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Science Advances Aug 2023Regulatory proteins play a crucial role in adaptation to environmental cues. Especially for lifestyle transitions, such as cell proliferation or apoptosis, switch-like...
Regulatory proteins play a crucial role in adaptation to environmental cues. Especially for lifestyle transitions, such as cell proliferation or apoptosis, switch-like characteristics are desirable. While nature frequently uses regulatory circuits to amplify or dampen signals, stand-alone protein switches are interesting for applications like biosensors, diagnostic tools, or optogenetics. However, such stand-alone systems frequently feature limited dynamic and operational ranges and suffer from slow response times. Here, we characterize a LOV-activated diguanylate cyclase (LadC) that offers precise temporal and spatial control of enzymatic activity with an exceptionally high dynamic range over four orders of magnitude. To establish this pronounced activation, the enzyme exhibits a two-stage activation process in which its activity is inhibited in the dark by caging its effector domains and stimulated upon illumination by the formation of an extended coiled-coil. These switch-like characteristics of the LadC system can be used to develop new optogenetic tools with tight regulation.
Topics: Light; Phosphorus-Oxygen Lyases; Escherichia coli Proteins; Photic Stimulation; Optogenetics
PubMed: 37531459
DOI: 10.1126/sciadv.adh4721 -
Zoological Research Jul 2023Feeding strategies of an organism depend on the multimodal sensory processing that most efficiently integrates available visual, chemosensory, and/or mechanoreceptive...
Feeding strategies of an organism depend on the multimodal sensory processing that most efficiently integrates available visual, chemosensory, and/or mechanoreceptive cues as part of their environmental adaptation. The blind cavefish morph of has developed sensory-dependent behaviors to find food more efficiently than their eyed, surface-morph counterparts while in darkness. In the absence of light, adult cavefish have evolved enhanced behaviors, such as vibration attraction behavior (VAB), and changes in feeding angle. Here, we identified evolved differences in cavefish larval prey capture (LPC) behavior. In the dark, LPC is more efficient in cavefish than in surface fish. Furthermore, different cave populations express laterality in their LPC and strike towards prey preferentially located on their left or right sides. This suggests the occurrence, to some extent, of divergent LPC evolution among cave populations. While LPC can be triggered exclusively by a vibration stimulus in both surface and cavefish, we provide evidence that LPC is, at least partially, a multimodal sensory process different from adult VAB. We also found that a lack of food may exacerbate the laterality of LPC. Thus, we proposed a mathematical model for explaining laterality based on a balance between: (1) enlarged range of foraging field (behavioral or perceptive) due to asymmetry, (2) food abundance, and (3) disadvantages caused by laterality (unequal lateral hydrodynamic resistance when swimming, allocation of resources for the brain and receptors, and predator escape).
Topics: Animals; Larva; Characidae; Behavior, Animal; Biological Evolution; Caves
PubMed: 37464932
DOI: 10.24272/j.issn.2095-8137.2022.466 -
Plant Communications Jun 2024After germination in the dark, plants produce a shoot apical hook and closed cotyledons to protect the quiescent shoot apical meristem (SAM), which is critical for...
After germination in the dark, plants produce a shoot apical hook and closed cotyledons to protect the quiescent shoot apical meristem (SAM), which is critical for seedling survival during skotomorphogenesis. The factors that coordinate these processes, particularly SAM repression, remain enigmatic. Plant cuticles, multilayered structures of lipid components on the outermost surface of the aerial epidermis of all land plants, provide protection against desiccation and external environmental stresses. Whether and how cuticles regulate plant development are still unclear. Here, we demonstrate that mutants of BODYGUARD1 (BDG1) and long-chain acyl-CoA synthetase2 (LACS2), key genes involved in cutin biosynthesis, produce a short hypocotyl with an opened apical hook and cotyledons in which the SAM is activated during skotomorphogenesis. Light signaling represses expression of BDG1 and LACS2, as well as cutin biosynthesis. Transcriptome analysis revealed that cuticles are critical for skotomorphogenesis, particularly for the development and function of chloroplasts. Genetic and molecular analyses showed that decreased HOOKLESS1 expression results in apical hook opening in the mutants. When hypoxia-induced expression of LITTLE ZIPPER2 at the SAM promotes organ initiation in the mutants, the de-repressed expression of cell-cycle genes and the cytokinin response induce the growth of true leaves. Our results reveal previously unrecognized developmental functions of the plant cuticle during skotomorphogenesis and demonstrate a mechanism by which light initiates photomorphogenesis through dynamic regulation of cuticle synthesis to induce coordinated and systemic changes in organ development and growth during the skotomorphogenesis-to-photomorphogenesis transition.
Topics: Arabidopsis; Arabidopsis Proteins; Gene Expression Regulation, Plant; Meristem
PubMed: 38409782
DOI: 10.1016/j.xplc.2024.100850 -
Plant Physiology Feb 2024In plants, sucrose nonfermenting 1 (SNF1)-related protein kinase 1 (SnRK1) is a key energy sensor that orchestrates large-scale transcriptional reprograming to maintain...
In plants, sucrose nonfermenting 1 (SNF1)-related protein kinase 1 (SnRK1) is a key energy sensor that orchestrates large-scale transcriptional reprograming to maintain cellular homeostasis under energy deficit. SnRK1 activity is under tight negative control, although the exact mechanisms leading to its activation are not well understood. We show that the Arabidopsis (Arabidopsis thaliana) DOMAIN OF UNKNOWN FUNCTION (DUF581) protein DUF581-9/FCS-like zinc finger 3 binds to the catalytic SnRK1.1 α subunit (KIN10) to inhibit its activation by geminivirus rep-interacting kinase (GRIK)-dependent T-loop phosphorylation. Overexpression of DUF581-9 in Arabidopsis dampens SnRK1 signaling and interferes with adaptation to dark-induced starvation. The presence of DUF581-9 significantly reduced SnRK1 activity in protoplasts and in vitro. This was accompanied by a reduction in T175 T-loop phosphorylation and also diminished KIN10 auto-phosphorylation. Furthermore, DUF581-9 reduced binding of the upstream activating kinase GRIK2 to KIN10, explaining the reduced KIN10 T-loop phosphorylation. Ectopically expressed DUF581-9 protein was rapidly turned over by the proteasome when Arabidopsis plants were subjected to starvation treatment, likely releasing its inhibitory activity on the SnRK1 complex. Taken together, our results support a model in which DUF581-9 negatively regulates SnRK1 activity under energy sufficient conditions. Turnover of the protein provides a rapid way for SnRK1 activation under energy deficit without the need of de novo protein synthesis.
Topics: Phosphorylation; Arabidopsis; Catalysis; Catalytic Domain; Cytoplasm; Protein Serine-Threonine Kinases; Arabidopsis Proteins
PubMed: 37936321
DOI: 10.1093/plphys/kiad594 -
Molecular Biology and Evolution Feb 2024Rainforest hunter-gatherers from Southeast Asia are characterized by specific morphological features including a particularly dark skin color (D), short stature (S),...
Rainforest hunter-gatherers from Southeast Asia are characterized by specific morphological features including a particularly dark skin color (D), short stature (S), woolly hair (W), and the presence of steatopygia (S)-fat accumulation localized in the hips (DSWS phenotype). Based on previous evidence in the Andamanese population, we first characterized signatures of adaptive natural selection around the calcium-sensing receptor gene in Southeast Asian rainforest groups presenting the DSWS phenotype and identified the R990G substitution (rs1042636) as a putative adaptive variant for experimental follow-up. Although the calcium-sensing receptor has a critical role in calcium homeostasis by directly regulating the parathyroid hormone secretion, it is expressed in different tissues and has been described to be involved in many biological functions. Previous works have also characterized the R990G substitution as an activating polymorphism of the calcium-sensing receptor associated with hypocalcemia. Therefore, we generated a knock-in mouse for this substitution and investigated organismal phenotypes that could have become adaptive in rainforest hunter-gatherers from Southeast Asia. Interestingly, we found that mouse homozygous for the derived allele show not only lower serum calcium concentration but also greater body weight and fat accumulation, probably because of enhanced preadipocyte differentiation and lipolysis impairment resulting from the calcium-sensing receptor activation mediated by R990G. We speculate that such differential features in humans could have facilitated the survival of hunter-gatherer groups during periods of nutritional stress in the challenging conditions of the Southeast Asian tropical rainforests.
Topics: Animals; Humans; Mice; Calcium; Phenotype; Polymorphism, Genetic; Receptors, Calcium-Sensing; Selection, Genetic
PubMed: 38285634
DOI: 10.1093/molbev/msae015 -
Brazilian Journal of Biology = Revista... 2023A little-studied characteristic of the Mexican native fish Dormitator latifrons is the effect that the color of the bottom or lining of ponds or tubs can have on their...
A little-studied characteristic of the Mexican native fish Dormitator latifrons is the effect that the color of the bottom or lining of ponds or tubs can have on their growth and blood parameters under controlled conditions. After a quarantine period in prophylactic treatment, an initial assay was performed. The organisms were grouped into four treatments (white, yellow, blue, and black) in triplicate, with 30 individuals with an average weight of 34.7± 2.5 g and average size of 12.5 ± 1.5 cm per tank. The trial lasted 60 days, after which a final biometry to all specimens and blood extractions to six random organisms per tank were performed. The following hematological and blood chemistry parameters were evaluated: erythrocytes, cell counts, and differential counts, as well as glucose, albumin, a/g ratio, and total proteins. Final weight, weight gain, and specific growth rate presented statistical differences between treatments (p<0.05), with dark bottoms (blue and black) above 80% of WG and above 1.0 of SGR. No statistically differences were found in hematological blood chemistry parameters (p>0.05). The growth results suggest that dark pond bottoms promote the adaptation of Dormitator latifrons by allowing it to avoid detection by predators through the adoption of a cryptic coloration. However, the species shows a great capacity for crypsis, being able to change its pigmentation to adapt to different bottom colors.
Topics: Animals; Ponds; Fishes; Perciformes; Mexico
PubMed: 37937625
DOI: 10.1590/1519-6984.274004 -
IScience Jun 2024Early modern humans lived as hunter-gatherers for millennia before agriculture, yet the genetic adaptations of these populations remain a mystery. Here, we investigate...
Early modern humans lived as hunter-gatherers for millennia before agriculture, yet the genetic adaptations of these populations remain a mystery. Here, we investigate selection in the ancient hunter-gatherer-fisher Jomon and contrast pre- and post-agricultural adaptation in the Japanese archipelago. Building on the successful validation of imputation with ancient Asian genomes, we identify selection signatures in the Jomon, particularly robust signals from variants, which may have influenced dark pigmentation evolution. The Jomon lacks well-known adaptive variants (, , and ), marking their emergence after the advent of farming in the archipelago. Notably, the and variants were prevalent in the archipelago 1,300 years ago, whereas the variant could have emerged later due to its absence in other ancient genomes. Overall, our study underpins local adaptation unique to the Jomon population, which in turn sheds light on post-farming selection that continues to shape contemporary Asian populations.
PubMed: 38883821
DOI: 10.1016/j.isci.2024.110050 -
Documenta Ophthalmologica. Advances in... Feb 2024Both rod and cone-driven signals contribute to the electroretinogram (ERG) elicited by a standard strong flash in the dark. Negative ERGs usually reflect inner retinal...
PURPOSE
Both rod and cone-driven signals contribute to the electroretinogram (ERG) elicited by a standard strong flash in the dark. Negative ERGs usually reflect inner retinal dysfunction. However, in diseases where rod photoreceptor function is selectively lost, a negative waveform might represent the response of the dark-adapted cone system. To investigate the dark-adapted cone-driven waveform in healthy individuals, we delivered flashes on a dim blue background, designed to saturate the rods, but minimally adapt the cones.
METHODS
ERGs were recorded, using conductive fibre electrodes, in adults from the TwinsUK cohort. Responses to 13 cd m s white xenon flashes (similar to the standard DA 10 flash), delivered on a blue background, were analysed. Photopic and scotopic strengths of the background were 1.3 and 30 cd m, respectively; through a dilated pupil, this is expected to largely saturate the rods, but adapt the cones much less than the standard ISCEV background.
RESULTS
Mean (SD) participant age was 62.5 (11.3) years (93% female). ERGs from 203 right and 204 left eyes were included, with mean (SD) b/a ratios of 1.22 (0.28) and 1.18 (0.28), respectively (medians, 1.19 and 1.17). Proportions with negative waveforms were 23 and 26%, respectively. Right and left eye b/a ratios were strongly correlated (correlation coefficient 0.74, p < 0.0001). We found no significant correlation of b/a ratio with age.
CONCLUSIONS
Over 20% of eyes showed b/a ratios less than 1, consistent with the notion that dark-adapted cone-driven responses to standard bright flashes can have negative waveforms. The majority had ratios greater than 1. Thus, whilst selective loss of rod function can yield a negative waveform (with reduced a-wave) in some, our findings also suggest that loss of rod function can occur without necessarily yielding a negative ERG. One potential limitation is possible mild cone system adaptation by the background.
Topics: Adult; Humans; Female; Middle Aged; Male; Electroretinography; Prevalence; Dark Adaptation; Photic Stimulation; Retinal Cone Photoreceptor Cells
PubMed: 37924416
DOI: 10.1007/s10633-023-09957-4 -
Zoological Letters Jan 2024Egg-laying mammals (monotremes) are considered "primitive" due to traits such as oviparity, cloaca, and incomplete homeothermy, all of which they share with reptiles....
Egg-laying mammals (monotremes) are considered "primitive" due to traits such as oviparity, cloaca, and incomplete homeothermy, all of which they share with reptiles. Two groups of monotremes, the terrestrial echidna (Tachyglossidae) and semiaquatic platypus (Ornithorhynchidae), have evolved highly divergent characters since their emergence in the Cenozoic era. These evolutionary differences, notably including distinct electrosensory and chemosensory systems, result from adaptations to species-specific habitat conditions. To date, very few studies have examined the visual adaptation of echidna and platypus. In the present study, we show that echidna and platypus have different light absorption spectra in their dichromatic visual sensory systems at the molecular level. We analyzed absorption spectra of monotreme color opsins, long-wavelength sensitive opsin (LWS) and short-wavelength sensitive opsin 2 (SWS2). The wavelength of maximum absorbance (λ) in LWS was 570.2 in short-beaked echidna (Tachyglossus aculeatus) and 560.6 nm in platypus (Ornithorhynchus anatinus); in SWS2, λ was 451.7 and 442.6 nm, respectively. Thus, the spectral range in echidna color vision is ~ 10 nm longer overall than in platypus. Natural selection analysis showed that the molecular evolution of monotreme color opsins is generally functionally conserved, suggesting that these taxa rely on species-specific color vision. In order to understand the usage of color vision in monotremes, we made 24-h behavioral observations of captive echidnas at warm temperatures and analyzed the resultant ethograms. Echidnas showed cathemeral activity and various behavioral repertoires such as feeding, traveling, digging, and self-grooming without light/dark environment selectivity. Halting (careful) behavior is more frequent in dark conditions, which suggests that echidnas may be more dependent on vision during the day and olfaction at night. Color vision functions have contributed to dynamic adaptations and dramatic ecological changes during the ~ 60 million years of divergent monotreme evolution. The ethogram of various day and night behaviors in captive echidnas also contributes information relevant to habitat conservation and animal welfare in this iconic species, which is locally endangered.
PubMed: 38167154
DOI: 10.1186/s40851-023-00224-7 -
Frontiers in Plant Science 2024Energy efficient lighting strategies have received increased interest from controlled environment producers. Long photoperiods (up to 24 h - continuous lighting (CL)) of...
Energy efficient lighting strategies have received increased interest from controlled environment producers. Long photoperiods (up to 24 h - continuous lighting (CL)) of lower light intensities could be used to achieve the desired daily light integral (DLI) with lower installed light capacity/capital costs and low electricity costs in regions with low night electricity prices. However, plants grown under CL tend to have higher carbohydrate and reactive oxygen species (ROS) levels which may lead to leaf chlorosis and down-regulation of photosynthesis. We hypothesize that the use of dynamic CL using a spectral change and/or light intensity change between day and night can negate CL-injury. In this experiment we set out to assess the impact of CL on pepper plants by subjecting them to white light during the day and up to 150 µmol m s of monochromatic blue light at night while controlling the DLI at the same level. Plants grown under all CL treatments had similar cumulative fruit number and weight compared to the 16h control indicating no reduction in production. Plants grown under CL had higher carbohydrate levels and ROS-scavenging capacity than plants grown under the 16h control. Conversely, the amount of photosynthetic pigment decreased with increasing nighttime blue light intensity. The maximum quantum yield of photosystem II (F/F), a metric often used to measure stress, was unaffected by light treatments. However, when light-adapted, the operating efficiency of photosystem II (ΦPSII) decreased and non-photochemical quenching (NPQ) increased with increasing nighttime blue light intensity. This suggests that both acclimated and instantaneous photochemistry during CL can be altered and is dependent on the nighttime light intensity. Furthermore, light-adapted chlorophyll fluorescence measurements may be more adept at detecting altered photochemical states than the conventional stress metric using dark-adapted measurements.
PubMed: 38882573
DOI: 10.3389/fpls.2024.1372886