nils-herrmann/clean_scirepeval huggingface dataset:
Utilising the Synergy between Plants and Rhizosphere Microorganisms to Enhance Breakdown of Organic Pollutants in the Environment (15 pp)
Venue: Environmental Science and Pollution Research

Phytoremediation is a promising technology for the cleanup of polluted environments. The technology has so far been used mainly to remove toxic heavy metals from contaminated soil, but there is a growing interest in broadening its applications to remove/degrade organic pollutants in the environment. Both plants and soil microorganisms have certain limitations with respect to their individual abilities to remove/breakdown organic compounds. A synergistic action by both rhizosphere microorganisms that leads to increased availability of hydrophobic compounds, and plants that leads to their removal and/or degradation, may overcome many of the limitations, and thus provide a useful basis for enhancing remediation of contaminated environments. The review of literature presented in this article provides an insight to the nature of plant-microbial interactions in the rhizosphere, with a focus on those processes that are relevant to the breakdown and/or removal of organic pollutants. Due consideration has been given to identify opportunities for utilising the plant-microbial synergy in the rhizosphere to enhance remediation of contaminated environments. The literature review has highlighted the existence of a synergistic interaction between plants and microbial communities in the rhizosphere. This interaction benefits both microorganisms through provision of nutrients by root exudates, and plants through enhanced nutrient uptake and reduced toxicity of soil contaminants. The ability of the plant-microbial interaction to tackle some of the most recalcitrant organic chemicals is of particular interest with regard to enhancing and extending the scope of remediation technologies. Plant-microbial interactions in the rhizosphere offer very useful means for remediating environments contaminated with recalcitrant organic compounds.Outlook A better knowledge of plant-microbial interactions will provide a basis for improving the efficacy of biological remediations. Further research is, however, needed to investigate different feedback mechanisms that select and regulate microbial activity in the rhizosphere.
Hierarchical organisation of the trap in the protocarnivorous plant Roridula gorgonias (Roridulaceae)
Venue: The Journal of Experimental Biology

The flypaper trap of the protocarnivorous plant Roridula gorgonias is known to capture various insects, even those having a considerable body size, by using an adhesive, visco-elastic resinous secretion released by glandular trichomes of different dimensions. However, recent experimental studies have shown that the adhesion of long tentacle-shaped trichome secretion is not as strong as previously assumed. One may then ask why this flypaper trap is so highly effective. In the present study, we compared geometry, flexibility and the adhesive properties of secretion in different sized trichomes. We have analysed the gross morphology of the plant and its surfaces using light and cryo-scanning electron microscopy. Trichomes' stiffness and the adhesive properties of their secretion on different surfaces were measured. A combination of structural and experimental results, presented in this study, let us suggest that R. gorgonias represents a three-dimensional trap consisting of three functional hierarchical levels (plant, leaves and trichomes). According to their size, we classified three types of trichomes having a particular arrangement on the leaf. The longest trichomes are more flexible and less adhesive compared with the shortest ones. The latter are 48 times stiffer and their secretion has a 9 times higher adhesive strength. Our data support the hypothesis that the shortest trichomes are adapted to strong, long-term adherence to prey insects, and that the longest trichomes are responsible for initial trapping and entanglement function.
Proteinaceous adhesive secretions from insects, and in particular the egg attachment glue of Opodiphthera sp. moths.
Venue: Archives of Insect Biochemistry and Physiology

Biochemical and electrophoretic screening of 29 adhesive secretions from Australian insects identified six types that appeared to consist largely of protein. Most were involved in terrestrial egg attachment. Hydrogel glues were subjected to gravimetric analyses and assessed for overall amino acid composition. When 32 proteins in glues from eight insect species were analyzed individually, many proved to be rich in Gly, Ser, and/or Pro, and some contained substantial levels of 4-hydroxyproline. A few proteins were heavily glycosylated. Abundant protein-based secretions were tested as adhesives, mainly by measuring dry shear strength on wood. The strongest (1-2 MPa) was an egg attachment glue produced by saturniid gum moths of the genus Opodiphthera. It was harvested from female colleterial gland reservoirs as a treacle-like liquid that underwent irreversible gelation, and recovered from the capsules of laid eggs as a highly elastic orange-brown hydrogel that could also display high tack. Its protein-based nature was confirmed and explored by spectroscopy, enzymatic degradation, and 2D gel electrophoresis. Its proteins are mostly 80-95 kDa, and sequences (almost all novel) were established for 23 tryptic peptides. Scanning probe microscopy of Opodiphthera hydrogel in water returned median values of 0.83 nN for adhesion, 63 kPa for modulus, and 87% for resilience. Recombinant mimics of this material might be useful as biodegradable commodity adhesives or as specialty biomedical products.
Probing the molecular and electronic structure of norhipposudoric and hipposudoric acids from the red sweat of Hippopotamus amphibius: a DFT investigation.
Venue: Journal of Physical Chemistry A

Molecular structure and tautomeric/conformational preferences of norhipposudoric and hipposudoric acids, the recently isolated pigments of the Hippopotamus amphibius' sweat, were investigated using the density functional theory (DFT) PBE0 formalism. Among a large variety of possible structures, two similar keto-enol tautomer/conformers are nearly isoenergetic and markedly more stable than the others both in the gas phase and aqueous solution. The bulk solvent effect was accounted for with the polarizable continuum model (PCM). A distinctive structural feature is the strong intramolecular hydrogen bonding in the keto-enol O-H...O bridge, as shown by analysis of the atoms-in-molecules topological properties of the electron density. To elucidate the claimed strong acidity of these pigments, the site-specific microscopic dissociation constants were also calculated using the cluster-continuum model, a hybrid approach based on inclusion of explicit solvent molecules and solvation of the cluster by the dielectric continuum. Notably, the first deprotonation should occur predominantly from the enolic group with a remarkably low pk(i) value. This factor could play an important role in the potent antibiotic activity of the pigments. The absorption spectra of the undissociated and dissociated compounds in aqueous solution were interpreted with time-dependent DFT/PCM calculations. The pi-pi* diquinoid excitations, mainly occurring in the fluorenoid nucleus, are the major contributors to the color and strong absorption bands in the UVA and UVB regions, which are closely related to the efficient sunscreen activity exerted by the pigments.
Interactions of woody and herbaceous vegetation in a southern African Savanna
Venue: Journal of Ecology

(1) A number of plots were set up in two natural savanna communities, with identical climates but different soils, to examine possible competition between the woody and herbaceous components of the vegetation. The community on the more sandy soil is a broad-leaf woody savanna and the other a more open microphyllous Acacia community. (2) Vegetative growth and soil water were monitored over a 2-year period in control plots and in plots cleared of one of the vegetation components. (3) In the broad-leaf community the effect of the herbaceous vegetation on the woody plants is negligible. (4) In the Acacia community with seven times more herbaceous biomass, mature woody-plant growth was reduced by competition from the grass-dominated herb layer particularly in the first (wetter) year. The vertical root distributions and soil-water data indicate that the grasses take up topsoil (0-30 cm) water sufficiently rapidly to reduce drainage into the subsoil (30-130 cm), and that they also take up subsoil water directly, thus lowering the amount of subsoil water available to woody plants. (5) The different herbaceous to woody-plant biomass ratios in the two sites and the different intensity of competition during the 2 years can be explained in terms of the effects of the soil properties and of the rainfall intensity on the ratio of water in the topsoil to that in the subsoil.
High-resolution polarisation vision in a cuttlefish
Venue: Current Biology

For animals that can see it, the polarisation of light adds another dimension to vision, analogous to adding colour to a black and white image . Whilst some animals use the orientation of the electric field vector (e-vector) for navigation and orientation , the ability to discriminate angular differences in e-vector has been implicated in object recognition for predator/prey detection  as well as signalling and communication . In all animals previously tested, however, the resolution of e-vector angle discrimination has been found to be in the range 10–20° [5,7,8], which is inadequate for the typical e-vector differences measured in relevant natural visual scenes . In this study, we found that mourning cuttlefish ( Sepia plangon ) are able to detect differences between e-vector orientations as small as 1°. Not only is this the most acute e-vector angle discrimination measured behaviourally in any animal, but it provides a high enough resolution to be relevant to real world visual tasks. We analysed natural underwater scenes using computer based polarisation imaging. When we increased the resolution of our system, we discovered information not detected using normal-resolution imaging polarimetry and invisible to animals lacking fine e-vector angle discrimination. For example, we found that high-resolution e-vector discrimination provides a new way of breaking typical intensity-based background matching. S. plangon lacks colour vision, like most other cephalopods, and high-resolution polarisation vision may provide an alternative source of contrast information that is just as fine-scale.
Skeletal development in sloths and the evolution of mammalian vertebral patterning
Venue: Proceedings of the National Academy of Sciences of the United States of America

Mammals show a very low level of variation in vertebral count, particularly in the neck. Phenotypes exhibited at various stages during the development of the axial skeleton may play a key role in testing mechanisms recently proposed to explain this conservatism. Here, we provide osteogenetic data that identify developmental criteria with which to recognize cervical vs. noncervical vertebrae in mammals. Except for sloths, all mammals show the late ossification of the caudal-most centra in the neck after other centra and neural arches. In sloths with 8–10 ribless neck vertebrae, the caudal-most neck centra ossify early, matching the pattern observed in cranial thoracic vertebrae of other mammals. Accordingly, we interpret the ribless neck vertebrae of three-toed sloths caudal to V7 as thoracic based on our developmental criterion. Applied to the unusual vertebral phenotype of long-necked sloths, these data support the interpretation that elements of the axial skeleton with origins from distinct mesodermal tissues have repatterned over the course of evolution.
Honeybee flight: a novel ‘streamlining’ response
Venue: The Journal of Experimental Biology

Animals that move rapidly through the air can save considerable energy by reducing the drag that they need to overcome during flight. We describe a novel ‘streamlining’ response in tethered, flying honeybees in which the abdomen is held in a raised position when the visual system is exposed to a pattern of image motion that is characteristic of forward flight. This visually evoked response, which can be elicited without exposing the insect to any airflow, presumably serves to reduce the aerodynamic drag that would otherwise be produced by the abdomen during real flight. The response is critically dependent on the presence of appropriate image motion everywhere within the large field of view of the insect. Thus, our results also underscore the importance of using panoramic stimulation for the study of visually guided flight in insects, and reveal the relative importance of various regions of the visual field in assessing the speed of flight through the environment.
Phantom hunter of the fjords: Camouflage by counterillumination in a shark (Etmopterus spinax)
Venue: Journal of Experimental Marine Biology and Ecology

Many midwater animals emit ventral light to hide their silhouette in the water column. This phenomenon known as counterillumination typically requires fine control over light emission since it needs a luminescence that closely matches the properties of downwelling light (intensity, angular distribution and wavelength). Here we provide evidence that, although lacking complex structures of counterilluminating animals, the deepwater luminescent shark Etmopterus spinax could, in Norwegian fjords, efficiently cloak its silhouette from downwelling ambient light to remain hidden from predator and prey. This represents the first experimentally tested function of luminescence in a shark and illustrates how evolution can take different routes to converge on identical complex behavior.
Iridescence impairs object recognition in bumblebees
Venue: Scientific Reports

Iridescence is a taxonomically widespread and striking form of animal coloration, yet despite advances in understanding its mechanism, its function and adaptive value are poorly understood. We test a counterintuitive hypothesis about the function of iridescence: that it can act as camouflage through interference with object recognition. Using an established insect visual model (Bombus terrestris), we demonstrate that both diffraction grating and multilayer iridescence impair shape recognition (although not the more subtle form of diffraction grating seen in some flowers), supporting the idea that both strategies can be effective means of camouflage. We conclude that iridescence produces visual signals that can confuse potential predators, and this might explain the high frequency of iridescence in many animal taxa.
Peptides controlling stifness of connective tissue in sea cucumbers.
Venue: The Biological Bulletin

We present the first evidence of a system of four bioactive peptides that affect the stiffness of sea cucumber dermis. The body wall dermis of sea cucumbers consists of catch connective tissue that is characterized by quick and drastic stiffness changes under nervous control. The peptides were isolated from the body wall, their amino acid sequences determined, and identical peptides synthesized. Two peptides, which we named holokinins, are homologous with bradykinin. We tested the effect of the peptides on the mechanical properties of sea cucumber dermis. Both of the holokinins softened the dermis, and a pentapeptide that we designated as NGIWYamide stiffened it. Both effects were reversibly suppressed by anesthesia with menthol. We called the fourth peptide stichopin; it had no direct effect on the stiffness of the dermis but suppressed action of the neurotransmitter acetylcholine reversibly. The results suggest that the peptides are neuropeptides and are part of a sophisticated system of neurotransmitters and neuromodulators that controls the connective tissue stiffness of sea cucumber dermis.
Surface tension prey transport in shorebirds: how widespread is it?
Venue: Ibis

Surface tension prey transport is a feeding mechanism employing the surface tension of water surrounding prey to transport prey from bill tip to mouth. Previously, it has been demonstrated only in the Red-necked Phalarope Phalaropus lobatus. On the basis of a model of the bill morphology necessary for this method of prey transport, I suggest that many species of shorebird should be capable of surface tension feeding. Laboratory investigations of the feeding mechanics of Wilson's Phalarope Phalaropus tricolor, Western Sandpiper Calidris mauri and Least Sandpiper Calidris minutilla demonstrated that all three use surface tension transport of prey when feeding in water. I examined interspecific variation in the performance of this feeding mechanism with a high-speed video system and a customized motion analysis system. Exploratory analyses indicated significant interspecific variation in distance the prey is transported per cycle of mandibular spreading, gape increase per unit transport, speed of transport, total number of cycles necessary to complete transport and total time to complete transport. The calidrid sandpipers also occasionally used other feeding mechanisms in conjunction with surface tension transport of prey. The discovery that these sandpipers, which normally obtain prey by probing, are capable of surface tension transport of prey implies that the capacity to employ this feeding mechanism may be widespread in the Scolopacidae and may have been a significant factor in the evolutionary radiation of phalaropes into aquatic environments.
Biomimetic Spider Leg Joints: A Review from Biomechanical Research to Compliant Robotic Actuators
Venue: Robotics

Due to their inherent compliance, soft actuated joints are becoming increasingly important for robotic applications, especially when human-robot-interactions are expected. Several of these flexible actuators are inspired by biological models. One perfect showpiece for biomimetic robots is the spider leg, because it combines lightweight design and graceful movements with powerful and dynamic actuation. Building on this motivation, the review article focuses on compliant robotic joints inspired by the function principle of the spider leg. The mechanism is introduced by an overview of existing biological and biomechanical research. Thereupon a classification of robots that are bio-inspired by spider joints is presented. Based on this, the biomimetic robot applications referring to the spider principle are identified and discussed.
Do western boxelder bugs sunbathe for sanitation? Inferences from in vitro experiments
Venue: Entomologia Experimentalis Et Applicata

When western boxelder bugs, Boisea rubrolineata (Barber) (Hemiptera: Rhopalidae), form aggregations in warm sunlight, they release from their posterior dorsal abdominal gland an odorous blend of monoterpenes with heretofore unknown biological function. In laboratory analyses and experiments, we show that bugs in warm sunlight, but not in shade, exude and spread copious amounts of monoterpenes onto their cuticle. These monoterpenes do not serve as a pheromone, but rather as a means of sanitation. They inhibit germination of conidia of the fungal pathogen Beauveria bassiana (Bals.‐Criv.) Vuill. (Hypocreales) as well as halt the growth of germinated spores. This prophylactic defense against pathogens appears adaptive for phytophagous insects, like B. rubrolineata, that are prone to infections by microbes thriving on leaf surfaces and in the insects' overwintering microhabitat.
Tree shrew lavatories: a novel nitrogen sequestration strategy in a tropical pitcher plant
Venue: Biology Letters

Nepenthes pitcher plants are typically carnivorous, producing pitchers with varying combinations of epicuticular wax crystals, viscoelastic fluids and slippery peristomes to trap arthropod prey, especially ants. However, ant densities are low in tropical montane habitats, thereby limiting the potential benefits of the carnivorous syndrome. Nepenthes lowii, a montane species from Borneo, produces two types of pitchers that differ greatly in form and function. Pitchers produced by immature plants conform to the ‘typical’ Nepenthes pattern, catching arthropod prey. However, pitchers produced by mature N. lowii plants lack the features associated with carnivory and are instead visited by tree shrews, which defaecate into them after feeding on exudates that accumulate on the pitcher lid. We tested the hypothesis that tree shrew faeces represent a significant nitrogen (N) source for N. lowii, finding that it accounts for between 57 and 100 per cent of foliar N in mature N. lowii plants. Thus, N. lowii employs a diversified N sequestration strategy, gaining access to a N source that is not available to sympatric congeners. The interaction between N. lowii and tree shrews appears to be a mutualism based on the exchange of food sources that are scarce in their montane habitat.
Molecular sabotage of plant defense by aphid saliva
Venue: Proceedings of the National Academy of Sciences of the United States of America

Aphids, which constitute one of the most important groups of agricultural pests, ingest nutrients from sieve tubes, the photoassimilate transport conduits in plants. Aphids are able to successfully puncture sieve tubes with their piercing mouthparts (stylets) and ingest phloem sap without eliciting the sieve tubes' normal occlusion response to injury. Occlusion mechanisms are calcium-triggered and may be prevented by chemical constituents in aphid saliva injected into sieve tubes before and during feeding. We recorded aphid feeding behavior with the electrical penetration graph (EPG) technique and then experimentally induced sieve tube plugging. Initiation of sieve tube occlusion caused a change in aphid behavior from phloem sap ingestion to secretion of watery saliva. Direct proof of “unplugging” properties of aphid saliva was provided by the effect of aphid saliva on forisomes. Forisomes are proteinaceous inclusions in sieve tubes of legumes that show calcium-regulated changes in conformation between a contracted state (below calcium threshold) that does not occlude the sieve tubes and a dispersed state (above calcium threshold) that occludes the sieve tubes. We demonstrated in vitro that aphid saliva induces dispersed forisomes to revert back to the nonplugging contracted state. Labeling Western-blotted saliva proteins with 45Ca2+ or ruthenium red inferred the presence of calcium-binding domains. These results demonstrate that aphid saliva has the ability to prevent sieve tube plugging by molecular interactions between salivary proteins and calcium. This provides aphids with access to a continuous flow of phloem sap and is a critical adaptation instrumental in the evolutionary success of aphids.
Honeybee combs: construction through a liquid equilibrium process?
Venue: Naturwissenschaften

Geometrical investigations of honeycombs and speculations on how honeybees measure and construct the hexagons and rhombi of their cells are centuries old. Here we show that honeybees neither have to measure nor construct the highly regular structures of a honeycomb, and that the observed pattern of combs can be parsimoniously explained by wax flowing in liquid equilibrium. The structure of the combs of honeybees results from wax as a thermoplastic building medium, which softens and hardens as a result of increasing and decreasing temperatures. It flows among an array of transient, close-packed cylinders which are actually the self-heated honeybees themselves. The three apparent rhomboids forming the base of each cell do not exist but arise as optical artefacts from looking through semi-transparent combs.