Development of ex vivo organ culture models to mimic human corneal scarring

PURPOSE: To develop ex vivo organ culture models of human corneal scarring suitable for pharmacological testing and the study of the molecular mechanisms leading to corneal haze after laser surgery or wounding. METHODS: Corneas from human donors were cultured ex vivo for 30 days, either at the air-liquid interface (AL) or immersed (IM) in the culture medium. Histological features and immunofluorescence for fibronectin, tenascin C, thrombospondin-1, and α-smooth muscle actin were graded from 0 to 3 for control corneas and for corneas wounded with an excimer laser. The effects of adding 10 ng/ml transforming growth factor-β1 (TGF-β1) to the culture medium and of prior complete removal of the epithelium and limbus, thus preventing reepithelialization, were also analyzed on wounded corneas. Collagen III expression was detected with real-time PCR. RESULTS: Wounding alone was sufficient to induce keratocyte activation and stromal disorganization, but it was only in the presence of added TGF-β1 that intense staining for fibronectin and tenascin C was found in the AL and IM models (as well as thrombospondin-1 in the AL model) and that α-smooth muscle actin became detectable. The scar-like appearance of the corneas was exacerbated when TGF-β1 was added and reepithelialization was prevented, resulting in the majority of corneas becoming opaque and marked upregulation of collagen III. CONCLUSIONS: THE MAIN FEATURES OF CORNEAL SCARRING WERE REPRODUCED IN THESE TWO COMPLEMENTARY MODELS: the AL model preserved differentiation of the epithelium and permits the topical application of active molecules, while the IM model ensures better perfusion by soluble compounds

Steric constraints in model proteins

A simple lattice model for proteins that allows for distinct sizes of the amino acids is presented. The model is found to lead to a significant number of conformations that are the unique ground state of one or more sequences or encodable. Furthermore, several of the encodable structures are highly designable and are the non-degenerate ground state of several sequences. Even though the native state conformations are typically compact, not all compact conformations are encodable. The incorporation of the hydrophobic and polar nature of amino acids further enhances the attractive features of the model.Comment: RevTex, 5 pages, 3 postscript figure

A transient homotypic interaction model for the influenza A virus NS1 protein effector domain

Influenza A virus NS1 protein is a multifunctional virulence factor consisting of an RNA binding domain (RBD), a short linker, an effector domain (ED), and a C-terminal 'tail'. Although poorly understood, NS1 multimerization may autoregulate its actions. While RBD dimerization seems functionally conserved, two possible apo ED dimers have been proposed (helix-helix and strand-strand). Here, we analyze all available RBD, ED, and full-length NS1 structures, including four novel crystal structures obtained using EDs from divergent human and avian viruses, as well as two forms of a monomeric ED mutant. The data reveal the helix-helix interface as the only strictly conserved ED homodimeric contact. Furthermore, a mutant NS1 unable to form the helix-helix dimer is compromised in its ability to bind dsRNA efficiently, implying that ED multimerization influences RBD activity. Our bioinformatical work also suggests that the helix-helix interface is variable and transient, thereby allowing two ED monomers to twist relative to one another and possibly separate. In this regard, we found a mAb that recognizes NS1 via a residue completely buried within the ED helix-helix interface, and which may help highlight potential different conformational populations of NS1 (putatively termed 'helix-closed' and 'helix-open') in virus-infected cells. 'Helix-closed' conformations appear to enhance dsRNA binding, and 'helix-open' conformations allow otherwise inaccessible interactions with host factors. Our data support a new model of NS1 regulation in which the RBD remains dimeric throughout infection, while the ED switches between several quaternary states in order to expand its functional space. Such a concept may be applicable to other small multifunctional proteins

Composite structural motifs of binding sites for delineating biological functions of proteins

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs which represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.Comment: 34 pages, 7 figure

Dietary α-linolenic acid diminishes experimental atherogenesis and restricts T cell-driven inflammation

Aims Epidemiological studies report an inverse association between plant-derived dietary α-linolenic acid (ALA) and cardiovascular events. However, little is known about the mechanism of this protection. We assessed the cellular and molecular mechanisms of dietary ALA (flaxseed) on atherosclerosis in a mouse model. Methods and results Eight-week-old male apolipoprotein E knockout (ApoE−/−) mice were fed a 0.21 % (w/w) cholesterol diet for 16 weeks containing either a high ALA [7.3 % (w/w); n = 10] or low ALA content [0.03 % (w/w); n = 10]. Bioavailability, chain elongation, and fatty acid metabolism were measured by gas chromatography of tissue lysates and urine. Plaques were assessed using immunohistochemistry. T cell proliferation was investigated in primary murine CD3-positive lymphocytes. T cell differentiation and activation was assessed by expression analyses of interferon-γ, interleukin-4, and tumour necrosis factor α (TNFα) using quantitative PCR and ELISA. Dietary ALA increased aortic tissue levels of ALA as well as of the n−3 long chain fatty acids (LC n−3 FA) eicosapentaenoic acid, docosapentaenoic acid, and docosahexaenoic acid. The high ALA diet reduced plaque area by 50% and decreased plaque T cell content as well as expression of vascular cell adhesion molecule-1 and TNFα. Both dietary ALA and direct ALA exposure restricted T cell proliferation, differentiation, and inflammatory activity. Dietary ALA shifted prostaglandin and isoprostane formation towards 3-series compounds, potentially contributing to the atheroprotective effects of ALA. Conclusion Dietary ALA diminishes experimental atherogenesis and restricts T cell-driven inflammation, thus providing the proof-of-principle that plant-derived ALA may provide a valuable alternative to marine LC n−3 F

Automata for true concurrency properties

We present an automata-theoretic framework for the model checking of true concurrency properties. These are specified in a fixpoint logic, corresponding to history-preserving bisimilarity, capable of describing events in computations and their dependencies. The models of the logic are event structures or any formalism which can be given a causal semantics, like Petri nets. Given a formula and an event structure satisfying suitable regularity conditions we show how to construct a parity tree automaton whose language is non-empty if and only if the event structure satisfies the formula. The automaton, due to the nature of event structure models, is usually infinite. We discuss how it can be quotiented to an equivalent finite automaton, where emptiness can be checked effectively. In order to show the applicability of the approach, we discuss how it instantiates to finite safe Petri nets. As a proof of concept we provide a model checking tool implementing the technique

Hetero-association of aromatic molecules in aqueous solution

Knowledge of the physical chemistry of small molecules complexation (the hetero-association) in aqueous solution is increasingly important in view of the rapidly emerging branch of supramolecular chemistry dealing with the formation of heterogeneous polymeric structures having specific functional roles. In this paper, the 50-year history of scientific studies of hetero-association of heterocyclic aromatic molecules in aqueous solution has been reviewed. Some important correlations of structural and thermodynamic parameters of complexation have been reported based on large data-set of hetero-association parameters accumulated to date. The fundamental problem of ‘energetic composition’ of π-stacking is extensively discussed. The review has shown that there are some gaps in our understanding of heteroassociation, which provides a challenge for further studies in this are

Everyday vulnerabilities and ''social dispositions'' in the Malian Sahel, an indication for evaluating future adaptability to water crises?

International audienceSince the 1970s, precipitation in the Sahel has decreased and become very irregular, leading to widespread drought, whilst the human need for water has rapidly increased. A new ''dispositions''-based approach was adapted in order to analyse human interactions with environmental hazards and applied to the case of Hombori village in northeastern Mali. This article explores how the population and political stakeholders perceive, live with and respond to the increasing scarcity of water. It also explores how their current vulnerability and ability to cope with variations in available water resources indicate future adaptability to climate shocks. On the one hand, this research shows how the population copes with variations in water resource availability: the population's socio-spatial organisation explains the inhabitants' exposure to this problem and some of the factors affecting vulnerability, the elderly and women being the hardest hit. The water issue is generally managed on a ''day-to-day'' basis and considered a big problem only in the dry season, thus lowering any incentive for self-protection. The main two variables that could explain this kind of risk management are the conflicting local governance and current social rules. On the other hand, the discussion of results, based on a conceptual model of social responses, explains why these current ''social dispositions'' to cope with and even address the water scarcity issue do not guarantee future adaptability to climate change

Observations on flower and fruit anatomy in dioecious species of Cordia (Cordiaceae, Boraginales) with evolutionary interpretations

Detailed anatomical studies of flowers and fruits may render traits of phylogenetic importance, but are still rare in the Boraginales. An Old World clade of Cordia comprises many dioecious species, but the floral anatomy is largely unexplored and, hence, the structural basis for sex separation. Fresh material of buds, functionally unisexual flowers and fruits were studied using a stack shot camera. Fixed such material of Cordia crenata, C. cf. grandicalyx and C. sinensis was sectioned using a microtome and stained with safranin red and astra blue, and the gynoecial surface was studied using SEM. The stamens of the female flowers are largely intact, but do not produce pollen, whereas the gynoecium of the male flowers is highly reduced though develops ovules lacking an embryo sac. The morphologically rather unreduced stamens of the female flower may have undergone a shift of function from producing pollen towards attracting pollinators by optical signals. The outer parenchyma of the gynoecium is strongly stained and after fertilisation, one through three ovules are maturing towards seeds. The presence of more than a single seed enclosed in the undivided endocarp is rare in Cordiaceae

Scoring docking conformations using predicted protein interfaces

BACKGROUND: Since proteins function by interacting with other molecules, analysis of protein-protein interactions is essential for comprehending biological processes. Whereas understanding of atomic interactions within a complex is especially useful for drug design, limitations of experimental techniques have restricted their practical use. Despite progress in docking predictions, there is still room for improvement. In this study, we contribute to this topic by proposing T-PioDock, a framework for detection of a native-like docked complex 3D structure. T-PioDock supports the identification of near-native conformations from 3D models that docking software produced by scoring those models using binding interfaces predicted by the interface predictor, Template based Protein Interface Prediction (T-PIP). RESULTS: First, exhaustive evaluation of interface predictors demonstrates that T-PIP, whose predictions are customised to target complexity, is a state-of-the-art method. Second, comparative study between T-PioDock and other state-of-the-art scoring methods establishes T-PioDock as the best performing approach. Moreover, there is good correlation between T-PioDock performance and quality of docking models, which suggests that progress in docking will lead to even better results at recognising near-native conformations. CONCLUSION: Accurate identification of near-native conformations remains a challenging task. Although availability of 3D complexes will benefit from template-based methods such as T-PioDock, we have identified specific limitations which need to be addressed. First, docking software are still not able to produce native like models for every target. Second, current interface predictors do not explicitly consider pairwise residue interactions between proteins and their interacting partners which leaves ambiguity when assessing quality of complex conformations