Gene expression profiles of Japanese precious coral Corallium japonicum during gametogenesis

Background

Corallium japonicum, a prized resource in Japan, plays a vital role in traditional arts and fishing industries. Because of diminished stock due to overexploitation, ongoing efforts are focused on restoration through transplantation. This study aimed to enhance our understanding of the reproductive biology of these valuable corals and find more efficient methods for sex determination, which may significantly contribute to conservation initiatives.

Methods

We used 12 three-month aquarium reared C. japonicum colony fragments, conducted histological analysis for maturity and sex verification, and performed transcriptome analysis via de novo assembly and mapping using the C. rubrum transcriptome to explore gene expression differences between female and male C. japonicum.

Results

Our histological observations enabled sex identification in 33% of incompletely mature samples. However, the sex of the remaining 67% of samples, classified as immature, could not be identified. RNA-seq yielded approximately 21-31 million short reads from 12 samples. De novo assembly yielded 404,439 highly expressed transcripts. Among them, 855 showed significant differential expression, with 786 differentially expressed transcripts between females and males. Heatmap analysis highlighted 283 female-specific and 525 male-specific upregulated transcripts. Transcriptome assembly mapped to C. rubrum yielded 28,092 contigs, leading to the identification of 190 highly differentially expressed genes, with 113 upregulated exclusively in females and 70 upregulated exclusively in males. Blastp analysis provided putative protein annotations for 83 female and 72 male transcripts. Annotation analysis revealed that female biological processes were related to oocyte proliferation and reproduction, whereas those in males were associated with cell adhesion.

Discussion

Transcriptome analysis revealed sex-specific gene upregulation in incompletely mature C. japonicum and shared transcripts with C. rubrum, providing insight into its gene expression patterns. This study highlights the importance of using both de novo and reference-based assembly methods. Functional enrichment analysis showed that females exhibited enrichment in cell proliferation and reproduction pathways, while males exhibited enrichment in cell adhesion pathways. To the best of our knowledge, this is the first report on the gene expressions of each sex during the spawning season. Our findings offer valuable insights into the physiological ecology of incompletely mature red Japanese precious corals and suggest a method for identifying sex using various genes expressed in female and male individuals. In the future, techniques such as transplantation, artificial fertilization, and larval rearing may involve sex determination methods based on differences in gene expression to help conserve precious coral resources and ecosystems.

Songbirds avoid the oxidative stress costs of high blood glucose levels: a comparative study

Chronically high blood glucose levels (hyperglycaemia) can compromise healthy ageing and lifespan at the individual level. Elevated oxidative stress can play a central role in hyperglycaemia-induced pathologies. Nevertheless, the lifespan of birds shows no species-level association with blood glucose. This suggests that the potential pathologies of high blood glucose levels can be avoided by adaptations in oxidative physiology at the macroevolutionary scale. However, this hypothesis remains unexplored. Here, we examined this hypothesis using comparative analyses controlled for phylogeny, allometry and fecundity based on data from 51 songbird species (681 individuals with blood glucose data and 1021 individuals with oxidative state data). We measured blood glucose at baseline and after stress stimulus and computed glucose stress reactivity as the magnitude of change between the two time points. We also measured three parameters of non-enzymatic antioxidants (uric acid, total antioxidants and glutathione) and a marker of oxidative lipid damage (malondialdehyde). We found no clear evidence for blood glucose concentration being correlated with either antioxidant or lipid damage levels at the macroevolutionary scale, as opposed to the hypothesis postulating that high blood glucose levels entail oxidative costs. The only exception was the moderate evidence for species with a stronger stress-induced increase in blood glucose concentration evolving moderately lower investment into antioxidant defence (uric acid and glutathione). Neither baseline nor stress-induced glucose levels were associated with oxidative physiology. Our findings support the hypothesis that birds evolved adaptations preventing the (glyc)oxidative costs of high blood glucose observed at the within-species level. Such adaptations may explain the decoupled evolution of glycaemia and lifespan in birds and possibly the paradoxical combination of long lifespan and high blood glucose levels relative to mammals.

Photosynthetic electron transport in pitcher plants (Nepenthes mirabilis)

Pitcher plants (Nepenthes sp.) are insectivorous angiosperm plants with modified leaves known as pitchers best known as acting as traps for insects. Pitcher plants are typically found under boggy conditions under both forest cover and open areas with very poor nutrient status, particularly N-status. The pitchers have low photosynthetic activity. The Chl a content of the pitcher tissue of both Nepenthes mirabilis (green and red) varieties was very low. Chl b/a ratios of the green variety phyllodes (lamina) and pitchers were ≈ 0.24 to 0.29. In the red variety, the mature phyllodes had a Chl b/a ratio ≈ 0.28 but both the pitchers and the young phyllodes had Chl b/a ratios of nearly 0.5. Photosynthetic electron transport (ETR) was measured using PAM technology. Phyllodes of both varieties showed photoinhibition at supra-optimal irradiances [Nepenthes mirabilis (green variety), E_opt ≈ 200-250 µmol photon m^-2 s^-1; red variety, E_opt ≈ 100-150 µmol photon m^-2 s^-1]. Pitchers had low optimum irradiances (E_opt ≈ 40-90 µmol photon m^-2 s^-1). Maximum ETR (ETR_max) of phyllodes of both varieties was low (ETR_max ≈ 50 µmol e^- g^-1 Chl a s^-1); ETR_max was higher for pitchers on a Chl a basis (ETR_max ≈ 80-100 µmol e^- g^-1 Chl a s^-1); a consequence of their low Chl a content on a surface area basis. ETR_max of cut disks of phyllodes did not respond strongly to incubation in NH₄⁺, glutamate or aspartate as N-sources but did respond positively to added urea.

Seasonal and elevational variation in thermal ecology of the crevice-dwelling knob-scaled lizard Xenosaurus fractus from central-eastern Mexico

There is strong covariation between the thermal physiology of ectothermic animals and their thermal environment. Spatial and temporal differences in the thermal environment across a species' range may result in changes in thermal preferences between populations of that species. Alternatively, thermoregulatory-based microhabitat selection can allow individuals to maintain similar body temperatures across a broad thermal gradient. Which strategy a species adopts is often dependent on taxon-specific levels of physiological conservatism or ecological context. Identifying which strategies species use in response to spatial and temporal variation in environmental temperatures requires empirical evidence, which then can support predictions as to how a species might respond to a changing climate. Here we present findings of our analyses of the thermal quality, thermoregulatory accuracy and efficiency for the lizard, Xenosaurus fractus, across an elevation-thermal gradient and over the temporal thermal variation associated with seasonal changes. Xenosaurus fractus is a strict crevice-dweller, a habitat that can buffer this lizard from extreme temperatures and is a thermal conformer (body temperatures reflect air and substrate temperatures). We found populations of this species differed in their thermal preferences along an elevation gradient and between seasons. Specifically, we found that habitat thermal quality, thermoregulatory accuracy and efficiency (all measures of how well the lizards' body temperatures compared to their preferred body temperatures) varied along thermal gradients and with season. Our findings indicate that this species has adapted to local conditions and shows seasonal flexibility in those spatial adaptations. Along with their strict crevice-dwelling habitat, these adaptations may provide some protection against a warming climate.

Fine-scale variation in microhabitat conditions influences physiology and metabolism in an Antarctic insect

Microhabitats with distinct biotic and abiotic properties exist within landscapes, and this microhabitat variation can have dramatic impacts on the phenology and physiology of the organisms occupying them. The Antarctic midge Belgica antarctica inhabits diverse microhabitats along the Western Antarctic Peninsula that vary in macrophyte composition, hygric qualities, nutrient input, and thermal patterns. Here, we compare seasonal physiological changes in five populations of B. antarctica living in close proximity but in different microhabitats in the vicinity of Palmer Station, Antarctica. Thermal regimes among our sample locations differed in both mean temperature and thermal stability. Between the warmest and coldest sites, seasonal mean temperatures differed by 2.6˚C and degree day accumulations above freezing differed by a factor of 1.7. Larval metabolic and growth rates varied among the sites, and adult emergence occurred at different times. Distinct microhabitats also corresponded with differences in body composition, as lipid and carbohydrate content of larvae differed across sites. Further, seasonal changes in carbohydrate and protein content were dependent on site, indicating fine-scale variation in the biochemical composition of larvae as they prepare for winter. Together, these results demonstrate that variation in microhabitat properties influences the ontogeny, phenology, physiology, and biochemical makeup of midge populations living in close proximity. These results have implications for predicting responses of Antarctic ecosystems to environmental change.

Genomic and physiological mechanisms underlying skin plasticity during water to air transition in an amphibious fish

The terrestrial radiation of vertebrates required changes in skin that resolved the dual demands of maintaining a mechanical and physiological barrier while also facilitating ion and gas transport. Using the amphibious killifish Kryptolebias marmoratus, we found that transcriptional regulation of skin morphogenesis was quickly activated upon air exposure (1 h). Rapid regulation of cell-cell adhesion complexes and pathways that regulate stratum corneum formation was consistent with barrier function and mechanical reinforcement. Unique blood vessel architecture and regulation of angiogenesis likely supported cutaneous respiration. Differences in ionoregulatory transcripts and ionocyte morphology were correlated with differences in salinity acclimation and resilience to air exposure. Evolutionary analyses reinforced the adaptive importance of these mechanisms. We conclude that rapid plasticity of barrier, respiratory and ionoregulatory functions in skin evolved to support the amphibious lifestyle of K. marmoratus; similar processes may have facilitated the terrestrial radiation of other contemporary and ancient fishes.

The diving reflex and asphyxia: working across species in physiological ecology

Beginning in the mid-1930s the comparative physiologists Laurence Irving and Per Fredrik (Pete) Scholander pioneered the study of diving mammals, particularly harbor seals. Although resting on earlier work dating back to the late nineteenth century, their research was distinctive in several ways. In contrast to medically oriented physiology, the approaches of Irving and Scholander were strongly influenced by natural history, zoology, ecology, and evolutionary biology. Diving mammals, they argued, shared the cardiopulmonary physiology of terrestrial mammals, but evolution had modified these basic adaptive processes in extreme ways. In particular, seals' remarkable ability to hold breath, lower metabolism, produce energy anaerobically, and resist asphyxiation, provided a sharp contrast with terrestrial mammals, including humans. This diving physiology was an extreme elaboration of a general regulatory mechanism that allowed seals and other diving mammals to remain active underwater for extended periods. The decrease in heart rate referred to as bradycardia or the "diving reflex" was highly developed in diving mammals, but also found in less developed form in many other organisms faced by asphyxia. It therefore served as a kind of "master switch" for lowering metabolism in diving, hibernation, parturition, drowning, and other physiological responses involving lack of oxygen. Studying bradycardia unified a wide diversity of physiological phenomena, while also providing a context for contrasting the physiological responses of various species, including humans. Conducted in the laboratory and the field, this research served as a bridge between a comparative physiological ecology focused on non-human species and a human-centered general physiology.

Wind alters landing dynamics in bumblebees

Landing is an important but understudied behavior that flying animals must perform constantly. In still air, insects decelerate smoothly prior to landing by employing the relatively simple strategy of maintaining a constant rate of image expansion during their approach. However, it is unclear whether insects employ this strategy when faced with challenging flight environments. Here, we tested the effects of wind on bumblebees (Bombus impatiens) landing on flowers. We find that bees' approach paths to flowers shift from multidirectional in still air to unidirectional in wind, regardless of flower orientation. In addition, bees landing in a 3.5 m s^-1 headwind do not decelerate smoothly, but rather maintain a high flight speed until contact, resulting in higher peak decelerations upon impact. These findings suggest that wind has a strong influence on insect landing behavior and performance, with important implications for the design of micro aerial vehicles and the ecomechanics of insect flight.

Drivers of hibernation in the brown bear

BACKGROUND

Hibernation has been a key area of research for several decades, essentially in small mammals in the laboratory, yet we know very little about what triggers or ends it in the wild. Do climatic factors, an internal biological clock, or physiological processes dominate? Using state-of-the-art tracking and monitoring technology on fourteen free-ranging brown bears over three winters, we recorded movement, heart rate (HR), heart rate variability (HRV), body temperature (Tb), physical activity, ambient temperature (TA), and snow depth to identify the drivers of the start and end of hibernation. We used behavioral change point analyses to estimate the start and end of hibernation and convergent cross mapping to identify the causal interactions between the ecological and physiological variables over time.

RESULTS

To our knowledge, we have built the first chronology of both ecological and physiological events from before the start to the end of hibernation in the field. Activity, HR, and Tb started to drop slowly several weeks before den entry. Bears entered the den when snow arrived and when ambient temperature reached 0 °C. HRV, taken as a proxy of sympathetic nervous system activity, dropped dramatically once the bear entered the den. This indirectly suggests that denning is tightly coupled to metabolic suppression. During arousal, the unexpected early rise in Tb (two months before den exit) was driven by TA, but was independent of HRV. The difference between Tb and TA decreased gradually suggesting that bears were not thermoconforming. HRV increased only three weeks before exit, indicating that late activation of the sympathetic nervous system likely finalized restoration of euthermic metabolism. Interestingly, it was not until TA reached the presumed lower critical temperature, likely indicating that the bears were seeking thermoneutrality, that they exited the den.

CONCLUSIONS

We conclude that brown bear hibernation was initiated primarily by environmental cues, but terminated by physiological cues.

Three dimensional printing as an effective method of producing anatomically accurate models for studies in thermal ecology

Hollow copper models painted to match the reflectance of the animal subject are standard in thermal ecology research. While the copper electroplating process results in accurate models, it is relatively time consuming, uses caustic chemicals, and the models are often anatomically imprecise. Although the decreasing cost of 3D printing can potentially allow the reproduction of highly accurate models, the thermal performance of 3D printed models has not been evaluated. We compared the cost, accuracy, and performance of both copper and 3D printed lizard models and found that the performance of the models were statistically identical in both open and closed habitats. We also find that 3D models are more standard, lighter, durable, and inexpensive, than the copper electroformed models.

Variation in carbon isotope discrimination within and among Sphagnum species in a temperate wetland

Field samples of bryophytes are highly variable in carbon isotope discrimination values (Δ, a measure of ¹³CO₂ uptake relative to ¹²CO₂), but it is unknown what affects Δ under field conditions, or how variation in Δ relates to bryophyte performance. This study employed field and greenhouse common garden studies to evaluate the influence of microsite, seasonal, and genetic variation on Δ in peatmosses. Three species of Sphagnum that occupy hollow (S. recurvum), carpet (S. palustre), and hummock (S. tenerum) habitats were sampled for relative growth rates (RGR), C:N ratio, and Δ throughout a growing season. Values of Δ ranged from 19.0 to 27.1‰. This variation was unrelated to species (P=0.61). However, Δ varied seasonally (P<0.001), with lower discrimination in the spring (mean 22.5‰), followed by summer (23.8‰) and winter (24.7‰). There was also significant microsite variation (P=0.015) which disappeared when plants were grown in a common garden. In both spring and summer, microsite variation in Δ was inversely related to RGR (P<0.001), but unrelated to C:N ratios (P>0.08). These results suggest that environmental, not genetic, variation at microsites affects Δ in non-vascular plants. However, environmental control of Δ is unlike that in vascular plants where water limitation lowers chloroplastic demand and increases resistance to carbon uptake. In non-vascular plants, water limitation lowers chloroplastic demand and decreases resistance to carbon uptake. These processes have additive effects and generate high spatial and seasonal variability in Δ.