Predicting Antidisease Immunity Using Proteome Arrays and Sera from Children Naturally Exposed to Malaria

Malaria remains one of the most prevalent and lethal human infectious diseases worldwide. A comprehensive characterization of antibody responses to blood stage malaria is essential to support the development of future vaccines, sero-diagnostic tests, and sero-surveillance methods. We constructed a proteome array containing 4441 recombinant proteins expressed by the blood stages of the two most common human malaria parasites, P. falciparum (Pf) and P. vivax (Pv), and used this array to screen sera of Papua New Guinea children infected with Pf, Pv, or both (Pf/Pv) that were either symptomatic (febrile), or asymptomatic but had parasitemia detectable via microscopy or PCR. We hypothesized that asymptomatic children would develop antigen-specific antibody profiles associated with antidisease immunity, as compared with symptomatic children. The sera from these children recognized hundreds of the arrayed recombinant Pf and Pv proteins. In general, responses in asymptomatic children were highest in those with high parasitemia, suggesting that antibody levels are associated with parasite burden. In contrast, symptomatic children carried fewer antibodies than asymptomatic children with infections detectable by microscopy, particularly in Pv and Pf/Pv groups, suggesting that antibody production may be impaired during symptomatic infections. We used machine-learning algorithms to investigate the relationship between antibody responses and symptoms, and we identified antibody responses to sets of Plasmodium proteins that could predict clinical status of the donors. Several of these antibody responses were identified by multiple comparisons, including those against members of the serine enriched repeat antigen family and merozoite protein 4. Interestingly, both P. falciparum serine enriched repeat antigen-5 and merozoite protein 4 have been previously investigated for use in vaccines. This machine learning approach, never previously applied to proteome arrays, can be used to generate a list of potential seroprotective and/or diagnostic antigens candidates that can be further evaluated in longitudinal studies.Of the five species of malaria parasites that infect humans, Plasmodium falciparum (Pf)¹ and P. vivax (Pv) are the most common. Interventions aimed at reducing transmission and improving diagnosis and treatment have led to a dramatic reduction in morbidity and mortality (1, 2). For example, Pf fatalities have declined from an estimated one million to 655,000 annually (2). Although Pv is now recognized as the most widespread species worldwide and a significant cause of severe disease, this parasite, which can relapse months to years after the initial blood stage infection, is still largely ignored (3, 4). Furthermore, mixed-species infections, most commonly of Pf and Pv, are more frequent than previously thought. Although blood smears suggest that <2% of cases are mixed-species infections, PCR-based diagnoses suggest that 55–65% of infections in Thailand, Papua New Guinea (PNG), and other countries in south-east Asia (5–7) are mixed-species infections.Natural immunity can be subdivided into antidisease immunity and antiparasitic immunity. Antidisease immunity (defined as the absence of symptoms) develops quickly, sometimes requiring only one or two infections in high transmission areas (8–11). However, individuals living in high transmission areas develop non-sterile antiparasite immunity, resulting in low-level parasitemia and asymptomatic infections. This immunity is acquired much more slowly than antidisease immunity, may require repeated infections depending on the transmission rate, and is rarely sterilizing (12). Parasite densities in individuals that have acquired antiparasite immunity are average 10⁴- to 10⁶-fold lower than those in non-immune individuals (13).Blood stage parasites activate innate responses, which in turn lead to significant levels of humoral and cellular adaptive immunity (reviewed in (14)). Antiparasitic immunity appears to be mediated primarily by antibody responses against blood stage antigens (15, 16). Specific antimalarial antibodies can block invasion of host erythrocytes in vitro by both Pf (17) and Pv merozoites (18–21). Additionally, certain antibody isotypes, in particular IgG3, can induce antibody-dependent cellular inhibition (ADCI) of parasite invasion and development in erythrocytes, which is strongly associated with protection against malaria parasites (13, 22). Moreover, passive transfer of Pf antimalarial antibodies to infected patients can result in parasite clearance (15, 16). Evidence from field studies suggests that the slow acquisition of antibodies to genetically variant circulating strains over several years is associated with antidisease immunity to Pf (23), but to a lesser extent to Pv (24). Cell-mediated immune responses also play a role in protection, particularly early in the immune response. A strong pro-inflammatory response mediated primarily by interferon-gamma (IFN-γ) and tumor necrosis factor-α (TNF-α) contributes to the initial killing and clearance of parasite-infected red blood cells (25).Identifying antibody targets that are associated with infection, disease, or immunity will support the development of vaccines, diagnostics, and tools for sero-surveillance. By comparing the humoral response profiles of defined populations possessing varying degrees of antidisease and/or antiparasite immunity, it may be possible to identify combinations or responses that are associated with protection against clinical disease and/or parasitemia. These responses could guide selection of antigen(s) for blood stage vaccines. Here, we applied Plasmodium genome sequence, proteomics, bioinformatics, and proteome array fabrication technologies to construct a Pf/Pv blood stage proteome array. The Plasmodium genome encodes over 5000 proteins (5538 and 5435 in Pf and Pv, respectively (26)), nearly half of which have been identified via proteomics at the different stages of malaria parasite life cycle (27, 28). A total of 4441 recombinant proteins, representing 1922 Pf and 1936 Pv native proteins previously reported or predicted to be expressed by the blood stages of these parasites were included on the Pf/Pv proteome arrays, which were then used to analyze antibody responses to both Plasmodium species in naturally-exposed individuals with clinically characterized infections.The resulting data were interrogated using machine-learning algorithms to identify antibody responses that associated with disease status. We identified sets of antigen-specific antibody responses that can be used to distinguish between asymptomatic donors with parasitemias detectable by light microscopy or PCR and asymptomatic donors, some of which were identified by multiple comparisons. This study is a proof-of-concept of the power of applying machine learning algorithms to biomarker discovery, and paves the way for future, more robust studies to identify novel malaria vaccine targets.     

Contribution of left ventricular residual stress by myocytes and collagen: existence of inter-constituent mechanical interaction

We quantify the contribution of myocytes, collagen fibers and their interactions to the residual stress field found in the left ventricle (LV) using both experimental and theoretical methods. Ring tissue samples extracted from normal rat, male and female, LV were treated with collagenase and decellularization to isolate myocytes and collagen fibers, respectively. Opening angle tests were then performed on these samples as well as intact tissue samples containing both constituents that served as control. Our results show that the collagen fibers are the main contributor to the residual stress fields found in the LV. Specifically, opening angle measured in collagen-only samples (106.45\(^\circ \) ± 23.02\(^\circ \)) and myocytes-only samples (21.00\(^\circ \) ± 4.37\(^\circ \)) was significantly higher and lower than that of the control (57.88\(^\circ \) ± 12.29\(^\circ \)), respectively. A constrained mixture (CM) modeling framework was then used to infer these experimental results. We show that the framework cannot reproduce the opening angle found in the intact tissue with measurements made on the collagen-only and myocytes-only samples. Given that the CM framework assumes that each constituent contributes to the overall mechanics simply by their mere presence, this result suggests the existence of some myocyte–collagen mechanical interaction that cannot be ignored in the LV. We then propose an extended CM formulation that takes into account of the inter-constituent mechanical interaction in which constituents are deformed additionally when they are physically combined into a mixture. We show that the intact tissue opening angle can be recovered in this framework.     

A Real-Time Brain-Machine Interface Combining Motor Target and Trajectory Intent Using an Optimal Feedback Control Design

Real-time brain-machine interfaces (BMI) have focused on either estimating the continuous movement trajectory or target intent. However, natural movement often incorporates both. Additionally, BMIs can be modeled as a feedback control system in which the subject modulates the neural activity to move the prosthetic device towards a desired target while receiving real-time sensory feedback of the state of the movement. We develop a novel real-time BMI using an optimal feedback control design that jointly estimates the movement target and trajectory of monkeys in two stages. First, the target is decoded from neural spiking activity before movement initiation. Second, the trajectory is decoded by combining the decoded target with the peri-movement spiking activity using an optimal feedback control design. This design exploits a recursive Bayesian decoder that uses an optimal feedback control model of the sensorimotor system to take into account the intended target location and the sensory feedback in its trajectory estimation from spiking activity. The real-time BMI processes the spiking activity directly using point process modeling. We implement the BMI in experiments consisting of an instructed-delay center-out task in which monkeys are presented with a target location on the screen during a delay period and then have to move a cursor to it without touching the incorrect targets. We show that the two-stage BMI performs more accurately than either stage alone. Correct target prediction can compensate for inaccurate trajectory estimation and vice versa. The optimal feedback control design also results in trajectories that are smoother and have lower estimation error. The two-stage decoder also performs better than linear regression approaches in offline cross-validation analyses. Our results demonstrate the advantage of a BMI design that jointly estimates the target and trajectory of movement and more closely mimics the sensorimotor control system.     

Germline Mutations in MAP3K6 Are Associated with Familial Gastric Cancer

Gastric cancer is among the leading causes of cancer-related deaths worldwide. While heritable forms of gastric cancer are relatively rare, identifying the genes responsible for such cases can inform diagnosis and treatment for both hereditary and sporadic cases of gastric cancer. Mutations in the E-cadherin gene, CDH1, account for 40% of the most common form of familial gastric cancer (FGC), hereditary diffuse gastric cancer (HDGC). The genes responsible for the remaining forms of FGC are currently unknown. Here we examined a large family from Maritime Canada with FGC without CDH1 mutations, and identified a germline coding variant (p.P946L) in mitogen-activated protein kinase kinase kinase 6 (MAP3K6). Based on conservation, predicted pathogenicity and a known role of the gene in cancer predisposition, MAP3K6 was considered a strong candidate and was investigated further. Screening of an additional 115 unrelated individuals with non-CDH1 FGC identified the p.P946L MAP3K6 variant, as well as four additional coding variants in MAP3K6 (p.F849Sfs*142, p.P958T, p.D200Y and p.V207G). A somatic second-hit variant (p.H506Y) was present in DNA obtained from one of the tumor specimens, and evidence of DNA hypermethylation within the MAP3K6 gene was observed in DNA from the tumor of another affected individual. These findings, together with previous evidence from mouse models that MAP3K6 acts as a tumor suppressor, and studies showing the presence of somatic mutations in MAP3K6 in non-hereditary gastric cancers and gastric cancer cell lines, point towards MAP3K6 variants as a predisposing factor for FGC.     

IgG1 as a Potential Biomarker of Post-chemotherapeutic Relapse in Visceral Leishmaniasis,and Adaptation to a Rapid Diagnostic Test

Background

Visceral leishmaniasis (VL), caused by protozoa of the Leishmania donovani complex, is a widespread parasitic disease of great public health importance; without effective chemotherapy symptomatic VL is usually fatal. Distinction of asymptomatic carriage from progressive disease and the prediction of relapse following treatment are hampered by the lack of prognostic biomarkers for use at point of care.

Methodology/Principal Findings

All IgG subclass and IgG isotype antibody levels were determined using unpaired serum samples from Indian and Sudanese patients with differing clinical status of VL, which included pre-treatment active VL, post-treatment cured, post-treatment relapsed, and post kala-azar dermal leishmaniasis (PKDL), as well as seropositive (DAT and/or rK39) endemic healthy controls (EHCs) and seronegative EHCs. L. donovani antigen-specific IgG1 levels were significantly elevated in relapsed versus cured VL patients (p<0.0001). Using paired Indian VL sera, consistent with the known IgG1 half-life, IgG1 levels had not decreased significantly at day 30 after the start of treatment (p = 0.8304), but were dramatically decreased by 6 months compared to day 0 (p = 0.0032) or day 15 (p<0.0001) after start of treatment. Similarly, Sudanese sera taken soon after treatment did not show a significant change in the IgG1 levels (p = 0.3939). Two prototype lateral flow immunochromatographic rapid diagnostic tests (RDTs) were developed to detect IgG1 levels following VL treatment: more than 80% of the relapsed VL patients were IgG1 positive; at least 80% of the cured VL patients were IgG1 negative (p<0.0001).

Conclusions/Significance

Six months after treatment of active VL, elevated levels of specific IgG1 were associated with treatment failure and relapse, whereas no IgG1 or low levels were detected in cured VL patients. A lateral flow RDT was successfully developed to detect anti-Leishmania IgG1 as a potential biomarker of post-chemotherapeutic relapse.     

Dissolved oxygen and dissolved inorganic carbon stable isotope composition and concentration fluxes across several shallow floodplain aquifers and in a diffusion experiment

Recent studies have documented the occurrence of dissolved molecular oxygen (DO) in shallow groundwater that is isotopically lighter than can be explained by atmospheric gas exchange or by biogeochemical reactions that consume ¹⁶O¹⁶O faster than ¹⁶O¹⁸O. In the present study, spatial gradients in the isotopic composition of DO (δ¹⁸O-DO) and dissolved inorganic carbon (δ¹³C-DIC) were measured in three shallow floodplain aquifers: (1) the Nyack aquifer, of the Middle Fork of the Flathead River in northwest Montana; (2) the Silver Bow Creek floodplain in southwest Montana; and (3) the Umatilla River floodplain in northeast Oregon. The field data show general trends of increasing DIC concentration, decreasing δ¹³C-DIC, and decreasing DO concentration with increase in groundwater path length. These trends are consistent with consumption of DO and production of DIC by microbial respiration. Although the expected trend of an increase in δ¹⁸O-DO with increase in path length was found at an area adjacent to hyporheic recharge at the Nyack floodplain, the majority of groundwater samples collected at Nyack and from the other sites distal to recharge zones had anomalously low δ¹⁸O-DO values well below 24.2 ‰, the value corresponding to atmospheric isotopic equilibrium. At the Nyack site, ³H-³He dates were used to estimate groundwater travel time: all groundwater samples with apparent age >1 year had δ¹⁸O-DO<24.2 ‰. Previously it has been suggested that diffusion of O₂ could be a viable mechanism to explain the existence of isotopically light DO in shallow groundwater. To test this hypothesis, laboratory experiments were conducted to measure the isotopic fractionation of O₂ as it diffuses from air across a simulated capillary fringe (made from a floating layer of foam beads) into a stirred, initially anoxic, water column. As expected, ¹⁶O¹⁶O diffused faster than ¹⁶O¹⁸O, and the magnitude of isotope fractionation associated with diffusion increased with a decrease in temperature. Fractionation factors (α) calculated from these diffusion experiments were 1.0030 at 15–19 °C and 1.0048 at 8 °C. The combined field and laboratory data suggest that diffusion is an important mechanism to maintain aerobic conditions in shallow groundwater systems, allowing microbial respiration to continue at long distances (km scale) from the source of groundwater recharge.     

Refuge-mediated apparent competition in plant–consumer interactions

At the intersection of consumer behaviour and plant competition is the concept of refuge-mediated apparent competition: an indirect interaction whereby plants provide a refuge for a shared consumer, subsequently increasing consumer pressure on another plant species. Here, we use a simple model and empirical examples to develop and illustrate the concept of refuge-mediated apparent competition. We find that the likelihood that an inferior competitor will succeed via refuge-mediated apparent competition is greater when competitors have similar resource requirements and when consumers exhibit a strong response to the refuge and high attack rates on the superior competitor. Refuge-mediated apparent competition may create an emergent Allee effect, such that a species invades only if it is sufficiently abundant to alter consumer impact on resident species. This indirect interaction may help explain unresolved patterns observed in biological invasion, such as the different physical structure of invasive exotic plants, the lag phase, and the failure of restoration efforts. Given the ubiquity of refuge-seeking behaviour by consumers and the ability of consumers to alter the outcome of direct competition among plants, refuge-mediated apparent competition may be an underappreciated mechanism affecting the composition and diversity of plant communities.
Ecology Letters (2010) 13: 11–20     

“Spider Monkey Cotton”: Bridging Waiwai and Scientific Ontologies to Characterize Spider Monkey (Ateles paniscus) Filariasis in the Konashen Community Owned Conservation Area,Guyana

International Journal of Primatology - Zoonotic disease risk is greatly influenced by cultural practices and belief systems. Yet, few studies have investigated how different ways of knowing are...