Testing attachment point theory: diatom attachment on microtextured polyimide biomimics

This paper explores diatom attachment to a range of laser etched polyimide surfaces to directly test 'attachment point theory'. Static bioassays were conducted on microtextured polyimide surfaces using four diatom species, Fallacia carpentariae, Nitzschia cf. paleacea, Amphora sp. and Navicula jeffreyi with cell sizes ranging from 1-14 microm. The microtextured polyimides were modelled from natural fouling resistant bivalve surfaces and had wavelengths above, below and at the same scale as the diatom cell sizes. Diatoms attached in significantly higher numbers to treatments where the numbers of attachment points was highest. The lowest diatom attachment occurred where cells were slightly larger than the microtexture wavelength, resulting in only two theoretical points of attachment. The results support attachment point theory and highlight the need to address larval/cell size in relation to the number of attachment points on a surface. Further studies examining a range of microtexture scales are needed to apply attachment point theory to a suite of fouling organisms and to develop structured surfaces to control the attachment and development of fouling communities.     

Topographic cues guide the attachment of diatom cells and algal zoospores

Surface topography plays a key role in the colonization of substrata by the colonizing stages of marine fouling organisms. For the innovation of marine antifouling coatings, it is essential to understand how topographic cues affect the settlement of these organisms. In this study, tapered, spiked microstructures and discrete honeycombs of varying feature dimensions were designed and fabricated in order to examine the influence of topography on the attachment of zoospores of the green macroalga Ulva linza and cells of the diatom (microalga) Navicula incerta. Contrasting results were obtained with these two species of algae. Indeed, the preferred location of cells of N. incerta was dominated by attachment point theory, which suggested a positive correlation between the density of cells adhering and the amount of available attachment points, while the settlement of spores of U. linza was mainly regulated by both Wenzel roughness and local binding geometry.     

The effects of fine-scale substratum roughness on diatom community structure in estuarine biofilms

Benthic diatoms are a major component of biofilms that form on surfaces submerged in marine environments. Roughness of the underlying substratum affects the settlement of both diatoms and subsequent macrofouling colonizers. This study reports the effects of roughness on estuarine diatom communities established in situ in the Indian River Lagoon, FL, USA. Natural communities were established on acrylic panels with a range of surface roughnesses. Smoother substrata exhibited higher cell density, species richness, and diversity. Twenty-three of 58 species were found either exclusively or more abundantly on the smooth surfaces compared to one or both roughened treatments. The results suggest a greater ability of benthic diatoms to recruit and colonize smooth surfaces, which is probably explained by a higher degree of contact between the cells and the surface.     

Discerning devotion: Testing the signaling theory of religion

Religious rituals often entail significant investments of time, energy, and money, and can risk bodily harm. Instead of being evolutionarily inexplicable, such costly religious acts have been argued to be honest signals of commitment to the beliefs and values of the community, helping individuals establish good reputations and foster trusting, cooperative relationships. Most tests of this hypothesis have evaluated whether religious signalers are more prosocial; here I investigate whether signal receivers actually perceive religious signalers as such. I do this with data collected over 20 months of ethnographic fieldwork in two villages in South India, where Hindu and Christian residents engage in different modes of religious practice, including dramatic acts of firewalking and spirit possession as well as the more subtle but consistent act of worshipping at a church or temple each week. Each mode of religious practice is found to be informative of a distinct set of reputational qualities. Broadly speaking, in the long term, individuals who invest more in the religious life of the village are not only seen as more devout, but also as having a suite of prosocial, other-focused traits. In the short term, individuals who perform greater and costlier acts in the annual Hindu festival show a slight increase in the percent of villagers recognizing them as physically strong and hardworking. These results suggest that people are attending to the full suite of religious acts carried out by their peers, using these signals to discern multiple aspects of their character and intentions.     

Copepod grazing during an iron-induced diatom bloom in the Antarctic Circumpolar Current (EisenEx): I. Feeding patterns and grazing impact on prey populations

Feeding activity, selective grazing and the potential grazing impact of two dominant grazers of the Polar Frontal Zone, Calanus simillimus and Rhincalanus gigas, and of copepods < 2 mm were investigated with incubation experiments in the course of an iron fertilized diatom bloom in November 2000. All grazers were already actively feeding in the low chlorophyll waters prior to the onset of the bloom. C. simillimus maintained constant clearance rates and fed predominantly on diatoms. R. gigas and the small copepods strongly increased clearance and ingestion of diatoms in response to their enhanced availability. All grazers preyed on microzooplankton, most steadily on ciliates, confirming the view that pure herbivory appears to be the exception rather than the rule in copepod feeding. The grazers exhibited differences in feeding behavior based on selectivity indices. C. simillimus and R. gigas showed prey switching from dinoflagellates to diatoms in response to the phytoplankton bloom. All grazers most efficiently grazed on large diatoms leading to differences in daily losses for large and small species, e.g. Corethron sp. or Thalassionema nitzschioides. Species-specific diatom mortality rates due to grazing suggest that the high feeding activity of C. simillimus prior to and during the bloom played a role in shaping diatom population dynamics.     

A general theory on fish aggregation to floating objects: An alternative to the meeting point hypothesis

An immense variety of fish may, on occasions, aggregate around or beassociated with floating structures such as drifting algae, jelliedzooplankton, whales, floats or anchored fish aggregating devices (ineffect, there are over 333 fish species belonging to 96 familiesrecorded in the literature).Several hypotheses have been advanced to explain this behaviour ofpelagic fish, although the most widely accepted theory is that fish usefloating materials, to some extent, to protect themselves frompredators. However, we think that aggregation under floats may be theresult of behaviour that has evolved to safeguard the survival of eggs,larvae and juvenile stages, during dispersion to other areas. Naturalfloating structures (e.g., algae, branches of trees) drift in seacurrents that originate in places where the floating objects arefrequently found (e.g., river estuaries, coastal areas). These same seacurrents also introduce some of the planktonic production generated inthese areas into the oligotrophic pelagic environment. Fish associatedwith drifting floating structures probably feed on invertebratesassociated with the structures. However, they may also benefit from theaccumulated plankton in the converging waters. Adult fish of somemigratory species (tuna, dolphinfish, etc.) have also developed similarassociative behaviour around drifting objects for other reasons (e.g.,resting places, presence of bait fish, geographical references andschool recomposition). In this context, the meeting point hypothesis isonly applicable to one specific case, the tuna and tuna-like species.Aggregative and associative behaviour, under and around floatingdevices, may be the result of convergent behaviors that result fromdifferent motivations. However, generally this behaviour can beexplained by the fact that drifting floating objects represent a meansof reaching relatively rich areas, where larvae and juvenile fish havean increased chance of survival.     

Testing the 'free radical theory of aging' hypothesis: physiological differences in long-lived and short-lived colubrid snakes

We test the 'free radical theory of aging' using six species of colubrid snakes (numerous, widely distributed, non-venomous snakes of the family Colubridae) that exhibit long (> 15 years) or short (< 10 years) lifespans. Because the 'rate of living theory' predicts metabolic rates to be correlated with rates of aging and oxidative damage results from normal metabolic processes we sought to answer whether physiological parameters and locomotor performance (which is a good predictor of survival in juvenile snakes) mirrored the evolution of lifespans in these colubrid snakes. We measured whole animal metabolic rate (oxygen consumption Vo2), locomotor performance, cellular metabolic rate (mitochondrial oxygen consumption), and oxidative stress potential (hydrogen peroxide production by mitochondria). Longer-lived colubrid snakes have greater locomotor performance and reduced hydrogen peroxide production than short-lived species, while whole animal metabolic rates and mitochondrial efficiency did not differ with lifespan. We present the first measures testing the 'free radical theory of aging' using reptilian species as model organisms. Using reptiles with different lifespans as model organisms should provide greater insight into mechanisms of aging.     

Bone orientation and position estimation errors using Cosserat point elements and least squares methods: Application to gait

The aim of this study was to analyze the accuracy of bone pose estimation based on sub-clusters of three skin-markers characterized by triangular Cosserat point elements (TCPEs) and to evaluate the capability of four instantaneous physical parameters, which can be measured non-invasively in vivo, to identify the most accurate TCPEs. Moreover, TCPE pose estimations were compared with the estimations of two least squares minimization methods applied to the cluster of all markers, using rigid body (RBLS) and homogeneous deformation (HDLS) assumptions. Analysis was performed on previously collected in vivo treadmill gait data composed of simultaneous measurements of the gold-standard bone pose by bi-plane fluoroscopy tracking the subjects' knee prosthesis and a stereophotogrammetric system tracking skin-markers affected by soft tissue artifact. Femur orientation and position errors estimated from skin-marker clusters were computed for 18 subjects using clusters of up to 35 markers. Results based on gold-standard data revealed that instantaneous subsets of TCPEs exist which estimate the femur pose with reasonable accuracy (median root mean square error during stance/swing: 1.4/2.8 deg for orientation, 1.5/4.2 mm for position). A non-invasive and instantaneous criteria to select accurate TCPEs for pose estimation (4.8/7.3 deg, 5.8/12.3 mm), was compared with RBLS (4.3/6.6 deg, 6.9/16.6 mm) and HDLS (4.6/7.6 deg, 6.7/12.5 mm). Accounting for homogeneous deformation, using HDLS or selected TCPEs, yielded more accurate position estimations than RBLS method, which, conversely, yielded more accurate orientation estimations. Further investigation is required to devise effective criteria for cluster selection that could represent a significant improvement in bone pose estimation accuracy.     

Effect of site-directed point mutations on protein misfolding: A simulation study

A Monte Carlo simulation based sequence design method is proposed to investigate the role of site-directed point mutations in protein misfolding. Site-directed point mutations are incorporated in the designed sequences of selected proteins. While most mutated sequences correctly fold to their native conformation, some of them stabilize in other nonnative conformations and thus misfold/unfold. The results suggest that a critical number of hydrophobic amino acid residues must be present in the core of the correctly folded proteins, whereas proteins misfold/unfold if this number of hydrophobic residues falls below the critical limit. A protein can accommodate only a particular number of hydrophobic residues at the surface, provided a large number of hydrophilic residues are present at the surface and critical hydrophobicity of the core is preserved. Some surface sites are observed to be equally sensitive toward site-directed point mutations as the core sites. Point mutations with highly polar and charged amino acids increases the misfold/unfold propensity of proteins. Substitution of natural amino acids at sites with different number of nonbonded contacts suggests that both amino acid identity and its respective site-specificity determine the stability of a protein. A clash-match method is developed to calculate the number of matching and clashing interactions in the mutated protein sequences. While misfolded/unfolded sequences have a higher number of clashing and a lower number of matching interactions, the correctly folded sequences have a lower number of clashing and a higher number of matching interactions. These results are valid for different SCOP classes of proteins.     

The presence of thiolated compounds allows the immobilization of enzymes on glyoxyl agarose at mild pH values: New strategies of stabilization by multipoint covalent attachment

Highly activated glyoxyl-supports rapidly immobilize proteins at pH 10 (where the -amino groups of the Lys groups of the protein surface are very reactive), and stabilize them by multipoint covalent attachment. However, they do not immobilize proteins at pH 8. This paper shows that the enzyme immobilization at this mild pH value is possible by incubation of the enzymes in the presence of different thiolated compounds (dithiothreitol, DTT; was selected as optimal reagent). The thiolated compounds (even the not reducing ones) stabilized the imino bonds formed at pH 8 between the aldehydes in the support and the amino groups of the protein. However, thiolated compounds are unable to reduce the imino bonds or the aldehyde groups and a final reduction step (e.g., using sodium borohydride) was always necessary. After enzyme immobilization through the most reactive amino group of the protein, the further incubation of this immobilized enzyme at pH 10 would improve the reactivity of the -amino groups of the Lys residues of the protein surface. Then, an intense multipoint covalent reaction of the enzyme with the dense layer of glyoxyl groups in the support could be obtained, increasing the stability of the immobilized enzyme. Using three different industrially relevant enzymes (penicillin G acylase from Escherichia coli (PGA), lipase from Bacillus thermocatenulatus (BTL2) and glutaryl acylase from Pseudomonas sp. (GA)), new immobilized-stabilized biocatalysts of the enzymes were produced. After reduction, the preparations incubated at pH 10 were more stable than those that were only immobilized and reduced at pH 8. In the case of the PGA, this preparation was even 4–5-fold more stable than those obtained by direct immobilization at pH 10 (around 40,000–50,000-fold more stable than the soluble enzyme).     

Testing intraguild predation theory in a field system: does numerical dominance shift along a gradient of productivity?

Although ecological theory exists to predict dynamics in communities with intraguild predation (IGP), few empirical tests have examined this theory. IGP theory, in particular, predicts that when two competitors interact via IGP, with increasing resource productivity: (1) the IG predator will increase in abundance as the IG prey declines, and (2) increasing dominance of the IG predator will cause resource density to increase. Here, we provide a first test of these predictions in a field community consisting of a scale insect and its two specialist parasitoids, Aphytis melinus (the IG predator) and Encarsia perniciosi (the IG prey). The shared resource, California red scale, is a pest of citrus, and its productivity varies across a threefold range among citrus cultivars. We examined both absolute and relative densities of parasitoids along this natural gradient of scale productivity in three citrus cultivars (orange, grapefruit and lemon). Although both parasitoid species were found in all three cultivars, their abundances reflected those predicted by IGP theory: the IG prey species dominated at low productivity and the IG predator dominated at high productivity. This relationship was caused by an increase in Aphytis density with productivity. In addition, the density of scale increased with the dominance of the IG predator. These results from a field system demonstrate the important dynamic outcomes for food webs with IGP.     

Trypanosoma gambiense: Blocking ability of parasite and macrophage homogenates on attachment during phagocytosis

This study deals with the ability of the parasite and macrophage homogenates, each fractionated into soluble and insoluble parts, to block the attachment of Trypanosoma gambiense on the macrophage in the process of phagocytosis. The soluble parasite fraction and the insoluble macrophage fraction both showed a high blocking ability. However, the ability of the parasite fraction was completely lost on trypsin digestion, while that of the macrophage was not changed at all. In addition, sonication of the macrophage did not change its blocking ability.     

Effect of curli expression and hydrophobicity of Escherichia coli O157:H7 on attachment to fresh produce surfaces

Aim: To investigate the effect of curli expression on cell hydrophobicity, biofilm formation and attachment to cut and intact fresh produce surfaces. Methods and Results: Five Escherichia coli O157:H7 strains were evaluated for curli expression, hydrophobicity, biofilm formation and attachment to intact and cut fresh produce (cabbage, iceberg lettuce and Romaine lettuce) leaves. Biofilm formation was stronger when E. coli O157:H7 were grown in diluted tryptic soy broth (1 : 10). In general, strong curli‐expressing E. coli O157:H7 strains 4406 and 4407 were more hydrophobic and attached to cabbage and iceberg lettuce surfaces at significantly higher numbers than other weak curli‐expressing strains. Overall, E. coli O157:H7 populations attached to cabbage and lettuce (iceberg and Romaine) surfaces were similar (P > 0·05), indicating produce surfaces did not affect (P < 0·05) bacterial attachment. All E. coli O157:H7 strains attached rapidly on intact and cut produce surfaces. Escherichia coli O157:H7 attached preferentially to cut surfaces of all produce types; however, the difference between E. coli O157:H7 populations attached to intact and cut surfaces was not significant (P > 0·05) in most cases. Escherichia coli O157:H7 attachment and attachment strength (S_R) to intact and cut produce surfaces increased with time. Conclusions: Curli‐producing E. coli O157:H7 strains attach at higher numbers to produce surfaces. Increased attachment of E. coli O157:H7 on cut surfaces emphasizes the need for an effective produce wash to kill E. coli O157:H7 on produce. Significance and Impact of the Study: Understanding the attachment mechanisms of E. coli O157:H7 to produce surfaces will aid in developing new intervention strategies to prevent produce outbreaks.     

Substratum/bacterial interactions and larval attachment: Films and exopolysaccharides of Halomonas marina (ATCC 25374) and their effect on barnacle cyprid larvae,Balanus amphitrite Darwin

Laboratory experiments were conducted to study the interaction between adhesion of the bacterium Halomonas marina to substrata of different wettabilities, the combination of which has been demonstrated to influence the attachment response of cyprid larvae of the barnacle Balanus amphitrite. Cyprid attachment in the presence of bacterial films was shown to be inhibited when films were on polystyrene but not on tissue‐culture polystyrene or glass. Using an enzyme‐linked lectin assay, bacteria on polystyrene showed an increase in binding of the lectin concanavalin A compared to bacteria on tissue‐culture treated polystyrene, indicating a difference in surface polymers associated with H. marina when attached to different substrata. Although bacterial growth supernatants when adsorbed to polystyrene were inhibitory to barnacle attachment, exopolysaccharides, to which the lectins may be binding, were not inhibitory. The data indicate that adhesion of films of bacteria to polystyrene alters the exopolymer production by H. marina and it is suggested that this change may be involved in the inhibition of cyprid attachment. However, the inhibition of cyprid larvae does not appear to be associated with the exopolysaccharides of the bacterium.     

Ectomycorrhiza and nitrogen effects on root IAA: results contrary to current theory

Summary Indole-3-acetic acid (IAA) concentrations of mycorrhizal and non-mycorrhizal Scots pine roots under moderate and high-nitrogen nutrition were assayed using mass spectrometry with an internal standard. Contrary to current theory, IAA was lower in mycorrhizal roots than in the controls, and higher during highnitrogen nutrition.     

Natural attachment duration of nymphs of the tick Ixodes uriae (Acari: Ixodidae) on kittiwake Rissa tridactyla nestlings

Daily searches of the plumage of 62 kittiwake (Rissa tridactyla) chicks were carried out for 3 weeks to determine the attachment duration of the tick Ixodes uriae. All ticks recorded were nymphs and their mean duration of attachment was 5.2±1.7 days (n=93). Seventy-four per cent of the ticks survived to engorgement and were assumed to have fed successfully. The mean duration of attachment of successful ticks was 5.8±1.0 days (n=69), significantly longer than that of unsuccessful ticks (3.3±2.1 days, n=24). There was no difference in survival rates to engorgement between ticks attached to feathered and unfeathered parts of the body (78.3 and 79.2%, respectively), but the duration of attachment of successful ticks was significantly longer on unfeathered compared to feathered areas. There were no significant differences in the survival to engorgement or duration of attachment between ticks found on young (c.11 days) and old (>11 days) kittiwake nestlings. The attachment duration was not related to the total number of ticks found on the host or the number of ticks present in the immediate vicinity of the site of attachment. This work provides important data on the parameter of attachment durations of nymphal I. uriae on free-living kittiwakes; the data can be used for incorporation into the application of population modelling.     

Reduced point charge models of proteins: assessment based on molecular dynamics simulations

A reduced point charge distribution is used to model Ubiquitin and two complexes, Vps27 UIM-1–Ubiquitin and Barnase–Barstar. It is designed from local extrema in charge density distributions obtained from the Poisson equation applied to smoothed molecular electrostatic potentials. A variant distribution is built by locating point charges on atoms. Various charge fitting conditions are selected, i.e. from either electrostatic Amber99 (Assisted Model Building with Energy Refinement) Coulomb potential or forces, considering reference grid points located within various distances from the protein atoms, with or without separate treatment of main and side chain charges. The program GROMACS (Groningen Machine for Chemical Simulations) is used to generate Amber99SB molecular dynamics (MD) trajectories of the solvated proteins modelled using the various reduced point charge models (RPCMs) so obtained. Point charges that are not located on atoms are considered as virtual sites. Some RPCMs lead to stable MD trajectories. They, however, involve a partial loss in the protein secondary structure and lead to a less-structured solute solvation shell. The model built by fitting charges on Coulomb forces calculated at grid points ranging between 1.4 and 2.0 times the van der Waals radius of the atoms, with a separate treatment of main chain and side chain charges, appears to best approximate all-atom MD trajectories.     

Bat point counts: A novel sampling method shines light on flying bat communities

Emerging technologies based on the detection of electro‐magnetic energy offer promising opportunities for sampling biodiversity. We exploit their potential by showing here how they can be used in bat point counts—a novel method to sample flying bats—to overcome shortcomings of traditional sampling methods, and to maximize sampling coverage and taxonomic resolution of this elusive taxon with minimal sampling bias. We conducted bat point counts with a sampling rig combining a thermal scope to detect bats, an ultrasound recorder to obtain echolocation calls, and a near‐infrared camera to capture bat morphology. We identified bats with a dedicated identification key combining acoustic and morphological features, and compared bat point counts with the standard bat sampling methods of mist‐netting and automated ultrasound recording in three oil palm plantation sites in Indonesia, over nine survey nights. Based on rarefaction and extrapolation sampling curves, bat point counts were similarly effective but more time‐efficient than the established methods for sampling the oil palm species pool in our study. Point counts sampled species that tend to avoid nets and those that are not echolocating, and thus cannot be detected acoustically. We identified some bat sonotypes with near‐infrared imagery, and bat point counts revealed strong sampling biases in previous studies using capture‐based methods, suggesting similar biases in other regions might exist. Our method should be tested in a wider range of habitats and regions to assess its performance. However, while capture‐based methods allow to identify bats with absolute and internal morphometry, and unattended ultrasound recorders can effectively sample echolocating bats, bat point counts are a promising, non‐invasive, and potentially competitive new tool for sampling all flying bats without bias and observing their behavior in the wild.     

Water and molecular chaperones act as weak links of protein folding networks: energy landscape and punctuated equilibrium changes point towards a game theory of proteins

Water molecules and molecular chaperones efficiently help the protein folding process. Here we describe their action in the context of the energy and topological networks of proteins. In energy terms water and chaperones were suggested to decrease the activation energy between various local energy minima smoothing the energy landscape, rescuing misfolded proteins from conformational traps and stabilizing their native structure. In kinetic terms water and chaperones may make the punctuated equilibrium of conformational changes less punctuated and help protein relaxation. Finally, water and chaperones may help the convergence of multiple energy landscapes during protein-macromolecule interactions. We also discuss the possibility of the introduction of protein games to narrow the multitude of the energy landscapes when a protein binds to another macromolecule. Both water and chaperones provide a diffuse set of rapidly fluctuating weak links (low affinity and low probability interactions), which allow the generalization of all these statements to a multitude of networks.