Biology subjects

Popovic, G.

Publications and source records attributed to Popovic, G..

4 recordsLinked to original sources

bioRxiv2022

Chorography and conformational dynamism of the Soluble Human Fibrinogen in solution

Fibrinogen is a soluble, multi-subunit and multi-domain dimeric protein, which, upon its proteolytic cleavage by thrombin, is converted to insoluble fibrin initiating polymerization that substantially contributes to clot growth. The consentaneous structural view of the soluble form of fibrinogen is relatively straight and rigid-like. However, fibrinogen contains numerous, transiently-accessible "cryptic" epitopes for hemostatic and immunologic proteins, suggesting that fibrinogen exhibits conformational flexibility, which may play functional roles in its temporal and spatial interactions. Hitherto, there has been limited information on the solution structure and internal flexibility of soluble fibrinogen. Here, utilizing an integrative, biophysical approach involving temperature-dependent hydrogen-deuterium exchange mass spectrometry, small angle X-ray scattering, and negative stain electron microscopy, we present a holistic, conformationally dynamic model of human fibrinogen in solution. Our data reveal a high degree of internal flexibility, accommodated by four major and distinct flexible sites along the central axis of the protein. We propose that the fibrinogen structure in solution consists of a complex, conformational landscape with multiple local minima, rather than a single, rigid topology. This is further supported by the location of numerous point mutations that are linked to dysfibrinogenemia, and post-translational modifications, residing near fibrinogen flexions. This work provides a molecular basis for the structural "dynamism" of fibrinogen that is expected to influence the broad swath of functionally diverse macromolecular interactions and fine-tune the structural and mechanical properties of blood clots.

biochemistry↗

bioRxiv2022

Effects of hydrological change in fire-prone wetland vegetation: an empirical simulation

Upland swamps are peat-accumulating, groundwater-dependent and fire-prone wetland ecosystems. Drying caused by anthropogenic processes such as underground mining, ditching and climate change may disrupt surface and groundwater flows effecting a bottom-up control on wetland expression. Fire is an endogenous, recurring disturbance that drives a top-down consumptive force in many of these systems. When compounded with anthropogenic drying, fire may facilitate permanent community transitions. A dearth of ecological data and temporal lags have hampered our ability to predict risks associated with multiple disturbances in wetland plant communities. We collected intact wetland mesocosms from valley floors and lower slopes of four undisturbed swamp sites. We transferred the mesocosms to a glasshouse and established three different soil moisture availability levels to simulate wetland drainage. After 20 months of the hydrological treatment, we simulated a fire event by sequentially applying biomass removal (clipping), heat and smoke to half of the mesocosms. We monitored species biomass, richness and composition over a 3.5-year time frame. We found evidence of a temporal lag in biomass response to low water availability and synergistic hydrological and fire effects on species richness. In unburnt conditions, richness declined with low water availability but was maintained under high and medium water availability. After simulated fire in medium water availability, however, richness also declined and converged with depauperate low water mesocosm richness. Representation by many obligate swamp species declined in low compared with high water availability mesocosms over time, an effect that was amplified by the fire treatment. SynthesisOur evidence of lagged effects of hydrological change on wetland vegetation and compounding effects of fire should be considered in impact assessments, monitoring programs and ecosystem management to avoid irreversible wetland change in drying environments.

ecology↗

bioRxiv2021

Longitudinal characterisation of phagocytic and neutralisation functions of anti-Spike antibodies in plasma of patients after SARS-CoV-2 infection.

Phagocytic responses by effector cells to antibody or complement-opsonised viruses have been recognized to play a key role in anti-viral immunity. These include antibody dependent cellular phagocytosis mediated via Fc-receptors, phagocytosis mediated by classically activated complement-fixing IgM or IgG1 antibodies and antibody independent phagocytosis mediated via direct opsonisation of viruses by complement products activated via the mannose-binding lectin pathway. Limited data suggest these phagocytic responses by effector cells may contribute to the immunological and inflammatory responses in SARS-CoV-2 infection, however, their development and clinical significance remain to be fully elucidated. In this cohort of 62 patients, acutely ill individuals were shown to mount phagocytic responses to autologous plasma-opsonised SARS-CoV-2 Spike protein-coated microbeads as early as 10 days post symptom onset. Heat inactivation of the plasma prior to use as an opsonin caused 77-95% abrogation of the phagocytic response, and pre-blocking of Fc-receptors on the effector cells showed only 18-60% inhibition. These results suggest that SARS-CoV-2 can provoke early phagocytosis, which is primarily driven by heat labile components, likely activated complements, with variable contribution from anti-Spike antibodies. During convalescence, phagocytic responses correlated significantly with anti-Spike IgG titers. Older patients and patients with severe disease had significantly higher phagocytosis and neutralisation functions when compared to younger patients or patients with asymptomatic, mild, or moderate disease. A longitudinal study of a subset of these patients over 12 months showed preservation of phagocytic and neutralisation functions in all patients, despite a drop in the endpoint antibody titers by more than 90%. Interestingly, surface plasmon resonance showed a significant increase in the affinity of the anti-Spike antibodies over time correlating with the maintenance of both the phagocytic and neutralisation functions suggesting that improvement in the antibody quality over the 12 months contributed to the retention of effector functions. Author SummaryLimited data suggest antibody dependent effector functions including phagocytosis may contribute to the immunological and inflammatory responses in SARS CoV-2 infection, however, their development, maintenance, and clinical significance remain unknown. In this study we show: O_LIPatients with acute SARS CoV-2 infection can mount phagocytic responses as early as 10 days post symptom onset and these responses were primarily driven by heat labile components of the autologous plasma. These results indicate that the current approach of studying phagocytosis using purified or monoclonal antibodies does not recapitulate contribution by all components in the plasma. C_LIO_LIIn convalescent patients, high phagocytic responses significantly correlated with increasing age, increasing disease severity, high neutralisation functions and high anti-Spike antibody titers, particularly IgG1. C_LIO_LILongitudinal study of convalescent patients over a 12-month period showed maintenance of phagocytic and neutralisation functions, despite a drop in the anti-Spike endpoint antibody titers by more than 90%. However, we found significant increase in the affinity of the anti-Spike antibodies over the 12-month period and these correlated with the maintenance of functions suggesting that improvement in the antibody quality over time contributed to the retention of effector functions. Clinically, measuring antibody titers in sera but not the quality of antibodies is considered a gold standard indicator of immune protection following SARS-CoV 2 infection or vaccination. Our results challenge this notion and recommends change in the current clinical practice. C_LI

immunology↗

bioRxiv2018

Untangling direct species associations from mediator species effects with graphical models

Ecologists often investigate co-occurrence patterns in multi-species data in order to gain insight into the ecological causes of observed co-occurrences. Apart from direct associations between two species, two species may co-occur because they both respond in similar ways to environmental variables, or due to the presence of other (mediator) species.\n\nA wide variety of methods are now available for modelling how environmental filtering drives species distributions. In contrast, methods for studying other causes of co-occurence are much more limited. \"Graphical\" methods, which can be used to study how mediator species impact co-occurrence patterns, have recently been proposed for use in ecology. However, available methods are limited to presence/absence data and methods assuming multivariate normality, which is problematic when analysing abundances.\n\nWe propose Gaussian copula graphical models (GCGMs) for studying the effect of mediator species on co-occurence patterns. GCGMs are a flexible type of graphical model which naturally accommodates all data types - binary (presence/absence), counts, as well as ordinal data and biomass, in a unified framework. Simulations for count data demonstrate that GCGMs are better able to distinguish effects of mediator species from direct associations than using existing methods designed for multivariate normal data.\n\nWe apply GCGMs to counts of hunting spiders, in order to visualise associations between species. We then analyze abundance data of New Zealand native forest cover (on an ordinal scale) to show how GCGMs can be used analyze large and complex datasets. In these data, we were able to reproduce known species relationships as well as generate new ecological hypotheses about species associations.

ecology↗