had a revision arthroplasty rate of 7.0% compared to a rate of 3.2% among those with conservatively managed fractures. CONCLUSION: ASFs are infrequent complications that can occur after RTSA. Preoperative factors that affect the quality of bone independently increase the fracture risk. Moreover, this risk can be minimized by avoiding shoulder corticosteroid injections 3 months before surgery and delaying physical therapy exercises among patients with osteoporosis. Surgical fixation of these fractures should be reserved for instances when conservative management has failed given high rates of infection, instability, and revision shoulder arthroplasty.

The Need for Historical Fluency in Pandemic Law and Policy.

The primary claim of this essay is that historical fluency is required for effective work in crafting legal and policy interventions as a part of public health emergency preparedness and response (PHEPR). At a broad level, public health law is explicitly recognized as a key systems-level component of PHEPR practice.1 This essay therefore focuses on the extent to which historical fluency is necessary or at least useful to all aspects of PHEPR that draw on or deploy legal and policy mechanisms (e.g., design, planning, implementation, dissemination, monitoring and evaluation, etc.). The essay collectively refers to these legal and policy mechanisms as epidemic law and policy response (ELAPR). Part I explains the concept of historical fluency. Part II explores the foundations of public health law both as a way of highlighting key structural features of ELAPR and in supporting the claim that historical fluency is critical for ELAPR. Part III applies the previous arguments to a specific case study to highlight the promise and power of historical fluency - the outbreak of bubonic plague in San Francisco in 1900. Tracking this essay's pragmatic focus, part IV offers several recommendations for how specifically historical fluency in public health law and ethics can be operationalized in PHEPR practice and policy. Part V summarizes and concludes.

The nepenthesin insert in the Plasmodium falciparum aspartic protease plasmepsin V is necessary for enzyme function.

Plasmepsin V (PM V) is a pepsin-like aspartic protease essential for growth of the malarial parasite Plasmodium falciparum. Previous work has shown PM V to be an endoplasmic reticulum-resident protease that processes parasite proteins destined for export into the host cell. Depletion or inhibition of the enzyme is lethal during asexual replication within red blood cells as well as during the formation of sexual stage gametocytes. The structure of the Plasmodium vivax PM V has been characterized by X-ray crystallography, revealing a canonical pepsin fold punctuated by structural features uncommon to secretory aspartic proteases; however, the function of this unique structure is unclear. Here, we used parasite genetics to probe these structural features by attempting to rescue lethal PM V depletion with various mutant enzymes. We found an unusual nepenthesin 1-type insert in the PM V gene to be essential for parasite growth and PM V activity. Mutagenesis of the nepenthesin insert suggests that both its amino acid sequence and one of the two disulfide bonds that undergird its structure are required for the insert's role in PM V function. Furthermore, molecular dynamics simulations paired with Markov state modeling suggest that mutations to the nepenthesin insert may allosterically affect PM V catalysis through multiple mechanisms. Taken together, these data provide further insights into the structure of the P. falciparum PM V protease.

Enzymatic and structural characterization of HAD5, an essential phosphomannomutase of malaria-causing parasites.

The malaria-causing parasite Plasmodium falciparum is responsible for over 200 million infections and 400,000 deaths per year. At multiple stages during its complex life cycle, P. falciparum expresses several essential proteins tethered to its surface by glycosylphosphatidylinositol (GPI) anchors, which are critical for biological processes such as parasite egress and reinvasion of host red blood cells. Targeting this pathway therapeutically has the potential to broadly impact parasite development across several life stages. Here, we characterize an upstream component of parasite GPI anchor biosynthesis, the putative phosphomannomutase (PMM) (EC 5.4.2.8), HAD5 (PF3D7_1017400). We confirmed the PMM and phosphoglucomutase activities of purified recombinant HAD5 by developing novel linked enzyme biochemical assays. By regulating the expression of HAD5 in transgenic parasites with a TetR-DOZI-inducible knockdown system, we demonstrated that HAD5 is required for malaria parasite egress and erythrocyte reinvasion, and we assessed the role of HAD5 in GPI anchor synthesis by autoradiography of radiolabeled glucosamine and thin layer chromatography. Finally, we determined the three-dimensional X-ray crystal structure of HAD5 and identified a substrate analog that specifically inhibits HAD5 compared to orthologous human PMMs in a time-dependent manner. These findings demonstrate that the GPI anchor biosynthesis pathway is exceptionally sensitive to inhibition in parasites and that HAD5 has potential as a specific, multistage antimalarial target.

Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu.

X-ray crystallography often requires non-native constructs involving mutations or truncations, and is challenged by membrane proteins and large multicomponent complexes. We present here a bottom-up endogenous structural proteomics approach whereby near-atomic-resolution cryo electron microscopy (cryoEM) maps are reconstructed ab initio from unidentified protein complexes enriched directly from the endogenous cellular milieu, followed by identification and atomic modeling of the proteins. The proteins in each complex are identified using cryoID, a program we developed to identify proteins in ab initio cryoEM maps. As a proof of principle, we applied this approach to the malaria-causing parasite Plasmodium falciparum, an organism that has resisted conventional structural-biology approaches, to obtain atomic models of multiple protein complexes implicated in intraerythrocytic survival of the parasite. Our approach is broadly applicable for determining structures of undiscovered protein complexes enriched directly from endogenous sources.

PMLB v1.0: an open-source dataset collection for benchmarking machine learning methods.

MOTIVATION: Novel machine learning and statistical modeling studies rely on standardized comparisons to existing methods using well-studied benchmark datasets. Few tools exist that provide rapid access to many of these datasets through a standardized, user-friendly interface that integrates well with popular data science workflows. RESULTS: This release of PMLB (Penn Machine Learning Benchmarks) provides the largest collection of diverse, public benchmark datasets for evaluating new machine learning and data science methods aggregated in one location. v1.0 introduces a number of critical improvements developed following discussions with the open-source community. AVAILABILITY AND IMPLEMENTATION: PMLB is available at https://github.com/EpistasisLab/pmlb. Python and R interfaces for PMLB can be installed through the Python Package Index and Comprehensive R Archive Network, respectively.

The Perils of Medicalization for Population Health and Health Equity.

Policy Points Medicalization is a historical process by which personal, behavioral, and social issues are increasingly viewed through a biomedical lens and "diagnosed and treated" as individual pathologies and problems by medical authorities. Medicalization in the United States has led to a conflation of "health" and "health care" and a confusion between individual social needs versus the social, political, and economic determinants of health. The essential and important work of population health science, public health practice, and health policy writ large is being thwarted by a medicalized view of health and an overemphasis on personal health services and the health care delivery system as the major focal point for addressing societal health issues and health inequality. Increased recognition of the negative consequences of a medicalized view of health is essential, with a focus on education and training of clinicians and health care managers, journalists, and policymakers.

Ethnoracial Disparities in Nitrogen Dioxide Pollution in the United States: Comparing Data Sets from Satellites, Models, and Monitors.

In the United States (U.S.), studies on nitrogen dioxide (NO2) trends and pollution-attributable health effects have historically used measurements from in situ monitors, which have limited geographical coverage and leave 66% of urban areas unmonitored. Novel tools, including remotely sensed NO2 measurements and estimates of NO2 estimates from land-use regression and photochemical models, can aid in assessing NO2 exposure gradients, leveraging their complete spatial coverage. Using these data sets, we find that Black, Hispanic, Asian, and multiracial populations experience NO2 levels 15-50% higher than the national average in 2019, whereas the non-Hispanic White population is consistently exposed to levels that are 5-15% lower than the national average. By contrast, the in situ monitoring network indicates more moderate ethnoracial NO2 disparities and different rankings of the least- to most-exposed ethnoracial population subgroup. Validating these spatially complete data sets against in situ observations reveals similar performance, indicating that all these data sets can be used to understand spatial variations in NO2. Integrating in situ monitoring, satellite data, statistical models, and photochemical models can provide a semiobservational record, complete geospatial coverage, and increasingly high spatial resolution, enhancing future efforts to characterize, map, and track exposure and inequality for highly spatially heterogeneous pollutants like NO2.

Bioethics, (Funding) Priorities, and the Perpetuation of Injustice.

If funding allocation is an indicator of a field's priorities, then the priorities of the field of bioethics are misaligned because they perpetuate injustice. Social justice mandates priority for the factors that drive systematic disadvantage, which tend not to be the areas supported by funding within academic bioethics. Current funding priorities violate social justice by overemphasizing technologies that aim to enhance the human condition without addressing underlying structural inequalities grounded in racism, and by deemphasizing areas of inquiry most frequently pursued by Scholars of Color. This lack of attention to upstream determinants of health in bioethics research perpetuates a gap in the resources needed to understand the experiences of communities disproportionately experiencing poor health, which is itself a form of epistemic injustice. Both social and epistemic injustices are apparent in the impact of these funding priorities on people of color, both in the public and in the bioethics community.

A python script for longitudinally measuring the duration of vacant land uses.

Populating and depopulating cities have some degree of underutilised land. The duration of vacancy, or length of time a property remains unused, more strongly influences urban decline than the amount of vacant land. Assessment of the duration of vacancy is seldom conducted, due to a lack of linking longitudinal data. This research creates and applies a Python script to track the duration of vacancy in Minneapolis, MN, U.S.A, to create a tool that can be utilised by cities with vacant land inventories. The tool can be used globally to prioritise treatment areas for urban regeneration plans.