nils-herrmann/clean_scirepeval huggingface dataset:
Electrical and behavioral courtship displays in the mormyrid fish Brienomyrus brachyistius
Venue: The Journal of Experimental Biology

Mormyrid electric fish rely on the waveform of their electric organ discharges (EODs) for communicating species, sex, and social status, while they use the sequences of pulse intervals (SPIs) for communicating rapidly changing behavioral states and motivation. Little is known of electric signaling during courtship behavior because of two major difficulties: (1) the fish are not easily bred in captivity and (2) there is no reliable means of separating electric signals from several individuals in natural communication settings. Through simulating artificial rain conditions, we have successfully induced courtship and succeeded in breeding a mormyrid electric fish (Brienomyrus brachyistius) in the laboratory. We have also developed a system of video recording and editing combined with cross correlation analysis to precisely record and view behavior and separate EODs from two individuals in non-breeding and breeding contexts. Knowing the electrical and motor patterns during courtship allows for further exploration of topics such as mate choice and neural basis of pattern generation in these fish. Here we describe nine common motor displays and 11 SPIs. Analysis of frequency of occurrences suggests that some SPI patterns are sex and season specific. We also observed electrical duetting called `rasp matching' during courtship signaling among pairs; males and females exchange `rasps' and `bursts', respectively, in alternation. Our study employs new techniques to separate and document SPIs in the context of courtship. We show that some SPIs correlate with specific behavioral acts around the time of spawning.
Aerodynamics of saccate pollen and its implications for wind pollination.
Venue: American Journal of Botany

Pollen grains of many wind-pollinated plants contain 1-3 air-filled bladders, or sacci. Sacci are thought to help orient the pollen grain in the pollination droplet. Sacci also increase surface area of the pollen grain, yet add minimal mass, thereby increasing dispersal distance; however, this aerodynamic hypothesis has not been tested in a published study. Using scanning electron and transmission electron microscopy, mathematical modeling, and the saccate pollen of three extant conifers with structurally different pollen grains (Pinus, Falcatifolium, Dacrydium), we developed a computational model to investigate pollen flight. The model calculates terminal settling velocity based on structural characters of the pollen grain, including lengths, widths, and depths of the main body and sacci; angle of saccus rotation; and thicknesses of the saccus wall, endoreticulations, intine, and exine. The settling speeds predicted by the model were empirically validated by stroboscopic photography. This study is the first to quantitatively demonstrate the adaptive significance of sacci for the aerodynamics of wind pollination. Modeling pollen both with and without sacci indicated that sacci can reduce pollen settling speeds, thereby increasing dispersal distance, with the exception of pollen grains having robust endoreticulations and those with thick saccus walls. Furthermore, because the mathematical model is based on structural characters and error propagation methods show that the model yields valid results when sample sizes are small, the flight dynamics of fossil pollen can be investigated. Several fossils were studied, including bisaccate (Pinus, Pteruchus, Caytonanthus), monosaccate (Gothania), and nonsaccate (Monoletes) pollen types.
Characterization of two new multiforms of Trametes pubescens laccase.
Venue: Bioorganic Chemistry

Electrochemical properties of two multiforms of laccase from Trametes pubescens basidiomycete (LAC1 and LAC2) have been studied. The standard redox potentials of the T1 sites of the enzymes were found to be 746 and 738 mV vs. NHE for LAC1 and LAC2, respectively. Bioelectroreduction of oxygen based on direct electron transfer between each of the two forms of Trametes pubescens laccase and spectrographic graphite electrodes has been demonstrated and studied. It is concluded that the T1 site of laccase is the first electron acceptor, both in solution (homogeneous case) and when the enzymes are adsorbed on the surface of the graphite electrode (heterogeneous case). Thus, the previously proposed mechanism of oxygen bioelectroreduction by adsorbed fungal laccase was additionally confirmed using two forms of the enzyme. Moreover, the assumed need for extracellular laccase to communicate directly and electronically with a solid matrix (lignin) in the course of lignin degradation is discussed. In summary, the possible roles of multiforms of the enzyme based on their electrochemical, biochemical, spectral, and kinetic properties have been suggested to consist in broadening of the substrate specificity of the enzyme, in turn yielding the possibility to dynamically regulate the process of lignin degradation according to the real-time survival needs of the organism.
Diel variation in ammonia excretion, glutamine levels, and hydration status in two species of terrestrial isopods
Venue: Journal of Comparative Physiology B-biochemical Systemic and Environmental Physiology

Terrestrial isopods (suborder Oniscidea) excrete most nitrogen diurnally as volatile ammonia, and ammonia-loaded animals accumulate nonessential amino acids, which may constitute the major nocturnal nitrogen pool. This study explored the relationship between ammonia excretion, glutamine storage/mobilization, and water balance, in two sympatric species Ligidium lapetum (section Diplocheta), a hygric species; and Armadillidium vulgare (Section Crinocheta), a xeric species capable of water-vapor absorption (WVA). Ammonia excretion (12-h), tissue glutamine levels, and water contents were measured following field collection of animals at dusk and dawn. In both species, diurnal ammonia excretion exceeded nocturnal excretion four- to fivefold while glutamine levels increased four- to sevenfold during the night. Most glutamine was accumulated in the somatic tissues (“body wall”). While data support the role of glutamine in nocturnal nitrogen storage, potential nitrogen mobilization from glutamine breakdown (162 μmol g−1 in A. vulgare) exceeds measured ammonia excretion (2.5 μmol g−1) over 60-fold. This may serve to generate the high hemolymph ammonia concentrations % MathType!Translator!2!1!AMS LaTeX.tdl!TeX -- AMS-LaTeX! % MathType!MTEF!2!1!+- % feaafeart1ev1aqatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn % hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr % 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9 % vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x % fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaaiikaiaabg % gacaqGUbGaaeizaiaabccacaqGObGaaeyAaiaabEgacaqGObGaaGjb % VlaadcfadaWgaaWcbaGaaeOtaiaabIeadaWgaaadbaGaaG4maaqaba % aaleqaaOGaaiykaaaa!437A! $$({\text{and high}}\;P_{{\text{NH}}_3 } )$$ seen during volatilization. The energetic cost of ammonia volatilization is discussed in the light of these findings. Mean water contents were similar at dusk and dawn in both species, indicating that diel cycles of water depletion and replenishment were not occurring.
Biological Activities of Rice Allelochemicals Momilactone A and B
Venue: Rice Research: Open Access

Momilactone A and B had been demonstrated to play critical roles in rice allelopathy by the findings of 
physiological and genetical approaches. Rice plants secrete momilactones into the rhizosphere over their entire life cycle at phytotoxic levels, and momilactones are able to account for the majority of the observed rice allelopathy. However, allelopathic activities of momilactones were determined on only a few test plant species. Therefore, this study was to determine the allelopathic activities of momilactones against nine test plant species including weed species, and four rice cultivars. 
Momilactone A and B inhibited Arabidopsis, alfalfa, lettuce, cress, timothy, barnyard grass, E. colonum, crabgrass and ryegrass at concentrations greater than 3 and 0.3 μM, respectively. The inhibition on those test plants was concentration dependent. On the other hand, effectiveness of momilactone A and B on rice cultivars, Koshihikari, Nipponbare, Norin 8 and Sasanishiki was very weak. Those rice cultivars were only inhibited by momilactone A and B at concentrations greater than 300 and 100 μM, respectively. Momilactone A and B may have potential as templates for the development of new plant control substances because of their selective inhibitory activities on weed plant 
species. More importantly, momilactone A and B as allelochemicals in rice may provide a molecular marker for 
breeding and/or engineering efforts directed at increasing allelopathic activity of this critical staple food crop.
Seasonal Adjustment of Solar Heat Gain Independent of Coat Coloration in a Desert Mammal
Venue: Physiological and Biochemical Zoology

Despite the apparent importance of solar radiation as a source of heat for free-living animals, there exists no substantial body of empirical data describing physiological responses to solar radiation under the range of convective conditions likely to occur in nature. We therefore quantified effects of simulated solar radiation and wind on metabolic heat production in the rock squirrel, Spermophilus variegatus. This diurnal mammal inhabits the Sonoran Desert and seasonally replaces its pelage in a fashion in which it retains constant external appearance but incorporates optical and structural changes that are thought to significantly alter heat-transfer properties of the coat. At a given wind speed, the presence of 950 W m⁻² of simulated solar radiation reduces metabolic heat production by 15% (at a wind speed of 4 m s⁻¹) to 37% (at a wind speed of 0.25 m s⁻¹). Independent of effects of irradiance, metabolic heat production significantly increases with wind speed such that as wind speed is increased from 0.25 m s⁻¹ to 4.0 m s⁻¹, metabolic heat production is elevated by 66% (sunlight absent) or 88% (sunlight present). Previous analyses demonstrated that when exposed to identical radiative and convective environments rock squirrels with summer pelages accrue solar heat loads 33%-71% lower than those experienced by animals with winter coats. This reduction of solar heat gain during the extremely hot Sonoran Desert summer apparently constitutes a previously unappreciated mode of thermal adaptation by seasonal adjustment of radiative heat gain without changes in the animal's appearance.
Antipredator Mechanisms of Australian Frogs
Venue: Journal of Herpetology

We examined the antipredator mechanisms of 19 Australian hylid species (two genera) and 23 myobatrachid species (nine genera). Frogs of 39 of the 42 species exhibited one or more defensive mech- anisms (other than escape), including postures, bright coloration, adhesive skin secretions, and/or calls. De- fensive posturing occurred in individuals of 38 species, and varied in relationship to morphology and lo- calization of skin glands. Bright colors, when present, typically were displayed during defensive postures. We documented dramatic geographic variation in the antipredator display of one species, Limnodynastes tasmaniensis. Defensive postures were accompanied by secretions from dorsal skin glands. These secretions were sometimes associated with a distinctive odor. Adhesive skin secretions were present in burrowing frogs of three genera. Defensive calls were emitted by most hylids but none of the myobatrachids. We offer a hypothesis of mimicry to explain the behavior pattern of exposing the bold black and white ventral surface in Pseudophryne and Crinia species.
Microtubule Assembly Dynamics at the Nanoscale
Venue: Current Biology

The labile nature of microtubules is critical for establishing cellular morphology and motility, yet the molecular basis of assembly remains unclear. Here we use optical tweezers to track microtubule polymerization against microfabricated barriers, permitting unprecedented spatial resolution.



We find that microtubules exhibit extensive nanometer-scale variability in growth rate and often undergo shortening excursions, in some cases exceeding five tubulin layers, during periods of overall net growth. This result indicates that the guanosine triphosphate (GTP) cap does not exist as a single layer as previously proposed. We also find that length increments (over 100 ms time intervals, n = 16,762) are small, 0.81 +/- 6.60 nm (mean +/- standard deviation), and very rarely exceed 16 nm (about two dimer lengths), indicating that assembly occurs almost exclusively via single-subunit addition rather than via oligomers as was recently suggested. Finally, the assembly rate depends only weakly on load, with the average growth rate decreasing only 2-fold as the force increases 7-fold from 0.4 pN to 2.8 pN.



The data are consistent with a mechanochemical model in which a spatially extended GTP cap allows substantial shortening on the nanoscale, while still preventing complete catastrophe in most cases.
Impact behaviour of freeze-dried and fresh pomelo (Citrus maxima) peel: influence of the hydration state
Venue: Royal Society Open Science

Pomelos (Citrus maxima) are known for their thick peel which—inter alia—serves as energy dissipator when fruits impact on the ground after being shed. It protects the fruit from splitting open and thus enables the contained seeds to stay germinable and to potentially be dispersed by animal vectors. The main part of the peel consists of a parenchymatous tissue that can be interpreted from a materials point of view as open pored foam whose struts are pressurized and filled with liquid. In order to investigate the influence of the water content on the energy dissipation capacity, drop weight tests were conducted with fresh and with freeze-dried peel samples. Based on the coefficient of restitution it was found that freeze-drying markedly reduces the relative energy dissipation capacity of the peel. Measuring the transmitted force during impact furthermore indicated a transition from a uniform collapse of the foam-like tissue to a progressive collapse due to water extraction. Representing the peel by a Maxwell model illustrates that freeze-drying not only drastically reduces the damping function of the dashpots but also stiffens the springs of the model.
First insights into the chemical defensive system of the erotylid beetle, Tritoma bipustulata
Venue: Chemoecology

The present study provides the first insights into the chemical defensive system of the erotylid beetle, Tritoma bipustulata, and furthermore reports the previously hardly known ability of abdominal reflex bleeding in this coleopteran family. The defensive chemistry of the secretion of pronotal glands, abdominal reflex blood as well as of the haemolymph were analysed by GC-MS. The different secretions were dominated by aromatic compounds; in addition, we detected alkenes, ketones, organic acids as well as a single sesquiterpene. The majority of these detected compounds had strong antimicrobial properties in microbiological assays with entomopathogenic micro-organisms. In feeding bioassays with ants, only benzyl alcohol, benzothiazole, indole and 3-methylindole, detected in the abdominal reflex blood, were significantly deterrent.
Forisomes: calcium-powered protein complexes with potential as 'smart' biomaterials.
Venue: Trends in Biotechnology

Sieve tubes in legumes contain forisomes, which are spindle-like bodies that are composed of ATP-independent, mechanically active proteins. Upon injury, forisomes occlude sieve tubes by dispersion and thus, help to prevent loss of nutrient-rich transport sap. Forisome enlargement by dispersion is brought about by Ca2+-induced conformational changes that confer radial expansion and longitudinal contraction. Forisomes recontract upon Ca2+ removal. In vitro, forisomes reversibly disperse and contract in the presence or absence of Ca2+, respectively, and at distinct pHs. Recently, forisomes have received renewed attention because of their unique capacity to convert chemical into mechanical energy independent of high-energy organic compounds. Forisome-based 'smart' materials can be used to produce self-powered monitoring and diagnostic systems. Here, we focus on physiological, chemical and physical aspects of forisomes and discuss their potential as biomimetic devices.
THE SPLASH-CUP DISPERSAL MECHANISM IN PLANTS
Venue: Botany

The late Prof. A. H. R. Buller regarded certain cup-shaped reproductive bodies found among cryptogams as "splash-cups" which make use of the energy of raindrops for the dispersal of spores, sperms, and gemmae. Buller's concepts are presented and supplemented by investigations carried out since his death. Raindrops cause the peridioles of the Nidulariaceae or bird's-nest fungi to be thrown about four feet by splash action. In the genus Cyathus, as a peridiole is jerked out of its cup, the funiculus is torn and this makes possible the expansion of a mass of adhesive hyphae (the hapteron) which clings to any object in the line of flight. The momentum of the peridiole causes a long cord to be pulled out of a sheath attached to the peridiole. The peridiole is checked in flight and the jerk causes the funicular cord to become wound around stems or entangled among plant hairs. Thus the peridiole becomes attached to vegetation and may be eaten subsequently by herbivorous animals. Several morphological features of...
Cooperating to compete: altruism, sexual selection and causes of male reproductive cooperation
Venue: Animal Behaviour

Competition among males for access to reproductive opportunities is a central tenet of behavioural biology that has critical implications for studies of mating systems, sexual selection and the evolution of numerous phenotypic traits. Given the expectation that males should compete vigorously for access to females, it may at first seem paradoxical that males in some species cooperate to reproduce, often resulting in the apparent sacrifice of direct fitness by some members of these cooperative partnerships. Because this form of cooperation lies at the interface between natural, sexual and kin selection, studies of the adaptive consequences of male reproductive cooperation may yield important insights into how complex and sometimes conflicting selective pressures shape individual behaviour. Here, we define and review examples of reproductive cooperation among male animals. We take an integrative approach to reviewing the potential causes of maleemale cooperation, including potential adaptive hypotheses, ecological correlates, phylogenetic patterns and physiological mechanisms. The impact of male reproductive cooperation on sexual selection theory is also discussed. We conclude by outlining several important directions for future research, including efforts to improve understanding of the ecological and demographic contexts in which male reproductive cooperation occurs. Collectively, such analyses promise to improve our understanding of multiple fundamental concepts in evolutionary biology.
Volumetric imaging of shark tail hydrodynamics reveals a three-dimensional dual-ring vortex wake structure
Venue: Proceedings of The Royal Society B: Biological Sciences

Understanding how moving organisms generate locomotor forces is fundamental to the analysis of aerodynamic and hydrodynamic flow patterns that are generated during body and appendage oscillation. In the past, this has been accomplished using two-dimensional planar techniques that require reconstruction of three-dimensional flow patterns. We have applied a new, fully three-dimensional, volumetric imaging technique that allows instantaneous capture of wake flow patterns, to a classic problem in functional vertebrate biology: the function of the asymmetrical (heterocercal) tail of swimming sharks to capture the vorticity field within the volume swept by the tail. These data were used to test a previous three-dimensional reconstruction of the shark vortex wake estimated from two-dimensional flow analyses, and show that the volumetric approach reveals a different vortex wake not previously reconstructed from two-dimensional slices. The hydrodynamic wake consists of one set of dual-linked vortex rings produced per half tail beat. In addition, we use a simple passive shark-tail model under robotic control to show that the three-dimensional wake flows of the robotic tail differ from the active tail motion of a live shark, suggesting that active control of kinematics and tail stiffness plays a substantial role in the production of wake vortical patterns.
Colour-producing β-keratin nanofibres in blue penguin (Eudyptula minor) feathers
Venue: Biology Letters

The colours of living organisms are produced by the differential absorption of light by pigments (e.g. carotenoids, melanins) and/or by the physical interactions of light with biological nanostructures, referred to as structural colours. Only two fundamental morphologies of non-iridescent nanostructures are known in feathers, and recent work has proposed that they self-assemble by intracellular phase separation processes. Here, we report a new biophotonic nanostructure in the non-iridescent blue feather barbs of blue penguins (Eudyptula minor) composed of parallel β-keratin nanofibres organized into densely packed bundles. Synchrotron small angle X-ray scattering and two-dimensional Fourier analysis of electron micrographs of the barb nanostructure revealed short-range order in the organization of fibres at the appropriate size scale needed to produce the observed colour by coherent scattering. These two-dimensional quasi-ordered penguin nanostructures are convergent with similar arrays of parallel collagen fibres in avian and mammalian skin, but constitute a novel morphology for feathers. The identification of a new class of β-keratin nanostructures adds significantly to the known mechanisms of colour production in birds and suggests additional complexity in their self-assembly.