nils-herrmann/clean_scirepeval huggingface dataset:
The Mechanosensitive Ion Channel MSL10 Potentiates Responses to Cell Swelling in Arabidopsis Seedlings
Venue: Social Science Research Network

The ability to respond to unanticipated increases in volume is a fundamental property of cells, essential for cellular integrity in the face of osmotic challenges. Plants must manage cell swelling during flooding, rehydration, and pathogenesis–but little is known about the mechanisms by which this occurs. It has been proposed that plant cells could sense and respond to cell swelling through the action of mechanosensitive ion channels. Here we develop and characterize a new assay to study the effects of cell swelling on Arabidopsis thaliana seedlings and to test the contributions of the mechanosensitive ion channel MscS-Like10 (MSL10). The assay incorporates both cell wall softening and hypo-osmotic treatment to induce cell swelling. We show that MSL10 is required for previously demonstrated responses to hypo-osmotic shock, including a cytoplasmic calcium transient within the first few seconds, accumulation of ROS within the first 30 minutes, and increased transcript levels of mechano-inducible genes within 60 minutes. We also show that cell swelling induces programmed cell death within 3 hours, also in a MSL10-dependent manner. Finally, we show that MSL10 is unable to potentiate cell swelling-induced death when phosphomimetic residues are introduced into its soluble N-terminus. Thus, MSL10 functions as a phospho-regulated membrane-based sensor that connects the perception of cell swelling to a downstream signaling cascade and programmed cell death.
The phytopathogenic fungus Sclerotinia sclerotiorum detoxifies plant glucosinolate hydrolysis products via an isothiocyanate hydrolase
Venue: Nature Communications

Brassicales plants produce glucosinolates and myrosinases that generate toxic isothiocyanates conferring broad resistance against pathogens and herbivorous insects. Nevertheless, some cosmopolitan fungal pathogens, such as the necrotrophic white mold Sclerotinia sclerotiorum, are able to infect many plant hosts including glucosinolate producers. Here, we show that S. sclerotiorum infection activates the glucosinolate-myrosinase system, and isothiocyanates contribute to resistance against this fungus. S. sclerotiorum metabolizes isothiocyanates via two independent pathways: conjugation to glutathione and, more effectively, hydrolysis to amines. The latter pathway features an isothiocyanate hydrolase that is homologous to a previously characterized bacterial enzyme, and converts isothiocyanate into products that are not toxic to the fungus. The isothiocyanate hydrolase promotes fungal growth in the presence of the toxins, and contributes to the virulence of S. sclerotiorum on glucosinolate-producing plants. Some plants produce toxic isothiocyanates that protect them against pathogens. Here, Chen et al. show that the plant pathogenic fungus Sclerotinia sclerotiorum converts isothiocyanates into non-toxic compounds via glutathione conjugation and, more effectively, via hydrolysis to amines using an isothiocyanate hydrolase.
Stochastic Mechanisms of Cell-Size Regulation in Bacteria.
Venue: Journal of Physical Chemistry Letters

How bacteria are able to maintain their sizes remains an open question. It is believed that cells have narrow distributions of sizes as a consequence of a homeostasis that allows bacteria to function at the optimal conditions. Several phenomenological approaches to explain these observations have been presented, but the microscopic origins of the cell-size regulation are still not understood. Here, we propose a new stochastic approach to investigate the molecular mechanisms of maintaining the cell sizes in bacteria. It is argued that the cell-size regulation is a result of coupling of two stochastic processes, cell growth and division, which eliminates the need for introducing the thresholds. Dynamic properties of the system are explicitly evaluated, and it is shown that the model is consistent with the experimentally supported adder principle of the cell-size regulation. In addition, theoretical predictions agree with experimental observations on E. coli bacteria. Theoretical analysis clarifies some important features of bacterial cell growth.
Architecture of a catalytically active homotrimeric plant cellulose synthase complex
Venue: Science

Plant cell wall construction crew Plants produce a complex cell wall in which cellulose, a glucose polymer, is a major component. Cellulose fibers are formed from close-packed single chains of cellulose that have been proposed to be formed by multimeric complexes (18 or more subunits) of the enzyme cellulose synthase, which exists in several isoforms. Purushotham et al. determined a cryo–electron microscopy structure of a trimer of a single isoform of cellulose synthase. A large channel forms a path for cellulose chains through the membrane-embedded complex. The structure also reveals oligomeric interfaces and provides a framework for modeling the larger complexes seen in plant membranes. The close arrangement of exit sites for nascent glycan chains is consistent with the enzyme complex playing a role in directing cellulose microfibril formation. Science, this issue p. 1089 The structure of a homotrimeric cellulose synthase complex provides molecular insights into cellulose fibril formation. Cellulose is an essential plant cell wall component and represents the most abundant biopolymer on Earth. Supramolecular plant cellulose synthase complexes organize multiple linear glucose polymers into microfibrils as load-bearing wall components. We determined the structure of a poplar cellulose synthase CesA homotrimer that suggests a molecular basis for cellulose microfibril formation. This complex, stabilized by cytosolic plant-conserved regions and helical exchange within the transmembrane segments, forms three channels occupied by nascent cellulose polymers. Secretion steers the polymers toward a common exit point, which could facilitate protofibril formation. CesA’s N-terminal domains assemble into a cytosolic stalk that interacts with a microtubule-tethering protein and may thus be involved in CesA localization. Our data suggest how cellulose synthase complexes assemble and provide the molecular basis for plant cell wall engineering.
Evolutionary diverse Chlamydomonas reinhardtii Old Yellow Enzymes reveal distinctive catalytic properties and potential for whole-cell biotransformations
Venue: Algal Research-Biomass Biofuels and Bioproducts

Old Yellow Enzymes (OYEs) selectively reduce carbon‑carbon double bonds of a broad range of substrates with excellent stereoselectivity. Current challenges of their application in bio-based industrial processes are the cost-efficient regeneration of the nicotinamide co-substrate and expanding the range of industrially relevant substrates. Microalgae represent a rich and mostly untapped source for OYEs with novel catalytic properties and are promising whole-cell factories that regenerate nicotinamide by photosynthesis. By comparative phylogenetics, we identified 20 putative OYEs in eleven algal species. Three recombinant OYEs from the unicellular green alga Chlamydomonas reinhardtii (CrOYEs) reveal diverse biocatalytic properties and potential for enzyme optimization. High substrate conversion activities of living algal wild type and mutant cells linked the biocatalytic profiles to in vivo functionality and demonstrate the potential of microalgae as sources for distinctive OYE activities and for light-driven biotransformations.
Life under quartz: Hypolithic mosses in the Mojave Desert
Venue: PLOS ONE

Several species of dryland cyanobacteria are known to occur as hypoliths under semi-translucent rocks. In the Mojave Desert, these organisms find refuge from intense solar radiation under milky quartz where moisture persists for a longer period of time than in adjacent soil surface habitat. Desert mosses, which are extremely desiccation-tolerant, can also occur in these hypolithic spaces, though little is known about this unique moss microhabitat and how species composition compares to that of adjacent soil surface communities. To address this question, we deployed microclimate dataloggers and collected moss samples from under and adjacent to 18 milky quartz rocks (quartz mean center thickness 26 ± 15 mm) in a western high elevation Mojave Desert site. Light transmission through Mojave quartz rocks may be as low as 1.2%, and data from microclimate loggers deployed for five months support the hypothesis that quartz provides thermal buffering and higher relative humidity compared to the soil surface. Of the 53 samples collected from hypolith and surface microhabitats, 68% were Syntrichia caninervis, the dominant bryophyte of the Mojave Desert biological soil crust. Tortula inermis accounted for 28% of the samples and 4% were Bryum argenteum. In a comparison of moss community composition, we found that S. caninervis was more likely to be on the soil surface, though it was abundant in both microhabitats, while T. inermis was more restricted to hypoliths, perhaps due to protection from temperature extremes. In our study site, the differences between hypolithic and surface microhabitats enable niche partitioning between T. inermis and S. caninervis, enhancing alpha diversity. This work points to the need to thoroughly consider microhabitats when assessing bryophyte species diversity and modelling species distributions. This focus is particularly important in extreme environments, where mosses may find refuge from the prevailing macroclimatic conditions in microhabitats such as hypoliths.
Chromatic neuronal jamming in a primitive brain
Venue: Nature Physics

Jamming models developed in inanimate matter have been widely used to describe cell packing in tissues 1 – 7 , but predominantly neglect cell diversity, despite its prevalence in biology. Most tissues, animal brains in particular, comprise a mix of many cell types, with mounting evidence suggesting that neurons can recognize their respective types as they organize in space 8 – 11 . How cell diversity revises the current jamming paradigm is unknown. Here, in the brain of the flatworm planarian Schmidtea mediterranea , which exhibits remarkable tissue plasticity within a simple, quantifiable nervous system 12 – 16 , we identify a distinct packing state, ‘chromatic’ jamming. Combining experiments with computational modelling, we show that neurons of distinct types form independent percolating networks barring any physical contact. This jammed state emerges as cell packing configurations become constrained by cell type-specific interactions and therefore may extend to describe cell packing in similarly complex tissues composed of multiple cell types. An imaging study of planarian flatworm brains demonstrates that densely packed neural tissues seem to have packing configurations commensurate with a jammed state.
A dynamic broadband reflector built from microscopic silica spheres in the ‘disco’ clam Ctenoides ales
Venue: Journal of the Royal Society Interface

The ‘disco’ or ‘electric’ clam Ctenoides ales (Limidae) is the only species of bivalve known to have a behaviourally mediated photic display. This display is so vivid that it has been repeatedly confused for bioluminescence, but it is actually the result of scattered light. The flashing occurs on the mantle lip, where electron microscopy revealed two distinct tissue sides: one highly scattering side that contains dense aggregations of spheres composed of silica, and one highly absorbing side that does not. High-speed video confirmed that the two sides act in concert to alternate between vivid broadband reflectance and strong absorption in the blue region of the spectrum. Optical modelling suggests that the diameter of the spheres is nearly optimal for scattering visible light, especially at shorter wavelengths which predominate in their environment. This simple mechanism produces a striking optical effect that may function as a signal.
A Clerodane Diterpene from Callicarpa americana Resensitizes Methicillin-Resistant Staphylococcus aureus to ß-Lactam Antibiotics.
Venue: ACS Infectious Diseases

The rise of antibiotic resistance presents a significant healthcare challenge and precludes the use of many otherwise valuable antibiotics. One potential solution to this problem is the use of antibiotics in combination with resistance-modifying agents, compounds that act synergistically with existing antibiotics to resensitize previously resistant bacteria. In this study, 12(S),16ξ-dihydroxycleroda-3,13-dien-15,16-olide, a clerodane diterpene isolated from the medicinal plant Callicarpa americana, was found to synergize with oxacillin against methicillin-resistant Staphylococcus aureus. This synergy was confirmed by checkerboard (FICI = 0.125) and time-kill assays, with a sub-inhibitory dose of 12(S),16ξ-dihydroxycleroda-3,13-dien-15,16-olide causing the effective concentration of oxacillin to fall below the susceptibility breakpoint for S. aureus, a > 32-fold decrease in both cases.
Fires prime terrestrial organic carbon for riverine export to the global oceans
Venue: Nature Communications

Black carbon (BC) is a recalcitrant form of organic carbon (OC) produced by landscape fires. BC is an important component of the global carbon cycle because, compared to unburned biogenic OC, it is selectively conserved in terrestrial and oceanic pools. Here we show that the dissolved BC (DBC) content of dissolved OC (DOC) is twice greater in major (sub)tropical and high-latitude rivers than in major temperate rivers, with further significant differences between biomes. We estimate that rivers export 18 ± 4 Tg DBC year −1 globally and that, including particulate BC fluxes, total riverine export amounts to 43 ± 15 Tg BC year −1 (12 ± 5% of the OC flux). While rivers export ~1% of the OC sequestered by terrestrial vegetation, our estimates suggest that 34 ± 26% of the BC produced by landscape fires has an oceanic fate. Biogeochemical models require modification to account for the unique dynamics of BC and to predict the response of recalcitrant OC export to changing environmental conditions. Black carbon is a recalcitrant and unique form of organic carbon formed from incomplete combustion. Here the authors use global sampling to reduce uncertainty in the flux of terrestrial black carbon to the oceans, predicting that 34% of black carbon produced by fires has an oceanic fate.
Ice-nucleating bacteria control the order and dynamics of interfacial water
Venue: Science Advances

Specialized bacteria trigger ice formation by controlling the molecular structure and energy transfer in interfacial water. Ice-nucleating organisms play important roles in the environment. With their ability to induce ice formation at temperatures just below the ice melting point, bacteria such as Pseudomonas syringae attack plants through frost damage using specialized ice-nucleating proteins. Besides the impact on agriculture and microbial ecology, airborne P. syringae can affect atmospheric glaciation processes, with consequences for cloud evolution, precipitation, and climate. Biogenic ice nucleation is also relevant for artificial snow production and for biomimetic materials for controlled interfacial freezing. We use interface-specific sum frequency generation (SFG) spectroscopy to show that hydrogen bonding at the water-bacteria contact imposes structural ordering on the adjacent water network. Experimental SFG data and molecular dynamics simulations demonstrate that ice-active sites within P. syringae feature unique hydrophilic-hydrophobic patterns to enhance ice nucleation. The freezing transition is further facilitated by the highly effective removal of latent heat from the nucleation site, as apparent from time-resolved SFG spectroscopy.
Viburnum tinus Fruits Use Lipids to Produce Metallic Blue Structural Color
Venue: Current Biology

Viburnum tinus is an evergreen shrub that is native to the Mediterranean region but cultivated widely in Europe and around the world. It produces ripe metallic blue fruits throughout winter . Despite its limited fleshy pulp , its high lipid content [3] makes it a valuable resource to the small birds [4] that act as its seed-dispersers . Here, we find that the metallic blue appearance of the fruits is produced by globular lipid inclusions arranged in a disordered multilayer structure. This structure is embedded in the cell walls of the epicarp and underlaid with a dark layer of anthocyanin pigments. The presence of such large, organized lipid aggregates in plant cell walls represents a new mechanism for structural coloration and may serve as an honest signal of nutritional content.
Comparative Analysis of Tear Composition in Humans, Domestic Mammals, Reptiles, and Birds
Venue: Frontiers in Veterinary Science

Tears are an important component of the ocular surface protection mechanism and are in close contact with the corneal epithelium and the environment. Their composition is well-known in humans; however, there are few investigations on the composition and function of tears in reptiles, birds and others mammals, which would elucidate the mechanisms governing the maintenance of ocular homeostasis. In this work, electrophoretic profiles and an evaluation of total protein, albumin, urea, glucose, and cholesterol concentrations in tears of semi-aquatic, terrestrial, and marine reptiles (Caiman latirostris, Chelonia mydas, Caretta caretta, Eretmochelys imbricata, Lepidochelys olivacea, and Chelonoidis carbonaria), birds (Tyto furcata, Rupornis magnirostris and Ara ararauna), and mammals (Equus caballus and Canis lupus familiaris) were apresented. Human tear components and respective blood serum samples were used as references. The electrophoretic analysis revealed similarities whithin same Classes. The results of the tear–blood serum relationship and the comparison to human tear components showed particularities that are potentially derived from a homeostatic response to the environment. When the tear compositions of animals belonging to different ecological clusters were compared, marked differences were observed in total protein and urea concentrations. Thus, reptile, bird, and mammalian tears are complex fluids with differing concentrations of biochemical components that are potentially a result of the animals' adaptation to different environments.
Human sperm uses asymmetric and anisotropic flagellar controls to regulate swimming symmetry and cell steering.
Venue: Science Advances

Flagellar beating drives sperm through the female reproductive tract and is vital for reproduction. Flagellar waves are generated by thousands of asymmetric molecular components; yet, paradoxically, forward swimming arises via symmetric side-to-side flagellar movement. This led to the preponderance of symmetric flagellar control hypotheses. However, molecular asymmetries must still dictate the flagellum and be manifested in the beat. Here, we reconcile molecular and microscopic observations, reconnecting structure to function, by showing that human sperm uses asymmetric and anisotropic controls to swim. High-speed three-dimensional (3D) microscopy revealed two coactive transversal controls: An asymmetric traveling wave creates a one-sided stroke, and a pulsating standing wave rotates the sperm to move equally on all sides. Symmetry is thus achieved through asymmetry, creating the optical illusion of bilateral symmetry in 2D microscopy. This shows that the sperm flagellum is asymmetrically controlled and anisotropically regularized by fast-signal transduction. This enables the sperm to swim forward.
A symbiotic bacterium of shipworms produces a compound with broad spectrum anti-apicomplexan activity
Venue: PLOS Pathogens

Apicomplexan parasites cause severe disease in both humans and their domesticated animals. Since these parasites readily develop drug resistance, development of new, effective drugs to treat infection caused by these parasites is an ongoing challenge for the medical and veterinary communities. We hypothesized that invertebrate-bacterial symbioses might be a rich source of anti-apicomplexan compounds because invertebrates are susceptible to infections with gregarines, parasites that are ancestral to all apicomplexans. We chose to explore the therapeutic potential of shipworm symbiotic bacteria as they are bona fide symbionts, are easily grown in axenic culture and have genomes rich in secondary metabolite loci . Two strains of the shipworm symbiotic bacterium, Teredinibacter turnerae, were screened for activity against Toxoplasma gondii and one strain, T7901, exhibited activity against intracellular stages of the parasite. Bioassay-guided fractionation identified tartrolon E (trtE) as the source of the activity. TrtE has an EC50 of 3 nM against T. gondii, acts directly on the parasite itself and kills the parasites after two hours of treatment. TrtE exhibits nanomolar to picomolar level activity against Cryptosporidium, Plasmodium, Babesia, Theileria, and Sarcocystis; parasites representing all branches of the apicomplexan phylogenetic tree. The compound also proved effective against Cryptosporidium parvum infection in neonatal mice, indicating that trtE may be a potential lead compound for preclinical development. Identification of a promising new compound after such limited screening strongly encourages further mining of invertebrate symbionts for new anti-parasitic therapeutics.
Ultra-black Camouflage in Deep-Sea Fishes
Venue: Current Biology

At oceanic depths >200 m, there is little ambient sunlight, but bioluminescent organisms provide another light source that can reveal animals to visual predators and prey [1-4]. Transparency and mirrored surfaces-common camouflage strategies under the diffuse solar illumination of shallower waters-are conspicuous when illuminated by directed bioluminescent sources due to reflection from the body surface [5, 6]. Pigmentation allows animals to absorb light from bioluminescent sources, rendering them visually undetectable against the dark background of the deep sea . We present evidence suggesting pressure to reduce reflected bioluminescence led to the evolution of ultra-black skin (reflectance <0.5%) in 16 species of deep-sea fishes across seven distantly related orders. Histological data suggest this low reflectance is mediated by a continuous layer of densely packed melanosomes in the exterior-most layer of the dermis [7, 8] and that this layer lacks the unpigmented gaps between pigment cells found in other darkly colored fishes [9-13]. Using finite-difference, time-domain modeling and comparisons with melanosomes found in other ectothermic vertebrates [11, 13-21], we find the melanosomes making up the layer in these ultra-black species are optimized in size and shape to minimize reflectance. Low reflectance results from melanosomes scattering light within the layer, increasing the optical path length and therefore light absorption by the melanin. By reducing reflectance, ultra-black fish can reduce the sighting distance of visual predators more than 6-fold compared to fish with 2% reflectance. This biological example of efficient light absorption via a simple architecture of strongly absorbing and highly scattering particles may inspire new ultra-black materials.