nils-herrmann/clean_scirepeval huggingface dataset:
Bacterial Recognition of Mineral Surfaces: Nanoscale Interactions Between Shewanella and α-FeOOH
Venue: Science

Force microscopy has been used to quantitatively measure the infinitesimal forces that characterize interactions betweenShewanella oneidensis (a dissimilatory metal-reducing bacterium) and goethite (α-FeOOH), both commonly found in Earth near-surface environments. Force measurements with subnanonewton resolution were made in real time with living cells under aerobic and anaerobic solutions as a function of the distance, in nanometers, between a cell and the mineral surface. Energy values [in attojoules (10−18 joules)] derived from these measurements show that the affinity between S. oneidensis and goethite rapidly increases by two to five times under anaerobic conditions in which electron transfer from bacterium to mineral is expected. Specific signatures in the force curves suggest that a 150-kilodalton putative iron reductase is mobilized within the outer membrane of S. oneidensis and specifically interacts with the goethite surface to facilitate the electron transfer process.
Overcoming the brittleness of glass through bio-inspiration and micro-architecture.
Venue: Nature Communications

Highly mineralized natural materials such as teeth or mollusk shells boast unusual combinations of stiffness, strength and toughness currently unmatched by engineering materials. While high mineral contents provide stiffness and hardness, these materials also contain weaker interfaces with intricate architectures, which can channel propagating cracks into toughening configurations. Here we report the implementation of these features into glass, using a laser engraving technique. Three-dimensional arrays of laser-generated microcracks can deflect and guide larger incoming cracks, following the concept of 'stamp holes'. Jigsaw-like interfaces, infiltrated with polyurethane, furthermore channel cracks into interlocking configurations and pullout mechanisms, significantly enhancing energy dissipation and toughness. Compared with standard glass, which has no microstructure and is brittle, our bio-inspired glass displays built-in mechanisms that make it more deformable and 200 times tougher. This bio-inspired approach, based on carefully architectured interfaces, provides a new pathway to toughening glasses, ceramics or other hard and brittle materials.
Extreme impact and cavitation forces of a biological hammer: strike forces of the peacock mantis shrimp Odontodactylus scyllarus
Venue: The Journal of Experimental Biology

Mantis shrimp are renowned for their unusual method of breaking shells with brief, powerful strikes of their raptorial appendages. Due to the extreme speeds of these strikes underwater, cavitation occurs between their appendages and hard-shelled prey. Here we examine the magnitude and relative contribution of the impact and cavitation forces generated by the peacock mantis shrimp Odontodactylus scyllarus. We present the surprising finding that each strike generates two brief, high-amplitude force peaks, typically 390–480 μs apart. Based on high-speed imaging, force measurements and acoustic analyses, it is evident that the first force peak is caused by the limb's impact and the second force peak is due to the collapse of cavitation bubbles. Peak limb impact forces range from 400 to 1501 N and peak cavitation forces reach 504 N. Despite their small size, O. scyllarus can generate impact forces thousands of times their body weight. Furthermore, on average, cavitation peak forces are 50% of the limb's impact force, although cavitation forces may exceed the limb impact forces by up to 280%. The rapid succession of high peak forces used by mantis shrimp suggests that mantis shrimp use a potent combination of cavitation forces and extraordinarily high impact forces to fracture shells. The stomatopod's hammer is fundamentally different from typical shell-crushing mechanisms such as fish jaws and lobster claws, and may have played an important and as yet unexamined role in the evolution of shell form.
Characterization of cork warts and aerenchyma in leaves of Rhizophora mangle and Rhizophora racemosa
Venue: Journal of The Torrey Botanical Society

Mangroves are a diverse group of plants that inhabit tidal zones in the tropics and sub-tropics. Some mangrove species occupy the lower tidal zone in which the substrate is anoxic for long time periods while some mangroves inhabit the upper tidal zone in which the substrate should be less anoxic. Recent research has shown that about 12 species of mangroves from the Americas and from Australia transport air internally from openings in leaves called cork warts, as air enters leaves it collects within leaf aerenchyma (special air spaces within leaves) where the air expands when heated by sunlight. Aerenchyma in leaves is connected to aerenchyma in stems and stilt roots that lead to small roots in the substrate. Eventually, youngest root tissues are aerated while they grow within the anoxic substrate. Data of this study show that cork warts and leaf aerenchyma develop during leaf initiation in both shoot terminals of branches as well as in viviparous seedlings. The number of cork warts per leaf is similar for leaf primordia and for fully enlarged leaves for both Rhizophora species. Tissue sections of leaves of less than 30 mm2 area show an area of more translucent cells. Leaves with a surface area of 200 mm2 show a distinct aerenchyma tissue in which cells have no contents. For such leaves the depth of aerenchyma was 54 µm with a total leaf depth of 230 µm. Fully enlarged leaves had an aerenchyma depth of about 81 µm while the total leaf thickness was about 660 µm. For all leaves above 30 mm2, aerenchyma comprised 25% of total leaf volume. Densities of cork warts were the same for emerging leaf primordia as for fully enlarged leaves. The results of this study show that cork warts and aerenchyma develop in leaf primordia of both terminal buds and viviparous seedlings. Aerenchyma and cork warts become active once they emerge from their stipular coverings.
Analysis of preload-dependent reversible mechanical interlocking using beetle-inspired wing locking device.
Venue: Langmuir

We report an analysis of preload-dependent reversible interlocking between regularly arrayed, high aspect ratio (AR) polymer micro- and nanofibers. Such a reversible interlocking is inspired from the wing-locking device of a beetle where densely populated microhairs (termed microtrichia) on the cuticular surface form numerous hair-to-hair contacts to maximize lateral shear adhesion. To mimic this, we fabricate various high AR, vertical micro- and nanopillars on a flexible substrate and investigate the shear locking force with different preloads (0.1-10 N/cm(2)). A simple theoretical model is developed based on the competition between van der Waals (VdW) attraction and deflection forces of pillars, which can explain the preload-dependent maximum deflection, tilting angle, and total shear adhesion force.
Cutaneous Water Acquisition by the Thorny Devil (Moloch horridus: Agamidae)
Venue: Journal of Herpetology

The skin of the thorny devil readily absorbs water, like "blotting-paper." The volume of water held in the cutaneous capillary system is about 3.7% of the body mass. Water is conveyed to the mouth by the cutaneous capillary system, where it is imbibed. The low permeability of the skin to evaporative water loss and lack of dyed water absorption suggest that there is not any transcutaneous water absorption across the skin itself. Interscalar channels about 5-50 ;m wide, and an overlapping shelf around the edge of the scales that forms a sub-scalar channel, appear to be the primary cutaneous surface features that are responsible for the "blotting-paper" action of the skin. The capillarity force that absorbs water to the skin supports a pressure head of about 10 cm water. This capillary head is not consistent with the inter-scalar capillarity channel dimension of about 5-50 um, but to about 220 Am. One ecological role of the "blotting-paper" skin of the thorny devil is clearly the direct uptake of rain that falls on the skin or from puddles. In addition, the cutaneous capillary system of the thorny devil enables water absorption
The biology and ecology of the ocean sunfish Mola mola: a review of current knowledge and future research perspectives
Venue: Reviews in Fish Biology and Fisheries

Relatively little is known about the biology and ecology of the world’s largest (heaviest) bony fish, the ocean sunfish Mola mola, despite its worldwide occurrence in temperate and tropical seas. Studies are now emerging that require many common perceptions about sunfish behaviour and ecology to be re-examined. Indeed, the long-held view that ocean sunfish are an inactive, passively drifting species seems to be entirely misplaced. Technological advances in marine telemetry are revealing distinct behavioural patterns and protracted seasonal movements. Extensive forays by ocean sunfish into the deep ocean have been documented and broad-scale surveys, together with molecular and laboratory based techniques, are addressing the connectivity and trophic role of these animals. These emerging molecular and movement studies suggest that local distinct populations may be prone to depletion through bycatch in commercial fisheries. Rising interest in ocean sunfish, highlighted by the increase in recent publications, warrants a thorough review of the biology and ecology of this species. Here we review the taxonomy, morphology, geography, diet, locomotion, vision, movements, foraging ecology, reproduction and species interactions of M. mola. We present a summary of current conservation issues and suggest methods for addressing fundamental gaps in our knowledge.
Neurophysiology: Sensing temperature without ion channels
Venue: Nature

Mammals use cold-sensitive ion channels to translate information about the temperature of their surroundings into electrical signals that are taken up by thermoreceptor nerve cells. Here I investigate the thermoelectric properties of an extracellular gel removed from the electrosensors of sharks, and show that it develops significant voltages in response to tiny temperature gradients. This bulk property of the gel indicates that temperature can be translated into electrical information without the need for ion channels, a sensitivity that may help sharks to locate thermal fronts as feeding areas.
Death by small forces: a fracture and fatigue analysis of wave-swept macroalgae
Venue: The Journal of Experimental Biology

Wave-swept macroalgae are subjected to large hydrodynamic forces as each wave breaks on shore, loads that are repeated thousands of times per day. Previous studies have shown that macroalgae can easily withstand isolated impositions of maximal field forces. Nonetheless, macroalgae break frequently. Here we investigate the possibility that repeated loading by sub-lethal forces can eventually cause fracture by fatigue. We determine fracture toughness, in the form of critical strain energy release rate, for several flat-bladed macroalgae, thereby assessing their resistance to complete fracture in the presence of cracks. Critical energy release rates are evaluated through single-edge-notch, pull-to-break tests and single-edge-notch, repeated-loading tests. Crack growth at sub-critical energy release rates is measured in repeated-loading tests, providing a first assessment of algal breakage under conditions of repeated loading. We then estimate the number of imposed waves required for un-notched algal blades to reach the point of complete fracture. We find that, if not checked by repair, fatigue crack growth from repeated sub-lethal stresses may completely fracture individuals within days. Our results suggest that fatigue may play an important role in macroalgal breakage.
Microtubule assembly dynamics: new insights at the nanoscale.
Venue: Current Opinion in Cell Biology

Although the dynamic self-assembly behavior of microtubule ends has been well characterized at the spatial resolution of light microscopy (~200 nm), the single-molecule events that lead to these dynamics are less clear. Recently, a number of in vitro studies used novel approaches combining laser tweezers, microfabricated chambers, and high-resolution tracking of microtubule-bound beads to characterize mechanochemical aspects of MT dynamics at nanometer scale resolution. In addition, computational modeling is providing a framework for integrating these experimental results into physically plausible models of molecular scale microtubule dynamics. These nanoscale studies are providing new fundamental insights about microtubule assembly, and will be important for advancing our understanding of how microtubule dynamic instability is regulated in vivo via microtubule-associated proteins, therapeutic agents, and mechanical forces.
A poisonous surprise under the coat of the African crested rat
Venue: Proceedings of The Royal Society B: Biological Sciences

Plant toxins are sequestered by many animals and the toxicity is frequently advertised by aposematic displays to deter potential predators. Such ‘unpalatability by appropriation’ is common in many invertebrate groups and also found in a few vertebrate groups. However, potentially lethal toxicity by acquisition has so far never been reported for a placental mammal. Here, we describe complex morphological structures and behaviours whereby the African crested rat, Lophiomys imhausi, acquires, dispenses and advertises deterrent toxin. Roots and bark of Acokanthera schimperi (Apocynaceae) trees are gnawed, masticated and slavered onto highly specialized hairs that wick up the compound, to be delivered whenever the animal is bitten or mouthed by a predator. The poison is a cardenolide, closely resembling ouabain, one of the active components in a traditional African arrow poison long celebrated for its power to kill elephants.
Pyrolobus fumarii, gen. and sp. nov., represents a novel group of archaea, extending the upper temperature limit for life to 113°C
Venue: Extremophiles

A novel, irregular, coccoid-shaped archaeum was isolated from a hydrothermally heated black smoker wall at the TAG site at the Mid Atlantic Ridge (depth 3650 meters). It grew at between 90°C and 113°C (optimum 106°C) and pH 4.0–6.5 (optimum 5.5) and 1%–4% salt (optimum 1.7%). The organism was a facultatively aerobic obligate chemolithoautotroph gaining energy by H2-oxidation. Nitrate, S2O32–, and low concentrations of O2 (up to 0.3% v/v) served as electron acceptors, yielding NH+4, H2S, and H2O as end products, respectively. Growth was inhibited by acetate, pyruvate, glucose, starch, or sulfur. The new isolate was able to form colonies on plates (at 102°C) and to grow at a pressure of 25000 kPa (250 bar). Exponentially growing cultures survived a one-hour autoclaving at 121°C. The GC content was 53mol%. The core lipids consisted of glycerol–dialkyl glycerol tetraethers and traces of 2,3-di-O-phytanyl-sn-glycerol. The cell wall was composed of a surface layer of tetrameric protein complexes arranged on a p4-lattice (center-to-center distance 18.5nm). By its 16S rRNA sequence, the new isolate belonged to the Pyrodictiaceae. Based on its GC-content, DNA homology, S-layer composition, and metabolism, we describe here a new genus, which we name Pyrolobus (the "fire lobe"). The type species is Pyrolobus fumarii (type strain 1A; DSM).
Deep-Sea, Swimming Worms with Luminescent “Bombs”
Venue: Science

Several species of deep-sea polychaete worms have been discovered that have a bizarre predator distraction mechanism. By using remotely operated vehicles, we found seven previously unknown species of swimming annelid worms below 1800 meters. Specimens were large and bore a variety of elaborate head appendages. In addition, five species have pairs of ellipsoidal organs homologous to branchiae that produce brilliant green bioluminescence when autotomized. Five genes were used to determine the evolutionary relationships of these worms within Cirratuliformia. These species form a clade within Acrocirridae and were not closely related to either of the two known pelagic cirratuliforms. Thus, this clade represents a third invasion of the pelagic realm from Cirratuliformia. This finding emphasizes the wealth of discoveries to be made in pelagic and deep demersal habitats.
Elastic modulus of hard tissues.
Venue: Journal of Biomechanics

This work aims at evaluating the elastic modulus of hard biological tissues by considering their staggered platelet micro-structure. An analytical expression for the effective modulus along the stagger direction is formulated using three non-dimensional structural variables. Structures with a single staggered hierarchy (e.g. collagen fibril) are first studied and predictions are compared with the experimental results and finite element simulations from the literature. A more complicated configuration, such as an array of fibrils, is analyzed next. Finally, a mechanical model is proposed for tooth dentin, in which variations in the multi-scale structural hierarchy are shown to significantly affect the macroscopic mechanical properties.
Do epidermal lens cells facilitate the absorptance of diffuse light?
Venue: American Journal of Botany

Many understory plants rely on diffuse light for photosynthesis because direct light is usually scattered by upper canopy layers before it strikes the forest floor. There is a considerable gap in the literature concerning the interaction of direct and diffuse light with leaves. Some understory plants have well-developed lens-shaped epidermal cells, which have long been thought to increase the absorption of diffuse light. To assess the role of epidermal cell shape in capturing direct vs. diffuse light, we measured leaf reflectance and transmittance with an integrating sphere system using leaves with flat (Begonia erythrophylla, Citrus reticulata, and Ficus benjamina) and lens-shaped epidermal cells (B. bowerae, Colocasia esculenta, and Impatiens velvetea). In all species examined, more light was absorbed when leaves were irradiated with direct as opposed to diffuse light. When leaves were irradiated with diffuse light, more light was transmitted and more was reflected in both leaf types, resulting in absorptance values 2-3% lower than in leaves irradiated with direct light. These data suggest that lens-shaped epidermal cells do not aid the capture of diffuse light. Palisade and mesophyll cell anatomy and leaf thickness appear to have more influence in the capture and absorption of light than does epidermal cell shape.
Long-distance transport of gases in plants: a perspective on internal aeration and radial oxygen loss from roots
Venue: Plant Cell and Environment

Internal transport of gases is crucial for vascular plants inhabiting aquatic, wetland or flood-prone environments. Diffusivity of gases in water is approximately 10 000 times slower than in air; thus direct exchange of gases between submerged tissues and the environment is strongly impeded. Aerenchyma provides a low-resistance internal pathway for gas transport between shoot and root extremities. By this pathway, O2 is supplied to the roots and rhizosphere, while CO2, ethylene, and methane move from the soil to the shoots and atmosphere. Diffusion is the mechanism by which gases move within roots of all plant species, but significant pressurized through-flow occurs in stems and rhizomes of several emergent and floating-leaved wetland plants. Through-flows can raise O2 concentrations in the rhizomes close to ambient levels. In general, rates of flow are determined by plant characteristics such as capacity to generate positive pressures in shoot tissues, and resistance to flow in the aerenchyma, as well as environmental conditions affecting leaf-to-air gradients in humidity and temperature. O2 diffusion in roots is influenced by anatomical, morphological and physiological characteristics, and environmental conditions. Roots of many (but not all) wetland species contain large volumes of aerenchyma (e.g. root porosity can reach 55%), while a barrier impermeable to radial O2 loss (ROL) often occurs in basal zones. These traits act synergistically to enhance the amount of O2 diffusing to the root apex and enable the development of an aerobic rhizosphere around the root tip, which enhances root penetration into anaerobic substrates. The barrier to ROL in roots of some species is induced by growth in stagnant conditions, whereas it is constitutive in others. An inducible change in the resistance to O2 across the hypodermis/exodermis is hypothesized to be of adaptive significance to plants inhabiting transiently waterlogged soils. Knowledge on the anatomical basis of the barrier to ROL in various species is scant. Nevertheless, it has been suggested that the barrier may also impede influx of: (i) soil-derived gases, such as CO2, methane, and ethylene; (ii) potentially toxic substances (e.g. reduced metal ions) often present in waterlogged soils; and (iii) nutrients and water. Lateral roots, that remain permeable to O2, may be the main surface for exchange of substances between the roots and rhizosphere in wetland species. Further work is required to determine whether diversity in structure and function in roots of wetland species can be related to various niche habitats.
To bend a coralline: effect of joint morphology on flexibility and stress amplification in an articulated calcified seaweed
Venue: The Journal of Experimental Biology

Previous studies have demonstrated that fleshy seaweeds resist wave-induced drag forces in part by being flexible. Flexibility allows fronds to `go with the flow', reconfiguring into streamlined shapes and reducing frond area projected into flow. This paradigm extends even to articulated coralline algae, which produce calcified fronds that are flexible only because they have distinct joints (genicula). The evolution of flexibility through genicula was a major event that allowed articulated coralline algae to grow elaborate erect fronds in wave-exposed habitats. Here we describe the mechanics of genicula in the articulated coralline Calliarthron and demonstrate how segmentation affects bending performance and amplifies bending stresses within genicula. A numerical model successfully predicted deflections of articulated fronds by assuming genicula to be assemblages of cables connecting adjacent calcified segments (intergenicula). By varying the dimensions of genicula in the model, we predicted the optimal genicular morphology that maximizes flexibility while minimizing stress amplification. Morphological dimensions of genicula most prone to bending stresses (i.e. genicula near the base of fronds) match model predictions.