nils-herrmann/clean_scirepeval huggingface dataset:
A small proportion of Talin molecules transmit forces at developing muscle attachments in vivo
Venue: PLOS Biology

Cells in developing organisms are subjected to particular mechanical forces that shape tissues and instruct cell fate decisions. How these forces are sensed and transmitted at the molecular level is therefore an important question, one that has mainly been investigated in cultured cells in vitro. Here, we elucidate how mechanical forces are transmitted in an intact organism. We studied Drosophila muscle attachment sites, which experience high mechanical forces during development and require integrin-mediated adhesion for stable attachment to tendons. Therefore, we quantified molecular forces across the essential integrin-binding protein Talin, which links integrin to the actin cytoskeleton. Generating flies expressing 3 Förster resonance energy transfer (FRET)-based Talin tension sensors reporting different force levels between 1 and 11 piconewton (pN) enabled us to quantify physiologically relevant molecular forces. By measuring primary Drosophila muscle cells, we demonstrate that Drosophila Talin experiences mechanical forces in cell culture that are similar to those previously reported for Talin in mammalian cell lines. However, in vivo force measurements at developing flight muscle attachment sites revealed that average forces across Talin are comparatively low and decrease even further while attachments mature and tissue-level tension remains high. Concomitantly, the Talin concentration at attachment sites increases 5-fold as quantified by fluorescence correlation spectroscopy (FCS), suggesting that only a small proportion of Talin molecules are mechanically engaged at any given time. Reducing Talin levels at late stages of muscle development results in muscle–tendon rupture in the adult fly, likely as a result of active muscle contractions. We therefore propose that a large pool of adhesion molecules is required to share high tissue forces. As a result, less than 15% of the molecules experience detectable forces at developing muscle attachment sites at the same time. Our findings define an important new concept of how cells can adapt to changes in tissue mechanics to prevent mechanical failure in vivo.
Superhydrophobic diving flies (Ephydra hians) and the hypersaline waters of Mono Lake
Venue: Proceedings of the National Academy of Sciences of the United States of America

Superhydrophobic surfaces have been of key academic and commercial interest since the discovery of the so-called lotus effect in 1977. The effect of different ions on complex superhydrophobic biological systems, however, has received little attention. By bringing together ecology, biomechanics, physics, and chemistry our study provides insight into the ion-specific effects of wetting in the presence of sodium carbonate and its large-scale consequences. By comparing the surface structure and chemistry of the alkali fly—an important food source for migrating birds—to other species we show that their uniquely hydrophobic properties arise from very small physical and chemical changes, thereby connecting picoscale physics with globally important ecological impacts. The remarkable alkali fly, Ephydra hians, deliberately crawls into the alkaline waters of Mono Lake to feed and lay eggs. These diving flies are protected by an air bubble that forms around their superhydrophobic cuticle upon entering the lake. To study the physical mechanisms underlying this process we measured the work required for flies to enter and leave various aqueous solutions. Our measurements show that it is more difficult for the flies to escape from Mono Lake water than from fresh water, due to the high concentration of Na2CO3 which causes water to penetrate and thus wet their setose cuticle. Other less kosmotropic salts do not have this effect, suggesting that the phenomenon is governed by Hofmeister effects as well as specific interactions between ion pairs. These effects likely create a small negative charge at the air–water interface, generating an electric double layer that facilitates wetting. Compared with six other species of flies, alkali flies are better able to resist wetting in a 0.5 M Na2CO3 solution. This trait arises from a combination of factors including a denser layer of setae on their cuticle and the prevalence of smaller cuticular hydrocarbons compared with other species. Although superbly adapted to resisting wetting, alkali flies are vulnerable to getting stuck in natural and artificial oils, including dimethicone, a common ingredient in sunscreen and other cosmetics. Mono Lake’s alkali flies are a compelling example of how the evolution of picoscale physical and chemical changes can allow an animal to occupy an entirely new ecological niche.
Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology
Venue: Proceedings of the National Academy of Sciences of the United States of America

Vital biological processes such as gene transcription and cell division may be severely impaired by inevitable entanglements ensuing from the extreme length and confinement of the genome. The family of topoisomerase proteins has independently evolved in different organisms to resolve these topological problems, yet no existing model can explain how topoisomerase alone can reduce the topological complexity of DNA in vivo. We propose that a synergistic mechanism between topoisomerase and a family of slip-link–like proteins called structural maintenance of chromosomes (SMC) can provide a pathway to systematically resolve topological entanglements even under physiological crowding and confinement. Given the ubiquity of topoisomerase and SMC, we argue that the uncovered mechanism is at work throughout the cell cycle and across different organisms. Topological entanglements severely interfere with important biological processes. For this reason, genomes must be kept unknotted and unlinked during most of a cell cycle. Type II topoisomerase (TopoII) enzymes play an important role in this process but the precise mechanisms yielding systematic disentanglement of DNA in vivo are not clear. Here we report computational evidence that structural-maintenance-of-chromosomes (SMC) proteins—such as cohesins and condensins—can cooperate with TopoII to establish a synergistic mechanism to resolve topological entanglements. SMC-driven loop extrusion (or diffusion) induces the spatial localization of essential crossings, in turn catalyzing the simplification of knots and links by TopoII enzymes even in crowded and confined conditions. The mechanism we uncover is universal in that it does not qualitatively depend on the specific substrate, whether DNA or chromatin, or on SMC processivity; we thus argue that this synergy may be at work across organisms and throughout the cell cycle.
Geometry and self-righting of turtles
Venue: Proceedings of The Royal Society B: Biological Sciences

Terrestrial animals with rigid shells face imminent danger when turned upside down. A rich variety of righting strategies of beetle and turtle species have been described, but the exact role of the shell's geometry in righting is so far unknown. These strategies are often based on active mechanisms, e.g. most beetles self-right via motion of their legs or wings; flat, aquatic turtles use their muscular neck to flip back. On the other hand, highly domed, terrestrial turtles with short limbs and necks have virtually no active control: here shape itself may serve as a fundamental tool. Based on field data gathered on a broad spectrum of aquatic and terrestrial turtle species we develop a geometric model of the shell. Inspired by recent mathematical results, we demonstrate that a simple mechanical classification of the model is closely linked to the animals' righting strategy. Specifically, we show that the exact geometry of highly domed terrestrial species is close to optimal for self-righting, and the shell's shape is the predominant factor of their ability to flip back. Our study illustrates how evolution solved a far-from-trivial geometrical problem and equipped some turtles with monostatic shells: beautiful forms, which rarely appear in nature otherwise.
Spider dragline silk as torsional actuator driven by humidity
Venue: Science Advances

Spider dragline silk exhibits a self-powered torsion actuation driven by humidity, potentially acting as a novel torsional actuator. Self-powered actuation driven by ambient humidity is of practical interest for applications such as hygroscopic artificial muscles. We demonstrate that spider dragline silk exhibits a humidity-induced torsional deformation of more than 300°/mm. When the relative humidity reaches a threshold of about 70%, the dragline silk starts to generate a large twist deformation independent of spider species. The torsional actuation can be precisely controlled by regulating the relative humidity. The behavior of humidity-induced twist is related to the supercontraction behavior of spider dragline silk. Specifically, molecular simulations of MaSp1 and MaSp2 proteins in dragline silk reveal that the unique torsional property originates from the presence of proline in MaSp2. The large proline rings also contribute to steric exclusion and disruption of hydrogen bonding in the molecule. This property of dragline silk and its structural origin can inspire novel design of torsional actuators or artificial muscles and enable the development of designer biomaterials.
Detecting a Prey in a Spider Orb Web
Venue: Siam Journal on Applied Mathematics

We consider the inverse problem of localizing a prey hitting a spider orb-web from dynamic measurements taken near the center of the web, where the spider is supposed to stay. The actual discrete orb-web, formed by a finite number of radial and circumferential threads, is modelled as a continuous membrane. The membrane has a specific fibrous structure, which is inherited from the original discrete web, and it is subject to tensile pre-stress in the referential configuration. The transverse load describing the prey's impact is assumed of the form $g(t)f(x)$, where $g(t)$ is a known function of time and $f(x)$ is the unknown term depending on the position variable $x$. For axially-symmetric orb-webs supported at the boundary and undergoing infinitesimal transverse deformations, we prove a uniqueness result for $f(x)$ in terms of measurements of the transverse dynamic displacement taken on an arbitrarily small and thin ring centered at the origin of the web, for a sufficiently large interval of time.
Type-I collagen fibrils: From growth morphology to local order
Venue: European Physical Journal E

The length of type-I collagen fibrils in solution increases through the development and progress of pointed tips appearing successively at the two ends of an axis-symmetric shaft with constant diameter. Those tips, respectively fine ($\alpha$α) or coarse ($ \beta$β) have opposite molecular orientations. The $\alpha$α-pointed tips, the first to appear, are particularly remarkable as they all show, on most of their length, a common parabolic profile which stays constant during the growth. Assuming that the latter occurs by lateral accretion of individual molecules in staggered configuration, we propose to give account of this prominent morphological feature along a purely geometrical argument, the profile of a tip being linked to the shape of the trajectories followed all along the accretion process. Among several possible trajectories, Fermat spirals lead to a parabolic profile in perfect agreement with the one observed for $\alpha$α-pointed tips. This is to be put in relation with the presence of such spirals in phyllotactic patterns which ensure the best packing efficiency in cases of axis-symmetry, which is indeed that of dense collagen fibrils. Moreover, those patterns are structured by concentric circles of dislocations, constitutive of the structure itself, whose behaviour might contribute to the mechanical properties of the fibrils.
Delay of ice formation on penguin feathers
Venue: European Physical Journal-special Topics

Cold-weather penguins continually dive in and out of the water and get splashed by waves during the frigid Antarctic winter. Yet, even under these extreme sub-zero conditions, macroscopic ice crystals are typically not observed on their feathers. In this work, we hypothesize that the origin of the anti-icing properties of a cold-weather penguin’s feathers comes from a unique combination of the feather’s macroscopic structure, the nanoscale topography of its barbules, and the hydrophobicity of its preen oil. We show that, the combination of all three, make cold-weather penguin feathers both highly water repellant and icephobic. In this paper, we present the results from a series of droplet freezing experiments performed on feathers from a number of species of both cold-weather and warm-weather penguins. Compared to a smooth glass substrate, freezing was delayed by a factor of 30-times for drops deposited on warm-weather penguin feathers and 60-times for cold-weather penguins. The difference in freezing time between warm- and cold-weather penguins was statistically significant and can be attributed to the increase in the contact angle measured between the drop and the feather of the cold-weather penguin. This increased contact angle is the result of an increase in the hydrophobicity of the preen oil and the inclusion of nanoscale, air-trapping dimples on the surface of the barbules. The physics of this delay are explained through the development of a simple heat transfer model which demonstrates that increasing contact angle is a primary cause of increased freezing time and icephobicity. The results of this study can be used to motivate the designs of biomimetic surfaces to minimize ice formation in extreme conditions for a number of important engineering applications.
Copper-bottomed: electrochemically active bacteria exploit conductive sulphide networks for enhanced electrogeneity
Venue: Energy and Environmental Science

In this study, we demonstrate that anodic electroactive bacteria like Geobacter sulfurreducens generate copper(I) and copper(II) sulphides when grown on copper electrodes. The insoluble copper sulphides form a conductive network within the biofilms, strongly enhancing the biofilm electrogeneity – i.e., the ability of the biofilm to produce electric currents. Compared to biofilms grown on graphite, the average relative current density of copper-based biofilms was 237%, with a maximum geometric current density of 1.59 ± 0.23 mA cm−2. An additional electrochemical CuS deposition prior to biofilm cultivation further increased the bioelectrocatalytic current generation to 2 mA cm−2. The chemical deposition of CuS onto graphite allowed cultivating biofilms with current densities 134% higher than at unmodified graphite. This approach – the chemical CuS deposition onto inexpensive electrode materials – thus represents a promising pathway for the development of scalable, high-performance electrode materials for microbial electrochemical technologies.
Nickel hyperaccumulation mechanisms: a review on the current state of knowledge
Venue: Plant and Soil

BackgroundHyperaccumulator plants are unusual plants that accumulate particular metals or metalloids, such as nickel, zinc, cadmium and arsenic, in their living tissues to concentrations that are hundreds to thousands of times greater than what is normal for most plants. The hyperaccumulation phenomenon is rare (exhibited by less than 0.2% of all angiosperms), with most of the ~500 hyperaccumulator species known globally for nickel.ScopeThis review highlights the contemporary understanding of nickel hyperaccumulation processes, which include root uptake and sequestration, xylem loading and transport, leaf compartmentation and phloem translocation processes.ConclusionsHyperaccumulator plants have evolved highly efficient physiological mechanisms for taking up nickel in their roots followed by rapid translocation and sequestration into the aerial shoots. The uptake of nickel is mainly involved with low affinity transport systems, presumably from the ZIP family. The presence of high concentrations of histidine prevents nickel sequestration in roots. Nickel is efficiently loaded into the xylem, where it mainly presents as Ni2+. The leaf is the main storage organ, which sequestrates nickel in non-active sites, e.g. vacuoles and apoplast. Recent studies show that phloem translocates high levels of nickel, which has a strong impact on nickel accumulation in young growing tissues.
Universal elastic mechanism for stinger design
Venue: Nature Physics

Living organisms use stingers that vary in length L over eight orders of magnitude, from a few tens of nanometres to several metres, across a wide array of biological taxa. Despite the extreme variation in size, their structures are strikingly similar. However, the mechanism responsible for this remarkable morphological convergence remains unknown. Using basic physical arguments and biomimetic experiments, we reveal an optimal design strategy that links their length, base diameter d 0 , Young’s modulus E and friction force per unit area μ p 0 . This principle can be framed simply as $${d}_{0} \approx {(\mu {p}_{0}/E)}^{1/3}L$$ d 0 ≈ ( μ p 0 / E ) 1 / 3 L . Existing data from measurements on viruses, algae, marine invertebrates, terrestrial invertebrates, plants, terrestrial vertebrates, marine vertebrates—as well as man-made objects such as nails, needles and weapons—are consistent with our predictions. Our results highlight the evolutionary adaptation of mechanical traits to the constraints imposed by friction, elastic stability and cost. The structures of stingers of living organisms are surprisingly similar despite their vastly different lengths. Now, stingers are found to obey a unifying mechanistic principle that characterizes the stingers resistance to buckling.
Compact nanoscale textures reduce contact time of bouncing droplets
Venue: Science Advances

Compact nanoscale textures reduce contact time of bouncing droplets with implications in insect survival and miniature drones. Many natural surfaces are capable of rapidly shedding water droplets—a phenomenon that has been attributed to the presence of low solid fraction textures (Φs ~ 0.01). However, recent observations revealed the presence of unusually high solid fraction nanoscale textures (Φs ~ 0.25 to 0.64) on water-repellent insect surfaces, which cannot be explained by existing wetting theories. Here, we show that the contact time of bouncing droplets on high solid fraction surfaces can be reduced by reducing the texture size to ~100 nm. We demonstrated that the texture size–dependent contact time reduction could be attributed to the dominance of line tension on nanotextures and that compact arrangement of nanotextures is essential to withstand the impact pressure of raindrops. Our findings illustrate a potential survival strategy of insects to rapidly shed impacting raindrops, and suggest a previously unidentified design principle to engineering robust water-repellent materials for applications including miniaturized drones.
Undulation enables gliding in flying snakes
Venue: Nature Physics

When flying snakes glide, they use aerial undulation. To determine if aerial undulation is a flight control strategy or a non-functional behavioural vestige of lateral undulation, we measured snake glides using high-speed motion capture and developed a new dynamical model of gliding. Reconstructions of the snake’s wing-body reveal that aerial undulation is composed of horizontal and vertical waves, whose phases differ by 90° and whose frequencies differ by a factor of two. Using these results, we developed a three-dimensional mathematical model of snake flight that incorporates aerodynamic and inertial effects. Although simulated glides without undulation attained some horizontal distance, they are biologically unrealistic because they failed due to roll and pitch instabilities. In contrast, the inclusion of undulation stabilized the rotational motion and markedly increased glide performance. This work demonstrates that aerial undulation in snakes serves a different function than known uses of undulation in other animals, and suggests a new template of control for dynamic flying robots. Observations of flying snakes inform the development of a dynamical model of gliding taking undulation into account. This work suggests that aerial undulation has a different function in snakes than in other animals.
Social immunity in insects
Venue: Current Biology

When animals become sick, infected cells and an armada of activated immune cells attempt to eliminate the pathogen from the body. Once infectious particles have breached the body's physical barriers of the skin or gut lining, an initially local response quickly escalates into a systemic response, attracting mobile immune cells to the site of infection. These cells complement the initial, unspecific defense with a more specialized, targeted response. This can also provide long-term immune memory and protection against future infection. The cell-autonomous defenses of the infected cells are thus aided by the actions of recruited immune cells. These specialized cells are the most mobile cells in the body, constantly patrolling through the otherwise static tissue to detect incoming pathogens. Such constant immune surveillance means infections are noticed immediately and can be rapidly cleared from the body. Some immune cells also remove infected cells that have succumbed to infection. All this prevents pathogen replication and spread to healthy tissues. Although this may involve the sacrifice of some somatic tissue, this is typically replaced quickly. Particular care is, however, given to the reproductive organs, which should always remain disease free (immune privilege).