Evolution of the cellular stress proteome: from monophyletic origin to ubiquitous function

Molecular aspects of heat stress sensing in land plants

Heat stress impacts all aspects of life, from evolution to global food security. Therefore, it becomes essential to understand how plants respond to heat stress, especially in the context of climate change. The heat stress response (HSR) involves three main components: sensing, signal transduction, and cellular reprogramming. Here, I focus on the heat stress sensing component. How can cells detect heat stress if it is not a signalling particle? To answer this question, I have looked at the molecular definition of heat stress. It can be defined as any particular rise in the optimum growth temperature that leads to higher-than-normal levels of reactive molecular species and macromolecular damage to biological membranes, proteins, and nucleic acid polymers (DNA and RNA). It is precisely these stress-specific alterations that are detected by heat stress sensors, upon which they would immediately trigger the appropriate level of the HSR. In addition, the work towards thermotolerance is complemented by a second type of response, here called the cellular homeostasis response (CHR). Upon mild and extreme temperature changes, the CHR is triggered by plant thermosensors, which are responsible for monitoring temperature information. Heat stress sensors and thermosensors are distinct types of molecules, each with unique modes of activation and functions. While many recent reviews provide a comprehensive overview of plant thermosensors, there remains a notable gap in the review literature regarding an in-depth analysis of plant heat stress sensors. Here, I attempt to summarise our current knowledge of the cellular sensors involved in triggering the plant HSR.

Transcriptomics Unveil Canonical and Non-Canonical Heat Shock-Induced Pathways in Human Cell Lines

The cellular stress response (CSR) is a conserved mechanism that protects cells from -environmental and physiological stressors. The heat shock response (HSR), a critical component of the CSR, utilizes molecular chaperones to mitigate proteotoxic stress caused by elevated temperatures. We hypothesized that while the canonical HSR pathways are conserved across cell types, specific cell lines may exhibit unique transcriptional responses to heat shock. To test this, we compared the transcriptomic responses of HEK293, HepG2, and HeLa cells under control conditions immediately following heat shock and after an 8-h recovery period. RNA sequencing revealed the conserved activation of canonical HSR pathways, including the unfolded protein response, alongside the -enrichment of the non-canonical "Receptor Ligand Activity" pathway across all cell lines. Cell-line-specific variations were observed, with HepG2 cells exhibiting significantly higher ex-pression levels of certain genes compared to other cell lines under stress conditions, as well as greater fold changes in gene expression relative to its control conditions. Validation by qPCR confirmed the activation of key genes within the "Receptor Ligand Activity" pathway across time points. These findings provide insights into conserved and context-specific aspects of the HSR, contributing to a more comprehensive understanding of stress response mechanisms across mammalian cells.

Comparative Proteomics of Bacteria Under Stress Conditions

Bacteria are unicellular organisms with the ability to exist in the harshest of climate and cope with sub-optimal fluctuating environmental conditions. They accomplish this by modification of their internal cellular environment. When external conditions are varied, change in the cell is triggered at the transcriptional level, which usually leads to proteolysis and rewiring of the proteome. Changes in cellular homeostasis, modifications in proteome, and dynamics of such survival mechanisms can be studied using various scientific techniques. Our focus in this chapter would be on comparative proteomics of bacteria under stress conditions using approaches like 2D electrophoresis accompanied by N-terminal sequencing and recently, mass spectrometry. More than 170 such studies on bacteria have been accomplished till to date and involve analysis of whole cells as well as that of cellular fractions, i.e., outer membrane, inner membrane, cell envelope, cytoplasm, thylakoid, lipid bodies, etc. Similar studies conducted on gram-negative and gram-positive model organism, i.e., Escherichia coli and Bacillus subtilis, respectively, have been summarized. Vital information, hypothesis about conservation of stress-specific proteome, and conclusions are also presented in the light of research conducted over the last decades.

Future cattle production: Animal welfare as a critical component of sustainability and beef quality, a South American perspective

The demand for animal protein is rising, increasing pressure on animal production systems and ecological resources. Ethical and environmental concerns are also growing worldwide, pushing for more sustainable food production systems. The international scientific community has raised concerns about misinformation regarding meat production processes and their harmful impact on the environment, animal welfare and human health consumption. It is crucial to provide accurate information based on science, implement an active communication strategy, and foster collaboration across the meat supply chain to demonstrate that livestock farming is part of the solution to climate change and sustainability issues. As a fundamental pillar of sustainability, animal welfare plays a crucial role in this scrutiny. The "social license to farm" hinges on animal welfare issues and those related to climate change, the environment and biodiversity. Animal welfare is gaining relevance in the market of farm animals and their products, shaping a nation's standing in the international community. Considering the potential advantages of the Southern cone of South America production systems regarding sustainability and animal welfare, several countries prioritise them in their science, technology transfer, innovation, and public policy agendas. Scientific research indicates that implementing effective animal handling and welfare practices has a demonstrably positive impact on individual animal temperament, the quality of the human-animal relationship, overall productivity, and meat quality while reducing the risks of accidents. Caring for the welfare of animals is not only a moral imperative but can also be a business decision that benefits all stakeholders.

Transcriptomics Unveil Canonical and Non-Canonical Heat Shock-Induced Pathways in Human Cell Lines

The cellular stress response (CSR) is a conserved mechanism that protects cells from environmental and physiological stressors. The heat shock response (HSR), a critical component of the CSR, utilizes molecular chaperones to mitigate proteotoxic stress caused by elevated temperatures. We hypothesized that while the canonical HSR pathways are conserved across cell types, specific cell lines may exhibit unique transcriptional responses to heat shock. To test this, we compared the transcriptomic responses of HEK293, HepG2, and HeLa cells under control conditions immediately following heat shock and after an 8-hour recovery period. RNA sequencing revealed conserved activation of canonical HSR pathways, including the unfolded protein response, alongside enrichment of the non-canonical "Receptor Ligand Activity" pathway across all cell lines. Cell line-specific variations were also observed, with HepG2 cells displaying more uniquely expressed genes and elevated expression levels (fold changes) of shared genes under stress conditions. Validation by qPCR confirmed the activation of key genes within the "Receptor Ligand Activity" pathway across time points. These findings provide insights into conserved and context-specific aspects of the HSR, contributing to a more comprehensive understanding of stress response mechanisms across mammalian cells.

A Golgi-targeted fluorescent probe for monitoring polarity dynamic during programmed cell death

Programmed cell death (PCD) is a controlled form of cell death and it plays an essential role in maintaining homeostasis. Golgi apparatus works as the hotspot during the early event of PCD and Golgi polarity, a vital microenvironment factor, can be regarded as an indicator of physiological status. Combined Golgi-targeted group phenylsulfonamide as electron acceptor group and triphenylamine as electron donor group, a novel Golgi-targeted fluorescent probe GTO had been developed. GTO showed good sensitivity and selectivity to polarity and its remarkable photostability makes it potentially useful for long-term cellular monitoring. In practice, GTO demonstrated good cell permeability and Golgi targeting capabilities. According to our results, GTO was applied to reveal the polarity increase during the early event of PCD and the encouraging results illustrated that GTO was an imaging tool for monitoring polarity in Golgi apparatus and the exploration in early diagnosis and drug discovery.

The effects of marine heatwaves on a coral reef snapper: insights into aerobic and anaerobic physiology and recovery

Marine heatwaves (MHWs) are increasing in frequency and intensity. Coral reefs are particularly susceptible to MHWs, which cause mass coral bleaching and mortality. However, little is known about how MHWs affect coral reef fishes. Here, we investigated how MHWs affect the physiology of a coral reef mesopredator, Lutjanus carponotatus. Specifically, we exposed mature adults to two different MHW intensities, +1°C (29.5°C) and + 2°C (30.5°C) and measured physiological performance at 2 and 4 weeks of exposure and at 2 weeks post-exposure. At these time points, we measured oxygen consumption at rest and after a simulated fishing capture event, recovery time, excess post-exercise oxygen consumption (EPOC) and associated biochemical markers in the blood (baseline lactate, post-capture lactate, glucose, haemoglobin levels and haematocrit proportion). We found that 2 weeks of exposure to MHW conditions increased resting oxygen consumption (+1°C = 23%, +2°C = 37%), recovery time (+1°C = 62%, +2°C = 77%), EPOC (+1°C = 50%, +2°C = 68%), baseline lactate (+1°C = 27%, +2°C = 28%), post-capture lactate (+1°C = 62%, +2°C = 109%) and haemoglobin levels (+1°C = 13%, +2°C = 28%). This pattern was maintained at 4 weeks of exposure except for post-capture lactate which was reduced (+1°C = -37%, +2°C = 27%). In combination, these results suggest a greater reliance on anaerobic glycolysis to maintain homeostasis in MHW conditions. At 2 weeks post-exposure, when compared to control fish, we found that capture oxygen consumption was increased (+1°C = 25%, +2°C = 26%), recovery rate was increased (+2°C = 38%) and haemoglobin was still higher (+1°C = 15%, +2°C = 21%). These results show that MHW conditions have direct physiological demands on adult coral reef snapper and ecologically relevant residual effects can last for at least 2 weeks post-MHW; however, individuals appear to recover from the negative effects experienced during the MHW. This provides new insight into the effects of MHWs on the physiological performance of coral reef fishes.

Combined effects of norfloxacin and polystyrene nanoparticles on the oxidative stress and gut health of the juvenile horseshoe crab Tachypleus tridentatus

Pollution with anthropogenic contaminants including antibiotics and nanoplastics leads to gradual deterioration of the marine environment, which threatens endangered species such as the horseshoe crab Tachypleus tridentatus. We assessed the potential toxic mechanisms of an antibiotic (norfloxacin, 0, 0.5, 5 μg/L) and polystyrene nanoparticles (104 particles/L) in T. tridentatus using biomarkers of tissue redox status, molting, and gut microbiota. Exposure to single and combined pollutants led to disturbance of redox balance during short-term (7 days) exposure indicated by elevated level of a lipid peroxidation product, malondialdehyde (MDA). After prolonged (14-21 days) exposure, compensatory upregulation of antioxidants (catalase and glutathione but not superoxide dismutase) was observed, and MDA levels returned to the baseline in most experimental exposures. Transcript levels of molting-related genes (ecdysone receptor, retinoic acid X alpha receptor and calmodulin A) and a molecular chaperone (cognate heat shock protein 70) showed weak evidence of response to polystyrene nanoparticles and norfloxacin. The gut microbiota T. tridentatus was altered by exposures to norfloxacin and polystyrene nanoparticles shown by elevated relative abundance of Bacteroidetes. At the functional level, evidence of suppression by norfloxacin and polystyrene nanoparticles was found in multiple intestinal microbiome pathways related to the genetic information processing, metabolism, organismal systems, and environmental information processing. Future studies are needed to assess the physiological and health consequences of microbiome dysbiosis caused by norfloxacin and polystyrene nanoparticles and assist the environmental risk assessment of these pollutants in the wild populations of the horseshoe crabs.

Projected ocean temperatures impair key proteins used in vision of octopus hatchlings

Global warming is one of the most significant and widespread effects of climate change. While early life stages are particularly vulnerable to increasing temperatures, little is known about the molecular processes that underpin their capacity to adapt to temperature change during early development. Using a quantitative proteomics approach, we investigated the effects of thermal stress on octopus embryos. We exposed Octopus berrima embryos to different temperature treatments (control 19°C, current summer temperature 22°C, or future projected summer temperature 25°C) until hatching. By comparing their protein expression levels, we found that future projected temperatures significantly reduced levels of key eye proteins such as S-crystallin and retinol dehydrogenase 12, suggesting the embryonic octopuses had impaired vision at elevated temperature. We also found that this was coupled with a cellular stress response that included a significant elevation of proteins involved in molecular chaperoning and redox regulation. Energy resources were also redirected away from non-essential processes such as growth and digestion. These findings, taken together with the high embryonic mortality observed under the highest temperature, identify critical physiological functions of embryonic octopuses that may be impaired under future warming conditions. Our findings demonstrate the severity of the thermal impacts on the early life stages of octopuses as demonstrated by quantitative proteome changes that affect vision, protein chaperoning, redox regulation and energy metabolism as critical physiological functions that underlie the responses to thermal stress.

Tracking Karyotype Changes in Treatment-Induced Drug-Resistant Evolution

Karyotype coding, which encompasses the complete chromosome sets and their topological genomic relationships within a given species, encodes system-level information that organizes and preserves genes' function, and determines the macroevolution of cancer. This new recognition emphasizes the crucial role of karyotype characterization in cancer research. To advance this cancer cytogenetic/cytogenomic concept and its platforms, this study outlines protocols for monitoring the karyotype landscape during treatment-induced rapid drug resistance in cancer. It emphasizes four key perspectives: combinational analyses of phenotype and karyotype, a focus on the entire evolutionary process through longitudinal analysis, a comparison of whole landscape dynamics by including various types of NCCAs (including genome chaos), and the use of the same process to prioritize different genomic scales. This protocol holds promise for studying numerous evolutionary aspects of cancers, and it further enhances the power of karyotype analysis in cancer research.

Topoisomerase 1 Activity Is Reduced in Response to Thermal Stress in Fruit Flies and in Human HeLa Cells

In the modern world with climate changes and increasing pollution, different types of stress are becoming an increasing challenge. Hence, the identification of reliable biomarkers of stress and accessible sensors to measure such biomarkers are attracting increasing attention. In the current study, we demonstrate that the activity, but not the expression, of the ubiquitous enzyme topoisomerase 1 (TOP1), as measured in crude cell extracts by the REEAD sensor system, is markedly reduced in response to thermal stress in both fruit flies (Drosophila melanogaster) and cultivated human cells. This effect was observed in response to both mild-to-moderate long-term heat stress and more severe short-term heat stress in D. melanogaster. In cultivated HeLa cells a reduced TOP1 activity was observed in response to both cold and heat stress. The reduced TOP1 activity appeared dependent on one or more cellular pathways since the activity of purified TOP1 was unaffected by the utilized stress temperatures. We demonstrate successful quantitative measurement of TOP1 activity using an easily accessible chemiluminescence readout for REEAD pointing towards a sensor system suitable for point-of-care assessment of stress responses based on TOP1 as a biomarker.

WR1065 conjugated to thiol-PEG polymers as novel anticancer prodrugs: broad spectrum efficacy, synergism, and drug resistance reversal

The lack of anticancer agents that overcome innate/acquired drug resistance is the single biggest barrier to achieving a durable complete response to cancer therapy. To address this issue, a new drug family was developed for intracellular delivery of the bioactive aminothiol WR1065 by conjugating it to discrete thiol-PEG polymers: 4-star-PEG-S-S-WR1065 (4SP65) delivers four WR1065s/molecule and m-PEG6-S-S-WR1065 (1LP65) delivers one. Infrequently, WR1065 has exhibited anticancer effects when delivered via the FDA-approved cytoprotectant amifostine, which provides one WR1065/molecule extracellularly. The relative anticancer effectiveness of 4SP65, 1LP65, and amifostine was evaluated in a panel of 15 human cancer cell lines derived from seven tissues. Additional experiments assessed the capacity of 4SP65 co-treatments to potentiate the anticancer effectiveness and overcome drug resistance to cisplatin, a chemotherapeutic, or gefitinib, a tyrosine kinase inhibitor (TKI) targeting oncogenic EGFR mutations. The CyQUANT®-NF proliferation assay was used to assess cell viability after 48-h drug treatments, with the National Cancer Institute COMPARE methodology employed to characterize dose-response metrics. In normal human epithelial cells, 4SP65 or 1LP65 enhanced or inhibited cell growth but was not cytotoxic. In cancer cell lines, 4SP65 and 1LP65 induced dose-dependent cytostasis and cytolysis achieving 99% cell death at drug concentrations of 11.2 ± 1.2 µM and 126 ± 15.8 µM, respectively. Amifostine had limited cytostatic effects in 11/14 cancer cell lines and no cytolytic effects. Binary pairs of 4SP65 plus cisplatin or gefitinib increased the efficacy of each partner drug and surmounted resistance to cytolysis by cisplatin and gefitinib in relevant cancer cell lines. 4SP65 and 1LP65 were significantly more effective against TP53-mutant than TP53-wild-type cell lines, consistent with WR1065-mediated reactivation of mutant p53. Thus, 4SP65 and 1LP65 represent a unique prodrug family for innovative applications as broad-spectrum anticancer agents that target p53 and synergize with a chemotherapeutic and an EGFR-TKI to prevent or overcome drug resistance.

Roles of Oxidative Stress and Nrf2 Signaling in Pathogenic and Non-Pathogenic Cells: A Possible General Mechanism of Resistance to Therapy

The coordinating role of nuclear factor erythroid-2-related factor 2 (Nrf2) in cellular function is undeniable. Evidence indicates that this transcription factor exerts massive regulatory functions in multiple signaling pathways concerning redox homeostasis and xenobiotics, macromolecules, and iron metabolism. Being the master regulator of antioxidant system, Nrf2 controls cellular fate, influencing cell proliferation, differentiation, apoptosis, resistance to therapy, and senescence processes, as well as infection disease success. Because Nrf2 is the key coordinator of cell defence mechanisms, dysregulation of its signaling has been associated with carcinogenic phenomena and infectious and age-related diseases. Deregulation of this cytoprotective system may also interfere with immune response. Oxidative burst, one of the main microbicidal mechanisms, could be impaired during the initial phagocytosis of pathogens, which could lead to the successful establishment of infection and promote susceptibility to infectious diseases. There is still a knowledge gap to fill regarding the molecular mechanisms by which Nrf2 orchestrates such complex networks involving multiple pathways. This review describes the role of Nrf2 in non-pathogenic and pathogenic cells.

Comparative Analysis of Transcriptomic Response of Escherichia coli K-12 MG1655 to Nine Representative Classes of Antibiotics

The use of antibiotics leads to strong stresses to bacteria, leading to profound impact on cellular physiology. Elucidating how bacteria respond to antibiotic stresses not only helps us to decipher bacteria's strategies to resistant antibiotics but also assists in proposing targets for antibiotic development. In this work, a comprehensive comparative transcriptomic analysis on how Escherichia coli responds to nine representative classes of antibiotics (tetracycline, mitomycin C, imipenem, ceftazidime, kanamycin, ciprofloxacin, polymyxin E, erythromycin, and chloramphenicol) was performed, aimed at determining and comparing the responses of this model organism to antibiotics at the transcriptional level. On average, 39.71% of genes were differentially regulated by antibiotics at concentrations that inhibit 50% growth. Kanamycin leads to the strongest transcriptomic response (76.4% of genes regulated), whereas polymyxin E led to minimal transcriptomic response (4.7% of genes regulated). Further GO, KEGG, and EcoCyc enrichment analysis found significant transcriptomic changes in carbon metabolism, amino acid metabolism, nutrient assimilation, transport, stress response, nucleotide metabolism, protein biosynthesis, cell wall biosynthesis, energy conservation, mobility, and cell-environmental communications. Analysis of coregulated genes led to the finding of significant reduction of sulfur metabolism by all antibiotics, and analysis of transcription factor-coding genes suggested clustered regulatory patterns implying coregulation. In-depth analysis of regulated pathways revealed shared and unique strategies of E. coli resisting antibiotics, leading to the proposal of four different strategies (the pessimistic, the ignorant, the defensive, and the invasive). In conclusion, this work provides a comprehensive analysis of E. coli's transcriptomic response to antibiotics, which paves the road for further physiological investigation. IMPORTANCE Antibiotics are among the most important inventions in the history of humankind. They are the ultimate reason why bacterial infections are no longer the number one threat to people's lives. However, the wide application of antibiotics in the last half a century has led to aggravating antibiotic resistance, weakening the efficacy of antibiotics. To better comprehend the ways bacteria deal with antibiotics that may eventually turn into resistance mechanisms, and to identify good targets for potential antibiotics, knowledge on how bacteria regulate their physiology in response to different classes of antibiotics is needed. This work aimed to fill this knowledge gap by identifying changes of bacterial functions at the transcription level and suggesting strategies of bacteria to resist antibiotics.

Effects of environmental factors on the cellular and molecular parameters of the immune system in decapods

Crustaceans and in particular decapods (i.e. shrimp, crabs and lobsters) are a diverse, commercially and ecologically important group of organisms. They are exposed to a range of environmental factors whose abiotic and biotic components are prone to fluctuate beyond their optimum ranges and, in doing so, affect crustaceans' immune system and health. Changes in key environmental factors such as temperature, pH, salinity, dissolved oxygen, ammonia concentrations and pathogens can provoke stress and immune responses due to alterations in immune parameters. The mechanisms through which stressors mediate effects on immune parameters are not fully understood in decapods. Improved knowledge of the environmental factors - above all, their abiotic components - that influence the immune parameters of decapods could help mitigate or constrain their harmful effects that adversely affect the production of decapod crustaceans. The first part of this overview examines current knowledge and information gaps regarding the basic components and functions of the innate immune system of decapods. In the second part, we discuss various mechanisms provoked by environmental factors and categorize cellular and molecular immune responses to each environmental factor with special reference to decapods.

Integrative biology of injury in animals

Mechanical injury is a prevalent challenge in the lives of animals with myriad potential consequences for organisms, including reduced fitness and death. Research on animal injury has focused on many aspects, including the frequency and severity of wounding in wild populations, the short- and long-term consequences of injury at different biological scales, and the variation in the response to injury within or among individuals, species, ontogenies, and environmental contexts. However, relevant research is scattered across diverse biological subdisciplines, and the study of the effects of injury has lacked synthesis and coherence. Furthermore, the depth of knowledge across injury biology is highly uneven in terms of scope and taxonomic coverage: much injury research is biomedical in focus, using mammalian model systems and investigating cellular and molecular processes, while research at organismal and higher scales, research that is explicitly comparative, and research on invertebrate and non-mammalian vertebrate species is less common and often less well integrated into the core body of knowledge about injury. The current state of injury research presents an opportunity to unify conceptually work focusing on a range of relevant questions, to synthesize progress to date, and to identify fruitful avenues for future research. The central aim of this review is to synthesize research concerning the broad range of effects of mechanical injury in animals. We organize reviewed work by four broad and loosely defined levels of biological organization: molecular and cellular effects, physiological and organismal effects, behavioural effects, and ecological and evolutionary effects of injury. Throughout, we highlight the diversity of injury consequences within and among taxonomic groups while emphasizing the gaps in taxonomic coverage, causal understanding, and biological endpoints considered. We additionally discuss the importance of integrating knowledge within and across biological levels, including how initial, localized responses to injury can lead to long-term consequences at the scale of the individual animal and beyond. We also suggest important avenues for future injury biology research, including distinguishing better between related yet distinct injury phenomena, expanding the subjects of injury research to include a greater variety of species, and testing how intrinsic and extrinsic conditions affect the scope and sensitivity of injury responses. It is our hope that this review will not only strengthen understanding of animal injury but will contribute to building a foundation for a more cohesive field of 'injury biology'.

Heat stress tolerance in peas (Pisum sativum L.): Current status and way forward

In the era of climate change, the overall productivity of pea (Pisum sativum L.) is being threatened by several abiotic stresses including heat stress (HS). HS causes severe yield losses by adversely affecting several traits in peas. A reduction in pod yield has been reported from 11.1% to 17.5% when mean daily temperature increase from 1.4 to 2.2°C. High-temperature stress (30.5-33°C) especially during reproductive phase is known to drastically reduce both seed yield and germination. HS during germination and early vegetative stage resulted in poor emergence and stunted plant growth along with detrimental effects on physiological functions of the pea plant. To combat HS and continue its life cycle, plants use various defense strategies including heat escape, avoidance or tolerance mechanisms. Ironically, the threshold temperatures for pea plant and its responses are inconsistent and not yet clearly identified. Trait discovery through traditional breeding such as semi leaflessness (afila), upright growing habit, lodging tolerance, lower canopy temperature and small seeded nature has highlighted their utility for greater adaptation under HS in pea. Screening of crop gene pool and landraces for HS tolerance in a targeted environment is a simple approach to identify HS tolerant genotypes. Thus, precise phenotyping using modern phenomics tools could lead to increased breeding efficiency. The NGS (next generation sequencing) data can be associated to find the candidate genes responsible for the HS tolerance in pea. In addition, genomic selection, genome wide association studies (GWAS) and marker assisted selection (MAS) can be used for the development of HS tolerant pea genotypes. Additionally, development of transgenics could be an alternative strategy for the development of HS tolerant pea genotypes. This review comprehensively covers the various aspects of HS tolerance mechanisms in the pea plant, screening protocols, omic advances, and future challenges for the development of HS tolerant genotypes.

Stress - Regulation of SUMO conjugation and of other Ubiquitin-Like Modifiers

Stress is unavoidable and essential to cellular and organismal evolution and failure to adapt or restore homeostasis can lead to severe diseases or even death. At the cellular level, stress drives a plethora of molecular changes, of which variations in the profile of protein post-translational modifications plays a key role in mediating the adaptative response of the genome and proteome to stress. In this context, post-translational modification of proteins by ubiquitin-like modifiers, (Ubl), notably SUMO, is an essential stress response mechanism. In this review, aiming to draw universal concepts of the Ubls stress response, we will decipher how stress alters the expression level, activity, specificity and/or localization of the proteins involved in the conjugation pathways of the various type-I Ubls, and how this result in the modification of particular Ubl targets that will translate an adaptive physiological stress response and allow cells to restore homeostasis.

Observing protein degradation in solution by the PAN-20S proteasome complex: Astate-of-the-art example of bio-macromolecular TR-SANS

In the present book chapter we illustrate the state-of-the-art of time-resolved small-angle neutron scattering (TR-SANS) by a concrete example of a dynamic bio-macromolecular system, i.e., regulated protein degradation by the archaeal PAN-20S proteasome complex. We present the specific and unique structural information that can be obtained by this approach, in combination with bio-macromolecular deuteration and online spectrophotometric measurements of a fluorescent substrate (GFP). The complementarity with atomic-resolution structural biology techniques (SAXS, NMR, crystallography and cryo-EM) and with the advent of atomic structure prediction are discussed, as well as the respective limitations and future perspectives.

Indication of the impact of environmental stress on the responses of the bivalve mollusk Unio tumidus to ibuprofen and microplastics based on biomarkers of reductive stress and apoptosis

The vulnerability of bivalve mollusks to micropollutants is estimated mainly in single model exposures. However, chronic environmental stress and complex exposures can modulate their responses. To evaluate the impact of population-dependent adaptations on the ability to react to common micropollutants, we compared freshwater bivalves Unio tumidus from two distinct populations, pure (Pr) and contaminated (Ct), in their exposures to microplastics (MP, 1 mg L^-1, size 0.1-0.5 mm), pharmaceutical ibuprofen (IBU, 0.8 μg L^-1), or their combination (Mix) for 14 days. Control groups from both sites showed remarkable differences, with lower levels of total antioxidant capacity (TAC), metallothionein protein (MTSH), NADH and NAD⁺, cytochrome P450-related EROD, glutathione-S transferase (GST), and citrate synthase (CS) but higher levels of GSH, GSSG, caspase-3 and cathepsin D (CTD) in the Ct-control group. These data indicate a chronic stress impact in the Ct population. Under exposures, we found an almost common strategy in both populations for NAD⁺/NADH and MTSH suppression and CTD induction. Additionally, Mix exposure caused an increase in CS, and IBU did not change GSH in both populations. However, the expected response to IBU - the suppression of caspase-3 - was indicated only in PrIBU- and PrMix-mollusks. CTD efflux increased dramatically only in PrMP- and PrMix- groups, and suppression of EROD and GST was detected in the PrMix-group. According to discriminant analysis, exposed Pr-groups were highly differentiated from control, whereas Ct-control and exposed groups had common localization demonstrating high resistance to environmental stress. Thus, the same exposures resulted in different adverse outcome pathways depending on the population.

The Unfolded-Protein Response Triggers the Arthropod Immune Deficiency Pathway

The insect immune deficiency (IMD) pathway is a defense mechanism that senses and responds to Gram-negative bacteria. Ticks lack genes encoding upstream components that initiate the IMD pathway. Despite this deficiency, core signaling molecules are present and functionally restrict tick-borne pathogens. The molecular events preceding activation remain undefined. Here, we show that the unfolded-protein response (UPR) initiates the IMD network. The endoplasmic reticulum (ER) stress receptor IRE1α is phosphorylated in response to tick-borne bacteria but does not splice the mRNA encoding XBP1. Instead, through protein modeling and reciprocal pulldowns, we show that Ixodes IRE1α complexes with TRAF2. Disrupting IRE1α-TRAF2 signaling blocks IMD pathway activation and diminishes the production of reactive oxygen species. Through in vitro, in vivo, and ex vivo techniques, we demonstrate that the UPR-IMD pathway circuitry limits the Lyme disease-causing spirochete Borrelia burgdorferi and the rickettsial agents Anaplasma phagocytophilum and A. marginale (anaplasmosis). Altogether, our study uncovers a novel linkage between the UPR and the IMD pathway in arthropods. IMPORTANCE The ability of an arthropod to harbor and transmit pathogens is termed "vector competency." Many factors influence vector competency, including how arthropod immune processes respond to the microbe. Divergences in innate immunity between arthropods are increasingly being reported. For instance, although ticks lack genes encoding key upstream molecules of the immune deficiency (IMD) pathway, it is still functional and restricts causative agents of Lyme disease (Borrelia burgdorferi) and anaplasmosis (Anaplasma phagocytophilum). How the IMD pathway is activated in ticks without classically defined pathway initiators is not known. Here, we found that a cellular stress response network, the unfolded-protein response (UPR), functions upstream to induce the IMD pathway and restrict transmissible pathogens. Collectively, this explains how the IMD pathway can be activated in the absence of canonical pathway initiators. Given that the UPR is highly conserved, UPR-initiated immunity may be a fundamental principle impacting vector competency across arthropods.

Metabolic, proteomic and microbial changes postmortem and during beef aging

The purpose of this review is to provide an overview of the current knowledge about proteomic and metabolic changes in beef, the microbiological alteration postmortem and during aging, and observe the influence on beef quality parameters, such as tenderness, taste and flavor. This review will also focus on the different aging types (wet- and dry-aging), the aging or postmortem time of beef and their effect on the proteome and metabolome of beef. The Ca2+ homeostasis and adenosine 5'-triphosphate breakdown are the main reactions in the pre-rigor phase. After rigor mortis, the enzymatic degradation of connective tissues and breakdown of energy metabolism dominate molecular changes in beef. Important metabolic processes leading to the formation of saccharides, nucleotides, organic acids (e.g. lactic acid), creatine and fatty acids are considered in this context as possible flavor precursors or formers of beef flavor and taste. Flavor precursors are substrates for lipid oxidation, Strecker degradation and Maillard reaction during cooking or roasting. The findings presented should serve as a basis for a better understanding of beef aging and its molecular effects and are intended to contribute to meeting the challenges of improving beef quality.

Adaptation to chronic ER stress enforces pancreatic β-cell plasticity

Pancreatic β-cells are prone to endoplasmic reticulum (ER) stress due to their role in insulin secretion. They require sustainable and efficient adaptive stress responses to cope with this stress. Whether episodes of chronic stress directly compromise β-cell identity is unknown. We show here under reversible, chronic stress conditions β-cells undergo transcriptional and translational reprogramming associated with impaired expression of regulators of β-cell function and identity. Upon recovery from stress, β-cells regain their identity and function, indicating a high degree of adaptive plasticity. Remarkably, while β-cells show resilience to episodic ER stress, when episodes exceed a threshold, β-cell identity is gradually lost. Single cell RNA-sequencing analysis of islets from type 1 diabetes patients indicates severe deregulation of the chronic stress-adaptation program and reveals novel biomarkers of diabetes progression. Our results suggest β-cell adaptive exhaustion contributes to diabetes pathogenesis.

The effect of density on sex differentiation, sexual dimorphism, stress, and related gene expression in yellow perch

A 180-day experiment was conducted to evaluate the effects of density on sex differentiation, sexual dimorphism, cortisol level, and stress related gene expression. Yellow perch, Perca flavescens, with initial mean body weight of 0.03 ± 0.001 g were reared in three different stocking densities: 1, 2, and 4 fish/L, termed as low (LD), moderate (MD), and high (HD) density, respectively, in a flow-through tank system. Results showed no significant differences in sex ratio in all density groups compared to normal population 1:1, and sexual size dimorphism (SSD) appeared when male and female were as small as the mean size reaching 11.5 cm and 12.3 cm in total length (TL) or 13.2g and 16.9g in body weight (BW), respectively. This female-biased sexual growth dimorphism was more pronounced in LD, although it was observed across all density groups. A significantly higher condition factor (K) of females than males in the LD group, and significantly higher R values of LD and MD than HD with the length/weight (L/W) linear relationships in females, were observed. Parallelly, fish reared in LD showed significantly higher mean body weight than those in the MD and HD groups, but there were no significant differences between the MD and HD. Similar results were also observed in all the other parameters of weight gain, specific growth rate (SGR), condition factor (K), and survival. These findings suggested that high density not only affected growth itself, but also affected SSD, growth trajectory or body shape, and general wellbeing in fish, especially in females. There were no significant differences in gonadosomatic index (GSI) and viscerosomatic index (VSI) among all the density groups; however, the hepatosomatic index (HSI) of LD was significantly higher than MD and HD, suggesting high density affected liver reserves or functions. Physiologically, plasma cortisol level was significantly highest in the LD among all groups, followed by MD, and lowest in HD. At the molecular level, the expression of the 70-kDa heat shock protein (Hsp70), glutathione peroxidase (GPx), and superoxide dismutase (SOD) genes involved in cellular stress were significantly upregulated in the HD group. The most significantly downregulated expression of these genes was consistently observed in the MD when compared to the LD and HD groups. In conclusion, increasing density induced chronic stress in yellow perch without affecting sex differentiation, but negatively affected expression of stress-related genes and mobilization of liver reserve, resulting in poorer wellbeing and reduced SSD, growth, and survival.

Inflammation: A New Look at an Old Problem

Pro-inflammatory stress is inherent in any cells that are subject to damage or threat of damage. It is defined by a number of universal components, including oxidative stress, cellular response to DNA damage, unfolded protein response to mitochondrial and endoplasmic reticulum stress, changes in autophagy, inflammasome formation, non-coding RNA response, formation of an inducible network of signaling pathways, and epigenetic changes. The presence of an inducible receptor and secretory phenotype in many cells is the cause of tissue pro-inflammatory stress. The key phenomenon determining the occurrence of a classical inflammatory focus is the microvascular inflammatory response (exudation, leukocyte migration to the alteration zone). This same reaction at the systemic level leads to the development of life-critical systemic inflammation. From this standpoint, we can characterize the common mechanisms of pathologies that differ in their clinical appearance. The division of inflammation into alternative variants has deep evolutionary roots. Evolutionary aspects of inflammation are also described in the review. The aim of the review is to provide theoretical arguments for the need for an up-to-date theory of the relationship between key human pathological processes based on the integrative role of the molecular mechanisms of cellular and tissue pro-inflammatory stress.

Environment-driven shifts in inter-individual variation and phenotypic integration within subnetworks of the mussel transcriptome and proteome

The environment can alter the magnitude of phenotypic variation among individuals, potentially influencing evolutionary trajectories. However, environmental influences on variation are complex and remain understudied. Populations in heterogeneous environments might exhibit more variation, the amount of variation could differ between benign and stressful conditions, and/or variation might manifest in different ways among stages of the gene‐to‐protein expression cascade or among physiological functions. Here, we explore these three issues by quantifying patterns of inter‐individual variation in both transcript and protein expression levels among California mussels, Mytilus californianus Conrad. Mussels were exposed to five ecologically relevant treatments that varied in the mean and interindividual heterogeneity of body temperature. To target a diverse set of physiological functions, we assessed variation within 19 expression subnetworks, including canonical stress‐response pathways and empirically derived coexpression clusters that represent a diffuse set of cellular processes. Variation in expression was particularly pronounced in the treatments with high mean and heterogeneous body temperatures. However, with few exceptions, environment‐dependent shifts of variation in the transcriptome were not reflected in the proteome. A metric of phenotypic integration provided evidence for a greater degree of constraint on relative expression levels (i.e., stronger correlation) within expression subnetworks in benign, homogeneous environments. Our results suggest that environments that are more stressful on average – and which also tend to be more heterogeneous – can relax these expression constraints and reduce phenotypic integration within biochemical subnetworks. Context‐dependent “unmasking” of functional variation may contribute to interindividual differences in physiological phenotype and performance in stressful environments.

Physiological mechanisms of stress-induced evolution

Organisms mount the cellular stress response whenever environmental parameters exceed the range that is conducive to maintaining homeostasis. This response is critical for survival in emergency situations because it protects macromolecular integrity and, therefore, cell/organismal function. From an evolutionary perspective, the cellular stress response counteracts severe stress by accelerating adaptation via a process called stress-induced evolution. In this Review, we summarize five key physiological mechanisms of stress-induced evolution. Namely, these are stress-induced changes in: (1) mutation rates, (2) histone post-translational modifications, (3) DNA methylation, (4) chromoanagenesis and (5) transposable element activity. Through each of these mechanisms, organisms rapidly generate heritable phenotypes that may be adaptive, maladaptive or neutral in specific contexts. Regardless of their consequences to individual fitness, these mechanisms produce phenotypic variation at the population level. Because variation fuels natural selection, the physiological mechanisms of stress-induced evolution increase the likelihood that populations can avoid extirpation and instead adapt under the stress of new environmental conditions.

Impacts, Tolerance, Adaptation, and Mitigation of Heat Stress on Wheat under Changing Climates

Heat stress (HS) is one of the major abiotic stresses affecting the production and quality of wheat. Rising temperatures are particularly threatening to wheat production. A detailed overview of morpho-physio-biochemical responses of wheat to HS is critical to identify various tolerance mechanisms and their use in identifying strategies to safeguard wheat production under changing climates. The development of thermotolerant wheat cultivars using conventional or molecular breeding and transgenic approaches is promising. Over the last decade, different omics approaches have revolutionized the way plant breeders and biotechnologists investigate underlying stress tolerance mechanisms and cellular homeostasis. Therefore, developing genomics, transcriptomics, proteomics, and metabolomics data sets and a deeper understanding of HS tolerance mechanisms of different wheat cultivars are needed. The most reliable method to improve plant resilience to HS must include agronomic management strategies, such as the adoption of climate-smart cultivation practices and use of osmoprotectants and cultured soil microbes. However, looking at the complex nature of HS, the adoption of a holistic approach integrating outcomes of breeding, physiological, agronomical, and biotechnological options is required. Our review aims to provide insights concerning morpho-physiological and molecular impacts, tolerance mechanisms, and adaptation strategies of HS in wheat. This review will help scientific communities in the identification, development, and promotion of thermotolerant wheat cultivars and management strategies to minimize negative impacts of HS.

The transcriptional response to oxidative stress is independent of stress-granule formation

Cells respond to stress with translational arrest, robust transcriptional changes, and transcription-independent formation of mRNP assemblies termed stress granules (SGs). Despite considerable interest in the role of SGs in oxidative, unfolded protein and viral stress responses, whether and how SGs contribute to stress-induced transcription have not been rigorously examined. To address this, we characterized transcriptional changes in Drosophila S2 cells induced by acute oxidative-stress and assessed how these were altered under conditions that disrupted SG assembly. Oxidative stress for 3 h predominantly resulted in induction or up-regulation of stress-responsive mRNAs whose levels peaked during recovery after stress cessation. The stress transcriptome is enriched in mRNAs coding for chaperones including HSP70s, small heat shock proteins, glutathione transferases, and several noncoding RNAs. Oxidative stress also induced cytoplasmic SGs that disassembled 3 h after stress cessation. As expected, RNAi-mediated knockdown of the conserved G3BP1/Rasputin protein inhibited SG assembly. However, this disruption had no significant effect on the stress-induced transcriptional response or stress-induced translational arrest. Thus SG assembly and stress-induced gene expression alterations appear to be driven by distinctive signaling processes. We suggest that while SG assembly represents a fast, transient mechanism, the transcriptional response enables a slower, longer-lasting mechanism for adaptation to and recovery from cell stress.

The Unfolded Protein Response at the Tumor-Immune Interface

The tumor-immune interface has surged to primary relevance in an effort to understand the hurdles facing immune surveillance and cancer immunotherapy. Reports over the past decades have indicated a role for the unfolded protein response (UPR) in modulating not only tumor cell fitness and drug resistance, but also local immunity, with emphasis on the phenotype and altered function of immune cells such as myeloid cells and T cells. Emerging evidence also suggests that aneuploidy correlates with local immune dysregulation. Recently, we reported that the UPR serves as a link between aneuploidy and immune cell dysregulation in a cell nonautonomous way. These new findings add considerable complexity to the organization of the tumor microenvironment (TME) and the origin of its altered function. In this review, we summarize these data and also discuss the role of aneuploidy as a negative regulator of local immunity.

Evaluation of transcriptional biomarkers using a high-resolution regression approach: Concentration-dependence of selected transcripts in copper-exposed freshwater mussels (Anodonta anatina)

We tested concentration-dependence of selected gene transcripts (cat, gst, hsp70, hsp90, mt and sod) for evaluation as biomarkers of chemical stress. Contrary to the common approach of factorial designs and few exposure concentrations, we used regression across a high-resolution concentration series. Specifically, freshwater mussels (Anodonta anatina) were acutely (96 h) exposed to Cu (13 nominal concentrations, measuring 0.13-1 600 µg/L), and transcripts were measured by RT-qPCR. In digestive glands, cat, hsp90 and mt decreased with water Cu (p < 0.05), but response magnitudes saturated at < 2-fold decreases. In gills, gst, hsp70, hsp90 and mt increased with water Cu (p < 0.05). While hsp70, hsp90 and mt exceeded 2-fold increases within the exposure range, high Cu concentrations were required (38-160 µg/L). Although gill responses were generally more robust compared to digestive glands, overall small response magnitudes and moderate sensitivity may set limit for potential application as general biomarkers of chemical stress.

Niche breadth affects bacterial transcription patterns along a salinity gradient

Understanding the molecular mechanisms that determine a species' life history is important for predicting their susceptibility to environmental change. While specialist species with a narrow niche breadth (NB) maximize their fitness in their optimum habitat, generalists with broad NB adapt to multiple environments. The main objective of this study was to identify general transcriptional patterns that would distinguish bacterial strains characterized by contrasted NBs along a salinity gradient. More specifically, we hypothesized that genes encoding fitness-related traits, such as biomass production, have a higher degree of transcriptional regulation in specialists than in generalists, because the fitness of specialists is more variable under environmental change. By contrast, we expected that generalists would exhibit enhanced transcriptional regulation of genes encoding traits that protect them against cellular damage. To test these hypotheses, we assessed the transcriptional regulation of fitness-related and adaptation-related genes of 11 bacterial strains in relation to their NB and stress exposure under changing salinity conditions. The results suggested that transcriptional regulation levels of fitness- and adaptation-related genes correlated with the NB and/or the stress exposure of the inspected strains. We further identified a shortlist of candidate stress marker genes that could be used in future studies to monitor the susceptibility of bacterial populations or communities to environmental changes.

Transcriptome analysis provides the first insight into the molecular basis of temperature plasticity in Banggai cardinalfish, Pterapogon kauderni

Banggai cardinalfish, Pterapogon kauderni, is a tropical fish listed as an endangered species by IUCN. Its distribution and survival condition are extremely limited, and the changes of living environment caused by global warming may seriously threaten its geographical distribution. In order to understand the survival temperature range and the potential mechanism of temperature plasticity of P. kauderni, transcriptome analysis was performed under five temperature conditions (18 °C, 22 °C, 26 °C, 30 °C and 34 °C). A total of 432,444,497 clean reads were obtained from the mix tissues of whole head, viscera (except intestine), and muscle. All clean data were spliced into 194,832 unigenes. Compared with 26 °C, 57, 107, 187 and 174 differentially expressed genes (DEGs) were obtained at 18 °C, 22 °C, 30 °C and 34 °C, respectively. Gene Ontology (GO) analysis showed the most highly enriched in the DEGs were cellular processes, binding, metabolic processes and biological regulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated circadian rhythm, protein processing in endoplasmic reticulum, influenza A and prion disease were significantly enriched. 47 genes that may be related to temperature stress were identified, such as Per1, MLP, IGFBP1, HSP70, HSP90α, HSPA4, DNAJB1, CALR. This is the first RNA-Seq study of P. kauderni. This information should be valuable for further targeted studies on temperature tolerance, thereby assisting the protection and development of P. kauderni.

Caspase activity in post mortem muscle and its relation to cattle handling practices

BACKGROUND

Animal handling practices are one of the factors majorly affecting animal metabolism prior to slaughter. This phenomenon increases the occurrence of meat quality defects such as dark cutting-beef, causing high economical losses in the meat industry. Under this framework, the assessment of apoptosis onset in post mortem muscle was proposed as a novel approach to reveal biochemical characteristics in several Spanish bovine breeds (Asturiana de los Valles, Retinta and Rubia Gallega) managed under different production systems (intensive versus semi-extensive) and transport/lairage conditions (mixing versus not mixing with unfamiliar animals). To do so, the activities of initiator caspase 9 and executioner caspases 3/7 were determined in Longissimus thoracis et lumborum muscle at three early post mortem times (2, 8, and 24 h).

RESULTS

Breed effect and transport/lairage conditions were the most relevant factors that influenced both caspase activities over post mortem time, showing Rubia Gallega breed a completely different behavior compared to Asturiana de los Valles and Retinta breeds. Moreover, it is postulated that apoptosis cascade is initiated via the activation of caspase 9 under hypoxic or metabolic stress followed by the activation of executioner caspases 3/7.

CONCLUSIONS

Assessment of apoptosis on post mortem muscle can be a novel approach to study the influence of animal handling on muscle metabolism and post mortem cell death and its consequences on meat quality traits. © 2021 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Application of High Hydrostatic Pressure (HHP) to Improve Cryopreservation of Young Bull Semen

The objective of the study was to determine the effect of high hydrostatic pressure (HHP) on quality of cryopreserved semen of young bulls. Semen for this study was collected from 8 bulls aged between 13 and 18 months at monthly intervals, from June to September. After collection, semen was diluted in a commercial Bioxcell® extender (one part at 1:1 and a second part to give a sperm concentration of 20 million/0.2 mL), filled into straws and treated with HHP at 30 MPa for 90 min. After HHP treatment, pre-diluted semen (1:1) was diluted to a sperm concentration 20 million/0.2 mL and filled into straws. In addition, part of the semen diluted to a concentration of 20 million/0.2 mL was not treated with HHP (control). All of it was held at +4°C and frozen in a freezer after 2.5-h equilibration. Semen was thawed in a water bath at 38°C and subjected to estimation of the percentage of motile sperm both subjectively and using a computer-assisted semen analyzer and cytometric assessment of sperm cell membrane integrity. Subjective motility and fast progressive motility were significantly higher with pre-diluted (1:1) and HHP treated semen compared to control (P<0.05). No significant differences were observed in percentage of membraneintact spermatozoa between control and experimental groups. Additionally, the influence of HHP on the sperm of individual bulls was assessed. In bull number 2, the HHP treatment after semen pre-dilution significantly improved progressive motility from 54.1 to 63.4 percent (P<0.05). In bull number 4, the HHP treatment after semen pre-dilution significantly improved subjective motility, rapid motility and progressive motility by 12.5, 16.8 and 16.3 percent, respectively (P<0.05). No effect was seen for 6 bulls. It is concluded that for some bulls, the application of HHP before semen freezing may improve the cryopreservation outcome. However, this requires further research in this area, also to determine the fertilizing capacity of bull semen exposed to high hydrostatic pressure.

De Novo Transcriptome Analysis Reveals Potential Thermal Adaptation Mechanisms in the Cicada Hyalessa fuscata

Simple Summary

In metropolitan Seoul and its vicinity, cicadas of the species Hyalessa fuscata living in warmer areas could tolerate the heat better than those living in cooler areas, but genetic mechanisms involved in better heat tolerance remained unclear. In this study, we examined differences in gene expression of cicadas living in a warm urban area, a cool urban area and a suburban area in three experimental treatments: no heating, 10 min heating and heating until the cicadas lost their mobility. Cicadas from the warm urban area changed their gene expressions the most. Activated genes were mostly related to heat shock, energy metabolism, and detoxification. These results suggested that under heat stress, cicadas inhabiting warm areas could differentially express genes to increase their thermal tolerance.

Abstract

In metropolitan Seoul, populations of the cicada Hyalessa fuscata in hotter urban heat islands (“high UHIs”) exhibit higher thermal tolerance than those in cooler UHIs (“low UHIs”). We hypothesized that heat stress may activate the expression of genes that facilitate greater thermal tolerance in high-UHI cicadas than in those from cooler areas. Differences in the transcriptomes of adult female cicadas from high-UHI, low-UHI, and suburban areas were analyzed at the unheated level, after acute heat stress, and after heat torpor. No noticeable differences in unheated gene expression patterns were observed. After 10 min of acute heat stress, however, low-UHI and suburban cicadas expressed more heat shock protein genes than high-UHI counterparts. More specifically, remarkable changes in the gene expression of cicadas across areas were observed after heat torpor stimulus, as represented by a large number of up- and downregulated genes in the heat torpor groups compared with the 10 min acute heat stress and control groups. High-UHI cicadas expressed the most differentially expressed genes, followed by the low-UHI and suburban cicadas. There was a notable increase in the expression of heat shock, metabolism, and detoxification genes; meanwhile, immune-related, signal transduction, and protein turnover genes were downregulated in high-UHI cicadas versus the other cicada groups. These results suggested that under heat stress, cicadas inhabiting high-UHIs could rapidly express genes related to heat shock, energy metabolism, and detoxification to protect cells from stress-induced damage and to increase their thermal tolerance toward heat stress. The downregulation of apoptosis mechanisms in high-UHI cicadas suggested that there was less cellular damage, which likely contributed to their high tolerance of heat stress.

Nucleotide stress responses in neural crest cell fate and melanoma

Melanoma is the deadliest form of skin cancer. While clinical developments have significantly improved patient prognosis, effective treatment is often obstructed by limited response rates, intrinsic or acquired resistance to therapy, and adverse events. Melanoma initiation and progression are associated with transcriptional reprogramming of melanocytes to a cell state that resembles the lineage from which the cells are specified during development, that is the neural crest. Convergence to a neural crest cell (NCC)-like state revealed the therapeutic potential of targeting developmental pathways for the treatment of melanoma. Neural crest cells have a unique sensitivity to metabolic dysregulation, especially nucleotide depletion. Mutations in the pyrimidine biosynthesis enzyme dihydroorotate dehydrogenase (DHODH) particularly affect neural crest-derived tissues and cause Miller syndrome, a genetic disorder characterized by craniofacial malformations in patients. The developmental susceptibility of the neural crest to nucleotide deficiency is conserved in melanoma and provides a metabolic vulnerability that can be exploited for therapeutic purposes. We review the current knowledge on nucleotide stress responses in neural crest and melanoma and discuss how the recent scientific advances that have improved our understanding of transcriptional regulation during nucleotide depletion can impact melanoma treatment.

Coping with stress in a warming Gulf: the postlarval American lobster's cellular stress response under future warming scenarios

The Gulf of the Maine (GoM) is one of the fastest warming bodies of water in the world, posing serious physiological challenges to its marine inhabitants. Marine organisms can cope with the cellular and molecular stresses created by climate change through changes in gene expression. We used transcriptomics to examine how exposure to current summer temperatures (16 °C) or temperature regimes reflective of projected moderate and severe warming conditions (18 °C and 22 °C, respectively) during larval development alters expression of transcripts affiliated with the cellular stress response (CSR) in postlarval American lobsters (Homarus americanus). We identified 26 significantly differentially expressed (DE) transcripts annotated to CSR proteins. Specifically, transcripts for proteins affiliated with heat shock, the ubiquitin family, DNA repair, and apoptosis were significantly over-expressed in lobsters reared at higher temperatures relative to current conditions. Substantial variation in the CSR expression between postlarvae reared at 18 °C and those reared at 22 °C suggests that postlarvae reared under severe warming may have a hindered ability to cope with the physiological and molecular challenges of ocean warming. These results highlight that postlarval American lobsters may experience significant heat stress as rapid warming in the GoM continues, potentially compromising their ability to prevent cellular damage and inhibiting the reallocation of cellular energy towards other physiological functions beyond activation of the CSR. Moreover, this study establishes additional American lobster stress markers and addresses various knowledge gaps in crustacean biology, where sufficient 'omics research is lacking.

Molecular response of a sub-antarctic population of the blue mussel (Mytilus edulis platensis) to a moderate thermal stress

The Kerguelen Islands (49°26'S, 69°50'E) represent a unique environment due to their geographical isolation, which protects them from anthropogenic pollution. The ability of the endemic mussel, part of the Mytilus complex, to cope with moderate heat stress was explored using omic tools. Transcripts involved in six major metabolic functions were selected and the qRT-PCR data indicated mainly changes in aerobic and anaerobic energy metabolism and stress response. Proteomic comparisons revealed a typical stress response pattern with cytoskeleton modifications and elements suggesting increased energy metabolism. Results also suggest conservation of protein homeostasis by the long-lasting presence of HSP while a general decrease in transcription is observed. The overall findings are consistent with an adaptive response to moderate stresses in mussels in good physiological condition, i.e. living in a low-impact site, and with the literature concerning this model species. Therefore, local blue mussels could be advantageously integrated into biomonitoring strategies, especially in the context of Global Change.

Acclimation to cyclic hypoxia improves thermal tolerance and copper survival in the caridean shrimp Palaemon varians

In response to the continuous variation of environmental parameters, species must be able to adjust their physiology to overcome stressful conditions, a process known as acclimatization. Numerous laboratory studies have been conducted to understand and describe the mechanisms of acclimation to one environmental stressor (e.g. cyclic hypoxia), but currently our understanding of how acclimation to one stressor can change tolerance to a subsequent stressor is limited. Here, in two different experiments, we used the shrimp Palaemon varians to test how, following 28-days acclimation to cyclic hypoxia (mimicking a cyclic hypoxic regime currently found in its natural habitat), critical thermal maximum (CT_max) and sensitivity to copper (Cu²⁺) exposure (30 mgL^-1) changed in comparison to shrimp acclimated to normoxic conditions and then exposed to thermal stress or Cu²⁺. Acclimation to cyclic hypoxia improved both CT_max (~1 °C higher than controls) and survival to acute Cu²⁺ exposure (~30% higher than controls) and induced significant gene expression changes (i.e. up-regulation of heat shock protein 70 - HSP70, hypoxia inducible factor - HIF, phosphoenolpyruvate carboxykinase - PEPCK, glucose 6-P transporter - G6Pt, metallothionein - Mt, and down-regulation of hemocyanin - Hem) in animals acclimated to cyclic hypoxia. Our results demonstrate how acclimation to cyclic hypoxia improved tolerance to subsequent stressors, highlighting the complexity of predicting organismal performance in variable (i.e. where multiple parameters can simultaneously change during the day) environments.

Calcium homeostasis and stable fatty acid composition underpin heatwave tolerance of the keystone polychaete Hediste diversicolor

Extreme weather events, such as heatwaves, are becoming increasingly frequent, long-lasting and severe as global climate change continues, shaping marine biodiversity patterns worldwide. Increased risk of overheating and mortality across major taxa have been recurrently observed, jeopardizing the sustainability of ecosystem services. Molecular responses of species, which scale up to physiological and population responses, are determinant processes that modulate species sensitivity or tolerance to extreme weather events. Here, by integrating proteomic, fatty acid profiling and physiological approaches, we show that the tolerance of the intertidal ragworm Hediste diversicolor, a keystone species in estuarine ecosystems and an emergent blue bio-resource, to long-lasting heatwaves (24  vs 30 °C for 30 days) is shaped by calcium homeostasis, immune function and stability of fatty acid profiles. These features potentially enabled H. diversicolor to increase its thermal tolerance limit by 0.81 °C under the heatwave scenario and maintain survival. No growth trade-offs were detected, as wet weight remained stable across conditions. Biological variation of physiological parameters was lower when compared to molecular measures. Proteins showed an overall elevated coefficient of variation, although decreasing molecular variance under the heatwave scenario was observed for both proteins and fatty acids. This finding is consistent with the phenomenon of physiological canalization in extreme environments and contradicts the theory that novel conditions increase trait variation. Our results show that keystone highly valued marine polychaetes are tolerant to heatwaves, confirming the potential of H. diversicolor as a blue bio-resource and opening new avenues for sustainable marine aquaculture development.

Bioenergetics in environmental adaptation and stress tolerance of aquatic ectotherms: linking physiology and ecology in a multi-stressor landscape

Energy metabolism (encompassing energy assimilation, conversion and utilization) plays a central role in all life processes and serves as a link between the organismal physiology, behavior and ecology. Metabolic rates define the physiological and life-history performance of an organism, have direct implications for Darwinian fitness, and affect ecologically relevant traits such as the trophic relationships, productivity and ecosystem engineering functions. Natural environmental variability and anthropogenic changes expose aquatic ectotherms to multiple stressors that can strongly affect their energy metabolism and thereby modify the energy fluxes within an organism and in the ecosystem. This Review focuses on the role of bioenergetic disturbances and metabolic adjustments in responses to multiple stressors (especially the general cellular stress response), provides examples of the effects of multiple stressors on energy intake, assimilation, conversion and expenditure, and discusses the conceptual and quantitative approaches to identify and mechanistically explain the energy trade-offs in multiple stressor scenarios, and link the cellular and organismal bioenergetics with fitness, productivity and/or ecological functions of aquatic ectotherms.

Arthropods Under Pressure: Stress Responses and Immunity at the Pathogen-Vector Interface

Understanding what influences the ability of some arthropods to harbor and transmit pathogens may be key for controlling the spread of vector-borne diseases. Arthropod immunity has a central role in dictating vector competence for pathogen acquisition and transmission. Microbial infection elicits immune responses and imparts stress on the host by causing physical damage and nutrient deprivation, which triggers evolutionarily conserved stress response pathways aimed at restoring cellular homeostasis. Recent studies increasingly recognize that eukaryotic stress responses and innate immunity are closely intertwined. Herein, we describe two well-characterized and evolutionarily conserved mechanisms, the Unfolded Protein Response (UPR) and the Integrated Stress Response (ISR), and examine evidence that these stress responses impact immune signaling. We then describe how multiple pathogens, including vector-borne microbes, interface with stress responses in mammals. Owing to the well-conserved nature of the UPR and ISR, we speculate that similar mechanisms may be occurring in arthropod vectors and ultimately impacting vector competence. We conclude this Perspective by positing that novel insights into vector competence will emerge when considering that stress-signaling pathways may be influencing the arthropod immune network.

Maternal effects in gene expression of interspecific coral hybrids

Maternal effects have been well documented for offspring morphology and life history traits in plants and terrestrial animals, yet little is known about maternal effects in corals. Further, few studies have explored maternal effects in gene expression. In a previous study, F1 interspecific hybrid and purebred larvae of the coral species Acropora tenuis and Acropora loripes were settled and exposed to ambient or elevated temperature and pCO₂ conditions for 7 months. At this stage, the hybrid coral recruits from both ocean conditions exhibited strong maternal effects in several fitness traits. We conducted RNA-sequencing on these corals and showed that gene expression of the hybrid Acropora also exhibited clear maternal effects. Only 40 genes were differentially expressed between hybrids and their maternal progenitor. In contrast, ~2000 differentially expressed genes were observed between hybrids and their paternal progenitors, and between the reciprocal F1 hybrids. These results indicate that maternal effects in coral gene expression can be long-lasting. Unlike findings from most short-term stress experiments in corals, no genes were differentially expressed in the hybrid nor purebred offspring after seven months of exposure to elevated temperature and pCO₂ conditions.

Global gene expression patterns in Porites white patch syndrome: Disentangling symbiont loss from the thermal stress response in reef-building coral

The mechanisms resulting in the breakdown of the coral symbiosis once the process of bleaching has been initiated remain unclear. Distinguishing the process of symbiont loss from the thermal stress response may shed light on the cellular and molecular pathways involved in each process. This study examined physiological changes and global gene expression patterns associated with white patch syndrome (WPS) in Porites lobata, which manifests in localized bleaching independent of thermal stress. In addition, a meta-analysis of global gene expression studies in other corals and anemones was used to contrast differential regulation as a result of disease and thermal stress from patterns correlated with symbiotic state. Symbiont density, chlorophyll a content, holobiont productivity, instant calcification rate, and total host protein content were uniformly reduced in WPS relative to healthy tissue. While expression patterns associated with WPS were secondary to fixed effects of source colony, specific functional enrichments combined with a lack of immune regulation suggest that the viral infection putatively giving rise to this condition affects symbiont rather than host cells. Expression in response to WPS also clustered independently of patterns in white syndrome impacted A. hyacinthus, further supporting a distinct aetiology of this syndrome. Expression patterns in WPS-affected tissues were significantly correlated with prior studies that examined short-term thermal stress responses independent of symbiotic state, suggesting that the majority of expression changes reflect a nonspecific stress response. Across studies, the magnitude and direction of expression change among particular functional enrichments suggests unique responses to stressor duration and highlights distinct responses to bleaching in an anemone model.

Temperature-dependent life history and transcriptomic responses in heat-tolerant versus heat-sensitive Brachionus rotifers

Thermal stress response is an essential physiological trait that determines occurrence and temporal succession in nature, including response to climate change. We compared temperature-related demography in closely related heat-tolerant and heat-sensitive Brachionus rotifer species. We found significant differences in heat response, with the heat-sensitive species adopting a strategy of long survival and low population growth, while the heat-tolerant followed the opposite strategy. In both species, we examined the genetic basis of physiological variation by comparing gene expression across increasing temperatures. Comparative transcriptomic analyses identified shared and opposing responses to heat. Interestingly, expression of heat shock proteins (hsps) was strikingly different in the two species and mirrored differences in population growth rates, showing that hsp genes are likely a key component of a species' adaptation to different temperatures. Temperature induction caused opposing patterns of expression in further functional categories including energy, carbohydrate and lipid metabolism, and in genes related to ribosomal proteins. In the heat-sensitive species, elevated temperatures caused up-regulation of genes related to meiosis induction and post-translational histone modifications. This work demonstrates the sweeping reorganizations of biological functions that accompany temperature adaptation in these two species and reveals potential molecular mechanisms that might be activated for adaptation to global warming.

Supplementing resuscitation-promoting factor (Rpf) enhanced biodegradation of polychlorinated biphenyls (PCBs) by Rhodococcus biphenylivorans strain TG9T

The biodegradation of polychlorinated biphenyls (PCBs) occurs slowly when the degrading bacteria enter a low activity state, such as a viable but nonculturable (VBNC) state, under unfavorable environmental conditions. The introduction of resuscitation-promoting factor (Rpf) can re-activate VBNC bacteria. This study tested the feasibility of enhancing PCB biodegradation via supplementing Rpf in liquid culture and soil microcosms inoculated with Rhodococcus biphenylivorans strain TG9^T. Exogenous Rpf resuscitated TG9^T cells that had previously entered the VBNC state after 90 d of nutrient starvation, resulting in the significantly enhanced degradation of PCB by 24.3% over 60 h in liquid medium that originally contained 50 mg L^-1 Aroclor 1242. In soil microcosms containing 50 mg kg^-1 Aroclor 1242 and inoculated with VBNC TG9^T cells, after 49 d of supplementation with Rpf, degradation efficiency of PCB reached 34.2%, which was significantly higher than the control. Our results confirmed that exogenous Rpf resuscitated VBNC TG9^T cells by stimulating endogenous expression of rpf gene orthologs. The enhanced PCB-degrading capability was likely due to the increased cell numbers and the strong expression of PCB catabolic genes. This study demonstrated the role of Rpf in enhancing PCB degradation via resuscitating PCB-degrading bacteria, indicating a promising approach for the remediation of PCB contamination.