nils-herrmann/clean_scirepeval huggingface dataset:
STEM tomography analysis of the trypanosome transition zone.
Venue: Journal of structural biology

The protist Trypanosoma brucei is an emerging model for the study of cilia and flagella. Here, we used scanning transmission electron microscopy (STEM) tomography to describe the structure of the trypanosome transition zone (TZ). At the base of the TZ, nine transition fibres irradiate from the B microtubule of each doublet towards the membrane. The TZ adopts a 9 + 0 structure throughout its length of ∼300 nm and its lumen contains an electron-dense structure. The proximal portion of the TZ has an invariant length of 150 nm and is characterised by a collarette surrounding the membrane and the presence of electron-dense material between the membrane and the doublets. The distal portion exhibits more length variation (from 55 to 235 nm) and contains typical Y-links. STEM analysis revealed a more complex organisation of the Y-links compared to what was reported by conventional transmission electron microscopy. Observation of the very early phase of flagellum assembly demonstrated that the proximal portion and the collarette are assembled early during construction. The presence of the flagella connector that maintains the tip of the new flagellum to the side of the old was confirmed and additional filamentous structures making contact with the membrane of the flagellar pocket were also detected. The structure and potential functions of the TZ in trypanosomes are discussed, as well as its mode of assembly.
Structural characterization of ribT from Bacillus subtilis reveals it as a GCN5-related N-acetyltransferase.
Venue: Journal of structural biology

In bacteria, biosynthesis of riboflavin occurs through a series of enzymatic steps starting with one molecule of GTP and two molecules of ribulose-5-phosphate. In Bacillus subtilis (B. subtilis) the genes (ribD/G, ribE, ribA, ribH and ribT) which are involved in riboflavin biosynthesis are organized in an operon referred as rib operon. All the genes of rib operon are characterized functionally except for ribT. The ribT gene with unknown function is found at the distal terminal of rib operon and annotated as a putative N-acetyltransferase. Here, we report the crystal structure of ribT from B. subtilis (bribT) complexed with coenzyme A (CoA) at 2.1 Å resolution determined by single wavelength anomalous dispersion method. Our structural study reveals that bribT is a member of GCN5-related N-acetyltransferase (GNAT) superfamily and contains all the four conserved structural motifs that have been in other members of GNAT superfamily. The members of GNAT family transfers the acetyl group from acetyl coenzyme A (AcCoA) to a variety of substrates. Moreover, the structural analysis reveals that the residues Glu-67 and Ser-107 are suitably positioned to act as a catalytic base and catalytic acid respectively suggesting that the catalysis by bribT may follow a direct transfer mechanism. Surprisingly, the mutation of a non-conserved amino acid residue Cys-112 to alanine or serine affected the binding of AcCoA to bribT, indicating a possible role of Cys-112 in the catalysis.
Structural changes of homodimers in the PDB.
Venue: Journal of structural biology

Protein complexes are involved in various biological phenomena. These complexes are intrinsically flexible, and structural changes are essential to their functions. To perform a large-scale automated analysis of the structural changes of complexes, we combined two original methods. An application, SCPC, compares two structures of protein complexes and decides the match of binding mode. Another application, Motion Tree, identifies rigid-body motions in various sizes and magnitude from the two structural complexes with the same binding mode. This approach was applied to all available homodimers in the Protein Data Bank (PDB). We defined two complex-specific motions: interface motion and subunit-spanning motion. In the former, each subunit of a complex constitutes a rigid body, and the relative movement between subunits occurs at the interface. In the latter, structural parts from distinct subunits constitute a rigid body, providing the relative movement spanning subunits. All structural changes were classified and examined. It was revealed that the complex-specific motions were common in the homodimers, detected in around 40% of families. The dimeric interfaces were likely to be small and flat for interface motion, while large and rugged for subunit-spanning motion. Interface motion was accompanied by a drastic change in contacts at the interface, while the change in the subunit-spanning motion was moderate. These results indicate that the interface properties of homodimers correlated with the type of complex-specific motion. The study demonstrates that the pipeline of SCPC and Motion Tree is useful for the massive analysis of structural change of protein complexes.
In-air hearing in Hawaiian monk seals: implications for understanding the auditory biology of Monachinae seals
Venue: Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology

The auditory biology of Monachinae seals is poorly understood. Limited audiometric data and certain anatomical features suggest that these seals may have reduced sensitivity to airborne sounds compared to related species. Here, we describe the in-air hearing abilities of a Hawaiian monk seal (Neomonachus schauinslandi) trained to participate in a psychophysical paradigm. We report absolute (unmasked) thresholds for narrowband signals measured in quiet conditions across the range of hearing and masked thresholds measured in the presence of octave-band noise at two frequencies. The behavioral audiogram indicates a functional hearing range from 0.1 to 33 kHz and poor sensitivity, with detection thresholds above 40 dB re 20 µPa. Critical ratio measurements are elevated compared to those of other seals. The apparently reduced terrestrial hearing ability of this individual—considered with available auditory data for a northern elephant seal (Mirounga angustirostris)—suggests that hearing in Monachinae seals differs from that of the highly sensitive Phocinae seals. Exploration of phylogenetic relationships and anatomical traits support this claim. This work advances understanding of the evolution of hearing in amphibious marine mammals and provides updated information that can be used for management and conservation of endangered Hawaiian monk seals.
Lesions of abdominal connectives reveal a conserved organization of the calling song central pattern generator (CPG) network in different cricket species
Venue: Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology

Although crickets move their front wings for sound production, the abdominal ganglia house the network of the singing central pattern generator. We compared the effects of specific lesions to the connectives of the abdominal ganglion chain on calling song activity in four different species of crickets, generating very different pulse patterns in their calling songs. In all species, singing activity was abolished after the connectives between the metathoracic ganglion complex and the first abdominal ganglion A3 were severed. The song structure was lost and males generated only single sound pulses when connectives between A3 and A4 were cut. Severing connectives between A4 and A5 had no effect in the trilling species, it led to an extension of chirps in a chirping species and to a loss of the phrase structure in two Teleogryllus species. Cutting the connectives between A5 and A6 caused no or minor changes in singing activity. In spite of the species-specific pulse patterns of calling songs, our data indicate a conserved organisation of the calling song motor pattern generating network. The generation of pulses is controlled by ganglia A3 and A4 while A4 and A5 provide the timing information for the chirp and/or phrase structure of the song.
Individual variation in metabolic rate, locomotion capacity and hypoxia tolerance and their relationships in juveniles of three freshwater fish species.
Venue: Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology

Individual variations in metabolic rate, locomotion capacity and hypoxia tolerance and their relationships were investigated in three cyprinid species [crucian carp (Carassius auratus), common carp (Cyprinus carpio) and qingbo (Spinibarbus sinensis), in 60 individuals of each species]. Either the active metabolic rate (AMR) and critical swimming speed (Ucrit) (30 individuals) or critical oxygen tension (Pcrit) and loss of equilibrium (LOE) (30 individuals) were measured in each species after measuring the resting metabolic rate (RMR). Both the AMR and Ucrit were found to be significantly and positively correlated with the RMR in all three cyprinid species, indicating that high-RMR individuals have high aerobic capacity and thus good swimming performance. Pcrit was positively correlated with the RMR in all three species, whereas the LOE was highly positively correlated, weakly positively correlated and not correlated with the RMR in qingbo, common carp and crucian carp, respectively, possibly due to specialized morphological and biochemical adaptations involved in hypoxia tolerance in crucian and common carp. Crucian carp showed relatively poor swimming performance, i.e., a low Ucrit (relatively high variation), strong hypoxia tolerance, and low LOE (relatively low variation); qingbo showed relatively good swimming performance (relatively low variation) and weak hypoxia tolerance (relatively high variation); and common carp showed moderate swimming performance and relatively strong hypoxia tolerance (moderate variation). These interspecific differences may be due to the different lifestyles of these cyprinid fishes based on their associated fast-slow-flow regime and are outcomes of long-term selection.
Neuroanatomical differentiation associated with alternative reproductive tactics in male arid land bees, Centris pallida and Amegilla dawsoni.
Venue: Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology

Alternative reproductive tactics (ARTs) occur when there is categorical variation in the reproductive strategies of a sex within a population. These different behavioral phenotypes can expose animals to distinct cognitive challenges, which may be addressed through neuroanatomical differentiation. The dramatic phenotypic plasticity underlying ARTs provides a powerful opportunity to study how intraspecific nervous system variation can support distinct cognitive abilities. We hypothesized that conspecific animals pursuing ARTs would exhibit dissimilar brain architecture. Dimorphic males of the bee species Centris pallida and Amegilla dawsoni use alternative mate location strategies that rely primarily on either olfaction (large-morph) or vision (small-morph) to find females. This variation in behavior led us to predict increased volumes of the brain regions supporting their primarily chemosensory or visual mate location strategies. Large-morph males relying mainly on olfaction had relatively larger antennal lobes and relatively smaller optic lobes than small-morph males relying primarily on visual cues. In both species, as relative volumes of the optic lobe increased, the relative volume of the antennal lobe decreased. In addition, A. dawsoni large males had relatively larger mushroom body lips, which process olfactory inputs. Our results suggest that the divergent behavioral strategies in ART systems can be associated with neuroanatomical differentiation.
Effects of underwater and semi-aquatic environments on gut tissue and microbiota of the mudskipper Boleophthalmus pectinirostris.
Venue: Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology

In both underwater and semi-aquatic environments, the gut microbiota is of particular physiological importance for amphibious animals, given that the gut tract is among those organs in direct communication with the external environment. In this study, we examined the effects of these contrasting environments on the dominant bacteria in the guts of the amphibious mudskipper Boleophthalmus pectinirostris. Compared with the guts of normal mudskippers, in which the dominant bacteria were identified as Vibrio and Faecalibacterium, we found that Acinetobacter, Shigella, and Bacillus predominated in their guts after exposure to the semi-aquatic environment, whereas Escherichia, Bacteroides, and Bacillus were more prevalent in the guts in the underwater environment. The total number of cultured gut bacteria decreased significantly in the semi-aquatic environment. In semi-aquatic mudskippers, we also detected reductions and increases in the length and width of gut villi, respectively, whereas the width of gut villi declined and the number of goblet cells increased significantly in mudskippers maintained underwater. The mRNA expression of multiple gut transporters for glucose, long-chain fatty acids, and amino acids was found to increase markedly in both underwater and semi-aquatic environments, with the expression of most transporters being significantly higher in those mudskippers exposed to an underwater environment. Furthermore, we detected significant increases in the mRNA expression of pro-inflammatory cytokine transcripts in the guts of both underwater and semi-aquatic mudskippers on days 2, 4, and 6 of exposure, whereas the expression of IL-10 and TGFβ mRNA was more pronounced on days 4 and 8, respectively. Comparatively, we found that expression levels of cytokines in the guts of underwater mudskipper were substantially higher than those in the guts of semi-aquatic mudskippers. Collectively, our findings revealed notable differences in the gut microbiota and energy metabolism requirements of mudskippers exposed to underwater and semi-aquatic conditions, thereby providing a theoretical basis explaining the maintenance of a homeostatic state in mudskippers that constantly transition between these contrasting amphibious habitats.
The development of the O2-sensing system in an amphibious fish: consequences of variation in environmental O2 levels.
Venue: Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology

Proper development of the O2-sensing system is essential for survival. Here, we characterized the development of the O2-sensing system in the mangrove rivulus (Kryptolebias marmoratus), an amphibious fish that transitions between hypoxic aquatic environments and O2-rich terrestrial environments. We found that NECs formed in the gills and skin of K. marmoratus during embryonic development and that both NEC populations are retained from the embryonic stage to adulthood. We also found that the hyperventilatory response to acute hypoxia was present in embryonic K. marmoratus, indicating that functional O2-sensing pathways are formed during embryonic development. We then exposed embryos to aquatic normoxia, aquatic hyperoxia, aquatic hypoxia, or terrestrial conditions for the first 30 days of embryonic development and tested the hypothesis that environmental O2 availability during embryonic development modulates the development of the O2-sensing system in amphibious fishes. Surprisingly, we found that O2 availability during embryonic development had little impact on the density and morphology of NECs in the gills and skin of K. marmoratus. Collectively, our results demonstrate that, unlike the only other species of fish in which NEC development has been studied to date (i.e., zebrafish), NEC development in K. marmoratus is largely unaffected by environmental O2 levels during the embryonic stage, indicating that there is interspecies variation in O2-induced plasticity in the O2-sensing system of fishes.
Differential bone remodeling mechanism in hindlimb unloaded rats and hibernating Daurian ground squirrels: a comparison between artificial and natural disuse.
Venue: Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology

To determine that differential bone remodeling mechanism (especially Wnt signaling) in hindlimb unloaded rats and hibernating Daurian ground squirrels, the bone microstructure, mechanical properties, and expression levels of bone remodeling related proteins and key proteins of Wnt/β-catenin signaling were analyzed in this study. The thickness of cortical and trabecular bone was decreased in femur of hindlimb unloaded rats, while it was maintained in femur of hibernating ground squirrels. Interestingly, the ultimate bending energy and ultimate normalized displacement were reduced and the bending rigidity was increased in tibia of hibernating ground squirrels. Besides, the protein level of Runx2 was decreased in femur and tibia of unloaded rats, while it was maintained in tibia and even increased in femur of hibernating ground squirrels. The protein levels of RANKL and MMP-9 were increased in femur and tibia in unloaded rats, while they were maintained in both femur and tibia of hibernating ground squirrels. The protein level of GSK-3β was increased in femur and tibia of unloaded rats, while it was maintained in both femur and tibia of hibernating ground squirrels. The phospho-β-catenin expression was increased in both femur and tibia of unloaded rats, while it was only decreased in femur, but maintained in tibia of hibernating ground squirrels. In conclusion, the femur and tibia in hindlimb unloaded rats showed obvious bone loss, while they mitigated disuse-induced bone loss in hibernating ground squirrels, involving differential protein expression of key molecules in bone remodeling. In comparison with hindlimb unloaded rats, promoting osteoblast differentiation through activating canonical GSK-3β/β-catenin signaling involving Runx2 might be an adaptation to natural disuse in femur of hibernating Daurian ground squirrels. However, there was no statistical change in the protein levels of bone formation related proteins, GSK-3β and phospho-β-catenin in tibia of hibernating Daurian ground squirrels.
Lipid signature of neural tissues of marine and terrestrial mammals: consistency across species and habitats.
Venue: Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology

Marine mammals are exposed to O2-limitation and increased N2 gas concentrations as they dive to exploit habitat and food resources. The lipid-rich tissues (blubber, acoustic, neural) are of particular concern as N2 is five times more soluble in lipid than in blood or muscle, creating body compartments that can become N2 saturated, possibly leading to gas emboli upon surfacing. We characterized lipids in the neural tissues of marine mammals to determine whether they have similar lipid profiles compared to terrestrial mammals. Lipid profiles (lipid content, lipid class composition, and fatty acid signatures) were determined in the neural tissues of 12 cetacean species with varying diving regimes, and compared to two species of terrestrial mammals. Neural tissue lipid profile was not significantly different in marine versus terrestrial mammals across tissue types. Within the marine species, average dive depth was not significantly associated with the lipid profile of cervical spinal cord. Across species, tissue type (brain, spinal cord, and spinal nerve) was a significant factor in lipid profile, largely due to the presence of storage lipids (triacylglycerol and wax ester/sterol ester) in spinal nerve tissue only. The stability of lipid signatures within the neural tissue types of terrestrial and marine species, which display markedly different dive behaviors, points to the consistent role of lipids in these tissues. These findings indicate that despite large differences in the level of N2 gas exposure by dive type in the species examined, the lipids of neural tissues likely do not have a neuroprotective role in marine mammals.
Einstein, von Frisch and the honeybee: a historical letter comes to light
Venue: Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology

The work of the Nobel Laureate Karl von Frisch, the founder of this journal, was seminal in many ways. He established the honeybee as a key animal model for experimental behavioural studies on sensory perception, learning and memory, and first correctly interpreted its famous dance communication. Here, we report on a previously unknown letter by the Physicist and Nobel Laureate Albert Einstein that was written in October 1949. It briefly addresses the work of von Frisch and also queries how understanding animal perception and navigation may lead to innovations in physics. We discuss records proving that Einstein and von Frisch met in April 1949 when von Frisch visited the USA to present a lecture on bees at Princeton University. In the historical context of Einstein’s theories and thought experiments, we discuss some more recent discoveries of animal sensory capabilities alien to us humans and potentially valuable for bio-inspired design improvements. We also address the orientation of animals like migratory birds mentioned by Einstein 70 years ago, which pushes the boundaries of our understanding nature, both its biology and physics.
Ear morphology in two root-rat species (genus Tachyoryctes) differing in the degree of fossoriality.
Venue: Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology

It is supposed that the subterranean lifestyle in mammals is reflected in ear morphology and tuning of hearing to low frequencies. We studied two root-rat species to see if their ear morphology reflects the difference in the amount of their surface activity. Whereas the more subterranean Tachyoryctes splendens possesses shorter pinnae as expected, it has smaller bullae compared to the more epigeic Tachyoryctes macrocephalus. The ratio between the eardrum and the stapedial footplate area and the ratio between the mallear and the incudal lever were lower in T. splendens (19.3 ± 0.3 and 1.9 ± 0.0, respectively) than in T. macrocephalus (21.8 ± 0.6 and 2.1 ± 0.1), probably reflecting the latter's higher surface activity. The cochlea in both species has 3.5 coils, yet the basilar membrane is longer in the smaller T. splendens (13.0 ± 0.5 versus 11.4 ± 0.7 mm), which indicates its wider hearing range and/or higher sensitivity (to some frequencies). In both root-rat species, the highest density of outer hair cells (OHC) was in the apical part of the cochlea, while the highest density of inner hair cells (IHC) was in its middle part. This OHC density pattern corresponds with good low-frequency hearing, whereas the IHC pattern suggests sensitivity to higher frequencies.