nils-herrmann/clean_scirepeval huggingface dataset:
Bacterial biofilm shows persistent resistance to liquid wetting and gas penetration
Venue: Proceedings of the National Academy of Sciences of the United States of America

Most of the world’s bacteria exist in robust, sessile communities known as biofilms, ubiquitously adherent to environmental surfaces from ocean floors to human teeth and notoriously resistant to antimicrobial agents. We report the surprising observation that Bacillus subtilis biofilm colonies and pellicles are extremely nonwetting, greatly surpassing the repellency of Teflon toward water and lower surface tension liquids. The biofilm surface remains nonwetting against up to 80% ethanol as well as other organic solvents and commercial biocides across a large and clinically important concentration range. We show that this property limits the penetration of antimicrobial liquids into the biofilm, severely compromising their efficacy. To highlight the mechanisms of this phenomenon, we performed experiments with mutant biofilms lacking ECM components and with functionalized polymeric replicas of biofilm microstructure. We show that the nonwetting properties are a synergistic result of ECM composition, multiscale roughness, reentrant topography, and possibly yet other factors related to the dynamic nature of the biofilm surface. Finally, we report the impenetrability of the biofilm surface by gases, implying defense capability against vapor-phase antimicrobials as well. These remarkable properties of B. subtilis biofilm, which may have evolved as a protection mechanism against native environmental threats, provide a new direction in both antimicrobial research and bioinspired liquid-repellent surface paradigms.
The mechanics of explosive dispersal and self-burial in the seeds of the filaree, Erodium cicutarium (Geraniaceae)
Venue: The Journal of Experimental Biology

The filaree (Erodium cicutarium), a small, flowering plant related to geraniums, possesses a unique seed dispersal mechanism: the plant can fling its seeds up to half a meter away; and the seeds can bury themselves by drilling into the ground, twisting and untwisting in response to changes in humidity. These feats are accomplished using awns, helical bristles of dead but hygroscopically active tissue attached to the seeds. Here, we describe the kinematics of explosive dispersal and self-burial based on detailed high-speed and time-lapse videos. We use these observations to develop a simple mechanical model that accounts for the coiling behavior of the awn and allows comparison of the strain energy stored in the awn with the kinetic energy at launch. The model is used to examine tradeoffs between dispersal distance and reliability of the dispersal mechanism. The mechanical model may help in understanding the invasive potential of this species and provides a framework for examining other evolutionary tradeoffs in seed dispersal mechanisms among the Geraniaceae.
NO-mediated cytoprotection: instant adaptation to oxidative stress in bacteria.
Venue: Proceedings of the National Academy of Sciences of the United States of America

Numerous sophisticated systems have been described that protect bacteria from increased levels of reactive oxygen species. Although indispensable during prolonged oxidative stress, these response systems depend on newly synthesized proteins, and are hence both time and energy consuming. Here, we describe an "express" cytoprotective system in Bacillus subtilis which depends on nitric oxide (NO). We show that NO immediately protects bacterial cells from reactive oxygen species by two independent mechanisms. NO transiently suppresses the enzymatic reduction of free cysteine that fuels the damaging Fenton reaction. In addition, NO directly reactivates catalase, a major antioxidant enzyme that has been inhibited in vivo by endogenous cysteine. Our data also reveal a critical role for bacterial NO-synthase in adaptation to oxidative stress associated with fast metabolic changes, and suggest a possible role for NO in defending pathogens against immune oxidative attack.
Slippery surfaces of pitcher plants: Nepenthes wax crystals minimize insect attachment via microscopic surface roughness
Venue: The Journal of Experimental Biology

Pitcher plants of the genus Nepenthes efficiently trap and retain insect prey in highly specialized leaves. Besides a slippery peristome which inhibits adhesion of insects they employ epicuticular wax crystals on the inner walls of the conductive zone of the pitchers to hamper insect attachment by adhesive devices. It has been proposed that the detachment of individual crystals and the resulting contamination of adhesive organs is responsible for capturing insects. However, our results provide evidence in favour of a different mechanism, mainly based on the stability and the roughness of the waxy surface. First, we were unable to detect a large quantity of crystal fragments on the pads of insects detached from mature pitcher surfaces of Nepenthes alata. Second, investigation of the pitcher surface by focused ion beam treatment showed that the wax crystals form a compact 3D structure. Third, atomic force microscopy of the platelet-shaped crystals revealed that the crystals are mechanically stable, rendering crystal detachment by insect pads unlikely. Fourth, the surface profile parameters of the wax layer showed striking similarities to those of polishing paper with low grain size. By measuring friction forces of insects on this artificial surface we demonstrate that microscopic roughness alone is sufficient to minimize insect attachment. A theoretical model shows that surface roughness within a certain length scale will prevent adhesion by being too rough for adhesive pads but not rough enough for claws.
Young's modulus varies with differential orientation of keratin in feathers.
Venue: Journal of Structural Biology

Feathers are composed of a structure that, whilst being very light, is able to withstand the large aerodynamic forces exerted upon them during flight. To explore the contribution of molecular orientation to feather keratin mechanical properties, we have examined the nanoscopic organisation of the keratin molecules by X-ray diffraction techniques and have confirmed a link between this and the Young's modulus of the feather rachis. Our results indicate that along the rachis length, from calamus to tip, the keratin molecules become more aligned than at the calamus before returning to a state of higher mis-orientation towards the tip of the rachis. We have also confirmed the general trend of increasing Young's modulus with distance along the rachis. Furthermore, we report a distinct difference in the patterns of orientation of beta-keratin in the feathers of flying and flightless birds. The trend for increased modulus along the feathers of volant birds is absent in the flightless ostrich.
Structure and mechanical behavior of a toucan beak
Venue: Acta Materialia

The toucan beak, which comprises one third of the length of the bird and yet only about 1/20th of its mass, has outstanding stiffness. The structure of a Toco toucan (Ramphastos toco) beak was found to be a sandwich composite with an exterior of keratin and a fibrous network of closed cells made of calcium-rich proteins. The keratin layer is comprised of superposed hexagonal scales (50 μm diameter and 1 μm thickness) glued together. Its tensile strength is about 50 MPa and Young’s modulus is 1.4 GPa. Micro and nanoindentation hardness measurements corroborate these values. The keratin shell exhibits a strain-rate sensitivity with a transition from slippage of the scales due to release of the organic glue, at a low strain rate (5 × 10−5/s) to fracture of the scales at a higher strain rate (1.5 × 10−3/s). The closed-cell foam is comprised of fibers having a Young’s modulus twice as high as the keratin shells due to their higher calcium content. The compressive response of the foam was modeled by the Gibson–Ashby constitutive equations for open and closed-cell foam. There is a synergistic effect between foam and shell evidenced by experiments and analysis establishing the separate responses of shell, foam, and foam + shell. The stability analysis developed by Karam and Gibson, assuming an idealized circular cross section, was applied to the beak. It shows that the foam stabilizes the deformation of the beak by providing an elastic foundation which increases its Brazier and buckling load under flexure loading.
How Cats Lap: Water Uptake by Felis catus
Venue: Science

Lap Cats We all know that domestic cats lap milk, but perhaps fewer of us have thought about how they do this. Reis et al. (p. 1231, published online 11 November; see the cover) have discovered that cats curl their tongues so that the top surface touches the water. Then, by lifting their tongues rapidly, a column of liquid grows by inertia until gravity induces its breakage and the cats close their jaws to capture the liquid. Lapping frequency is tuned to maximize the volume ingested, depending on the animal's mass; a relationship that holds as true for tabby cats as it does for lions. Cats use fluid inertia to generate a liquid column that they catch in their mouths before gravity destroys it. Animals have developed a range of drinking strategies depending on physiological and environmental constraints. Vertebrates with incomplete cheeks use their tongue to drink; the most common example is the lapping of cats and dogs. We show that the domestic cat (Felis catus) laps by a subtle mechanism based on water adhesion to the dorsal side of the tongue. A combined experimental and theoretical analysis reveals that Felis catus exploits fluid inertia to defeat gravity and pull liquid into the mouth. This competition between inertia and gravity sets the lapping frequency and yields a prediction for the dependence of frequency on animal mass. Measurements of lapping frequency across the family Felidae support this prediction, which suggests that the lapping mechanism is conserved among felines.
Biomechanics: A pneumo-hydrostatic skeleton in land crabs
Venue: Nature

Like their aquatic counterparts, terrestrial crabs repeatedly shed their rigid exoskeleton during moulting. But in the case of land crabs, little water is available to provide a temporary hydrostatic skeleton before the new skeleton hardens, and air does not provide the buoyancy necessary to support the animal. Here we show that whenever its exoskeleton is shed, the blackback land crab Gecarcinus lateralis relies on an unconventional type of hydrostatic skeleton that uses both gas and liquid (a ‘pneumo-hydrostat’). To our knowledge, this is the first experimental evidence for a locomotor skeleton that depends on a gas. It establishes a new category of hydrostatic skeletal support and possibly a critical adaptation to life on land for the Crustacea.
Multifocal lenses compensate for chromatic defocus in vertebrate eyes
Venue: Journal of Comparative Physiology A-neuroethology Sensory Neural and Behavioral Physiology

The focal length of the vertebrate eye is a function of wavelength, i.e. the eye suffers from longitudinal chromatic aberration. Chromatic defocus is a particularly severe problem in eyes with high light-gathering ability, since depth of field is small due to a pupillary opening that is large in relation to the focal length of the eye. Calculations show that in such eyes only a narrow spectral band of light can be in focus on the retina. For the major part of the visual spectrum, spatial resolution should be limited by the optics of the eye and far lower than the resolving power achievable by the retinal cone photoreceptor mosaic. To solve this problem, fishes with irises unresponsive to light have developed lenses with multiple focal lengths. Well-focused images are created at the wavelengths of maximum absorbance of all spectral cone types. Multifocal lenses also appear to be present in some terrestrial species. In eyes with mobile irises, multifocal lenses are correlated with pupil shapes that allow all zones of the lens, with different refractive powers, to participate in the imaging process, irrespective of the state of pupil constriction.
The Transition from Stiff to Compliant Materials in Squid Beaks
Venue: Science

The beak of the Humboldt squid Dosidicus gigas represents one of the hardest and stiffest wholly organic materials known. As it is deeply embedded within the soft buccal envelope, the manner in which impact forces are transmitted between beak and envelope is a matter of considerable scientific interest. Here, we show that the hydrated beak exhibits a large stiffness gradient, spanning two orders of magnitude from the tip to the base. This gradient is correlated with a chemical gradient involving mixtures of chitin, water, and His-rich proteins that contain 3,4-dihydroxyphenyl-l-alanine (dopa) and undergo extensive stabilization by histidyl-dopa cross-link formation. These findings may serve as a foundation for identifying design principles for attaching mechanically mismatched materials in engineering and biological applications.
Whisker-like geometries and their force reduction properties
Venue: OCEANS Conference

This paper studies the effects of geometrical features on harbor seal whiskers on its force reduction ability. Each feature in the seal whisker is sequentially stripped from the original whisker shape. Four whisker-like geometries are created from such methodology. 3D simulations of flow around the structures are performed and the resulting forces on the structures are non-dimensionalized. The lift and drag coefficients of these structures are compared to the real whisker case. The undulations on minor and major axes are found to be necessary in reducing the lift forces. Existence of only one of the undulations fails to weaken the flow and break the vortex tubes and braids in the wake. The offset angle between leading edge and trailing edge are found to have slight effects on the lift and drag coefficients. The reduction in drag coefficient is found to be dependent on the existence of undulations in minor axis. The force responses of whisker-like geometries with undulations on one of their axes are found to be periodic. When the force response on whisker-like geometries with both undulations are found to be chaotic. Vortex shedding frequency of the structure is observed to decrease considerably when no offset angle is introduced into the geometry. This may result in longer lifespan of the structure.
Bacterial Surface Motility: Slime Trails, Grappling Hooks and Nozzles
Venue: Current Biology

We thank N. Bose, K. Collins, R. Brennan, T. Economou, H. Higgs, M. Koomey, G. O'Toole, M. Sheetz, J. Skerker, R. Taylor, and T. Yahr for critical discussion of the ideas in this review. We apologize to colleagues whose work was not cited due to space constraints. A.J.M. is supported by Fellowship DRG–1598 of the Cancer Research Fund of the Damon Runyon-Walter Winchell Foundation. K.T.F. is supported by the NIH (GM59721) and the W.M. Keck Foundation.
Animal communication: Tree-hole frogs exploit resonance effects
Venue: Nature

Animal mating calls that exert a comparatively high sound pressure propagate over greater distances and generally have greater attractive power. Here we show that calling male Bornean tree-hole frogs (Metaphrynella sundana) actively exploit the acoustic properties of cavities in tree trunks that are partially filled with water and which are primarily used as egg-deposition sites. By tuning their vocalizations to the resonant frequency of the hole, which varies with the amount of water that it contains, these frogs enhance their chances of attracting females.
Mechanics of cutting maneuvers by ostriches (Struthio camelus)
Venue: The Journal of Experimental Biology

We studied the strategies used by cursorial bipeds (ostriches) to maneuver during running. Eight ostriches were induced to run along a trackway and execute turns. Ground reaction forces and three-dimensional kinematics of the body and leg joints were simultaneously recorded, allowing calculation of joint angles and quasi-static net joint torques. Sidesteps, where the leg on the outside of the turn changes the movement direction, and crossovers using the inside leg, occurred with nearly equal frequency. Ostriches executed maneuvers using a simple control strategy that required minimal changes to leg kinematics or net torque production at individual joints. Although ostriches did use acceleration or braking forces to control body rotation, their morphology allowed for both crossovers and sidesteps to be accomplished with minimal net acceleratory/braking force production. Moreover, body roll and ab/adduction of the leg shifted the foot position away from the turn direction, reducing the acceleratory/braking forces required to prevent under- or over-rotation and aligning the leg with the ground reaction force.
The anatomy and ultrastructure of the suctorial organ of Solifugae (Arachnida).
Venue: Arthropod Structure & Development

Solifugae possess an evertable, adhesive pedipalpal organ (suctorial organ) at the tip of the distal tarsus of each pedipalp that is unique among arachnids. When inverted inside the pedipalp, the suctorial organ is covered with two cuticular lips, a dorsal upper lip and a ventral lower lip, but it can be protruded rapidly in order to facilitate grasping prey or climbing on bushes or even climbing on smooth surfaces due to its remarkable adhesive properties. In this study, the suctorial organs of different species from old world families Galeodidae and Karschiidae and new world families Ammotrechidae and Eremobatidae were investigated by means of light microscopy, scanning and transmission electron microscopy. In all representatives, the suctorial organ is formed by an evertable, cuticular pad with a complex internal stabilizing structure. The procuticle of this pad consists of a lattice-like basal plate and numerous stalked structures connected to this basal plate. The shafts of the stalked structures are regularly organized and ramify apically. The surface of the suctorial organ is constituted of a very thin epicuticle overlaying the ramifying apices forming ridges and furrows on the ventral side of the suctorial organ.
Polyphosphoprotein-Containing Marine Adhesives
Venue: Journal of Adhesion

Protein phosphorylation is an important regulator of both cellular and extracellular events. Recently, protein phosphorylation has also emerged as an important process in biological adhesives. During the last decade, Herbert Waite and his group have indeed characterized several polyphosphoproteins from the adhesive secretions of two different marine organisms, mussels and tube-building worms. This suggests the possibility that polyphosphoproteins could be important components of several bioadhesives and may, therefore, be widely distributed throughout the animal kingdom. Many amino acids can be targets for phosphorylation but only phosphoserine (pSer) has been detected to date in marine adhesive proteins. We investigated whether monoclonal antibodies directed against pSer could be used to specifically label polyphosphoproteins in marine adhesives. Antibodies were applied on histological sections through the foot of the mussel Mytilus edulis and through the building organ of the tube-worm Sabellaria alveolata. In both cases, anti-pSer binding was detected in the adhesive glands (phenol gland and cement gland, respectively). However, the intensity of the immunolabeling was different between the two species, being weak in the former and strong in the latter. With the use of these antibodies, a new pSer-rich bioadhesive has been detected in Cuvierian tubules, the sticky defense organs of sea cucumbers. Immunoblots and amino acid analyses confirmed the presence of polyphosphoproteins in the adhesive secretion of the Cuvierian tubules from three species of sea cucumber. These findings bring to three the number of animal groups in which adhesive processes involve polyphosphoproteins and raise interesting questions about the convergent evolution of these adhesives.
Self-cleaning in tree frog toe pads; a mechanism for recovering from contamination without the need for grooming
Venue: The Journal of Experimental Biology

Tree frogs use adhesive toe pads for climbing on a variety of surfaces. They rely on wet adhesion, which is aided by the secretion of mucus. In nature, the pads will undoubtedly get contaminated regularly through usage, but appear to maintain their stickiness over time. Here, we show in two experiments that the toe pads of White's tree frogs (Litoria caerulea) quickly recover from contamination through a self-cleaning mechanism. We compared adhesive forces prior to and after contamination of (1) the whole animal on a rotatable platform and (2) individual toe pads in restrained frogs mimicking individual steps using a motorised stage. In both cases, the adhesive forces recovered after a few steps but this took significantly longer in single toe pad experiments from restrained frogs, showing that use of the pads increases recovery. We propose that both shear movements and a ‘flushing’ effect of the secreted mucus play an important role in shedding particles/contaminants.
Ultrastructure, aggregation-state, and crystal growth of biogenic nanocrystalline sphalerite and wurtzite
Venue: American Mineralogist

In this study, we investigated the size, submicrometer-scale structure, and aggregation state of ZnS formed by sulfate-reducing bacteria (SRB) in a SRB-dominated biofilm growing on degraded wood in cold (T ~ 8 °C), circumneutral-pH (7.2−8.5) waters draining from an abandoned, carbonate-hosted Pb-Zn mine. High-resolution transmission electron microscope (HRTEM) data reveal that the earliest biologically induced precipitates are crystalline ZnS nanoparticles 1−5 nm in diameter. Although most nanocrystals have the sphalerite structure, nanocrystals of wurtzite are also present, consistent with a predicted size dependence for ZnS phase stability. Nearly all the nanocrystals are concentrated into 1−5 μm diameter spheroidal aggregates that display concentric banding patterns indicative of episodic precipitation and flocculation. Abundant disordered stacking sequences and faceted, porous crystalaggregate morphologies are consistent with aggregation-driven growth of ZnS nanocrystals prior to and/or during spheroid formation. Spheroids are typically coated by organic polymers or associated with microbial cellular surfaces, and are concentrated roughly into layers within the biofilm. Size, shape, structure, degree of crystallinity, and polymer associations will all impact ZnS solubility, aggregation and coarsening behavior, transport in groundwater, and potential for deposition by sedimentation. Results presented here reveal nanometer- to micrometer-scale attributes of biologically induced ZnS formation likely to be relevant to sequestration via bacterial sulfate reduction (BSR) of other potential contaminant metal(loid)s, such as Pb2+, Cd2+, As3+ and Hg2+, into metal sulfides. The results highlight the importance of basic mineralogical information for accurate prediction and monitoring of long-term contaminant metal mobility and bioavailability in natural and constructed bioremediation systems. Our observations also provoke interesting questions regarding the role of size-dependent phase stability in biomineralization and provide new insights into the origin of submicrometer- to millimeter-scale petrographic features observed in low-temperature sedimentary sulfide ore deposits.