Effective dynamics of microorganisms that interact with their own trail

Like ants, some microorganisms are known to leave trails on surfaces to communicate. We explore how trail-mediated self-interaction could affect the behavior of individual microorganisms when diffusive spreading of the trail is negligible on the timescale of the microorganism using a simple phenomenological model for an actively moving particle and a finite-width trail. The effective dynamics of each microorganism takes on the form of a stochastic integral equation with the trail interaction appearing in the form of short-term memory. For moderate coupling strength below an emergent critical value, the dynamics exhibits effective diffusion in both orientation and position after a phase of superdiffusive reorientation. We report experimental verification of a seemingly counterintuitive perpendicular alignment mechanism that emerges from the model.Comment: new figure with experimental results; expanded appendi

Dynamics of confined water reconstructed from inelastic x-ray scattering measurements of bulk response functions

Nanoconfined water and surface-structured water impacts a broad range of fields. For water confined between hydrophilic surfaces, measurements and simulations have shown conflicting results ranging from “liquidlike” to “solidlike” behavior, from bulklike water viscosity to viscosity orders of magnitude higher. Here, we investigate how a homogeneous fluid behaves under nanoconfinement using its bulk response function: The Green's function of water extracted from a library of S(q,ω) inelastic x-ray scattering data is used to make femtosecond movies of nanoconfined water. Between two confining surfaces, the structure undergoes drastic changes as a function of surface separation. For surface separations of ≈9 Å, although the surface-associated hydration layers are highly deformed, they are separated by a layer of bulklike water. For separations of ≈6 Å, the two surface-associated hydration layers are forced to reconstruct into a single layer that modulates between localized “frozen’ and delocalized “melted” structures due to interference of density fields. These results potentially reconcile recent conflicting experiments. Importantly, we find a different delocalized wetting regime for nanoconfined water between surfaces with high spatial frequency charge densities, where water is organized into delocalized hydration layers instead of localized hydration shells, and are strongly resistant to `freezing' down to molecular distances (<6 Å)

Electrostatics of Rigid Polyelectrolytes

Abstract The organization of rigid biological polyelectrolytes by multivalent ions and macroions are important for many fundamental problems in biology and biomedicine, such as cytoskeletal regulation and antimicrobial sequestration in cystic fibrosis. These polyelectrolytes have been used as model systems for understanding electrostatics in complex fluids. Here, we review some recent results in theory, simulations, and experiments. © 2007 Elsevier Ltd. All rights reserved. Electrostatics is important in biology because all nucleic acids and virtually all proteins and membranes are charged. Electrostatic interactions in water however are qualitatively different from those in a vacuum or a dielectric. The starting point for understanding these interactions is usually mean-field theories like the Poisson-Boltzmann (PB) formalism and their approximations, which are routinely employed in colloid science and computational biology. It can for example be used to computationally estimate the distribution of counterions around realistic models of biological macromolecules. This approximate approach, however, systematically ignores counterion correlations and finite ion sizes. (Recent work suggests that a partial cancellation between these two effects result in approximate agreement with experiments [1 •• ].) Within the PB description, like-charged objects such as polyelectrolytes always repel, in accord with intuition. In systems with strong electrostatic interactions (ex: high surface charge densities, multivalent ions), interactions between polyelectrolytes are controlled by the organization and dynamics of the condensed ions surrounding the polyelectrolyte. For example, using the hypernetted chain approximation, Kjellander and Marcelja •• ]. It is generally agreed that condensation of polyelectrolytes by multivalent ions or macroions is important for many fundamental problems in biology and biomedicine. One wellknown series of examples is nucleic acid packaging in viruses, bacteria, chromosomes, and artificial gene delivery systems [5 • ] In the last 10 years, theoretical investigations have focused on the electrostatic behavior of highly-charged polyelectrolytes that cannot be explained by mean-fields, such as overcharging, the collapse behavior of the polyelectrolyte itself, as well as the existence and form of multivalent ion induced like-charge attraction, using approaches such as density functional theories, integral equations, field theoretical calculations, as well as others. A number of excellent reviews with comprehensive references have been published [21 recent work on the structure, interactions, and phase behavior of primarily rigid polyelectrolytes. Rigid polyelectrolytes Anionic rigid biopolymers have been recently used as experimental systems for polyelectrolyte electrostatics. Due to their large persistence lengths (Nμm), they can be thought of as idealized charged rods, and are well-suited for comparison with theory. For example, the addition of divalent cations to a solution of anionic F-actin filaments will drive the ordering of close-packed bundles of twisted filaments [25 • ]. In the case of microtubules, a polymorphism of bundle structures can be formed via multivalent ions. Hexagonal bundles with controllable diameters are formed via interactions with trivalent and higher valence ions, whereas &apos;living necklace&apos; bundles with linear, branched, and looped morphologies are formed with divalent ions [26 • ] •• ]. Using a family of homologous diamine ions, &apos;dumbbell&apos;-shaped molecules with two cationic amine (+1) groups connected by a spacer of variable length, it was experimentally shown that the small divalent diamines condense M13 virus polyelectrolyte rods while the larger divalent diamines cannot. Moreover, the addition of a single CH 2 group to the spacer can enforce a transition between condensing and non-condensing behavior [34 • ]. A rough empirical criterion for condensation using these prototypical &apos;dumbbell&apos; ionic linkers was proposed, but clearly a rigorous microscopic understanding is still lacking. Phase behavior of polyelectrolytes Counterion-induced attractions strongly impinge on polyelectrolyte phase behavior. For example, the mechanisms described above for multivalent ion induced polyelectrolyte attraction are all relatively short-ranged, while the imperfectly compensated polyelectrolyte rods are mutually repulsive at long-range. The competition between long-range electrostatic repulsion and shortrange attractions can drive the formation of a rich polymorphism of structures. As a function of increasing divalent ion concentration, the global organization of cytoskeletal F-actin rods can convert between different liquid crystalline phases with different symmetries and packing densities. F-actin rods in isotropic or nematic phases will both organize into a lamellar liquid crystalline network phase of crosslinked rafts before fully condensing into bundles composed of close-packed F-actin rods [35 • ]. Interestingly, this liquid crystalline network phase can exist at physiological concentrations of divalent ions, which suggests that it may play a role in cytoskeletal organization. The physics of multi-axial liquid crystalline gels and networks have been engaged theoretically in a number of studies [36 •• 37-40]. In the presence of strong linkers such as multivalent ions that can form crosslinks between polyelectrolyte rods, where it is possible to effectively maintain a highdensity of repulsive rods, the repulsive interactions responsible for the orientational behavior are expected to be strong since the rods forced into proximity via crosslinking. Bruinsma extended the Onsager theory of nematic liquid crystals to rod-like polyelectrolytes crosslinked by multivalent ions, and found that a range of exotic multi-axial liquid crystalline phases can exist near regions of phase coexistence between the isotropic phase and dense bundle phase Since counterions play a central role in the generation of inter-polyelectrolyte forces, it is important to be able to probe their spatial distribution, correlations, and dynamics. In the last few years, progress has been made in this area. Role of counterions Although experiments show unambiguously that an attractive interaction exists, there has been little done on measuring actual counterion correlations, which are necessary for generating attractions. The organization of divalent Ba ions on actin filaments was studied using synchrotron x-ray diffraction [25 • ]. Interestingly, the counterions do not form a lattice that simply follows actin&apos;s helical symmetry; rather, they organize into onedimensional (1-D) counterion density waves (CDW) parallel to the actin filaments. Each monomer has a heterogeneous charge distribution, which is repeated along the symmetry a 13/6 helix, or 13 monomers in 6 full helical turns. The 1-D counterion density wave is coupled to torsional deformations of the oppositely charged actin polyelectrolyte, so that attractions are optimized via charge alignment with the counterion domains. It will be interesting to see how this counterion organization is modified under different conditions. For example, it has been shown that the structure of a counterion lattice within a condensed polyelectrolyte rod phase undergoes a series of shearing transitions as the spacing between the rods decreases [44 • ]. This general theme of a coupled mode between counterion density changes and polyelectrolyte distortions can also be seen in recent work on DNA. Kornyshev and Leikin developed a theory of interactions between DNA with explicitly defined helical charge patterns [45 •• ]. It was proposed that an &apos;electrostatic zipper&apos; can form when multivalent cations adsorb in the major groove of one DNA chain, and interact with the protrusive anionic ridges of the sugar-phosphate backbone on an adjacent DNA chain. Within this theoretical framework, it was shown that counterion-induced aggregation of DNA can be accompanied by significant torsional deformations of the DNA helix, in order to maintain registry between opposing DN

Cooperativity and Frustration in Protein-Mediated Parallel Actin Bundles

We examine the mechanism of bundling of cytoskeletal actin filaments by two representative bundling proteins, fascin and espin. Small-angle X-ray studies show that increased binding from linkers drives a systematic \textit{overtwist} of actin filaments from their native state, which occurs in a linker-dependent fashion. Fascin bundles actin into a continuous spectrum of intermediate twist states, while espin only allows for untwisted actin filaments and fully-overtwisted bundles. Based on a coarse-grained, statistical model of protein binding, we show that the interplay between binding geometry and the intrinsic \textit{flexibility} of linkers mediates cooperative binding in the bundle. We attribute the respective continuous/discontinous bundling mechanisms of fascin/espin to differences in the stiffness of linker bonds themselves.Comment: 5 pages, 3 figures, figure file has been corrected in v

Extended hopanoid loss reduces bacterial motility and surface attachment, and leads to heterogeneity in root nodule growth kinetics in a Bradyrhizobium-Aeschynomene symbiosis

Hopanoids are steroid-like bacterial lipids that enhance membrane rigidity and promote bacterial growth under diverse stresses. Roughly 10% of bacteria contain genes involved in hopanoid biosynthesis, and these genes are particularly conserved in plant-associated organisms. We previously found that the extended class of hopanoids (C35) in the nitrogen-fixing soil bacterium Bradyrhizobium diazoefficiens promotes its root nodule symbiosis with the tropical legume Aeschynomene afraspera. By quantitatively modeling root nodule development, we identify independent consequences of extended hopanoid loss in the initiation of root nodule formation and in the rate of root nodule maturation. In vitro studies demonstrate that extended hopanoids support B. diazoefficiens motility and surface attachment, which may correlate with stable root colonization in planta. Confocal microscopy of maturing root nodules reveals that root nodules infected with extended hopanoid-deficient B. diazoefficiens contain unusually low densities of bacterial symbionts, indicating that extended hopanoids are necessary for persistent, high levels of host infection

Functional Reciprocity of Amyloids and Antimicrobial Peptides: Rethinking the Role of Supramolecular Assembly in Host Defense, Immune Activation, and Inflammation

Pathological self-assembly is a concept that is classically associated with amyloids, such as amyloid-β (Aβ) in Alzheimer's disease and α-synuclein in Parkinson's disease. In prokaryotic organisms, amyloids are assembled extracellularly in a similar fashion to human amyloids. Pathogenicity of amyloids is attributed to their ability to transform into several distinct structural states that reflect their downstream biological consequences. While the oligomeric forms of amyloids are thought to be responsible for their cytotoxicity via membrane permeation, their fibrillar conformations are known to interact with the innate immune system to induce inflammation. Furthermore, both eukaryotic and prokaryotic amyloids can self-assemble into molecular chaperones to bind nucleic acids, enabling amplification of Toll-like receptor (TLR) signaling. Recent work has shown that antimicrobial peptides (AMPs) follow a strikingly similar paradigm. Previously, AMPs were thought of as peptides with the primary function of permeating microbial membranes. Consistent with this, many AMPs are facially amphiphilic and can facilitate membrane remodeling processes such as pore formation and fusion. We show that various AMPs and chemokines can also chaperone and organize immune ligands into amyloid-like ordered supramolecular structures that are geometrically optimized for binding to TLRs, thereby amplifying immune signaling. The ability of amphiphilic AMPs to self-assemble cooperatively into superhelical protofibrils that form structural scaffolds for the ordered presentation of immune ligands like DNA and dsRNA is central to inflammation. It is interesting to explore the notion that the assembly of AMP protofibrils may be analogous to that of amyloid aggregates. Coming full circle, recent work has suggested that Aβ and other amyloids also have AMP-like antimicrobial functions. The emerging perspective is one in which assembly affords a more finely calibrated system of recognition and response: the detection of single immune ligands, immune ligands bound to AMPs, and immune ligands spatially organized to varying degrees by AMPs, result in different immunologic outcomes. In this framework, not all ordered structures generated during multi-stepped AMP (or amyloid) assembly are pathological in origin. Supramolecular structures formed during this process serve as signatures to the innate immune system to orchestrate immune amplification in a proportional, situation-dependent manner

Functional Reciprocity of Amyloids and Antimicrobial Peptides: Rethinking the Role of Supramolecular Assembly in Host Defense, Immune Activation, and Inflammation

Pathological self-assembly is a concept that is classically associated with amyloids, such as amyloid-β (Aβ) in Alzheimer's disease and α-synuclein in Parkinson's disease. In prokaryotic organisms, amyloids are assembled extracellularly in a similar fashion to human amyloids. Pathogenicity of amyloids is attributed to their ability to transform into several distinct structural states that reflect their downstream biological consequences. While the oligomeric forms of amyloids are thought to be responsible for their cytotoxicity via membrane permeation, their fibrillar conformations are known to interact with the innate immune system to induce inflammation. Furthermore, both eukaryotic and prokaryotic amyloids can self-assemble into molecular chaperones to bind nucleic acids, enabling amplification of Toll-like receptor (TLR) signaling. Recent work has shown that antimicrobial peptides (AMPs) follow a strikingly similar paradigm. Previously, AMPs were thought of as peptides with the primary function of permeating microbial membranes. Consistent with this, many AMPs are facially amphiphilic and can facilitate membrane remodeling processes such as pore formation and fusion. We show that various AMPs and chemokines can also chaperone and organize immune ligands into amyloid-like ordered supramolecular structures that are geometrically optimized for binding to TLRs, thereby amplifying immune signaling. The ability of amphiphilic AMPs to self-assemble cooperatively into superhelical protofibrils that form structural scaffolds for the ordered presentation of immune ligands like DNA and dsRNA is central to inflammation. It is interesting to explore the notion that the assembly of AMP protofibrils may be analogous to that of amyloid aggregates. Coming full circle, recent work has suggested that Aβ and other amyloids also have AMP-like antimicrobial functions. The emerging perspective is one in which assembly affords a more finely calibrated system of recognition and response: the detection of single immune ligands, immune ligands bound to AMPs, and immune ligands spatially organized to varying degrees by AMPs, result in different immunologic outcomes. In this framework, not all ordered structures generated during multi-stepped AMP (or amyloid) assembly are pathological in origin. Supramolecular structures formed during this process serve as signatures to the innate immune system to orchestrate immune amplification in a proportional, situation-dependent manner

Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation

Bacterial biofilms are communities of bacteria that exist as aggregates that can adhere to surfaces or be free-standing. This complex, social mode of cellular organization is fundamental to the physiology of microbes and often exhibits surprising behavior. Bacterial biofilms are more than the sum of their parts: single-cell behavior has a complex relation to collective community behavior, in a manner perhaps cognate to the complex relation between atomic physics and condensed matter physics. Biofilm microbiology is a relatively young field by biology standards, but it has already attracted intense attention from physicists. Sometimes, this attention takes the form of seeing biofilms as inspiration for new physics. In this roadmap, we highlight the work of those who have taken the opposite strategy: we highlight the work of physicists and physical scientists who use physics to engage fundamental concepts in bacterial biofilm microbiology, including adhesion, sensing, motility, signaling, memory, energy flow, community formation and cooperativity. These contributions are juxtaposed with microbiologists who have made recent important discoveries on bacterial biofilms using state-of-the-art physical methods. The contributions to this roadmap exemplify how well physics and biology can be combined to achieve a new synthesis, rather than just a division of labor

A Hierarchical Cascade of Second Messengers Regulates Pseudomonas aeruginosa Surface Behaviors

Biofilms are surface-attached multicellular communities. Using single-cell tracking microscopy, we showed that apilY1 mutant of Pseudomonas aeruginosa is defective in early biofilm formation. We leveraged the observation that PilY1 pro- tein levels increase on a surface to perform a genetic screen to identify mutants altered in surface-grown expression of this pro- tein. Based on our genetic studies, we found that soon after initiating surface growth, cyclic AMP (cAMP) levels increase, depen- dent on PilJ, a chemoreceptor-like protein of the Pil-Chp complex, and the type IV pilus (TFP). cAMP and its receptor protein Vfr, together with the FimS-AlgR two-component system (TCS), upregulate the expression of PilY1 upon surface growth. FimS and PilJ interact, suggesting a mechanism by which Pil-Chp can regulate FimS function. The subsequent secretion of PilY1 is dependent on the TFP assembly system; thus, PilY1 is not deployed until the pilus is assembled, allowing an ordered signaling cascade. Cell surface-associated PilY1 in turn signals through the TFP alignment complex PilMNOP and the diguanylate cyclase SadC to activate downstream cyclic di-GMP (c-di-GMP) production, thereby repressing swarming motility. Overall, our data support a model whereby P. aeruginosa senses the surface through the Pil-Chp chemotaxis-like complex, TFP, and PilY1 to reg- ulate cAMP and c-di-GMP production, thereby employing a hierarchical regulatory cascade of second messengers to coordinate its program of surface behaviors