nils-herrmann/clean_scirepeval huggingface dataset:
Mitochondrial adaptations to utilize hydrogen sulfide for energy and signaling
Venue: Journal of Comparative Physiology B

Sulfur is a versatile molecule with oxidation states ranging from −2 to +6. From the beginning, sulfur has been inexorably entwined with the evolution of organisms. Reduced sulfur, prevalent in the prebiotic Earth and supplied from interstellar sources, was an integral component of early life as it could provide energy through oxidization, even in a weakly oxidizing environment, and it spontaneously reacted with iron to form iron–sulfur clusters that became the earliest biological catalysts and structural components of cells. The ability to cycle sulfur between reduced and oxidized states may have been key in the great endosymbiotic event that incorporated a sulfide-oxidizing α-protobacteria into a host sulfide-reducing Archea, resulting in the eukaryotic cell. As eukaryotes slowly adapted from a sulfidic and anoxic (euxinic) world to one that was highly oxidizing, numerous mechanisms developed to deal with increasing oxidants; namely, oxygen, and decreasing sulfide. Because there is rarely any reduced sulfur in the present-day environment, sulfur was historically ignored by biologists, except for an occasional report of sulfide toxicity. Twenty-five years ago, it became evident that the organisms in sulfide-rich environments could synthesize ATP from sulfide, 10 years later came the realization that animals might use sulfide as a signaling molecule, and only within the last 4 years did it become apparent that even mammals could derive energy from sulfide generated in the gastrointestinal tract. It has also become evident that, even in the present-day oxic environment, cells can exploit the redox chemistry of sulfide, most notably as a physiological transducer of oxygen availability. This review will examine how the legacy of sulfide metabolism has shaped natural selection and how some of these ancient biochemical pathways are still employed by modern-day eukaryotes.
Acoustic signal perception in a noisy habitat: lessons from synchronising insects
Venue: Journal of Comparative Physiology A

Acoustically communicating animals often have to cope with ambient noise that has the potential to interfere with the perception of conspecific signals. Here we use the synchronous display of mating signals in males of the tropical katydid Mecopoda elongata in order to assess the influence of nocturnal rainforest noise on signal perception. Loud background noise may disturb chorus synchrony either by masking the signals of males or by interaction of noisy events with the song oscillator. Phase-locked synchrony of males was studied under various signal-to-noise ratios (SNRs) using either native noise or the audio component of noise (<9 kHz). Synchronous entrainment was lost at a SNR of −3 dB when native noise was used, whereas with the audio component still 50 % of chirp periods matched the pacer period at a SNR of −7 dB. Since the chirp period of solo singing males remained almost unaffected by noise, our results suggest that masking interference limits chorus synchrony by rendering conspecific signals ambiguous. Further, entrainment with periodic artificial signals indicates that synchrony is achieved by ignoring heterospecific signals and attending to a conspecific signal period. Additionally, the encoding of conspecific chirps was studied in an auditory neuron under the same background noise regimes.
Osmoregulatory strategies in natural populations of the black-chinned tilapia Sarotherodon melanotheron exposed to extreme salinities in West African estuaries
Venue: Journal of Comparative Physiology B

The effect of salinity was studied in natural populations of the black-chinned tilapia (Sarotherodon melanotheron) from West Africa. This euryhaline species colonizes nearly all coastal environments from bays to lagoons characterized by salinities ranging from fresh water to hypersaline water over 100 ‰. Individuals were sampled during the dry season at several locations characterized by different levels of salinity (3–102 ‰). Their osmotic status and their gills were analyzed. The branchial mitochondria-rich cells (MRC), localized at the basis of the filaments and along the lamellae in fish taken from the saline stations, showed a wide plasticity with significant differences in their number and size. The most striking results were a significant larger area (≈3x) and a higher number (≈55x) of MRC at high salinity (102 ‰) compared to low salinity (3 ‰). The major ion transporters and channels were localized by immunocytochemistry and different expression patterns have been recorded between stations. Despite an increased Na+/K+-ATPase (NKA) α-subunit expression and NKA activity, pointing to an increased monovalent ion excretion, a severe osmotic imbalance was recorded in animals living in hypersaline environments.
Interpreting indices of physiological stress in free-living vertebrates
Venue: Journal of Comparative Physiology B

When vertebrate physiological ecologists use the terms ‘stress’ or ‘physiological stress’, they typically mean the level of hypothalamus–pituitary–adrenal (HPA-) axis activation. Measurements of stress hormone concentrations (e.g. glucocorticoids in blood, urine or faeces), leukocytes (e.g. the neutrophil–lymphocyte ratio or heterophil equivalent), immunofunction (e.g. innate, cell-mediated or humoral immunity measures) and regenerative anaemia (e.g. mean erythrocyte volume and red blood cell distribution width) have all been used to estimate HPA-axis activity in free-living vertebrates. Stress metrics have provided insights into aspects of autecology or population regulation that could not have been easily obtained using other indices of population wellbeing, such as body condition or relative abundance. However, short- and long-term stress (often problematically termed acute and chronic stress, respectively) can interact in unpredictable ways. When animals experience trapping and handling stress before blood, faeces and/or urine is sampled, the interaction of short- and long-term stress can confound interpretation of the data, a fact not always acknowledged in studies of stress in free-living vertebrates. This review examines how stress metrics can be confounded when estimates of HPA-axis activation are collected for free-living vertebrates and outlines some approaches that can be used to help circumvent the influence of potentially confounding factors.
Columnar cells necessary for motion responses of wide-field visual interneurons in Drosophila
Venue: Journal of Comparative Physiology A

Wide-field motion-sensitive neurons in the lobula plate (lobula plate tangential cells, LPTCs) of the fly have been studied for decades. However, it has never been conclusively shown which cells constitute their major presynaptic elements. LPTCs are supposed to be rendered directionally selective by integrating excitatory as well as inhibitory input from many local motion detectors. Based on their stratification in the different layers of the lobula plate, the columnar cells T4 and T5 are likely candidates to provide some of this input. To study their role in motion detection, we performed whole-cell recordings from LPTCs in Drosophila with T4 and T5 cells blocked using two different genetically encoded tools. In these flies, motion responses were abolished, while flicker responses largely remained. We thus demonstrate that T4 and T5 cells indeed represent those columnar cells that provide directionally selective motion information to LPTCs. Contrary to previous assumptions, flicker responses seem to be largely mediated by a third, independent pathway. This work thus represents a further step towards elucidating the complete motion detection circuitry of the fly.
Divergent strategies for adaptation to desiccation stress in two Drosophila species of immigrans group
Venue: Journal of Comparative Physiology B

Water balance mechanisms have been investigated in desert Drosophila species of the subgenus Drosophila from North America, but changes in mesic species of subgenus Drosophila from other continents have received lesser attention. We found divergent strategies for coping with desiccation stress in two species of immigrans group—D. immigrans and D. nasuta. In contrast to clinal variation for body melanization in D. immigrans, cuticular lipid mass showed a positive cline in D. nasuta across a latitudinal transect (10°46′–31°43′N). Based on isofemale lines variability, body melanization showed positive correlation with desiccation resistance in D. immigrans but not in D. nasuta. The use of organic solvents has supported water proofing role of cuticular lipids in D. nasuta but not in D. immigrans. A comparative analysis of water budget of these two species showed that higher water content, reduced rate of water loss and greater dehydration tolerance confer higher desiccation resistance in D. immigrans while the reduced rate of water loss is the only possible mechanism to enhance desiccation tolerance in D. nasuta. We found that carbohydrates act as metabolic fuel during desiccation stress in both the species, whereas their rates of utilization differ significantly between these two species. Further, acclimation to dehydration stress improved desiccation resistance due to increase in the level of carbohydrates in D. immigrans but not in D. nasuta. Thus, populations of D. immigrans and D. nasuta have evolved different water balance mechanisms under shared environmental conditions. Multiple measures of desiccation resistance in D. immigrans but reduction in water loss in D. nasuta are consistent with their different levels of adaptive responses to wet and dry conditions on the Indian subcontinent.
Calcium buffering and clearance in spider mechanosensory neurons
Venue: Journal of Comparative Physiology A

Spider VS-3 mechanoreceptor neurons have a low-voltage-activated Ca2+ current that raises intracellular calcium concentration [Ca2+] when they are depolarized by agonists of GABAA receptors or fire action potentials. The Ca2+ rise produces negative feedback by modulating the mechanoreceptor current and regulates Ca2+- and voltage-activated K+ currents. However, nothing is known about Ca2+ buffering in VS-3 neurons. Dynamic changes in VS-3 neuron intracellular [Ca2+] were measured using the fluorescent Ca2+ indicator Oregon Green BAPTA-1 (OG488) to understand Ca2+ buffering and clearance. Intracellular OG488 concentration increased slowly over more than 2 h as it diffused through a sharp intracellular microelectrode and spread through the cell. This slow increase was used to measure endogenous Ca2+ buffering and clearance by the added buffer technique, with OG488 acting as both added exogenous buffer and Ca2+ indicator. [Ca2+] was raised for brief periods by regular action potential firing, produced by pulsed electric current injection through the microelectrode. The resulting rise and fall of [Ca2+] were well fitted by the single compartment model of Ca2+ dynamics. With earlier ratiometric [Ca2+] estimates, these data gave an endogenous Ca2+ binding ratio of 684. Strong Ca2+ buffering may assist these neurons to deal with rapid changes in mechanical inputs.
Cloning, tissue expression pattern and daily rhythms of Period1, Period2, and Clock transcripts in the flatfish Senegalese sole, Solea senegalensis
Venue: Journal of Comparative Physiology B

An extensive network of endogenous oscillators governs vertebrate circadian rhythmicity. At the molecular level, they are composed of a set of clock genes that participate in transcriptional–translational feedback loops to control their own expression and that of downstream output genes. These clocks are synchronized with the environment, although entrainment by external periodic cues remains little explored in fish. In this work, partial cDNA sequences of clock genes representing both positive (Clock) and negative (Period1, Period2) elements of the molecular feedback loops were obtained from the nocturnal flatfish Senegalese sole, a relevant species for aquaculture and chronobiology. All of the above genes exhibited high identities with their respective teleost clock genes, and Per–Arnt–Sim or basic helix–loop–helix binding domains were recognized in their primary structure. They showed a widespread distribution through the animal body and some of them displayed daily mRNA rhythms in central (retina, optic tectum, diencephalon, and cerebellum) and peripheral (liver) tissues. These rhythms were most robust in retina and liver, exhibiting marked Period1 and Clock daily oscillations in transcript levels as revealed by ANOVA and cosinor analysis. Interestingly, expression profiles were inverted in retina and optic tectum compared to liver. Such differences suggest the existence of tissue-dependent zeitgebers for clock gene expression in this species (i.e., light for retina and optic tectum and feeding time for liver). This study provides novel insight into the location of the molecular clocks (central vs. peripheral) and their different phasing and synchronization pathways, which contributes to better understand the teleost circadian systems and its plasticity.
Photic resetting of the circadian clock is correlated with photic habitat in Anolis lizards
Venue: Journal of Comparative Physiology A

Circadian rhythms are regulated by an internal clock, which is itself synchronized to environmental cues such as light and temperature. It is widely assumed that the circadian system is adapted to local cues, which vary enormously across habitats, yet the comparative data necessary for testing this idea are lacking. We examined photic and thermal resetting of the circadian clock in five species of Anolis lizards whose microhabitats differ in the amounts of sun and shade. The primary circadian oscillator in Anolis is the pineal gland, which produces the hormone melatonin. A flow-through culture system was employed to measure rhythmic melatonin output from individually cultured pineal glands. All species showed temperature-compensated circadian rhythms of pineal melatonin. Light caused significant phase delays of the melatonin rhythm, and this effect varied among species. Controlling for phylogenetic differences, the results indicate that the pineal glands of shade-dwelling species are more sensitive to photic resetting than species living in more brightly illuminated habitats. The differences were not due to variation in free-running period, but may be due to variation in oscillator phase and/or robustness. Surprisingly, thermal resetting was not statistically significant. Overall, the results suggest that the Anolis circadian system is adapted to photic habitat.
Low social status impairs hypoxia tolerance in rainbow trout (Oncorhynchus mykiss)
Venue: Journal of Comparative Physiology B

In the present study, chronic behavioural stress resulting from low social status affected the physiological responses of rainbow trout (Oncorhynchus mykiss) to a subsequent acute stressor, exposure to hypoxia. Rainbow trout were confined in fork-length matched pairs for 48–72 h, and social rank was assigned based on behaviour. Dominant and subordinate fish were then exposed individually to graded hypoxia (final water PO2, PwO2 = 40 Torr). Catecholamine mobilization profiles differed between dominant and subordinate fish. Whereas dominant fish exhibited generally low circulating catecholamine levels until a distinct threshold for release was reached (PwO2 = 51.5 Torr corresponding to arterial PO2, PaO2 = 24.1 Torr), plasma catecholamine concentrations in subordinate fish were more variable and identification of a distinct threshold for release was problematic. Among fish that mobilized catecholamines (i.e. circulating catecholamines rose above the 95% confidence interval around the baseline value), however, the circulating levels achieved in subordinate fish were significantly higher (459.9 ± 142.2 nmol L−1, mean ± SEM, N = 12) than those in dominant fish (130.9 ± 37.9 nmol L−1, N = 12). The differences in catecholamine mobilization occurred despite similar P50 values in dominant (22.0 ± 1.5 Torr, N = 6) and subordinate (22.1 ± 2.2 Torr, N = 8) fish, and higher PaO2 values in subordinate fish under severely hypoxic conditions (i.e. PwO2 < 60 Torr). The higher PaO2 values of subordinate fish likely reflected the greater ventilatory rates and amplitudes exhibited by these fish during severe hypoxia. At the most severe level of hypoxia, subordinate fish were unable to defend arterial blood O2 content, which fell to approximately half (0.60 ± 0.13 mL O2 g−1 haemoglobin, N = 9) that of dominant fish (1.08 ± 0.09 mL O2 g−1 haemoglobin, N = 9). Collectively, these data indicate that chronic social stress impacts the ability of trout to respond to the additional, acute stress of hypoxia.
Seasonal changes in thermogenesis of a free-ranging afrotherian small mammal, the Western rock elephant shrew (Elephantulus rupestris)
Venue: Journal of Comparative Physiology B

We report on the seasonal metabolic adjustments of a small-sized member of the phylogenetically ancient Afrotheria, the Western rock elephant shrew (Elephantulus rupestris). We recorded body temperature (Tb) patterns and compared the capacity for adrenergically induced nonshivering thermogenesis (NST) in E. rupestris captured in the wild in summer and winter. Noradrenaline (NA) treatment (0.4–0.5 mg/kg, s.c.) induced a pronounced elevation in oxygen consumption compared to controls (saline), and the increase in oxygen consumption following injection of NA was 1.8-fold higher in winter compared to summer. This suggests that the smaller members of Afrotheria possess functional brown adipose tissue, which changes in thermogenic capacity depending on the season. Torpor was recorded in both seasons, but in winter the incidence of torpor was higher (n = 205 out of 448 observations) and minimal Tb during torpor was lower (Tbmin: 11.9°C) than in summer (n = 24 out of 674 observations; Tbmin: 26°C). In addition to cold, high air humidity emerged as a likely predictor for torpor entry. Overall, E. rupestris showed a high degree of thermoregulatory plasticity, which was mainly reflected in a variable timing of torpor entry and arousal. We conclude that E. rupestris exhibits seasonal metabolic adjustments comparable to what has been long known for many Holarctic rodents.
Peripheral circadian rhythms and their regulatory mechanism in insects and some other arthropods: a review
Venue: Journal of Comparative Physiology B

Many physiological functions of insects show a rhythmic change to adapt to daily environmental cycles. These rhythms are controlled by a multi-clock system. A principal clock located in the brain usually organizes the overall behavioral rhythms, so that it is called the “central clock”. However, the rhythms observed in a variety of peripheral tissues are often driven by clocks that reside in those tissues. Such autonomous rhythms can be found in sensory organs, digestive and reproductive systems. Using Drosophila melanogaster as a model organism, researchers have revealed that the peripheral clocks are self-sustained oscillators with a molecular machinery slightly different from that of the central clock. However, individual clocks normally run in harmony with each other to keep a coordinated temporal structure within an animal. How can this be achieved? What is the molecular mechanism underlying the oscillation? Also how are the peripheral clocks entrained by light–dark cycles? There are still many questions remaining in this research field. In the last several years, molecular techniques have become available in non-model insects so that the molecular oscillatory mechanisms are comparatively investigated among different insects, which give us more hints to understand the essential regulatory mechanism of the multi-oscillatory system across insects and other arthropods. Here we review current knowledge on arthropod’s peripheral clocks and discuss their physiological roles and molecular mechanisms.
Physiological constraints and the influence of diet on fatty acids in the yolk of gentoo penguins, Pygoscelis papua
Venue: Journal of Comparative Physiology B

Avian yolk fatty acids (FA) composition is influenced by two main factors: maternal diet and genetic factors that regulate FA metabolism. However, due to embryonic developmental requirements, yolk FA are thought to be physiologically constrained and less useful for dietary and trophic studies. We assessed the relative contributions of diet and physiological constraints in determining the yolk FA composition of a marine bird, the gentoo penguin (Pygoscelis papua) by comparing FA signatures of yolks and prey between a captive, controlled- feeding experiment and a wild population. Captive and wild yolk FA signatures differed even though both groups’ yolk lipids were composed primarily of three FA (16:0, 18:0 and 18:1n-9). Differences were due to FA occurring in relatively low abundance, but which mirrored differences in the FA composition of diets. However, yolk FA signatures were correlated across three penguin species suggesting that common developmental constraints can be relatively more important than species-specific differences in diet or egg-laying physiology. While yolk FA are constrained, several minor components of yolk FA are reflective of diets and the calibration coefficients resulting from this study have the potential to be incorporated into predictive models and allow for quantitative dietary and trophic studies using FA analysis of penguin egg yolks.
Coping with physiological oxidative stress: a review of antioxidant strategies in seals
Venue: Journal of Comparative Physiology B

While diving, seals are exposed to apnea-induced hypoxemia and repetitive cycles of ischemia/reperfusion. While on land, seals experience sleep apnea, as well as prolonged periods of food and water deprivation. Prolonged fasting, sleep apnea, hypoxemia and ischemia/reperfusion increase oxidant production and oxidative stress in terrestrial mammals. In seals, however, neither prolonged fasting nor apnea-induced hypoxemia or ischemia/reperfusion increase systemic or local oxidative damage. The strategies seals evolved to cope with increased oxidant production are reviewed in the present manuscript. Among these strategies, high antioxidant capacity and the oxidant-mediated activation of hormetic responses against hypoxia and oxidative stress are discussed. In addition to expanding our knowledge of the evolution of antioxidant defenses and adaptive responses to oxidative stress, understanding the mechanisms that naturally allow mammals to avoid oxidative damage has the potential to advance our knowledge of oxidative stress-induced pathologies and to enhance the translative value of biomedical therapies in the long term.