Evolution of resistance and virulence in plant-herbivore and plant-pathogen interactions

Herbivores and pathogens often attack or infect the same plant parts, and the same plant traits can affect the likelihood and degree of damage. Research on plant-herbivore and plant-pathogen interactions in natural systems have, however, proceeded largely independently of each other. Our understanding of both types of plant-enemy interaction would be enhanced by greater exposure of researchers to developments in both disciplines and by more studies of interactions between pathogen and herbivore species associated with the same hosts.     

Surface plasmon resonance spectroscopy: an emerging tool for the study of peptide-membrane interactions

The interactions between peptides and membranes mediate a wide variety of biological processes, and characterization of the molecular details of these interactions is central to our understanding of cellular events such as protein trafficking, cellular signaling and ion-channel formation. A wide variety of biophysical techniques have been combined with the use of model membrane systems to study peptide-membrane interactions, and have provided important information on the relationship between membrane-active peptide structure and their biological function. However, what has generally not been reported is a detailed analysis of the affinity of peptide for different membrane systems, which has largely been due to the difficulty in obtaining this information. To address this issue, surface plasmon resonance (SPR) spectroscopy has recently been applied to the study of biomembrane-based systems using both planar mono- or bilayers or liposomes. This article provides an overview of these recent applications that demonstrate the potential of SPR to enhance our molecular understanding of membrane-mediated peptide function.     

Interactions of amphipathic CPPs with model membranes

We have investigated the interactions between two carrier peptides and model membrane systems as well as the conformational consequences of these interactions. Studies performed with lipid monolayers at the air-water interface have enabled identification of the nature of the lipid-peptide interactions and characterization of the influence of phospholipids on the ability of these peptides to penetrate into lipidic media. Penetration experiments reveal that both peptides interact strongly with phospholipids. Conformational investigations indicate that the lipid-peptide interaction govern the conformational state of the peptides. Based on the ability of both peptides to promote ion permeabilization of both natural and artificial membranes, we propose a model illustrating the translocation process. For MPG, it is based on the formation of a β-barrel pore-like structure, while for Pep-1, it is based on association of helices.     

Pathfinding in a large vertebrate axon tract: isotypic interactions guide retinotectal axons at multiple choice points

Navigating axons respond to environmental guidance signals, but can also follow axons that have gone before - pioneer axons. Pioneers have been studied extensively in simple systems, but the role of axon-axon interactions remains largely unexplored in large vertebrate axon tracts, where cohorts of identical axons could potentially use isotypic interactions to guide each other through multiple choice points. Furthermore, the relative importance of axon-axon interactions compared with axon-autonomous receptor function has not been assessed. Here, we test the role of axon-axon interactions in retinotectal development, by devising a technique to selectively remove or replace early-born retinal ganglion cells (RGCs). We find that early RGCs are both necessary and sufficient for later axons to exit the eye. Furthermore, introducing misrouted axons by transplantation reveals that guidance from eye to tectum relies heavily on interactions between axons, including both pioneer-follower and community effects. We conclude that axon-axon interactions and ligand-receptor signaling have co-equal roles, cooperating to ensure the fidelity of axon guidance in developing vertebrate tracts.     

Interactions of amphipathic CPPs with model membranes

We have investigated the interactions between two carrier peptides and model membrane systems as well as the conformational consequences of these interactions. Studies performed with lipid monolayers at the air-water interface have enabled identification of the nature of the lipid-peptide interactions and characterization of the influence of phospholipids on the ability of these peptides to penetrate into lipidic media. Penetration experiments reveal that both peptides interact strongly with phospholipids. Conformational investigations indicate that the lipid-peptide interaction govern the conformational state of the peptides. Based on the ability of both peptides to promote ion permeabilization of both natural and artificial membranes, we propose a model illustrating the translocation process. For MPG, it is based on the formation of a beta-barrel pore-like structure, while for Pep-1, it is based on association of helices.     

Guidepost cells.

Guidepost cells, as classically defined in the grasshopper embryo have only rarely been found in other systems. If the concept of guidepost cells is expanded, recognizing that any special role of specific cells in axon guidance is a function of the entire landscape in which axons are growing, and that growth cone--guidepost interactions may share mechanisms with many other cell--cell interactions, then numerous examples are found in both the peripheral and central nervous systems of many species.     

Neuronal interactions between neuropeptide Y (NPY) and catecholaminergic systems in the rat arcuate nucleus as shown by dual immunocytochemistry

Several recent studies have suggested interactions between catecholamine (CA) and neuropeptide Y (NPY) neuronal systems in the rat brain. In order to obtain morphological evidence for such CA/NPY interactions in the arcuate nucleus, we have used a double immunostaining procedure using an anti-tyrosine hydroxylase (TH) antiserum as a marker for catecholamine neurons and an anti-NPY antiserum. This double staining, where the first staining is silver-gold intensified, was detectable at both light and electron microscopic levels. In semi-thin sections, a substantial overlap and close proximity of TH-immunopositive neurons and NPY neuronal elements could be seen within the arcuate nucleus. At the electron microscopic level, direct appositions between TH- and NPY-immunoreactive structures could be detected. These appositions were of axosomatic, axodendritic or axoaxonic types without any synaptic membrane differentiation. Moreover, direct appositions between NPY-immunoreactive structures have also been observed. This morphological study showing appositions between TH and NPY neuronal systems suggest direct interactions between these two systems in the arcuate nucleus.     

Surface plasmon resonance spectroscopy in the study of membrane-mediated cell signalling.

Peptide-membrane interactions contribute to many important biological processes such as cellular signaling, protein trafficking and ion-channel formation. During receptor-mediated signalling, activated intracellular signalling molecules are often recruited into receptor-induced signaling complexes at the cytoplasmic surface of the cell membrane. Such recruitment can depend upon protein-protein and protein-lipid interactions as well as protein acylation. A wide variety of biophysical techniques have been combined with the use of model membrane systems to study these interactions and have provided important information on the relationship between the structure of these proteins involved in cell signalling and their biological function. More recently, surface plasmon resonance (SPR) spectroscopy has also been applied to the study of biomembrane-based systems using both planar mono- or bilayers or liposomes. This article provides an overview of these recent applications, which demonstrate the potential of SPR to enhance our molecular understanding of membrane-mediated cellular signalling.     

A combined yeast/bacteria two-hybrid system: development and evaluation

Two-hybrid screening is a standard method used to identify and characterize protein-protein interactions and has become an integral component of many proteomic investigations. The two-hybrid system was initially developed using yeast as a host organism. However, bacterial two-hybrid systems have also become common laboratory tools and are preferred in some circumstances, although yeast and bacterial two-hybrid systems have never been directly compared. We describe here the development of a unified yeast and bacterial two-hybrid system in which a single bait expression plasmid is used in both organismal milieus. We use a series of leucine zipper fusion proteins of known affinities to compare interaction detection using both systems. Although both two-hybrid systems detected interactions within a comparable range of interaction affinities, each demonstrated unique advantages. The yeast system produced quantitative readout over a greater dynamic range than that observed with bacteria. However, the phenomenon of "autoactivation" by baits was less of a problem in the bacterial system than in the yeast. Both systems identified physiological interactors for a library screen with a cI-Ras test bait; however, non-identical interactors were obtained in yeast and bacterial screens. The ability to rapidly shift between yeast and bacterial systems provided by these new reagents should provide a marked advantage for two-hybrid investigations. In addition, the modified expression vectors we describe in this report should be useful for any application requiring facile expression of a protein of interest in both yeast and bacteria.     

The application of yeast hybrid systems in protein interaction analysis

Yeast hybrid systems have been widely used due to their convenience and low cost. Based on these systems, many methods have been developed to analyze protein–protein, protein–DNA and protein–RNA interactions. In this paper, we are reviewing these different yeast hybrid systems. According to the number of hybrid proteins, yeast hybrid systems can be divided into three categories, yeast one-hybrid, yeast two-hybrid and yeast three-hybrid systems. Alternatively, yeast hybrid systems can be categorized according to the subcellular localization of the protein interaction process in the cell into nuclear protein–protein interactions, cytosol protein–protein interactions and membrane protein–protein interactions. Throughout the review, we focus on the progress and limitations of each yeast hybrid system over the recent years.     

Substrate-mediated nucleic acid delivery from self-assembled monolayers

Substrate-mediated nucleic acid (NA) delivery involves the immobilization of NAs or NA delivery vehicles to biomaterials for localized transfection of cells. Self-assembled monolayers (SAMs) offer an easy system to immobilize delivery vectors. SAMs form well-defined surfaces; therefore, the effect of surface composition on vector immobilization and transfection efficiency can also be studied. To date, the most effective SAM-mediated delivery systems have utilized nonspecific interactions for immobilization; however, systems that rely on specific interactions between vector and surface can impart higher control of spatial and/or temporal delivery. This review summarizes systems that use both specific and nonspecific interactions for gene delivery from SAMs; highlights progress and remaining challenges; and explores other specific recognition modalities that might be employed for future applications in surface-mediated NA delivery.     

Protein recruitment systems for the analysis of protein +/- protein interactions

The yeast Saccharomyces cerevisiae serves as an excellent genetic tool for the analysis of protein +/- protein interactions. The most common system, used to date, is the two-hybrid system. Although proven very powerful, the two-hybrid system exhibits several inherent problems and limitations. Recently, two alternative systems have been described that take advantage of the fact that localization of signal transduction effectors to the inner leaflet of the plasma membrane is absolutely necessary for yeast viability. These effectors can either be the Ras guanyl nucleotide exchange factor or Ras itself. The yeast strain used in both systems is a temperature-sensitive mutant in the yeast Ras guanyl nucleotide exchange factor, CDC25. Membrane localization of these effectors is achieved via protein +/- protein interaction. Each system can be used to test interaction between known protein pairs, as well as for isolation of novel protein interactions. Described here are the scientific and technical steps to be considered for both protein recruitment systems.     

Interactions between a detrital resource pulse and a detritivore community

Detritivore communities influence the decomposition of detrital resources in virtually all natural systems. Conversely, detrital resources can also have considerable bottom-up effects on detritivore communities. While many investigations have examined detritivory and decomposition processes, few have considered interactions between detritivores and detritus as concurrent processes in the same system, or in the context of natural detrital pulses. In many systems, resource pulses contribute substantial detrital inputs to belowground systems. These detrital pulses may influence interactions between the detritivore community and detrital decomposition. I conducted field experiments to investigate interactions between detrital resource pulses of periodical cicada (Magicicada spp.) carcasses and scavenging detritivorous macroarthropods. Cicada litterfall pulses influenced several broad groups in the macroarthropod community, including relatively specialized necrophilous taxa and relatively generalized detritivores, omnivores and predators. Conversely, detritivore activity increased the rate of cicada carcass decomposition by 4,082% compared to caged control carcasses. These results suggest that interactions between pulses of cicada detritus and the detritivore community influence both the persistence of ephemeral detrital resources, and the distribution, abundance and behavior of detritivore populations.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

AFM for structure and dynamics of biomembranes

We review structure and dynamic measurements of biomembranes by atomic force microscopy (AFM). We focus mainly on studies involving supported lipid bilayers (SLBs), particularly formation by vesicle rupture on flat and corrugated surfaces, nucleation and growth of domains in phase-separated systems, anesthetic-lipid interactions, and protein/peptide interactions in multicomponent systems. We show that carefully designed experiments along with real-time AFM imaging with superior lateral and z resolution (0.1 nm) have revealed quantitative details of the mechanisms and factors controlling vesicle rupture, domain shape and size, phase transformations, and some model biological interactions. The AFM tip can also be used as a mechanical transducer and incorporated in electrochemical measurements of membrane components; therefore, we touch on these important applications in both model and cell membranes.     

A synthesis of subdisciplines: predator–prey interactions, and biodiversity and ecosystem functioning

The last 15 years has seen parallel surges of interest in two research areas that have rarely intersected: biodiversity and ecosystem functioning (BEF), and multispecies predator–prey interactions (PPI). Research addressing role of biodiversity in ecosystem functioning has focused primarily on single trophic‐level systems, emphasizing additive effects of diversity that manifest through resource partitioning and the sampling effect. Conversely, research addressing predator–prey interactions has focused on two trophic‐level systems, emphasizing indirect and non‐additive interactions among species. Here, we use a suite of consumer‐resource models to organize and synthesize the ways in which consumer species diversity affects the densities of both resources and consumer species. Specifically, we consider sampling effects, resource partitioning, indirect effects caused by intraguild interactions and non‐additive effects. We show that the relationship between consumer diversity and the density of resources and consumer species are broadly similar for systems with one vs. two trophic levels, and that indirect and non‐additive interactions generally do little more than modify the impacts of diversity established by the sampling effect and resource partitioning. The broad similarities between systems with one vs. two trophic levels argue for greater communication between researchers studying BEF, and researchers studying multispecies PPI.     

Lateral organization of biological membranes

The lateral organization of biological membranes is of great importance in many biological processes, both for the formation of specific structures such as super-complexes and for function as observed in signal transduction systems. Over the last years, AFM studies, particularly of bacterial photosynthetic membranes, have revealed that certain proteins are able to segregate into functional domains with a specific organization. Furthermore, the extended non-random nature of the organization has been suggested to be important for the energy and redox transport properties of these specialized membranes. In the work reported here, using a coarse-grained Monte Carlo approach, we have investigated the nature of interaction potentials able to drive the formation and segregation of specialized membrane domains from the rest of the membrane and furthermore how the internal organization of the segregated domains can be modulated by the interaction potentials. These simulations show that long-range interactions are necessary to allow formation of membrane domains of realistic structure. We suggest that such possibly non-specific interactions may be of great importance in the lateral organization of biological membranes in general and in photosynthetic systems in particular. Finally, we consider the possible molecular origins of such interactions and suggest a fundamental role for lipid-mediated interactions in driving the formation of specialized photosynthetic membrane domains. We call these lipid-mediated interactions a ‘lipophobic effect.’     

Unilamellar DMPC vesicles in aqueous glycerol: preferential interactions and thermochemistry

Glycerol is accumulated in response to environmental stresses in a diverse range of organisms. Understanding of favorable in vivo effects of this solute requires insight into its interactions with biological macromolecules, and one access to this information is the quantification of so-called preferential interactions in glycerol-biopolymer solutions. For model membrane systems, preferential interactions have been discussed, but not directly measured. Hence, we have applied a new differential vapor pressure equipment to quantify the isoosmotic preferential binding parameter, Gamma( micro 1), for systems of unilamellar vesicles of DMPC in aqueous glycerol. It is found that Gamma( micro 1) decreases linearly with the glycerol concentration with a slope of -0.14 +/- 0.014 per molal. This implies that glycerol is preferentially excluded from the membrane-solvent interface. Calorimetric investigations of the same systems showed that the glycerol-DMPC interactions are weakly endothermic, and the temperature of the main phase transition increases slightly (0.16 degrees C per molal) with the glycerol concentration. The results are discussed with respect to a molecular picture which takes into account both the partitioning of glycerol into the membrane and the preferential exclusion from the hydration layer, and it is concluded that the latter effect contributes about four times stronger than the former to the net interaction.     

Computational structural analysis of protein interactions and networks

Protein interactions have been at the focus of computational biology in recent years. In particular, interest has come from two different communities--structural and systems biology. Here, we will discuss key systems and structural biology methods that have been used for analysis and prediction of protein-protein interactions and the insight these approaches have provided on the nature and organization of protein-protein interactions inside cells.     

Analytical ultracentrifugation as a tool for studying protein interactions

The last two decades have led to significant progress in the field of analytical ultracentrifugation driven by instrumental, theoretical, and computational methods. This review will highlight key developments in sedimentation equilibrium (SE) and sedimentation velocity (SV) analysis. For SE, this includes the analysis of tracer sedimentation equilibrium at high concentrations with strong thermodynamic non-ideality, and for ideally interacting systems, the development of strategies for the analysis of heterogeneous interactions towards global multi-signal and multi-speed SE analysis with implicit mass conservation. For SV, this includes the development and applications of numerical solutions of the Lamm equation, noise decomposition techniques enabling direct boundary fitting, diffusion deconvoluted sedimentation coefficient distributions, and multi-signal sedimentation coefficient distributions. Recently, effective particle theory has uncovered simple physical rules for the co-migration of rapidly exchanging systems of interacting components in SV. This has opened new possibilities for the robust interpretation of the boundary patterns of heterogeneous interacting systems. Together, these SE and SV techniques have led to new approaches to study macromolecular interactions across the entire spectrum of affinities, including both attractive and repulsive interactions, in both dilute and highly concentrated solutions, which can be applied to single-component solutions of self-associating proteins as well as the study of multi-protein complex formation in multi-component solutions.