nils-herrmann/clean_scirepeval huggingface dataset:
Carotenoid fluorescence in Dunaliella salina
Venue: Journal of Applied Phycology

Dunaliella salina is a halotolerant green alga that is well known for its carotenoid producing capacity. The produced carotenoids are mainly stored in lipid globules. For various research purposes, such as production and extraction kinetics, we would like to determine and/or localise the carotenoid globules in vivo. In this study, we show that the carotenoid-rich globules emit clear green fluorescence, which can be used in, for example, fluorescence microscopy (e.g. CLSM) to obtain pictures of the cells and their carotenoid content.
The Molecular Basis of Nacre Formation
Venue: Science

A protein complex guides the process of nacre formation in mollusk shells. The mechanisms that determine the structural features of organisms are complex, and we are still far from predicting the structure of an organism by looking at its genetic makeup. An additional level of complexity exists for organisms that form body parts composed of mineralized structures such as sea shells, bone, and teeth. These organisms must also carefully control the interfaces between the soft body parts and the growing mineral. On page 1388 in this issue, Suzuki et al. (1) identify two novel proteins, Pif80 and Pif97, as key players in controlling the crystal structure of calcium carbonate (CaCO3) in the pearl-forming oyster Pinctada fucata. The work provides the most complete data set to date for the role of any known protein involved in mollusk biomineralization. The methods used in this study may be widely applied in future studies in this field.
Earthworm bioluminescence: characterization of high specific activity Diplocardia longa luciferase and the reaction it catalyzes.
Venue: Biochemistry

Diplocardia longa luciferase purified by an improved procedure differs from that first described by Bellisario et al. [Bellisario, R., Spencer, T. E., & Cormier, M. J. (1972) Biochemistry 11, 2256-2266] in having much higher specific activity (40X) and firmly bound, EPR-silent copper. Improved assay conditions suggest that this protein acts as a catalyst in a bioluminescent reaction involving the degradation of 3-(isovalerylamino)-1-hydroxypropane hydroperoxide. This substrate is formed spontaneously on the addition of hydrogen peroxide to D. longa luciferin (3-(isovalerylamino)propanal). The quantum yield of the bioluminescence for this substrate is 3%. Detailed physical and chemical analyses of high specific activity D. longa luciferase indicate that it is a large (300000 daltons), asymmetric (f/fo=1.63, with 0.4 g/g hydration), multisubunit enzyme. It contains carbohydrate (6%), lipid (2%), and copper (up to 4 mol/30000 daltons). The amino acid composition is unusual with 11% by weight of the residues being either proline or hydroxyproline.
Feeding mechanisms of adult Lepidoptera: structure, function, and evolution of the mouthparts.
Venue: Annual Review of Entomology

The form and function of the mouthparts in adult Lepidoptera and their feeding behavior are reviewed from evolutionary and ecological points of view. The formation of the suctorial proboscis encompasses a fluid-tight food tube, special linking structures, modified sensory equipment, and novel intrinsic musculature. The evolution of these functionally important traits can be reconstructed within the Lepidoptera. The proboscis movements are explained by a hydraulic mechanism for uncoiling, whereas recoiling is governed by the intrinsic proboscis musculature and the cuticular elasticity. Fluid uptake is accomplished by the action of the cranial sucking pump, which enables uptake of a wide range of fluid quantities from different food sources. Nectar-feeding species exhibit stereotypical proboscis movements during flower handling. Behavioral modifications and derived proboscis morphology are often associated with specialized feeding preferences or an obligatory switch to alternative food sources.
THE RESPONSES OF THE PUPIL OF GEKKO GEKKO TO EXTERNAL LIGHT STIMULUS
Venue: The Journal of General Physiology

1. The responses of the pupil of a nocturnal gecko (Gekko gekko) to external light stimulus were studied. 2. The responses of the pupil are determined by light entering the pupil and not by light acting directly on the iris. 3. The responses of the pupil are very uniform in sensitivity including spectral sensitivity for light coming in different directions to the eye. 4. The possible change in area of the pupil is more than 300-fold and probably represents an effort to shield the pure rod retina from saturating light intensities. 5. The pupil continues to contract sharply for changes in external light intensity which give retinal illuminations corresponding to 106 quanta/sec. striking a retinal rod. 6. There is a large degree of spatial summation of the response; circular external light fields subtending 5 and 140° giving the same illumination at the pupil give approximately the same pupil response. 7. The spectral sensitivity curve agrees with the absorption curve of an extracted pigment from a closely related gecko described by Crescitelli in the followig paper. It is similar to the human scotopic curve but its maximum is displaced about 20 to 30 mµ towards the red end of the spectrum. The fall in sensitivity towards the red end of the spectrum is described by the equation See PDF for Equation
Iron conservation by reduction of metalloenzyme inventories in the marine diazotroph Crocosphaera watsonii
Venue: Proceedings of the National Academy of Sciences of the United States of America

The marine nitrogen fixing microorganisms (diazotrophs) are a major source of nitrogen to open ocean ecosystems and are predicted to be limited by iron in most marine environments. Here we use global and targeted proteomic analyses on a key unicellular marine diazotroph Crocosphaera watsonii to reveal large scale diel changes in its proteome, including substantial variations in concentrations of iron metalloproteins involved in nitrogen fixation and photosynthesis, as well as nocturnal flavodoxin production. The daily synthesis and degradation of enzymes in coordination with their utilization results in a lowered cellular metalloenzyme inventory that requires ∼40% less iron than if these enzymes were maintained throughout the diel cycle. This strategy is energetically expensive, but appears to serve as an important adaptation for confronting the iron scarcity of the open oceans. A global numerical model of ocean circulation, biogeochemistry and ecosystems suggests that Crocosphaera’s ability to reduce its iron-metalloenzyme inventory provides two advantages: It allows Crocosphaera to inhabit regions lower in iron and allows the same iron supply to support higher Crocosphaera biomass and nitrogen fixation than if they did not have this reduced iron requirement.
The mechanics of the adhesive locomotion of terrestrial gastropods
Venue: The Journal of Experimental Biology

Research on the adhesive locomotion of terrestrial gastropods is gaining renewed interest as it provides a source of guidance for the design of soft biomimetic robots that can perform functions currently not achievable by conventional rigid vehicles. The locomotion of terrestrial gastropods is driven by a train of periodic muscle contractions (pedal waves) and relaxations (interwaves) that propagate from their tails to their heads. These ventral waves interact with a thin layer of mucus secreted by the animal that transmits propulsive forces to the ground. The exact mechanism by which these propulsive forces are generated is still a matter of controversy. Specifically, the exact role played by the complex rheological and adhesive properties of the mucus is not clear. To provide quantitative data that could shed light on this question, we use a newly developed technique to measure, with high temporal and spatial resolution, the propulsive forces that terrestrial gastropods generate while crawling on smooth flat surfaces. The traction force measurements demonstrate the importance of the finite yield stress of the mucus in generating thrust and are consistent with the surface of the ventral foot being lifted with the passage of each pedal wave. We also show that a forward propulsive force is generated beneath each stationary interwave and that this net forward component is balanced by the resistance caused by the outer rim of the ventral foot, which slides at the speed of the center of mass of the animal. Simultaneously, the animal pulls the rim laterally inward. Analysis of the traction forces reveals that the kinematics of the pedal waves is far more complex than previously thought, showing significant spatial variation (acceleration/deceleration) as the waves move from the tail to the head of the animal.
Botany: A record-breaking pollen catapult
Venue: Nature

The release of stored elastic energy often drives rapid movements in animal systems, and plant components employing this mechanism should be able to move with similar speed. Here we describe how the flower stamens of the bunchberry dogwood (Cornus canadensis) rely on this principle to catapult pollen into the air as the flower opens explosively. Our high-speed video observations show that the flower opens in less than 0.5 ms — to our knowledge, the fastest movement so far recorded in a plant.
Absence of eye shine and tapetum in the heterogeneous eye of Anthocharis butterflies (Pieridae)
Venue: The Journal of Experimental Biology

Insect eyes are composed of spectrally heterogeneous ommatidia, typically with three different types. The ommatidial heterogeneity in butterflies can be identified non-invasively by the colorful eye shine, the reflection from the tapetal mirror located at the proximal end of the ommatidia, which can be observed by epi-illumination microscopy. Since the color of eye shine is determined by the spectral properties of the ommatidia, it has been tentatively related to color vision. In the course of a survey of ommatidial heterogeneity in butterflies, we found that members of the pierid genus Anthocharis lack the eye shine. We therefore carried out anatomy of the eye of the yellow tip, Anthocharis scolymus, and correlated it with the absence of the tapetum. The butterfly tapetum is a remnant of the ancestral moth tapetum, a trait that has been completely lost in the papilionids and also, as now appears, in the genus Anthocharis. Anatomical investigations also revealed that, considering rhabdom shape, peri-rhabdomal pigment clusters and autofluorescence, the ommatidia can be divided in at least two different types, which are randomly distributed in the retina.
New functional insights into the internal architecture of the laminated anchor spicules of Euplectella aspergillum
Venue: Proceedings of the National Academy of Sciences of the United States of America

The remarkable properties of biological structural materials can often be attributed to the composite arrangement of their constituents. This paper focuses on the high-aspect-ratio, load-bearing, glassy skeletal fibers (spicules) of the marine sponge Euplectella aspergillum. Considering that the spicules’ internal architecture cannot be repaired or remodeled, we hypothesize that there is a connection between their internal structure and their strength. Using a newly developed structural mechanics model for composite beams, we demonstrate that the unique internal geometry that maximizes a beam’s strength correlates well with the geometry observed in the native spicules. This bio-inspired design strategy for increasing a beam's strength has implications for a new generation of man-made structural materials. To adapt to a wide range of physically demanding environmental conditions, biological systems have evolved a diverse variety of robust skeletal architectures. One such example, Euplectella aspergillum, is a sediment-dwelling marine sponge that is anchored into the sea floor by a flexible holdfast apparatus consisting of thousands of anchor spicules (long, hair-like glassy fibers). Each spicule is covered with recurved barbs and has an internal architecture consisting of a solid core of silica surrounded by an assembly of coaxial silica cylinders, each of which is separated by a thin organic layer. The thickness of each silica cylinder progressively decreases from the spicule’s core to its periphery, which we hypothesize is an adaptation for redistributing internal stresses, thus increasing the overall strength of each spicule. To evaluate this hypothesis, we created a spicule structural mechanics model, in which we fixed the radii of the silica cylinders such that the force transmitted from the surface barbs to the remainder of the skeletal system was maximized. Compared with measurements of these parameters in the native sponge spicules, our modeling results correlate remarkably well, highlighting the beneficial nature of this elastically heterogeneous lamellar design strategy. The structural principles obtained from this study thus provide potential design insights for the fabrication of high-strength beams for load-bearing applications through the modification of their internal architecture, rather than their external geometry.
In vitro study of magnesium-calcite biomineralization in the skeletal materials of the seastar Pisaster giganteus.
Venue: Chemistry: A European Journal

The mechanisms of formation of biogenic magnesium-rich calcite remain an enigma. Here we present ultrastructural and compositional details of ossicles from the seastar Pisaster giganteus (Echinodermata, Asteroidea). Powder X-ray diffraction, infrared spectroscopy and elemental analyses confirm that the ossicles are composed of magnesium-rich calcite, whilst also containing about 0.01 % (w/w) of soluble organic matrix (SOM) as an intracrystalline component. Amino acid analysis and N-terminal sequencing revealed that this mixture of intracrystalline macromolecules consists predominantly of glycine-rich polypeptides. In vitro calcium carbonate precipitation experiments indicate that the SOM accelerates the conversion of amorphous calcium carbonate (ACC) into its final crystalline product. From this observation and from the discovery of ACC in other closely related taxa, it is suggested that substitution of magnesium into the calcite lattice through a transient precursor phase may be a universal phenomenon prevalent across the phylum echinodermata.
The mammalian auditory hair cell: a simple electric circuit model.
Venue: Journal of the Acoustical Society of America

A model based on the potassium current pathway through the hair cell is used to analyze the electrical behavior of mammalian inner and outer hair cells. Without taking into account the effects of calcium it is possible to simulate experimental results concerning the shape and strength of the receptor potential and the frequency dependent ac (alternating current) and dc (direct current) components of the receptor current. This model and a simplified form of it are utilized to explain: (1) Transduction latencies: that the receptor potential follows a stimulating signal with a very short delay, under the assumption of a constant number of open K+ channels in the lateral part of the cell membrane. (2) Transduction gains: why higher potential changes are measured in inner hair cells than in outer hair cells, although the outer hair cells are expected to be exposed to higher stereociliary motions: in inner hair cells a decrease in the conductance of the basolateral membrane causes higher gain (receptor potential increases) and together with an increase of membrane capacitance slower reaction (a larger time constant). (3) Transduction channel kinetics: that the shortest (0.1 ms) as well as the longest (20 ms) possible open times of the transduction channels in the stereocilia have different frequency related effects on the shape of the receptor potentials.
Ultraviolet reflecting photonic microstructures in the King Penguin beak
Venue: Biology Letters

King and emperor penguins (Aptenodytes patagonicus and Aptenodytes forsteri) are the only species of marine birds so far known to reflect ultraviolet (UV) light from their beaks. Unlike humans, most birds perceive UV light and several species communicate using the near UV spectrum. Indeed, UV reflectance in addition to the colour of songbird feathers has been recognized as an important signal when choosing a mate. The king penguin is endowed with several highly coloured ornaments, notably its beak horn and breast and auricular plumage, but only its beak reflects UV, a property considered to influence its sexual attraction. Because no avian UV-reflecting pigments have yet been identified, the origin of such reflections is probably structural. In an attempt to identify the structures that give rise to UV reflectance, we combined reflectance spectrophotometry and morphological analysis by both light and electron microscopy, after experimental removal of surface layers of the beak horn. Here, we characterize for the first time a multilayer reflector photonic microstructure that produces the UV reflections in the king penguin beak.
Geographic variation in halogenated furanones from the red alga Delisea pulchra and associated herbivores and epiphytes
Venue: Marine Ecology Progress Series

We examine patterns of quantitative variation in halogenated furanones, secondary metabolites of Delisea pulchra (Rhodophyta; Bonnemaisoniales), and how this relates to variation in local abundance of herbivores and epiphytes. Fifteen populations of D. pulchra covering a distance of 650 km of temperate southeastern Australia were sampled. Concentrations of the 4 main furanones in D. pulchra (Compounds 1 to 4) showed large variability but there was no latitudinal trend to this variation. We found significant variation in the concentrations of both total and individual furanones among locations, between summer and winter, and between different life-history stages. Importantly, the range of total furanone concentration among plants within locations was large, often varying by an order of magnitude or more. A total of 5 species of herbivorous fish, 7 species of macroinvertebrate grazer and 6 groups of mesograzer (of varying taxonomic level) were found at the 15 locations. The abundance of both total macroinvertebrate grazers and total mesograzers known to consume D. pul- chra varied significantly among locations. However, correlations between furanones and the abun- dance of macroinvertebrate grazers and mesograzers at the scale of location were all weak and non- significant, as was the correlation between furanones and the abundance of epiphytes on D. pulchra. The large variability in concentrations of furanones, and the absence of any positive relationships between furanones, herbivores and epiphytes, suggest that quantitative variation in furanones in D. pulchra is not driven by population-level selection or induction, but is more likely to be a result of small-scale variation in environmental factors such as nutrients and light, and genetic differences among individual plants.
The eyes of oilbirds (Steatornis caripensis): pushing at the limits of sensitivity
Venue: Naturwissenschaften

An extreme example of a low light-level lifestyle among flying birds is provided by the oilbird, Steatornis caripensis (Steatornithidae, Caprimulgiformes). Oilbirds breed and roost in caves, often at sufficient depth that no daylight can penetrate, and forage for fruits at night. Using standard microscopy techniques we investigated the retinal structure of oilbird eyes and used an ophthalmoscopic reflex technique to determine the parameters of these birds’ visual fields. The retina is dominated by small rod receptors (diameter 1.3±0.2 μm; length 18.6±0.6 μm) arranged in a banked structure that is unique among terrestrial vertebrates. This arrangement achieves a photoreceptor density that is the highest so far recorded (≈1,000,000 rods mm−2) in any vertebrate eye. Cone photoreceptors are, however, present in low numbers. The eye is relatively small (axial length 16.1±0.2 mm) with a maximum pupil diameter of 9.0±0.0 mm, achieving a light-gathering capacity that is the highest recorded in a bird (f-number ≈1.07). The binocular field has a maximum width of 38° and extends vertically through 100° with the bill projecting towards the lower periphery; a topography that suggests that vision is not used to control bill position. We propose that oilbird eyes are at one end of the continuum that juxtaposes the conflicting fundamental visual capacities of sensitivity and resolution. Thus, while oilbird visual sensitivity may be close to a maximum, visual resolution must be low. This explains why these birds employ other sensory cues, including olfaction and echolocation, in the control of their behaviour in low-light-level environments.
Function of blue iridescence in tropical understorey plants
Venue: Journal of the Royal Society Interface

The blue colouration seen in the leaves of Selaginella willdenowii is shown to be iridescent. Transmission electron microscopy studies confirm the presence of a layered lamellar structure of the upper cuticle of iridescent leaves. Modelling of these multi-layer structures suggests that they are responsible for the blue iridescence, confirming the link between the observed lamellae and the recorded optical properties. Comparison of blue and green leaves from the same plant indicates that the loss of the blue iridescence corresponds to a loss of the multi-layer structure. The results reported here do not support the idea that iridescence in plants acts to enhance light capture of photosynthetically important wavelengths. The reflectance of light in the range 600–700 nm is very similar for both iridescent and non-iridescent leaves. However, owing to the occurrence of blue colouration in a wide variety of shade dwelling plants it is probable that this iridescence has some adaptive benefit. Possible adaptive advantages of the blue iridescence in these plants are discussed.
Conservation of essential design features in coiled coil silks.
Venue: Molecular Biology and Evolution

Silks are strong protein fibers produced by a broad array of spiders and insects. The vast majority of known silks are large, repetitive proteins assembled into extended beta-sheet structures. Honeybees, however, have found a radically different evolutionary solution to the need for a building material. The 4 fibrous proteins of honeybee silk are small ( approximately 30 kDa each) and nonrepetitive and adopt a coiled coil structure. We examined silks from the 3 superfamilies of the Aculeata (Hymenoptera: Apocrita) by infrared spectroscopy and found coiled coil structure in bees (Apoidea) and in ants (Vespoidea) but not in parasitic wasps of the Chrysidoidea. We subsequently identified and sequenced the silk genes of bumblebees, bulldog ants, and weaver ants and compared these with honeybee silk genes. Each species produced orthologues of the 4 small fibroin proteins identified in honeybee silk. Each fibroin contained a continuous predicted coiled coil region of around 210 residues, flanked by 23-160 residue length N- and C-termini. The cores of the coiled coils were unusually rich in alanine. There was extensive sequence divergence among the bee and ant silk genes (<50% similarity between the alignable regions of bee and ant sequences), consistent with constant and equivalent divergence since the bee/ant split (estimated to be 155 Myr). Despite a high background level of sequence diversity, we have identified conserved design elements that we propose are essential to the assembly and function of coiled coil silks.