nils-herrmann/clean_scirepeval huggingface dataset:
Evolution of the metathoracic tympanal ear and its mesothoracic homologue in the Macrolepidoptera (Insecta)
Venue: Zoomorphology

Two independent methods of comparison, serial homology and phylogenetic character mapping, are employed to investigate the evolutionary origin of the noctuoid moth (Noctuoidea) ear sensory organ. First, neurobiotin and Janus green B staining techniques are used to describe a novel mesothoracic chordotonal organ in the hawkmoth, Manduca sexta, which is shown to be serially homologous to the noctuoid metathoracic tympanal organ. This chordotonal organ comprises a proximal scolopidial region with three bipolar sensory cells, and a long flexible strand (composed of attachment cells) that connects peripherally to an unspecialized membrane ventral to the axillary cord of the fore-wing. Homology to the tympanal chordotonal organ in the Noctuoidea is proposed from anatomical comparisons of the meso- and metathoracic nerve branches and their corresponding peripheral attachment sites. Second, the general structure (noting sensory cell numbers, gross anatomy, and location of peripheral attachment sites) of both meso- and metathoracic organs is surveyed in 23 species representing seven superfamilies of the Lepidoptera. The structure of the wing-hinge chordotonal organ in both thoracic segments was found to be remarkably conserved in all superfamilies of the Macrolepidoptera examined except the Noctuoidea, where fewer than three cells occur in the metathoracic ear (one cell in representatives of the Notodontidae and two cells in those of other families examined), and at the mesothoracic wing-hinge (two cells) in the Notodontidae only. By mapping cell numbers onto current phylogenies of the Macrolepidoptera, we demonstrate that the three-celled wing-hinge chordotonal organ, believed to be a wing proprioceptor, represents the plesiomorphic state from which the tympanal organ in the Noctuoidea evolved. This ’trend toward simplicity’ in the noctuoid ear contrasts an apparent ’trend toward complexity’ in several other insect hearing organs where atympanate homologues have been studied. The advantages to having fewer rather than more cells in the moth ear, which functions primarily to detect the echolocation calls of bats, is discussed.
Use of an Oligoribonucleotide Containing the Polypurine Tract Sequence as a Primer by HIV Reverse Transcriptase (*)
Venue: Journal of Biological Chemistry

A primary site for initiation of plus strand DNA synthesis in human immunodeficiency virus (HIV) corresponds to a 19-nucleotide-long purine rich sequence located just upstream of the U3 region, designated the polypurine tract (PPT). The HIV reverse transcriptase (RT) uses its RNase H activity to cut the genomic RNA after minus strand DNA synthesis. A plus strand PPT primer is formed, extended, and then removed. In vitro, the HIV-RT recognizes this primer specifically, using it much more efficiently than other RNA primers. However, the PPT still primes significantly less efficiently than DNA primers. The 19-nucleotide PPT primer is partially resistant to degradation when compared with other oligoribonucleotides. Prior to initiation of DNA synthesis, several nucleotides are removed by the RT from the 3′ ends of some of the PPT primers. Cleavage is enhanced in the absence of dNTPs. We suggest that DNA synthesis suppresses primer degradation, so that primer extension and cleavage occur in proper sequence. As a result of 3′ end degradation, PPT elongation products contain 5′-RNA segments from 16 to 19 nucleotides in length. These shorter segments are also generated from a longer transcript containing the PPT sequence, indicating that they are not created as a result of binding of the RT to the 5′ end of the PPT oligoribonucleotide. Full-length and shorter versions of the PPT primers are cleaved from the extended DNA by RT. These experiments show that HIV-RT has a specificity to generate a primer in the region of the PPT but that the ends of the primer are not well defined.
How Delisea pulchra furanones affect quorum sensing and swarming motility in Serratia liquefaciens MG1.
Venue: Microbiology

Halogenated furanones produced by the benthic marine macroalga Delisea pulchra inhibit swarming motility of Serratia liquefaciens MG1. This study demonstrates that exogenously added furanones control transcription of the quorum sensing regulated gene swrA in competition with the cognate signal molecule N:-butanoyl-L-homoserine lactone. This in turn results in reduced production of the surface-active compound serrawettin W2, which is crucial for surface translocation of the differentiated swarm cells. It is demonstrated that furanones interfere with interspecies communication during swarming of mixed cultures and that the mode of interference in quorum-sensing control and interspecies communication is not through inhibition of autoinducer synthesis.
Coral Fluorescent Proteins as Antioxidants
Venue: PLOS ONE

A wide array of fluorescent proteins (FP) is present in anthozoans, although their biochemical characteristics and function in host tissue remain to be determined. Upregulation of FP's frequently occurs in injured or compromised coral tissue, suggesting a potential role of coral FPs in host stress responses.  The presence of FPs was determined and quantified for a subsample of seven healthy Caribbean coral species using spectral emission analysis of tissue extracts. FP concentration was correlated with the in vivo antioxidant potential of the tissue extracts by quantifying the hydrogen peroxide (H2O2) scavenging rates. FPs of the seven species varied in both type and abundance and demonstrated a positive correlation between H2O2 scavenging rate and FP concentration. To validate this data, the H2O2 scavenging rates of four pure scleractinian FPs, cyan (CFP), green (GFP), red (RFP) and chromoprotein (CP), and their mutant counterparts (without chromophores), were investigated. In vitro, each FP scavenged H2O2 with the most efficient being CP followed by equivalent activity of CFP and RFP. Scavenging was significantly higher in all mutant counterparts.  Both naturally occurring and pure coral FPs have significant H2O2 scavenging activity. The higher scavenging rate of RFP and the CP in vitro is consistent with observed increases of these specific FPs in areas of compromised coral tissue. However, the greater scavenging ability of the mutant counterparts suggests additional roles of scleractinian FPs, potentially pertaining to their color. This study documents H2O2 scavenging of scleractinian FPs, a novel biochemical characteristic, both in vivo across multiple species and in vitro with purified proteins. These data support a role for FPs in coral stress and immune responses and highlights the multi-functionality of these conspicuous proteins.
Does cooperation increase helpers' later success as breeders? A test of the skills hypothesis in the cooperatively displaying lance-tailed manakin.
Venue: Journal of Animal Ecology

Experience improves individual performance in many tasks. Pre-breeding cooperation may provide important experience that improves later success as a breeder, offering one compelling explanation for why some individuals delay reproduction to help others breed (the 'skills hypothesis'). However, confounding effects of age, quality and alternative selective benefits have complicated rigorous tests of this hypothesis. Male lance-tailed manakins perform cooperative courtship displays involving partnerships between unrelated alpha and beta males, and alphas monopolize resulting copulations. Beta males therefore do not receive immediate direct or indirect fitness benefits, but may gain skills during cooperation that increase their later success as an alpha. To date, however, the effect of cooperative experience on later success as a breeder has never been tested in any cooperatively displaying taxon. The effects of prior cooperative experience on reproductive success of alpha lance-tailed manakins were analysed in a mixed model framework using 12 years of information on cooperative experience and annual and lifetime genetic reproductive success for 57 alpha males. Models included previously identified effects of age and alpha tenure. Individual-level random effects controlled for quality differences to test for an independent influence of beta experience on success. Males accumulated up to 5 years of beta experience before becoming alphas, but 42·1% of alphas had no prior beta experience. Betas became alphas later in life, and experienced significantly lower reproductive success in their final year as alpha than males that were never beta, but did not have higher lifetime success or longer alpha tenures. Differences in patterns of annual siring success were best explained by age-dependent patterns of reproductive improvement and senescence among alphas, not beta experience. Cooperative experience does not increase relative breeding success for male lance-tailed manakins. Importantly, beta cooperation seems to be an alternative reproductive tactic that yields fitness payoffs equivalent to a non-cooperative route to alpha status, if population growth rate is stable.
Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation.
Venue: Biochimica et Biophysica Acta

Conceptually, the simplest way to synthesize an organic molecule is to construct it one carbon at a time. The Wood-Ljungdahl pathway of CO(2) fixation involves this type of stepwise process. The biochemical events that underlie the condensation of two one-carbon units to form the two-carbon compound, acetate, have intrigued chemists, biochemists, and microbiologists for many decades. We begin this review with a description of the biology of acetogenesis. Then, we provide a short history of the important discoveries that have led to the identification of the key components and steps of this usual mechanism of CO and CO(2) fixation. In this historical perspective, we have included reflections that hopefully will sketch the landscape of the controversies, hypotheses, and opinions that led to the key experiments and discoveries. We then describe the properties of the genes and enzymes involved in the pathway and conclude with a section describing some major questions that remain unanswered.
The functional morphology and attachment mechanism of pandarid adhesion pads (Crustacea: Copepoda: Pandaridae)
Venue: Zoologischer Anzeiger – A Journal of Comparative Zoology

The attachment mechanism of pandarid adhesion pads is described from observations of their externally ridged structure and internal construction in three species; Pandarus bicolor Leach, 1816, Dinemoura latifolia (Steenstrup and Lutken, 1861) and Echthrogaleus coleoptratus (Guerin-Meneville, 1837). The host's external skin morphology was also examined, since parasite attachment mechanism and host surface can be considered as components of a single system. The results emphasise the importance of the physical nature of the pad's surface. This is inferred from the compliance of the cuticle and subsurface structure, and the presence of cuticular ridging. The pads probably prevent pandarids from being dislodged by hydrodynamic drag, by increasing overall adhesion. It is proposed that this is achieved in different ways, by two types of adhesion pad identified here, distinguishable by their external structure and location. Type I pads are suggested to remove interfacial water and increase surface contact by one of two contrasting methods. The ridges may act as tyre treads, by channelling water from the contact surface. Alternatively, the channels between ridges may be hydrophobic and behave as dewetting structures, preventing water from entering in the same way that troughs between surface nodules function to produce superhydrophobicity on lotus leaves. Type I adhesion pads are also suggested to aid attachment by hindering the process of peeling, by which they are thought to be removed by hydrodynamic drag. Type II pads are more likely to function as one-way frictional attachments. Both types of pad appear to be attached passively, since they lack muscles inserting into them. The adhesive mechanism of each, which functions most effectively on hard surfaces, may explain why pads are absent or reduced on pandarids which parasitise the softer, unscaled surfaces of hosts. Pandarids predominantly parasitise the skin and fins of fast-swimming sharks. This may be because the scales are characteristically smaller in these species and are more easily encircled by the primary attachment appendages, the maxillipeds. This is thought to be the first published report to reveal frictional attachment structures from the Crustacea, which have convergently evolved in many terrestrial Arthropoda.
Jackrabbit ears: surface temperatures and vascular responses.
Venue: Science

Blood flow to the ear pinnae is curtailed at ambient temperatures of between 1.4 degrees and 24 degrees C, which minimizes heat loss across the pinnae and allows the surfaces of erect pinnae to approach ambient temperature. The pinnae are warmed by steady or pulsatile vasodilation in some animals when the ambient temperature is between 1 degree and 9 degrees C below body temperature, a response favoring heat loss. When ambient temperature exceeds body temperature by 4 degrees to 5 degrees C, the pinnae are circulated with blood cooler than ambient temperature; this response favors heat influx.
The winter diet of the Atlantic Puffin Fratercula arctica around the Faroe Islands
Venue: Ibis

Most mortality of Atlantic Puffins occurs outside the breeding season but little is known about the species’ diet at that time. The stomach contents of 176 Puffins shot legally for food around the Faroe Islands between October and January in three winters were examined. The remains of 20 species of fish, six species of crustacea and single species of polychaete, chaetognathid and squid were identified. The most frequently recorded prey in terms of frequency of occurrence were 0 group (<1 year old) Lesser Sandeel Ammodytes marinus (82% of stomachs), followed by mesopelagic fish (52%), nereid worms (41%), Silver Rockling Gaidropsarus argentatus (36%), crustacea (35%), large sandeel (32%) and other large fish (32%). In terms of calculated biomass, nereids (41%), large sandeel (23%) and other large fish (17%) made up the bulk of the diet but the latter two prey types were most important in energetic terms (46% despite accounting for only 9% of items). Stomach contents collected on the same day and location were significantly more similar than those collected on different dates and locations, suggesting that during the winter, Puffins are generalists, taking any prey they encounter.
The detection of carbonation by the Drosophila gustatory system
Venue: Nature

There are five known taste modalities in humans: sweet, bitter, sour, salty and umami (the taste of monosodium glutamate). Although the fruitfly Drosophila melanogaster tastes sugars, salts and noxious chemicals, the nature and number of taste modalities in this organism is not clear. Previous studies have identified one taste cell population marked by the gustatory receptor gene Gr5a that detects sugars, and a second population marked by Gr66a that detects bitter compounds. Here we identify a novel taste modality in this insect: the taste of carbonated water. We use a combination of anatomical, calcium imaging and behavioural approaches to identify a population of taste neurons that detects CO2 and mediates taste acceptance behaviour. The taste of carbonation may allow Drosophila to detect and obtain nutrients from growing microorganisms. Whereas CO2 detection by the olfactory system mediates avoidance, CO2 detection by the gustatory system mediates acceptance behaviour, demonstrating that the context of CO2 determines appropriate behaviour. This work opens up the possibility that the taste of carbonation may also exist in other organisms.
Force production and flow structure of the leading edge vortex on flapping wings at high and low Reynolds numbers
Venue: The Journal of Experimental Biology

The elevated aerodynamic performance of insects has been attributed in part to the generation and maintenance of a stable region of vorticity known as the leading edge vortex (LEV). One explanation for the stability of the LEV is that spiraling axial flow within the vortex core drains energy into the tip vortex, forming a leading-edge spiral vortex analogous to the flow structure generated by delta wing aircraft. However, whereas spiral flow is a conspicuous feature of flapping wings at Reynolds numbers (Re) of 5000, similar experiments at Re=100 failed to identify a comparable structure. We used a dynamically scaled robot to investigate both the forces and the flows created by a wing undergoing identical motion at Re of∼ 120 and ∼1400. In both cases, motion at constant angular velocity and fixed angle of attack generated a stable LEV with no evidence of shedding. At Re=1400, flow visualization indicated an intense narrow region of spanwise flow within the core of the LEV, a feature conspicuously absent at Re=120. The results suggest that the transport of vorticity from the leading edge to the wake that permits prolonged vortex attachment takes different forms at different Re.
Analysis of an ultra hard magnetic biomineral in chiton radular teeth
Venue: Materials Today

Recent analyses of the ultrastructural and mechanical properties of mineralized biological materials have demonstrated some common architectural features that can help explain their observed damage tolerance. Nature has accomplished this feat through the precise control of anisotropic crystal nucleation and growth processes in conjunction with nanoscale control over the self-assembly of spatially distinct organic and inorganic phases, resulting in effective inhibition of crack propagation through these materials. One such example is found in the hyper-mineralized and abrasion resistant radular teeth of the chitons, a group of herbivorous marine mollusks who have the surprising capacity to erode away the rocky substrates on which they graze 1-4 . Through the use of modern microscopy and nanomechanical characterization techniques, we describe the architectural and mechanical properties of the radular teeth from Cryptochiton stelleri. Chiton teeth are shown to exhibit the largest hardness and stiffness of any biominerals reported to date, being notably as much as three-fold harder than human enamel and the calcium carbonate-based shells of mollusks. We explain how the unique multi-phasic design of these materials contributes not only to their functionality, but also highlights some interesting design principles that might be applied to the fabrication of synthetic composites.
Intraspecific Directed Deterrence by the Mustard Oil Bomb in a Desert Plant
Venue: Current Biology

Plant secondary metabolites (SMs) acting as defensive chemicals in reproductive organs such as fruit tissues play roles in both mutualistic and antagonistic interactions between plants and seed dispersers/predators. The directed-deterrence hypothesis states that SMs in ripe fruits deter seed predators but have little or no effect on seed dispersers. Indeed, studies have demonstrated that birds are able to cope with fruit SMs whereas rodents are deterred by them. However, this mechanism was only demonstrated at the class level, i.e., between birds and mammals, based on differences in the vanilloid receptors. Here we present experimental and behavioral data demonstrating the use of the broad-range, class-independent "mustard oil bomb" mechanism in Ochradenus baccatus fruits to force a behavioral change at an ecological timescale, converting rodents from seed predators to seed dispersers. This is achieved by a unique compartmentalization of the mustard oil bomb, causing activation of the system only upon seed and pulp coconsumption, encouraging seed dispersal via seed spitting by rodents. Our findings demonstrate the power of SMs to shift the animal-plant relationship from predation to mutualism and provide support for the directed-deterrence hypothesis at the intraspecific level, in addition to the interspecific level.
Water Transport by Sandgrouse
Venue: BioScience

Water transport in the feathers of birds is not unique to the sandgrouse, but the sandgrouse have developed the technique to a stage far beyond that of any other bird. That this should have happened in birds of arid zones is not surprising; what is not immediately obvious is how it happened. The first documented accounts of water transport in sandgrouse are of captive males carrying water in their belly feathers to their young (Meade-Waldo 1896, 1897, 1906, 1921, St. Quintin 1905). These observations were disbelieved and discredited by later ornithologists (e.g., Hile and Etch6copar 1957, Meinertzhagen 1954, Stegmann 1969). Meinertzhagen even went so far as to initiate the myth that the male sandgrouse regurgitates water from his crop to the incubating female and that both sexes provide their young with water in this way. This has since proven to be patently untrue. Why it should have been necessary to fabricate a story when the truth was so much more fascinating and worthy of investigation, is hard to understand.
Battle in the Amazon: Arapaima versus Piranha
Venue: Advanced Engineering Materials

The scales of the Arapaimas, a large freshwater fish (up to 200 kg), are a superb example of a natural material that has evolved to provide protection against predators. The Arapaimas lives primarily in Amazon basin lakes that become infested with piranhas as the dry season advances and is covered with scales having up to 10 cm length. They have a collagen interior with a highly mineralized external layer. The collagen fibers form a cross-lamellar arrangement which produces a laminate composite. The internal collagenous layer provides the flexibility to the scales, which can undergo significant elastic deformation prior to failure, providing considerable toughness. The mineralized exterior provides the required protection against predation. The flexibility of the biomineral is enabled by two factors: (i) a corrugated configuration in which the tensile strains are minimized; (ii) a graded composition. We propose herein that the structure of the scales, a composite consisting of a mineralized external layer with surface corrugations and an internal flexible collagenous foundation, can serve as inspiration for the design of flexible composites having a hard ceramic surface. The piranha (Serrasalminae) is one of the principal predators in seasonal lakes, in which fish get trapped. Its teeth form triangular arrays creating a guillotine action that is highly effective in slicing through muscle. The bite force is calculated for a piranha with a mass of 1 kg from estimated maximum force values applied by three muscle groups connecting the jaw to the mandible: it is ≈20 N. Mechanical tests on the scales and teeth demonstrate that the cutting and puncturing ability of the piranha teeth cannot penetrate the Arapaimas scales.