Adsorption of chain molecules in pores with crystalline walls: a density functional approach

A microscopic density functional theory of adsorption of chain molecules on the attractive solid surfaces of crystalline symmetry is developed. The proposed approach is based on the expansions of one-particle functions into two-dimensional Fourier series. Illustrative calculations for dimers, 8- and 16-mers adsorbed on a (100) fcc crystal surface indicate the effect of the periodicity of the adsorbing potential on the structure of the adsorbed layer and thermodynamics of adsorption.Розвинуто мiкроскопiчну теорiю функцiоналу густини для вивчення адсорбцiї ланцюгових молекул на притягальних твердих поверхнях кристалiчної симетрiї. Запропонований пiдхiд ґрунтується на розкладах одночастинкових функцiй у двовимiрнi ряди Фур’є. Для iлюстрацiї проведено обчислення для димерiв, 8- i 16-мерiв, що адсорбованi на кристалiчнiй поверхнi (100) fcc, якi демонструють вплив перiодичностi адсорбуючого потенцiалу на структуру адсорбованого шару i термодинамiку адсорбцiї

Self-recognition and Ca2+-dependent carbohydrate–carbohydrate cell adhesion provide clues to the Cambrian explosion

Author Posting. © The Authors, 2009. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Molecular Biology and Evolution 26 (2009): 2551-2561, doi:10.1093/molbev/msp170.The Cambrian explosion of life was a relatively short period ca. 540 million years ago that marked a generalized acceleration in the evolution of most animal phyla, but the trigger of this key biological event remains elusive. Sponges are the oldest extant Precambrian metazoan phylum and thus a valid model to study factors that could have unleashed the rise of multicellular animals. One such factor is the advent of self/non-self recognition systems, which would be evolutionarily beneficial to organisms to prevent germ cell parasitism or the introduction of deleterious mutations resulting from fusion with genetically different individuals. However, the molecules responsible for allorecognition probably evolved gradually before the Cambrian period, and some other (external) factor remains to be identified as the missing triggering event. Sponge cells associate through calcium-dependent, multivalent carbohydrate-carbohydrate interactions of the g200 glycan found on extracellular proteoglycans. Single molecule force spectroscopy analysis of g200-g200 binding indicates that calcium affects the lifetime (+Ca/-Ca: 680 s/3 s) and bond reaction length (+Ca/-Ca: 3.47 Å/2.27 Å). Calculation of mean g200 dissociation times in low and high calcium within the theoretical framework of a cooperative binding model indicates the non-linear and divergent characteristics leading to either disaggregated cells or stable multicellular assemblies, respectively. This fundamental phenomenon can explain a switch from weak to strong adhesion between primitive metazoan cells caused by the well documented rise in ocean calcium levels at the end of Precambrian time. We propose that stronger cell adhesion allowed the integrity of genetically uniform animals composed only of “self” cells, facilitating genetic constitutions to remain within the metazoan individual and be passed down inheritance lines. The Cambrian explosion might have been triggered by the coincidence in time of primitive animals endowed with self/non-self recognition, and of a surge in sea water calcium that increased the binding forces between their calcium-dependent cell adhesion molecules.D.A. and A.K. acknowledge financial support from the Collaborative Research Center SFB 613 from the Deutsche Forschungsgemeinschaft (DFG), and X.F.-B. acknowledges financial support from grants BIO2002-00128, BIO2005-01591, and CSD2006-00012 from the Ministerio de Ciencia y Tecnología, Spain, which included Fondo Europeo de Desarrollo Regional funds, and from grant 2005SGR-00037 from the Generalitat de Catalunya, Spain

Phase separation of an asymmetric binary fluid mixture confined in a nanoscopic slit pore: Molecular-dynamics simulations

As a generic model system of an asymmetric binary fluid mixture, hexadecane dissolved in carbon dioxide is considered, using a coarse-grained bead-spring model for the short polymer, and a simple spherical particle with Lennard-Jones interactions for the carbon dioxide molecules. In previous work, it has been shown that this model reproduces the real phase diagram reasonable well, and also the initial stages of spinodal decomposition in the bulk following a sudden expansion of the system could be studied. Using the parallelized simulation package ESPResSo on a multiprocessor supercomputer, phase separation of thin fluid films confined between parallel walls that are repulsive for both types of molecules are simulated in a rather large system (1356 x 1356 x 67.8 A^3, corresponding to about 3.2 million atoms). Following the sudden system expansion, a complicated interplay between phase separation in the directions perpendicular and parallel to the walls is found: in the early stages the hexadecane molecules accumulate mostly in the center of the slit pore, but as the coarsening of the structure in the parallel direction proceeds, the inhomogeneity in the perpendicular direction gets much reduced. Studying then the structure factors and correlation functions at fixed distances from the wall, the densities are essentially not conserved at these distances, and hence the behavior differs strongly from spinodal decomposition in the bulk. Some of the characteristic lengths show a nonmonotonic variation with time, and simple coarsening described by power-law growth is only observed if the domain sizes are much larger than the film thickness.Comment: accepted for publication in PR

Pseudomonas aeruginosa Pili and Flagella Mediate Distinct Binding and Signaling Events at the Apical and Basolateral Surface of Airway Epithelium

Pseudomonas aeruginosa, an important opportunistic pathogen of man, exploits numerous factors for initial attachment to the host, an event required to establish bacterial infection. In this paper, we rigorously explore the role of two major bacterial adhesins, type IV pili (Tfp) and flagella, in bacterial adherence to distinct host receptors at the apical (AP) and basolateral (BL) surfaces of polarized lung epithelial cells and induction of subsequent host signaling and pathogenic events. Using an isogenic mutant of P. aeruginosa that lacks flagella or utilizing beads coated with purified Tfp, we establish that Tfp are necessary and sufficient for maximal binding to host N-glycans at the AP surface of polarized epithelium. In contrast, experiments utilizing a P. aeruginosa isogenic mutant that lacks Tfp or using beads coated with purified flagella demonstrate that flagella are necessary and sufficient for maximal binding to heparan sulfate (HS) chains of heparan sulfate proteoglycans (HSPGs) at the BL surface of polarized epithelium. Using two different cell-free systems, we demonstrate that Tfp-coated beads show highest binding affinity to complex N-glycan chains coated onto plastic plates and preferentially aggregate with beads coated with N-glycans, but not with single sugars or HS. In contrast, flagella-coated beads bind to or aggregate preferentially with HS or HSPGs, but demonstrate little binding to N-glycans. We further show that Tfp-mediated binding to host N-glycans results in activation of phosphatidylinositol 3-kinase (PI3K)/Akt pathway and bacterial entry at the AP surface. At the BL surface, flagella-mediated binding to HS activates the epidermal growth factor receptor (EGFR), adaptor protein Shc, and PI3K/Akt, and induces bacterial entry. Remarkably, flagella-coated beads alone can activate EGFR and Shc. Together, this work provides new insights into the intricate interactions between P. aeruginosa and lung epithelium that may be potentially useful in the development of novel treatments for P. aeruginosa infections

Monte Carlo Methods for Estimating Interfacial Free Energies and Line Tensions

Excess contributions to the free energy due to interfaces occur for many problems encountered in the statistical physics of condensed matter when coexistence between different phases is possible (e.g. wetting phenomena, nucleation, crystal growth, etc.). This article reviews two methods to estimate both interfacial free energies and line tensions by Monte Carlo simulations of simple models, (e.g. the Ising model, a symmetrical binary Lennard-Jones fluid exhibiting a miscibility gap, and a simple Lennard-Jones fluid). One method is based on thermodynamic integration. This method is useful to study flat and inclined interfaces for Ising lattices, allowing also the estimation of line tensions of three-phase contact lines, when the interfaces meet walls (where "surface fields" may act). A generalization to off-lattice systems is described as well. The second method is based on the sampling of the order parameter distribution of the system throughout the two-phase coexistence region of the model. Both the interface free energies of flat interfaces and of (spherical or cylindrical) droplets (or bubbles) can be estimated, including also systems with walls, where sphere-cap shaped wall-attached droplets occur. The curvature-dependence of the interfacial free energy is discussed, and estimates for the line tensions are compared to results from the thermodynamic integration method. Basic limitations of all these methods are critically discussed, and an outlook on other approaches is given

The Evolution of Extracellular Matrix

We present a perspective on the molecular evolution of the extracellular matrix (ECM) in metazoa that draws on research publications and data from sequenced genomes and expressed sequence tag libraries. ECM components do not function in isolation, and the biological ECM system or “adhesome” also depends on posttranslational processing enzymes, cell surface receptors, and extracellular proteases. We focus principally on the adhesome of internal tissues and discuss its origins at the dawn of the metazoa and the expansion of complexity that occurred in the chordate lineage. The analyses demonstrate very high conservation of a core adhesome that apparently evolved in a major wave of innovation in conjunction with the origin of metazoa. Integrin, CD36, and certain domains predate the metazoa, and some ECM-related proteins are identified in choanoflagellates as predicted sequences. Modern deuterostomes and vertebrates have many novelties and elaborations of ECM as a result of domain shuffling, domain innovations and gene family expansions. Knowledge of the evolution of metazoan ECM is important for understanding how it is built as a system, its roles in normal tissues and disease processes, and has relevance for tissue engineering, the development of artificial organs, and the goals of synthetic biology

Bacterial Flagella: Twist and Stick, or Dodge across the Kingdoms

The flagellum organelle is an intricate multiprotein assembly best known for its rotational propulsion of bacteria. However, recent studies have expanded our knowledge of other functions in pathogenic contexts, particularly adherence and immune modulation, e.g., for Salmonella enterica, Campylobacter jejuni, Pseudomonas aeruginosa, and Escherichia coli. Flagella-mediated adherence is important in host colonisation for several plant and animal pathogens, but the specific interactions that promote flagella binding to such diverse host tissues has remained elusive. Recent work has shown that the organelles act like probes that find favourable surface topologies to initiate binding. An emerging theme is that more general properties, such as ionic charge of repetitive binding epitopes and rotational force, allow interactions with plasma membrane components. At the same time, flagellin monomers are important inducers of plant and animal innate immunity: variation in their recognition impacts the course and outcome of infections in hosts from both kingdoms. Bacteria have evolved different strategies to evade or even promote this specific recognition, with some important differences shown for phytopathogens. These studies have provided a wider appreciation of the functions of bacterial flagella in the context of both plant and animal reservoirs

The Second Type VI Secretion System of Pseudomonas aeruginosa Strain PAO1 Is Regulated by Quorum Sensing and Fur and Modulates Internalization in Epithelial Cells

The genome of Pseudomonas aeruginosa PAO1 contains three type VI secretion systems (T6SSs) called H1-, H2-, and H3-T6SS. The H1-T6SS secretes three identified toxins that target other bacteria, providing a fitness advantage for P. aeruginosa, and likely contributes to bacterial pathogenesis in chronic infections. However, no specific substrates or defined roles have been described for the two other systems. Here, we demonstrate that the expression of H2-T6SS genes of strain PAO1 is up-regulated during the transition from exponential to stationary phase growth and regulated by the Las and Rhl quorum sensing systems. In addition, we identify two putative Fur boxes in the promoter region and find that H2-T6SS transcription is negatively regulated by iron. We also show that the H2-T6SS system enhances bacterial uptake into HeLa cells (75% decrease in internalization with a H2-T6SS mutant) and into lung epithelial cells through a phosphatidylinositol 3-kinase-dependent pathway that induces Akt activation in the host cell (50% decrease in Akt phosphorylation). Finally, we show that H2-T6SS plays a role in P. aeruginosa virulence in the worm model. Thus, in contrast to H1-T6SS, H2-T6SS modulates interaction with eukaryotic host cells. Together, T6SS can carry out different functions that may be important in establishing chronic P. aeruginosa infections in the human host

Co się dzieje w wodach jezior Warnowo, Rabiąż, Czajcze i Domysłowskie w Wolińskim Parku Narodowym podczas stagnacji letnich?

In 2007, 2008 and 2010, water temperature and water saturation by O2 profiles were determined in summer in the Warnowo, Rabiaz, Czajcze and Domyslowskie Lakes interconnected by inlets being situated within the Wolin National Park in the Warnowo-Kolczewo Lake District on the Wolin Island. The occurrence of homothermy and practically constant water oxygenation from 0.5 m below the surface to 0.5 m above the bottom, with the waters under analysis being characterised by strong oxygen deficiency which differed however in consecutive lakes. The results of determinations of general parameters, biogenic substance concentrations and mineralisation indices also showed small but yet clear differences in the chemistry of the lakes under analysis, which was connected with different anthropogenic pressure on respective ecosystems and limitation of the water flow through consecutive lakes down the drainage basin. It was showed that the occurrence of low water saturation by O2 in the body of water of the lakes under analysis was connected with progressive dystrophication of the analysed ecosystems, being manifested as exuberant growth of rush vegetation and, first of all, floating plants.W latach 2007, 2008 i 2010 w okresach letnich wyznaczano profile temperaturowe i natlenienia wód w połączonych ze sobą przesmykami jeziorach Warnowo, Rabiąż, Czajcze i Domysłowskie leżących w granicach Wolińskiego Parku Narodowego na wyspie Wolin na Pojezierzu Warnowsko-Kołczewskim. Wykazano występowanie homotermii i praktycznie stałego natlenienia wód od 0.5 m od powierzchni do 0.5 m powyżej dna, przy czym badane wody cechowały się zdecydowanym niedotlenieniem, które było jednakże w kolejnych jeziorach zróżnicowane. Wyniki oznaczeń wskaźników ogólnych, stężeń biogenów i wskaźników mineralizacji, wskazywały także na niewielkie, niemniej wyraźne zróżnicowanie chemizmu badanych jezior, co było związane ze zróżnicowaniem antropopresji na poszczególne ekosystemy oraz z ograniczeniem przepływu wód przez kolejne ww. jeziora w dół zlewni. Wskazano, że występowanie niskiego natlenienia wód w toni wodnej badanych jezior związane było z postępującą dystrofizacją badanych ekosystemów jeziornych, uwidaczniającą się jako bujny rozwój roślinności szuwarowej i przede wszystkim roślinności pływającej