Coreferentiality: A New Method for the Hypothesis-Based Analysis of Phenotypes Characterized by Multivariate Data

Many multifactorial biologic effects, particularly in the context of complex human diseases, are still poorly understood. At the same time, the systematic acquisition of multivariate data has become increasingly easy. The use of such data to analyze and model complex phenotypes, however, remains a challenge. Here, a new analytic approach is described, termed coreferentiality, together with an appropriate statistical test. Coreferentiality is the indirect relation of two variables of functional interest in respect to whether they parallel each other in their respective relatedness to multivariate reference data, which can be informative for a complex effect or phenotype. It is shown that the power of coreferentiality testing is comparable to multiple regression analysis, sufficient even when reference data are informative only to a relatively small extent of 2.5%, and clearly exceeding the power of simple bivariate correlation testing. Thus, coreferentiality testing uses the increased power of multivariate analysis, however, in order to address a more straightforward interpretable bivariate relatedness. Systematic application of this approach could substantially improve the analysis and modeling of complex phenotypes, particularly in the context of human study where addressing functional hypotheses by direct experimentation is often difficult

FGB1 and WSC3 are in planta-induced beta-glucan-binding fungal lectins with different functions

In the root endophyte Serendipita indica, several lectin-like members of the expanded multigene family of WSC proteins are transcriptionally induced in planta and are potentially involved in beta-glucan remodeling at the fungal cell wall. Using biochemical and cytological approaches we show that one of these lectins, SiWSC3 with three WSC domains, is an integral fungal cell wall component that binds to long-chain beta 1-3-glucan but has no affinity for shorter beta 1-3- or beta 1-6-linked glucose oligomers. Comparative analysis with the previously identified beta-glucan-binding lectin SiFGB1 demonstrated that whereas SiWSC3 does not require beta 1-6-linked glucose for efficient binding to branched beta 1-3-glucan, SiFGB1 does. In contrast to SiFGB1, the multivalent SiWSC3 lectin can efficiently agglutinate fungal cells and is additionally induced during fungus-fungus confrontation, suggesting different functions for these two beta-glucan-binding lectins. Our results highlight the importance of the beta-glucan cell wall component in plant-fungus interactions and the potential of beta-glucan-binding lectins as specific detection tools for fungi in vivo

Insights into β-glucan biology in mutualistic plant-microbe interactions

Plants are constantly surrounded by pathogenic and mutualistic microbes, for example fungi. To defend against fungal invaders plants rely on the innate immunity of each cell which is activated in response to the perception of microbe-associated molecular patterns, so called MAMPs, by specific plant surface receptors. Fungal cell wall derived polysaccharides like branched β-1,3/1,6-glucans are perceived as MAMPs and identify a fungal cell as non-self. The fungal cell wall is a highly dynamic organelle that is constantly reshaped to tailor its structure and composition to circumvent the activation of the plant defense while ensuring cell wall integrity especially during plant colonization. This study aimed to characterize proteins of the mutualistic root endophyte Serendipita indica and its experimental host plant A. thaliana that are engaged in β-glucan biology. The WSC-domain containing lectin WSC3, a member of a multigene family in S. indica is transcriptionally induced during plant colonization and in contact with a second fungus. The fusion protein WSC3-GFP localizes to the cell wall of S. indica, reduces the exposure of β-1,3-glucan and increases cell wall stress resistance in the yeast Pichia pastoris. Isothermal titration calorimetry revealed that WSC3-His binds the MAMP laminarin, a branched β-1,3/1,6-glucan and is able to agglutinate various fungal cells. Furthermore WSC3-His efficiently competes with the unknown plant receptor and thus prevents the induction of the production of reactive oxygen species (ROS) by laminarin but does not increase colonization of barley roots by S. indica. Additionally the secreted β-1,6-glucan specific lectin FGB1 of S. indica was shown to universally suppress ROS production in barley in response to the MAMPs laminarin, chitin and flg22. The investigation of the laminarin-induced ROS production in A. thaliana revealed great natural variation among 100 tested accession. A genome wide association screen identified several genetic loci that are potentially involved in laminarin-triggered defense responses in A. thaliana. Collectively these results suggest that WSC3 might act as a structural component of the fungal cell wall to maintain cell wall integrity while FGB1 is acting as universal suppressor of MAMP-triggered ROS production. Both proteins underline the pivotal role of the fungal cell wall in general and especially of β-glucans during plant-microbe interactions. The responsiveness of A. thaliana to laminarin is subject of great natural variation and potentially represents a multigenetic trait

Correlating New Physics Effects in Semileptonic ΔC=1\Delta C = 1 and ΔS=1\Delta S = 1 Processes

We present constraints on the left-handed dimension-6 interactions that contribute to semileptonic and leptonic decays of $K$, $D$, pions and to nuclear beta decay. We employ the flavour covariant description of the effective couplings, identify universal CP phases of New Physics and derive constraints from decay rates and CP-odd quantities. As a result, we can predict the maximal effects of such flavoured NP in $D$ decays from stringent $K$ decay constraints and vice-versa.Comment: 18 pages, 10 figure

Clusters of cytokines determine malaria severity in Plasmodium falciparum - Infected patients from endemic areas of central India

We investigated the role of interferon (IFN)- gamma , interleukin (IL)-1 beta , IL-2, IL-4, IL-5, IL-6, IL-10, IL-12, tumor necrosis factor (TNF)- alpha , and transforming growth factor (TGF)- beta in clinically well-defined groups of Plasmodium falciparum-infected patients manifesting mild malaria (MM), severe noncerebral malaria (SM), or cerebral malaria (CM) and in control subjects from Gondia, a malaria-endemic site in India, as well as in healthy subjects from non-malaria-endemic areas. Two-way coupled cluster analysis revealed 2 clusters of cytokines relevant to clinical subgroups of disease. The first cluster was composed of IFN- gamma , IL-2, IL-5, IL-6, and IL-12, the levels of which were significantly increased during infection but were predominant in patients with MM and allowed us to distinguish them from patients with SM or CM. The second cluster was composed of TGF- beta , TNF- alpha , IL-10, and IL-1 beta , the levels of which were highly correlated with each other in the different clinical groups of patients and significantly increased with disease severity, particularly in CM. Discriminant analyses allowed us to propose a minimal model. Levels of cytokines such as IL-5, IL-1 beta , IL-10, and IL-2 increase with infection. Levels of IL-12, IL-5, and IL-6 discriminate severe forms of malaria from MM. Finally, levels of IL-1 beta , IL-12, and IFN- gamma are relevant for the discrimination of CM from SM: high IL-1 beta levels are associated with CM, and high IL-12 and IFN- gamma levels are associated with S

Anti-brain protein autoantibodies are detectable in extraparenchymal but not parenchymal neurocysticercosis

Neurocysticercosis (NC) presents a spectrum of clinical manifestations, with two broad clinical entities based on the central nervous system location of the parasite: extraparenchymal (EP-NC) and parenchymal (P-NC). In this work, using quantitative immunoblot methodology, we demonstrate the presence of autoantibodies to brain proteins in CSF from EP-NC, but not P-NC, patients. There was striking correlation between the level of autoantibodies and the levels of the secreted metacestode glycoprotein HP-10, suggesting that the level of stimulation of the autoantibody response may be a function of the number of viable parasites. Nine corresponding proteins autoantigens were provisionally identified by mass spectroscopy. © 2020 Elsevier B.V.Neurocysticercosis (NC) presents a spectrum of clinical manifestations, with two broad clinical entities based on the central nervous system location of the parasite: extraparenchymal (EP-NC) and parenchymal (P-NC). In this work, using quantitative immunoblot methodology, we demonstrate the presence of autoantibodies to brain proteins in CSF from EP-NC, but not P-NC, patients. There was striking correlation between the level of autoantibodies and the levels of the secreted metacestode glycoprotein HP-10, suggesting that the level of stimulation of the autoantibody response may be a function of the number of viable parasites. Nine corresponding proteins autoantigens were provisionally identified by mass spectroscopy. © 2020 Elsevier B.V

Total and functional parasite specific IgE responses in Plasmodium falciparum-infected patients exhibiting different clinical status

Blood samples were collected from controls and P. falciparum-infected patients before treatment on the day of hospitalization (day 0) in India and, in addition, on days 7 and 30 after treatment in Gabon. Total IgE levels were determined by ELISA and functional P. falciparum-specific IgE were estimated using a mast cell line RBL-2H3 transfected with a human Fcε RI α-chain that triggers degranulation upon human IgE cross-linking. Mann Whitney and Kruskall Wallis tests were used to compare groups and the Spearman test was used for correlations. Total IgE levels were confirmed to increase upon infection and differ with level of transmission and age but were not directly related to the disease phenotype. All studied groups exhibited functional parasite-specific IgEs able to induce mast cell degranulation in vitro in the presence of P. falciparum antigens. Plasma IgE levels correlated with those of IL-10 in uncomplicated malaria patients from Gabon. In Indian patients, plasma IFN-γ , TNF and IL-10 levels were significantly correlated with IgE concentrations in all groups

Asymptomatic Plasmodium falciparum infection in children is associated with increased auto-antibody production, high IL-10 plasma levels and antibodies to merozoite surface protein 3

Background Mechanisms of acquired protection to malaria in asymptomatic Plasmodium falciparum carriers are only partially understood. Among them, the role plays by the self-reactive antibodies has not been clarified yet. In this study, the relationship between repertoires of circulating self-reactive and parasite-specific immunoglobulin G (IgG), their correlation with cytokine levels, and their association with protection against malaria was investigated in asymptomatic Plasmodium falciparum-infected Gabonese children. Methods The diversity of P. falciparum-specific antibody repertoire was analysed using a protein micro-array immunoassay, the total auto-antibody repertoire by quantitative immunoblotting and circulating cytokine levels were measured by ELISA in endemic controls (EC) and P. falciparum-infected children from Gabon with asymptomatic (AM) or mild malaria (MM). The association of self- and parasite-specific antibody repertoires with circulating cytokines was evaluated using single linkage hierarchical clustering, Kruskal – Wallis tests and Spearman’s rank correlation. Results Children with AM exhibited an IgG response to merozoite surface protein 3 (MSP3) but not to MSP1-19, although their levels of total P. falciparum-specific IgG were similar to those in the MM group. Moreover, the asymptomatic children had increased levels of autoantibodies recognising brain antigens. In addition, a correlation between IL-10 levels and parasite load was found in AM and MM children. These two groups also exhibited significant correlations between plasma levels of IL-10 and IFN-γ with age and with total plasma IgG levels. IL-10 and IFN-γ levels were also associated with auto-antibody responses in AM. Conclusions Altogether, these results indicate that a self-reactive polyclonal response associated with increased IgG to MSP3 and high plasma levels of IL-10 and IFN-γ may contribute to protective immune mechanisms triggered in asymptomatic P. falciparum infection in Gabonese children

Increased polyclonal immunoglobulin reactivity toward human and bacterial proteins is associated with clinical protection in human Plasmodium infection

BACKGROUND: Polyclonal B-cell activation is well known to occur in Plasmodium infections, but its role in pathogenesis or protection remains unclear. However, protective properties of natural antibodies have previously been demonstrated in other contexts. METHODS: Sera from asymptomatic and symptomatic Plasmodium-infected subjects locally detected in a survey study in the Brazilian Amazon, and from unexposed and exposed but presently uninfected control subjects, were assayed by a standardized quantitative immunoblot method allowing simultaneous detection of IgG or IgM reactivity to a large number of parasite-unrelated proteins. RESULTS: In subjects free of coinfection with hepatitis B virus, IgG reactivity to human brain antigens and Escherichia coli proteins was strikingly enhanced in asymptomatic Plasmodium-infected individuals when compared to such with clinical malaria symptoms, or to uninfected control subjects. This difference was most characteristic for limited exposure times (less than ten years locally, or 20 years in endemic areas). It was more significant than a similar trend found for IgG to Plasmodium falciparum antigens, and unrelated to parasitaemia levels. Asymptomatic subjects with comparatively short exposure characteristically showed relatively elevated IgG versus IgM reactivity. Polyclonal IgG reactivity appears triggered by previous P. falciparum but not Plasmodium vivax malaria. CONCLUSION: The observed difference in polyclonal antibody production seems related to intrinsic activation states of infected individuals, rather than to parasite-antigen specific immune responses. However, it appears influenced by preceding stimuli. This supports the idea that acquired clinical immunity may not exclusively depend on antigen-specific responses, but also on the individual polyclonal reaction