nils-herrmann/clean_scirepeval huggingface dataset:
Using ecosystem engineers as tools in habitat restoration and rewilding: beaver and wetlands.
Venue: Science of The Total Environment

Potential for habitat restoration is increasingly used as an argument for reintroducing ecosystem engineers. Beaver have well known effects on hydromorphology through dam construction, but their scope to restore wetland biodiversity in areas degraded by agriculture is largely inferred. Our study presents the first formal monitoring of a planned beaver-assisted restoration, focussing on changes in vegetation over 12years within an agriculturally-degraded fen following beaver release, based on repeated sampling of fixed plots. Effects are compared to ungrazed exclosures which allowed the wider influence of waterlogging to be separated from disturbance through tree felling and herbivory. After 12years of beaver presence mean plant species richness had increased on average by 46% per plot, whilst the cumulative number of species recorded increased on average by 148%. Heterogeneity, measured by dissimilarity of plot composition, increased on average by 71%. Plants associated with high moisture and light conditions increased significantly in coverage, whereas species indicative of high nitrogen decreased. Areas exposed to both grazing and waterlogging generally showed the most pronounced change in composition, with effects of grazing seemingly additive, but secondary, to those of waterlogging. Our study illustrates that a well-known ecosystem engineer, the beaver, can with time transform agricultural land into a comparatively species-rich and heterogeneous wetland environment, thus meeting common restoration objectives. This offers a passive but innovative solution to the problems of wetland habitat loss that complements the value of beavers for water or sediment storage and flow attenuation. The role of larger herbivores has been significantly overlooked in our understanding of freshwater ecosystem function; the use of such species may yet emerge as the missing ingredient in successful restoration.
Alteration of North American streams by beaver
Venue: BioScience

organic matter in the channel, create and maintain wetlands, modify nutrient cycling and decomposition dynamics, modify the structure and dynamics of the riparian zone, influence the character of water and materials transported downstream, and ultimately influence plant and animal community composition and diversity (Naiman and Melillo 1984, Naiman et al. 1986). In addition to their importance at the ecosystem level, these effects have a significant impact on the landscape and must be interpreted over broad spatial and temporal scales as beaver population dynamics shift in response to disturbance, food supply, disease, and predation. Although once more prevalent than they are today, beaver-induced alterations to drainage networks are not localized or unusual. Where beaver
Interaction of liquid epicuticular hydrocarbons and tarsal adhesive secretion in Leptinotarsa decemlineata Say (Coleoptera: Chrysomelidae)
Venue: Journal of Comparative Physiology A-neuroethology Sensory Neural and Behavioral Physiology

Species of various insect orders possess specialised tarsal adhesive structures covered by a thin liquid film, which is deposited in the form of footprints. This adhesive liquid has been suggested to be chemically and physiologically related to the epicuticular lipid layer, which naturally covers the body of insects and acts as the prime barrier to environmental stresses, such as desiccation. The functional efficiency of the layer, however, is jeopardised by partial melting that may occur at physiological temperatures. In this study, light microscopic images of elytral prints show that the epicuticular lipid layer of the Colorado potato beetle Leptinotarsa decemlineata actually is partially liquid and chemical investigations reveal the high similarity of the epicuticular hydrocarbon pattern and the tarsal liquid. By means of chemical manipulation of the surface hydrocarbon composition of live beetles, the substance exchange between their tarsal adhesive hairs and the body surface is monitored. Histological sections of L. decemlineata tarsi, furthermore, reveal glandular cells connected to individual adhesive setae and departing from these results, an idea of a general mechanism of tarsal secretion is developed and discussed in a functional–ecological context.
The mechanics of slithering locomotion
Venue: Proceedings of the National Academy of Sciences of the United States of America

In this experimental and theoretical study, we investigate the slithering of snakes on flat surfaces. Previous studies of slithering have rested on the assumption that snakes slither by pushing laterally against rocks and branches. In this study, we develop a theoretical model for slithering locomotion by observing snake motion kinematics and experimentally measuring the friction coefficients of snakeskin. Our predictions of body speed show good agreement with observations, demonstrating that snake propulsion on flat ground, and possibly in general, relies critically on the frictional anisotropy of their scales. We have also highlighted the importance of weight distribution in lateral undulation, previously difficult to visualize and hence assumed uniform. The ability to redistribute weight, clearly of importance when appendages are airborne in limbed locomotion, has a much broader generality, as shown by its role in improving limbless locomotion.
Deployment of hagfish slime thread skeins requires the transmission of mixing forces via mucin strands
Venue: The Journal of Experimental Biology

Hagfishes are benthic marine protovertebrates that secrete copious quantities of slime when threatened. The slime originates as a two-component glandular exudate comprised of coiled bundles of cytoskeletal intermediate filaments (thread skeins) and mucin vesicles. Holocrine secretion of the slime into seawater results in the rapid deployment of both fibrous and mucin components, resulting in about a liter of dilute slime. Deployment of the thread skeins involves their unraveling in a fraction of a second from a 150 μm-long ellipsoid bundle to a thread that is 100× longer. We hypothesized that thread skein deployment requires both vigorous hydrodynamic mixing and the presence of mucin vesicles, both of which are required for whole slime deployment. Here we provide evidence that mixing and mucin vesicles are indeed crucial for skein unraveling. Specifically, we show that mucin vesicles mixed into seawater swell and elongate into high-aspect ratio mucin strands that attach to the thread skeins, transmit hydrodynamic forces to them and effect their unraveling by loading them in tension. Our discovery of mucin strands in hagfish slime not only provides a mechanism for the rapid deployment of thread skeins in vivo, it also helps explain how hagfish slime is able to trap such impressive volumes of seawater via viscous entrainment. We believe that the deployment of thread skeins via their interaction with shear-elongated mucins represents a unique mechanism in biology and may lead to novel technologies for transmitting hydrodynamic forces to microscale particles that would typically be immune to such forces.
Energy and time optimal trajectories in exploratory jumps of the spider Phidippus regius
Venue: Scientific Reports

Jumping spiders are proficient jumpers that use jumps in a variety of behavioural contexts. We use high speed, high resolution video to measure the kinematics of a single regal jumping spider for a total of 15 different tasks based on a horizontal gap of 2–5 body lengths and vertical gap of +/−2 body lengths. For short range jumps, we show that low angled trajectories are used that minimise flight time. For longer jumps, take-off angles are steeper and closer to the optimum for minimum energy cost of transport. Comparison of jump performance against other arthropods shows that Phidippus regius is firmly in the group of animals that use dynamic muscle contraction for actuation as opposed to a stored energy catapult system. We find that the jump power requirements can be met from the estimated mass of leg muscle; hydraulic augmentation may be present but appears not to be energetically essential.
Understanding stress concentration about a nutrient foramen.
Venue: Journal of Biomechanics

We investigated the microstructural basis of a reduced stress concentration around the primary nutrient foramen of the equine third metacarpus. We quantified the spatial variations of compositional parameters (mineral content, volume fraction, histological architecture, and osteonal trajectories) from microradiographs and polarizing microscopic images of thin sections. These variations in composition and organization in turn cause variations in mechanical properties of cortical bone. We modeled the spatially inhomogeneous anisotropic elastic properties based on the measured compositional parameters and used the properties as inputs to a finite element model of the bone containing the foramen. This model, spatially constructed solely from the microscopic images, was subsequently validated by our mechanical test results. We found that: (1) a primary mechanism for stress concentration reduction appears to be due to an increased compliance near the foramen: the sharp discontinuity represented by the hole is softened by embedding it in a compliant region; (2) a reinforcing ring of increased stiffness exists at some distance from the foramen; and (3) a ring of lamellar bone exists along the foramen inside edge, which might serve to reduce the chance of cracks forming there. Our work is allowing us to design biomimetic structures with holes by mimicking the microstructure near the nutrient foramen.
Mechanism, kinematic performance, and fitness consequences of jumping behavior in entomopathogenic nematodes (Steinernema spp.)
Venue: Canadian Journal of Zoology

The mechanism enabling entomopathogenic nematodes (Steinernema spp.) to jump is described. Jumping performance is measured and the contribution of jumping to host finding is estimated. We used the entomopathogenic nematode Steinernema carpocapsae as a model species for the genus. Nematodes jump using a two-step process of forming and contracting a loop. During loop formation, the nematode bends the anterior half of its body until the head region makes contact with the side of the body. The two body regions are held fast by the surface tension of the water film covering the nematode. When the loop is contracted, the body becomes contorted so that the cuticle kinks. This extreme bending generates and stores sufficient energy that when the surface-tension force is broken the nematode is propelled through the air. The nematode (0.558 mm in length) can jump a distance of 4.8 ± 0.8 mm (mean ± SEM) and a height of 3.9 ± 0.1 mm. The contribution of jumping to host finding varies among species and is related to th...
FOXO-dependent regulation of innate immune homeostasis
Venue: Nature

The innate immune system represents an ancient host defence mechanism that protects against invading microorganisms. An important class of immune effector molecules to fight pathogen infections are antimicrobial peptides (AMPs) that are produced in plants and animals. In Drosophila, the induction of AMPs in response to infection is regulated through the activation of the evolutionarily conserved Toll and immune deficiency (IMD) pathways. Here we show that AMP activation can be achieved independently of these immunoregulatory pathways by the transcription factor FOXO, a key regulator of stress resistance, metabolism and ageing. In non-infected animals, AMP genes are activated in response to nuclear FOXO activity when induced by starvation, using insulin signalling mutants, or by applying small molecule inhibitors. AMP induction is lost in foxo null mutants but enhanced when FOXO is overexpressed. Expression of AMP genes in response to FOXO activity can also be triggered in animals unable to respond to immune challenges due to defects in both the Toll and IMD pathways. Molecular experiments at the Drosomycin promoter indicate that FOXO directly binds to its regulatory region, thereby inducing its transcription. In vivo studies in Drosophila, but also studies in human lung, gut, kidney and skin cells indicate that a FOXO-dependent regulation of AMPs is evolutionarily conserved. Our results indicate a new mechanism of cross-regulation of metabolism and innate immunity by which AMP genes can be activated under normal physiological conditions in response to the oscillating energy status of cells and tissues. This regulation seems to be independent of the pathogen-responsive innate immunity pathways whose activation is often associated with tissue damage and repair. The sparse production of AMPs in epithelial tissues in response to FOXO may help modulating the defence reaction without harming the host tissues, in particular when animals are suffering from energy shortage or stress.
The effect of molluscan glue proteins on gel mechanics
Venue: The Journal of Experimental Biology

Several molluscs have been shown to alternate between a non-adhesive trail mucus and a similar gel that forms a strong glue. The major structural difference between the two secretions is the presence of specific proteins in the adhesive mucus. The present study identifies similar proteins from the glue of the slug Arion subfuscus and the land snail Helix aspersa. To investigate the role played by these proteins in adhesion, the proteins were isolated from the adhesive mucus of different molluscs and added to commercial polymer solutions. The effect was observed qualitatively, and quantified using a dynamic rheometer. The isolated proteins triggered gelling or visible stiffening of agar, pectin and polygalacturonic acid. The effect was stronger on more negatively charged polymers. The effect of the proteins was concentration dependent with an optimal concentration of 1–1.5 mg ml–1, and was weakened when their structure changed. Other proteins and carbohydrates found in the adhesive mucus had no clear mechanical effect on gels. These findings show that the addition of these proteins to large, anionic polymers plays a central role in the formation of a glue from a mucus-like secretion. Such a mechanism may be common among invertebrates, and it may guide biomimetic approaches in the development of glues and gels.
Ultrastructure and permeability characteristics of the membranes of mucous granules of the hagfish.
Venue: Tissue & Cell

Mucous granules secreted by the slime glands of the hagfish. Eptatretus stouti, were studied after ultrarapid cryofixation and freeze substitution in diverse media (osmium tetroxide in acetone; several aqueous glutaraldehyde-based media with or without osmium). Only freeze substitution with osmium tetroxide-acetone preserved the granules intact, allowing visualization of its single unit membrane. Tests of the rupture or stability of freshly secreted mucous granules in sea water and other aqueous media showed the membranes of the granules are permeable to all inorganic cations tested, ranging in relative mass from ammonium to barium. They are permeable to the univalent anions chloride, nitrate, and bicarbonate, but not to the di- or trivalent anions sulfate, phosphate, and citrate. Moreover, in solutions where nonpenetrant anions were present, rupture occurred if the osmotic pressure was below a critical level (about 800 mOsmol/l). The structural and permeability characteristics of the granules account for the explosive speed with which they rupture, releasing their mucous contents, on contact with sea water.
Restoration of tensile strength in bark samples of Ficus benjamina due to coagulation of latex during fast self-healing of fissures.
Venue: Annals of Botany

The functions of plant latex have been discussed for a long time. Today, many studies support a defence mechanism as being its main function. A role as a self-healing mechanism was never attributed to the coagulation of latex. In this study we quantified the contribution of the coagulation of Ficus benjamina (weeping fig) latex to a restoration of the mechanical properties of the bark after external lesions.



Tensile tests of F. benjamina bark were conducted either immediately after injury or at various latency times after injury.



A significant increase in the tensile strength of bark samples until 30 min after injury was found, and this effect could be attributed to the coagulation of plant latex alone. The tensile strength remains nearly constant until several hours or days after injury. Then, very probably due to other mechanisms such as cell growth and cell proliferation, the tensile strength begins to increase slightly again.



The coagulation of latex seals lesions and serves as a quick and effective pre-step of subsequent, more effective, long-lasting self-healing mechanisms such as cell growth and proliferation. Thus, a fast self-healing effect can be included in the list of functions of plant latex.
How do sucker-footed bats hold on, and why do they roost head-up?
Venue: Biological Journal of The Linnean Society

Individuals of most bat species hang head-down by their toenails from rough surfaces, but Madagascar’s endemic sucker-footed bat (Myzopoda aurita) clings head-up to smooth leaves using specialized pads on its wrists and ankles. We investigated the adhesive performance of 28 individuals and found that attachment performance on brass was not affected by the presence or absence of a seal around the pad–surface interface. Furthermore, on smooth acrylic, the wrist pads were more than nine-fold weaker when lifted perpendicular to the surface than when pulled parallel to it. The unimportance of a seal and the difference in strength in those directions on a smooth surface are characteristic of wet adhesion, but not of suction. Thus, despite its name, the sucker-footed bat appears to adhere using wet adhesion. We observed that when wrist pads were pushed anteriorly, they unpeeled easily from the surface because of deformation of the pads. This most likely permits rapid detachment during crawling, but would also cause passive detachment if bats roosted head-down. This provides an ecomorphological explanation to the head-up roosting behaviour of these unique bats. The results obtained in the present study thus link morphology, behaviour, and roosting ecology for an enigmatic Malagasy endemic.  detachment – ecomorphology – head-up posture – Myzopoda – roosting posture – suction – Thyroptera – wet adhesion.
Companion planting with French marigolds protects tomato plants from glasshouse whiteflies through the emission of airborne limonene
Venue: PLOS ONE

Horticulturalists and gardeners in temperate regions often claim that planting marigolds next to tomato plants protects the tomatoes from the glasshouse whitefly (Trialeurodes vaporariorum Westwood). If shown to hold true, this technique could be used in larger-scale tomato production, protecting the crop and helping to introduce greater plant diversity into these agro-ecosystems. Here we present two large-scale glasshouse trials corresponding to the two main ways growers are likely to use marigolds to control whiteflies. In the first, marigolds are grown next to tomato throughout the growing period and we quantify whitefly population growth from the seedling stage over a 48 day infestation period. Here we show that association with marigolds significantly slows whitefly population development. Introducing additional whitefly-attractive ‘pull’ plants around the perimeter of plots has little effect, but reducing the proportion of marigolds and introducing other non-hosts of whiteflies (basil, nasturtium and Chinese cabbage) also reduces whitefly populations on tomato. The second experiment assesses the efficacy of marigolds when used as an ‘emergency’ measure. Here we allow whitefly populations to build to a high density on unprotected tomatoes then introduce marigolds and assess whitefly population over a further period. Following laboratory work showing limonene to be a major chemical component of French marigolds and a negative behaviour response of whiteflies to this compound, limonene dispensers are added as an additional treatment to this experiment. “Emergency” marigold companion planting yielded minimal reductions in whitefly performance, but the use of limonene dispensers was more effective. Our work indicates that companion planting short vine tomatoes with French marigolds throughout the growing season will slow development of whitefly populations. Introducing marigolds to unprotected tomatoes after significant whitefly build-up will be less effective. The use of limonene dispensers placed near to tomato plants also shows promise. It is argued that this work supports the possibility of the development of a mixture of tomato companion plants that infer ‘associational resistance’ against many major invertebrate pests of tomato. Such a mixture, if comprising edible or ornamental plants, would be economically viable, would reduce the need for additional chemical and biological control, and, if used outdoors, would generate plant-diverse agro-ecosystems that are better able to harbour invertebrate wildlife.
The Calvin cycle revisited
Venue: Photosynthesis Research

The sequence of reactions in the Calvin cycle, and the biochemical characteristics of the enzymes involved, have been known for some time. However, the extent to which any individual enzyme controls the rate of carbon fixation has been a long standing question. Over the last 10 years, antisense transgenic plants have been used as tools to address this and have revealed some unexpected findings about the Calvin cycle. It was shown that under a range of environmental conditions, the level of Rubisco protein had little impact on the control of carbon fixation. In addition, three of the four thioredoxin regulated enzymes, FBPase, PRKase and GAPDH, had negligible control of the cycle. Unexpectedly, non-regulated enzymes catalysing reversible reactions, aldolase and transketolase, both exerted significant control over carbon flux. Furthermore, under a range of growth conditions SBPase was shown to have a significant level of control over the Calvin cycle. These data led to the hypothesis that increasing the amounts of these enzymes may lead to an increase in photosynthetic carbon assimilation. Remarkably, photosynthetic capacity and growth were increased in tobacco plants expressing a bifunctional SBPase/FBPase enzyme. Future work is discussed which will further our understanding of this complex and important pathway, particularly in relation to the mechanisms that regulate and co-ordinate enzyme activity.
Sacrificial bonds and hidden length: unraveling molecular mesostructures in tough materials.
Venue: Biophysical Journal

Sacrificial bonds and hidden length in structural molecules and composites have been found to greatly increase the fracture toughness of biomaterials by providing a reversible, molecular-scale energy-dissipation mechanism. This mechanism relies on the energy, of order 100 eV, needed to reduce entropy and increase enthalpy as molecular segments are stretched after being released by the breaking of weak bonds, called sacrificial bonds. This energy is relatively large compared to the energy needed to break the polymer backbone, of order a few eV. In many biological cases, the breaking of sacrificial bonds has been found to be reversible, thereby additionally providing a "self-healing" property to the material. Due to the nanoscopic nature of this mechanism, single molecule force spectroscopy using an atomic force microscope has been a useful tool to investigate this mechanism. Especially when investigating natural molecular constructs, force versus distance curves quickly become very complicated. In this work we propose various types of sacrificial bonds, their combination, and how they appear in single molecule force spectroscopy measurements. We find that by close analysis of the force spectroscopy curves, additional information can be obtained about the molecules and their bonds to the native constructs.