Molecular Mechanisms Of Adaptation Research Articles

Erratum for the Research Article: "Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity" by Jurdzinski et al.

Erratum for the Research Article: "Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity" by Jurdzinski et al.

In search of the molecular mechanisms of adaptation memory in rods: basic activity of phosphodiesterase

Retinal rods, the photoreceptors responsible for twilight vision, are capable of adapting to a wide range of light levels. The molecular mechanisms of light adaptation have been well studied, but an interesting question is what changes occur in the phototransduction cascade after the adaptive light stimuli are eliminated. Previously, we showed the phenomenon of adaptation memory in amphibian rods: after background illumination photoreceptor sensitivity to light remained reduced for several minutes, while the dark current recovered within 20—30 s. This suggests the existence of additional, as yet unknown, regulatory mechanisms of the phototransduction cascade that act after the adaptive effect of light. In search of specific mechanisms that could explain the effect of adaptation memory, we performed electrophysiological experiments on isolated frog rods to evaluate the basal activity of the effector enzyme of the phototransduction cascade, the phosphodiesterase type 6, in the dark and after saturating background illumination. It was found that the post-adaptation state of rods was characterized by increased basal phosphodiesterase activity, which gradually decreased to the dark level within tens of seconds after turning off the adaptive illumination. These results also suggest that the components of the phototransduction cascade may undergo some unstudied changes after light adaptation.

The differential expression of the P5CR and αTPS6 genes in cowpea plants increases tolerance to water-deficit and high temperatures

Plants exposed to adverse environmental conditions develop molecular mechanisms of adaptation and/or defense, the osmoprotectors, which function as compatible solutes and contribute to tolerance via prevention systems and protection against cellular damage caused by these abiotic stresses. This study aimed to identify and characterize the osmoprotectors proline and trehalose in cowpea plants cv. Carijó under controlled conditions of water-deficit and heat stress based on the IPCC scenario of 4.8 °C increase in temperature, evaluating their structure and function through computational methods, as well as gene expression by RT-qPCR. The experimental assays were carried out in growth chambers under controlled conditions with different levels of soil water availability, phenological phases and temperature regimes. From the in silico analyses, ten TPS genes and one P5CR gene were identified in Vigna unguiculata, and these were named according to their chromosomal location. The VuP5CR and VuTPS genes play roles in hormone pathway signaling and in the response to light and biotic and abiotic stresses. The genes P5CR (proline) and αTPS6 (trehalose) were induced with increased temperature and lower water availability in the vegetative phase of cowpeas. In addition, P5CR also showed induction with 50% water availability at high temperatures. In the pod filling phase, the P5CR and αTPS6 genes were repressed with water availability of 75%, while only the P5CR gene was induced when water availability was reduced to 25% under heat stress. P5CR and TPS6 genes were induced in cowpea cv. Carijó in response to associated abiotic stresses (water-deficit and high temperatures), which suggests their participation in the mechanisms of adaptation of the species in adverse environmental conditions.

Comparative transcriptomics combined with physiological and functional analysis reveals the regulatory mechanism of rainbow trout (Oncorhynchus mykiss) under acute hypoxia stress

Hypoxia, largely triggered by global warming and water contamination, has become an environmental issue of great concern, posing a great threat to aquatic ecosystem. As one of the world's most economically important fish, rainbow trout (Oncorhynchus mykiss) is extremely intolerant of hypoxic environments, however, little is known about the roles of non-coding RNAs (ncRNAs) in the response of rainbow trout to hypoxia stress. Herein, effects of moderate (Tm12L) and severe hypoxia for 12 h (Ts12L) and 12 h reoxygenation on histology, biochemical parameters (antioxidant, metabolism and immunity) and transcriptome (lncRNA, miRNA and mRNA) in rainbow trout liver were investigated. We further validated the regulatory relationships between LOC110519952, novel-m0023-5p and glut1a via dual‑luciferase reporter, overexpression and silencing assays. Compared with Tm12L, the liver in Ts12L showed more severe oxidative damage. Anaerobic, lipid and protein metabolism was enhanced under hypoxia stress, especially in Ts12L. We also found that Tm12L could strengthen innate immune response, which was inhibited in Ts12L. Besides, several hypoxia-related genes (glut1a, vegfaa, hmox, epoa, foxo1a and igfbp1) and ceRNA networks were identified from 1824, 427 and 545 differentially expressed mRNAs, miRNAs and lncRNAs, including LOC118965299-novel-m0179-3p-epoa, LOC110519952-novel-m0023-5p-glut1a, MSTRG.7382.2-miR-184-y-hmox and LOC110520012-miR-206-y-vegfaa. Through in vitro and in vivo functional analysis, we demonstrated that glut1a is a target of novel-m0023-5p, and LOC110519952 can positively regulate glut1a by targeting novel-m0023-5p. Introduction of LOC110519952 could attenuate the promoting effects of novel-m0023-5p on rainbow trout liver cell viability and proliferation. This study highlights the differences in the regulatory mechanism of rainbow trout under different concentrations of hypoxia stress and provides valuable data for further research on the molecular mechanisms of fish adaptation to hypoxic environments.

Proline metabolism and its osmotic regulatory role in enhancing hypersalinity tolerance of the razor clam (Sinonovacula constricta)

Proline serves as an important osmolyte in maintaining osmotic pressure and stabilizing cellular structure in aquatic organisms, and is essential for adaptation to salinity stress. This study focuses on the razor clam (Sinonovacula constricta), and investigated the metabolism and synthesis of proline in response to changing salinity. The proline content in gill tissues of razor clams significantly increased over time and with different levels of salinity exposure. The key genes involved in proline metabolism, including (Aminotransferase (ScOAT), Δ1-pyrroline-5-carboxylic acid synthase (ScP5CS), and proline dehydrogenase (ScProDH) were investigated, as well as enzyme activities associated with these genes in razor clams. The expression and activity of P5CS increased significantly under hypersalinity conditions, whereas that of OAT enzyme activity decreased. This suggested that the glutamate pathway had an important role in the proline synthesis during hypersalinity. ProDH activity was negatively correlated with salinity and regulated by the proline content, indicating a significant role of ProDH in proline accumulation under hypersalinity conditions. ScP5CS was heterologously expressed in yeast Saccharomyces cerevisiae, followed by exogenous proline supplementation studies. Recombinant S. cerevisiae incubated with ScP5CS exhibited elevated levels of proline, with the growth performance of recombinant strain surpassing that of the control group after salinity stress. In addition, razor clams exposed to exogenous proline under high salinity conditions showed expedite osmotic regulation, whereby the hemolymph pressure reached equilibrium more quickly. Together, these results indicated that the proline content increased under high salinity, which could improve the tolerance of razor clams to hypersalinity, offering novel perspectives into molecular mechanism of salinity adaptation in shellfish.

Apolipoprotein E controls Dectin-1-dependent development of monocyte-derived alveolar macrophages upon pulmonary β-glucan-induced inflammatory adaptation

The lung is constantly exposed to the outside world and optimal adaptation of immune responses is crucial for efficient pathogen clearance. However, mechanisms that lead to lung-associated macrophages’ functional and developmental adaptation remain elusive. To reveal such mechanisms, we developed a reductionist model of environmental intranasal β-glucan exposure, allowing for the detailed interrogation of molecular mechanisms of pulmonary macrophage adaptation. Employing single-cell transcriptomics, high-dimensional imaging and flow cytometric characterization paired with in vivo and ex vivo challenge models, we reveal that pulmonary low-grade inflammation results in the development of apolipoprotein E (ApoE)-dependent monocyte-derived alveolar macrophages (ApoE+CD11b+ AMs). ApoE+CD11b+ AMs expressed high levels of CD11b, ApoE, Gpnmb and Ccl6, were glycolytic, highly phagocytic and produced large amounts of interleukin-6 upon restimulation. Functional differences were cell intrinsic, and myeloid cell-specific ApoE ablation inhibited Ly6c+ monocyte to ApoE+CD11b+ AM differentiation dependent on macrophage colony-stimulating factor secretion, promoting ApoE+CD11b+ AM cell death and thus impeding ApoE+CD11b+ AM maintenance. In vivo, β-glucan-elicited ApoE+CD11b+ AMs limited the bacterial burden of Legionella pneumophilia after infection and improved the disease outcome in vivo and ex vivo in a murine lung fibrosis model. Collectively these data identify ApoE+CD11b+ AMs generated upon environmental cues, under the control of ApoE signaling, as an essential determinant for lung adaptation enhancing tissue resilience.

Genome-wide identification of bHLH gene family and screening of candidate gene in response to salt stress in kiwifruit

As the second largest family of transcription factors in plants, bHLH is widely involved in the growth and development of organisms and their response to stress. In the past, there was no systematic division of this gene family in kiwifruit. In this study, we identified 206 AcbHLH genes, divided into 22 subfamilies, and analyzed chromosomal localization, physicochemical properties, conserved domains, and intron/exon composition. In addition, the repeat events of the AcbHLH gene in kiwifruit and the evolutionary relationship with Arabidopsis thaliana and Oryza sativa were further analyzed. We analyzed the expression levels of the AcbHLH genes under biotic and abiotic stresses (heat, low temperature, drought, and Bacillus anthracis infection). In addition, we also investigated the biological function of AcbHLH146 under salt stress using a VIGS-mediated gene silencing method. In the AcbHLH146-VIGS line, the content of H2O2 and O2- was lower and the damage was less. SOD, POD, and CAT enzyme activities are higher. These results suggest that AcbHLH146 may play a negative moderating role in the response of kiwifruit to salt stress. Our findings provide new insights into the potential role of AcbHLH146 under abiotic stress, and provide a theoretical basis for the molecular mechanism of Kiwifruit adaptation to salt stress.

Multi-scale analysis of heat stress acclimation in Arabidopsis seedlings highlights the primordial contribution of energy-transducing organelles.

Much progress has been made in understanding the molecular mechanisms of plant adaptation to heat stress. However, the great diversity of models and stress conditions, and the fact that analyses are often limited to a small number of approaches, complicate the picture. We took advantage of a liquid culture system in which Arabidopsis seedlings are arrested in their development, thus avoiding interference with development and drought stress responses, to investigate through an integrative approach seedlings' global response to heat stress and acclimation. Seedlings perfectly tolerate a noxious heat shock (43°C) when subjected to a heat priming treatment at a lower temperature (38°C) the day before, displaying a thermotolerance comparable to that previously observed for Arabidopsis. A major effect of the pre-treatment was to partially protect energy metabolism under heat shock and favor its subsequent rapid recovery, which was correlated with the survival of seedlings. Rapid recovery of actin cytoskeleton and mitochondrial dynamics were another landmark of heat shock tolerance. The omics confirmed the role of the ubiquitous heat shock response actors but also revealed specific or overlapping responses to priming, heat shock, and their combination. Since only a few components or functions of chloroplast and mitochondria were highlighted in these analyses, the preservation and rapid recovery of their bioenergetic roles upon acute heat stress do not require extensive remodeling of the organelles. Protection of these organelles is rather integrated into the overall heat shock response, thus allowing them to provide the energy required to elaborate other cellular responses toward acclimation.

Acute hypoxia and reoxygenation alters glucose and lipid metabolic patterns in Hulong hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂)

Dissolved oxygen (DO) is crucial for fish's biological functions, affecting metabolism, growth, and survival. Intensive aquaculture and live fish transportation, prevalent in the growing live fish market, often expose Hulong hybrid groupers (Epinephelus fuscoguttatus♀ × E. lanceolatus♂) to acute hypoxic stress. This study explores the impact of acute hypoxia and subsequent reoxygenation on these groupers, focusing on their metabolic response and the underlying mechanisms in different tissues. By inducing acute hypoxic stress until mobility loss and then allowing recovery to normal DO levels, we comprehensively assessed glycolipid metabolism using RNA-seq to map regulatory networks in stress and recovery phases. This revealed significant transcriptional regulation related to hypoxic stress and glycolipid metabolism, with pathways like Insulin, HIF-1, FoxO, and cAMP playing key roles. Gill and brain tissues showed rapid changes, with significant upregulation in genes like irs, pi3k, hif-1α, and hk, whereas the liver had a more subdued response, upregulating genes linked to glycolipid metabolism like gdpd5 and amy1. During reoxygenation, lipid metabolism genes were downregulated in gills and brain, while the liver showed enhanced lipid oxidation, upregulating genes like apoa1 and fabp3, suggesting a metabolic shift from anaerobic to aerobic processes. These findings illuminate the molecular mechanisms of grouper adaptation to DO fluctuations, offering insights to mitigate acute hypoxia damage in aquaculture.

Differential Expression of Stress Adaptation Genes in a Diatom Ulnaria acus under Different Culture Conditions.

Diatoms are a group of unicellular eukaryotes that are essential primary producers in aquatic ecosystems. The dynamic nature of their habitat necessitates a quick and specific response to various stresses. However, the molecular mechanisms of their physiological adaptations are still underexplored. In this work, we study the response of the cosmopolitan freshwater diatom Ulnaria acus (Bacillariophyceae, Fragilariophycidae, Licmophorales, Ulnariaceae, Ulnaria) in relation to a range of stress factors, namely silica deficiency, prolonged cultivation, and interaction with an algicidal bacterium. Fluorescent staining and light microscopy were used to determine the physiological state of cells under these stresses. To explore molecular reactions, we studied the genes involved in the stress response-type III metacaspase (MC), metacaspase-like proteases (MCP), death-specific protein (DSP), delta-1-pyrroline-5-carboxylate dehydrogenase (ALDH12), and glutathione synthetase (GSHS). We have described the structure of these genes, analyzed the predicted amino acid sequences, and measured their expression dynamics in vitro using qRT-PCR. We demonstrated that the expression of UaMC1, UaMC3, and UaDSP increased during the first five days of silicon starvation. On the seventh day, it was replaced with the expression of UaMC2, UaGSHS, and UaALDH. After 45 days of culture, cells stopped growing, and the expression of UaMC1, UaMC2, UaGSHS, and UaDSP increased. Exposure to an algicidal bacterial filtrate induced a higher expression of UaMC1 and UaGSHS. Thus, we can conclude that these proteins are involved in diatoms' adaptions to environmental changes. Further, these data show that the molecular adaptation mechanisms in diatoms depend on the nature and exposure duration of a stress factor.

Population structure and adaptability analysis of Schizothorax o’connori based on whole-genome resequencing

BackgroundSchizothorax o’connori is an endemic fish distributed in the upper and lower reaches of the Yarlung Zangbo River in China. It has experienced a fourth round of whole gene replication events and is a good model for exploring the genetic differentiation and environmental adaptability of fish in the Qinghai-Tibet Plateau. The uplift of the Qinghai-Tibet Plateau has led to changes in the river system, thereby affecting gene exchange and population differentiation between fish populations. With the release of fish whole genome data, whole genome resequencing has been widely used in genetic evolutionary analysis and screening of selected genes in fish, which can better elucidate the genetic basis and molecular environmental adaptation mechanisms of fish. Therefore, our purpose of this study was to understand the population structure and adaptive characteristics of S. o’connori using the whole-genome resequencing method.ResultsThe results showed that 23,602,746 SNPs were identified from seven populations, mostly distributed on chromosomes 2 and 23. There was no significant genetic differentiation between the populations, and the genetic diversity was relatively low. However, the Zangga population could be separated from the Bomi, Linzhi, and Milin populations in the cluster analysis. Based on historical dynamics analysis of the population, the size of the ancestral population of S. o’connori was affected by the late accelerated uplift of the Qinghai Tibet Plateau and the Fourth Glacial Age. The selected sites were mostly enriched in pathways related to DNA repair and energy metabolism.ConclusionOverall, the whole-genome resequencing analysis provides valuable insights into the population structure and adaptive characteristics of S. o’connori. There was no obvious genetic differentiation at the genome level between the S. o’connori populations upstream and downstream of the Yarlung Zangbo River. The current distribution pattern and genetic diversity are influenced by the late accelerated uplift of the Qinghai Tibet Plateau and the Fourth Ice Age. The selected sites of S. o’connori are enriched in the energy metabolism and DNA repair pathways to adapt to the low temperature and strong ultraviolet radiation environment at high altitude.

Freezing stress response of wild and cultivated chickpeas.

Chickpea is an economically and nutritionally important grain legume globally, however, cold stress has adverse effects on its growth. In cold countries, like Canada where the growing season is short, having cold stress-tolerant varieties is crucial. Crop wild relatives of chickpea, especially Cicer reticulatum, can survive in suboptimal environments and are an important resource for crop improvement. In this study, we explored the performance of eleven C. reticulatum wild accessions and two chickpea cultivars, CDC Leader and CDC Consul, together with a cold sensitive check ILC533 under freezing stress. Freezing tolerance was scored based on a 1-9 scale. The wild relatives, particularly Kesen_075 and CudiA_152, had higher frost tolerance compared to the cultivars, which all died after frost treatment. We completed transcriptome analysis via mRNA sequencing to assess changes in gene expression in response to freezing stress and identified 6,184 differentially expressed genes (DEGs) in CDC Consul, and 7,842 DEGs in Kesen_075. GO (gene ontology) analysis of the DEGs revealed that those related to stress responses, endogenous and external stimuli responses, secondary metabolite processes, and photosynthesis were significantly over-represented in CDC Consul, while genes related to endogenous stimulus responses and photosynthesis were significantly over-represented in Kesen_075. These results are consistent with Kesen_075 being more tolerant to freezing stress than CDC Consul. Moreover, our data revealed that the expression of CBF pathway-related genes was impacted during freezing conditions in Kesen_075, and expression of these genes is believed to alleviate the damage caused by freezing stress. We identified genomic regions associated with tolerance to freezing stress in an F2 population derived from a cross between CDC Consul and Kesen_075 using QTL-seq analysis. Eight QTLs (P<0.05) on chromosomes Ca3, Ca4, Ca6, Ca7, Ca8, and two QTLs (P<0.01) on chromosomes Ca4 and Ca8, were associated with tolerance to freezing stress. Interestingly, 58 DEGs co-located within these QTLs. To our knowledge, this is the first study to explore the transcriptome and QTLs associated with freezing tolerance in wild relatives of chickpea under controlled conditions. Altogether, these findings provide comprehensive information that aids in understanding the molecular mechanism of chickpea adaptation to freezing stress and further provides functional candidate genes that can assist in breeding of freezing-stress tolerant varieties.

Metabolomics and transcriptomics of embryonic livers reveal hypoxia adaptation of Tibetan chickens

BackgroundExploring the hypoxia adaptation mechanism of Tibetan chicken is of great significance for revealing the survival law of Tibetan chicken and plateau animal husbandry production. To investigate the hypoxia adaptation of Tibetan chickens (TBCs), an integrative metabolomic-transcriptomic analysis of the liver on day 18 of embryonic development was performed. Dwarf laying chickens (DLCs), a lowland breed, were used as a control.ResultsA total of 1,908 metabolites were identified in both TBCs and DLCs. Energy metabolism and amino acid metabolism related differentially regulated metabolites (DRMs) were significantly enriched under hypoxia. Important metabolic pathways including the TCA cycle and arginine and proline metabolism were screened; PCK1, SUCLA2, and CPS1 were found to be altered under hypoxic conditions. In addition, integrated analysis suggested potential differences in mitochondrial function, which may play a crucial role in the study of chicken oxygen adaptation.ConclusionsThese results suggest that hypoxia changed the gene expression and metabolic patterns of embryonic liver of TBCs compared to DLCs. Our study provides a basis for uncovering the molecular regulation mechanisms of hypoxia adaptation in TBCs with the potential application of hypoxia adaptation research for other animals living on the Qinghai-Tibet plateau, and may even contribute to the study of diseases caused by hypoxia.

Multi-omics integration analysis reveals the molecular mechanisms of drought adaptation in homologous tetraploid alfalfa(Medicago sativa 'Xinjiang-Daye').

Drought stress is a predominant abiotic factor leading to decreased alfalfa yield. Genomic ploidy differences contribute to varying adaptation mechanisms of different alfalfa cultivars to drought conditions. This study employed a multi-omics approach to characterize the molecular basis of drought tolerance in a tetraploid variant of alfalfa (Medicago sativa, Xinjiang-Daye). Under drought treatment, a total of 4446 genes, 859 proteins, and 524 metabolites showed significant differences in abundance. Integrative analysis of the multi-omics data revealed that regulatory modules involved in flavonoid biosynthesis, plant hormone signalling transduction, linoleic acid metabolism, and amino acid biosynthesis play crucial roles in alfalfa adaptation to drought stress. The severity of drought led to the substantial accumulation of flavonoids, plant hormones, free fatty acids, amino acids, and their derivatives in the leaves. Genes such as PAL, 4CL, CHI, CHS, PP2C, ARF_3, and AHP_4 play pivotal regulatory roles in flavonoid biosynthesis and hormone signalling pathways. Differential expression of the LOX gene emerged as a key factor in the elevated levels of free fatty acids. Upregulation of P5CS_1 and GOT1/2 contributed significantly to the accumulation of Pro and Phe contents. ERF19 emerged as a principal positive regulator governing the synthesis of the aforementioned compounds. Furthermore, observations suggest that Xinjiang-Daye alfalfa may exhibit widespread post-transcriptional regulatory mechanisms in adapting to drought stress. The study findings unveil the critical mechanisms by which Xinjiang-Daye alfalfa adapts to drought stress, offering novel insights for the improvement of alfalfa germplasm resources.

Differential protein analysis of saline-alkali promoting the oil accumulation in Nitzschia palea

BackgroundThe increasingly severe salinization of the aquatic environment has led to serious damage to the habitats of aquatic organisms. Benthic diatoms are commonly employed as indicator species for assessing water quality and serve as a reflection of the overall health of the aquatic ecosystem. Nitzschia palea is a common diatom found in freshwater, with high oil content, rapid reproductive rate, and it is a commonly dominant species in various rivers.ResultsThe results showed that after 4 days (d) of saline-alkali stress, the cell density and chlorophyll a content of Nitzschia palea reached their maximum values. Therefore, we selected Nitzschia palea under 4 d stress for Tandem Mass Tag (TMT) quantitative proteomic analysis to explore the molecular adaptation mechanism of freshwater diatoms under saline-alkali stress. Totally, 854 proteins were enriched, of which 439 differentially expressed proteins were identified. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and subcellular fractionation analysis revealed that these proteins were mainly enriched in the photosynthesis pathway, citric acid cycle (TCA cycle), fatty acid synthesis, and glutathione cycle.ConclusionsThis study aims to reveal the physiological, biochemical and proteomic mechanisms of salt and alkali tolerance and molecular adaptation of Nitzschia palea under different saline-alkali concentrations. This study showed that Nitzschia palea is one candidate of the environmental friendly, renewable bioenergy microalgae. Meantime, Nitzschiapalea reveals for the proteome of the freshwater and provides the basis, it became a model algal species for freshwater diatoms.

Transcriptome profiling of the gills to air exposure in mud crab Scylla paramamosain

The mud crab Scylla paramamosain is a valuable commercial mariculture crab worldwide. During the ebb tide or when transported to market, crabs suffer underlying air exposure stress. Gills tissue is the first tissue to cope with this stress. In this study, the transcriptome of S. paramamosain gills from the control group (CG) and experimental group (EG) were sequenced, assembled, and compared. A total of 7,425,620,293 bp and 6,741,616,977 bp clean data were found in EG and CG, respectively. A total of 38,507 unigenes (42.78%) were annotated successfully. 13,626 differentially expressed genes (DEGs) were up-regulated, and 6,502 DEGs were down-regulated. The DEGs related to immunity, apoptosis, metabolism, and ion exchange were detected. DEGs were enriched significantly into the KEGG pathways related to metabolism and immunity. These results proved that more material and energy were required, and immune defense was enhanced when the crab was under air exposure stress. The present study provides the first-gill transcriptomic analysis challenged with air exposure stress in S. paramamosain under air exposure stress, which will be useful to clarify the molecular mechanisms of air exposure adaptation.

Integrated Transcriptomics and Metabolomics Reveal Changes in Cell Homeostasis and Energy Metabolism in Trachinotus ovatus in Response to Acute Hypoxic Stress.

Trachinotus ovatus is an economically important mariculture fish, and hypoxia has become a critical threat to this hypoxia-sensitive species. However, the molecular adaptation mechanism of T. ovatus liver to hypoxia remains unclear. In this study, we investigated the effects of acute hypoxic stress (1.5 ± 0.1 mg·L-1 for 6 h) and re-oxygenation (5.8 ± 0.3 mg·L-1 for 12 h) in T. ovatus liver at both the transcriptomic and metabolic levels to elucidate hypoxia adaptation mechanism. Integrated transcriptomics and metabolomics analyses identified 36 genes and seven metabolites as key molecules that were highly related to signal transduction, cell growth and death, carbohydrate metabolism, amino acid metabolism, and lipid metabolism, and all played key roles in hypoxia adaptation. Of these, the hub genes FOS and JUN were pivotal hypoxia adaptation biomarkers for regulating cell growth and death. During hypoxia, up-regulation of GADD45B and CDKN1A genes induced cell cycle arrest. Enhancing intrinsic and extrinsic pathways in combination with glutathione metabolism triggered apoptosis; meanwhile, anti-apoptosis mechanism was activated after hypoxia. Expression of genes related to glycolysis, gluconeogenesis, amino acid metabolism, fat mobilization, and fatty acid biosynthesis were up-regulated after acute hypoxic stress, promoting energy supply. After re-oxygenation for 12 h, continuous apoptosis favored cellular function and tissue repair. Shifting from anaerobic metabolism (glycolysis) during hypoxia to aerobic metabolism (fatty acid β-oxidation and TCA cycle) after re-oxygenation was an important energy metabolism adaptation mechanism. Hypoxia 6 h was a critical period for metabolism alteration and cellular homeostasis, and re-oxygenation intervention should be implemented in a timely way. This study thoroughly examined the molecular response mechanism of T. ovatus under acute hypoxic stress, which contributes to the molecular breeding of hypoxia-tolerant cultivars.

'Against all floods': plant adaptation to flooding stress and combined abiotic stresses.

Current climate change brings with it a higher frequency of environmental stresses, which occur in combination rather than individually leading to massive crop losses worldwide. In addition to, for example, drought stress (low water availability), also flooding (excessive water) can threaten the plant, causing, among others, an energy crisis due to hypoxia, which is responded to by extensive transcriptional, metabolic and growth-related adaptations. While signalling during flooding is relatively well understood, at least in model plants, the molecular mechanisms of combinatorial flooding stress responses, for example, flooding simultaneously with salinity, temperature stress and heavy metal stress or sequentially with drought stress, remain elusive. This represents a significant gap in knowledge due to the fact that dually stressed plants often show unique responses at multiple levels not observed under single stress. In this review, we (i) consider possible effects of stress combinations from a theoretical point of view, (ii) summarize the current state of knowledge on signal transduction under single flooding stress, (iii) describe plant adaptation responses to flooding stress combined with four other abiotic stresses and (iv) propose molecular components of combinatorial flooding (hypoxia) stress adaptation based on their reported dual roles in multiple stresses. This way, more future emphasis may be placed on deciphering molecular mechanisms of combinatorial flooding stress adaptation, thereby potentially stimulating development of molecular tools to improve plant resilience towards multi-stress scenarios.

Changes in the astronaut serum proteome during prolonged spaceflight.

The molecular mechanisms associated with spaceflight-induced biological adaptations that may affect many healthy tissue functions remain poorly understood. In this study, we analyzed temporal changes in the serum proteome of six astronauts during prolonged spaceflight missions using quantitative comprehensive proteome analysis performed with the data-independent acquisition method of mass spectrometry (DIA-MS). All six astronauts participated in a spaceflight mission for approximately 6 months and showed a decreasing trend in T-scores at almost all sites where dual-energy X-ray absorptiometry scans were performed. DIA-MS successfully identified 624 nonredundant proteins in sera and further quantitative analysis for each sampling point provided information on serum protein profiles closely related to several time points before (pre-), during (in-), and after (post-) spaceflight. Changes in serum protein levels between spaceflight and on the ground suggest that abnormalities in bone metabolism are induced in astronauts during spaceflight. Furthermore, changes in the proteomic profile occurring during spaceflight suggest that serum levels of bone metabolism-related proteins, namely ALPL, COL1A1, SPP1, and POSTN, could serve as highly responsive indicators of bone metabolism status in spaceflight missions. This study will allow us to accelerate research to improve our understanding of the molecular mechanisms of biological adaptations associated with prolonged spaceflight.

Genomic Analysis of Earwigs and Their Ecological Adaptation: From Genome Assembly to Molecular Mechanisms of Environmental Adaptation

Genomic Analysis of Earwigs and Their Ecological Adaptation: From Genome Assembly to Molecular Mechanisms of Environmental Adaptation