Shining a light on bacterial environmental cue integration and its relation to metabolism.

The ability of a bacterium to successfully colonize its host is dependent on proper adaptation to its local environment. Environmental cues are diverse in nature, ranging from ions to bacterial-produced signals, and to host immune responses that can also be exploited by the bacteria as cues. Simultaneously, bacterial metabolism must be matched to the carbon and nitrogen sources available at a given time and location. While initial characterization of a bacterium's response to a given environmental cue or its ability to utilize a particular carbon/nitrogen source requires study of the signal in question in isolation, actual infection poses a situation where multiple signals are present concurrently. This perspective focuses on the untapped potential in uncovering and understanding how bacteria integrate their response to multiple concurrent environmental cues, and in elucidating the possible intrinsic coordination of bacterial environmental response with its metabolism.

Targeting Mycobacterium tuberculosis pH-driven adaptation.

Mycobacterium tuberculosis (Mtb) senses and adapts to host environmental cues as part of its pathogenesis. One important cue sensed by Mtb is the acidic pH of its host niche - the macrophage. Acidic pH induces widespread transcriptional and metabolic remodelling in Mtb. These adaptations to acidic pH can lead Mtb to slow its growth and promote pathogenesis and antibiotic tolerance. Mutants defective in pH-dependent adaptations exhibit reduced virulence in macrophages and animal infection models, suggesting that chemically targeting these pH-dependent pathways may have therapeutic potential. In this review, we discuss mechanisms by which Mtb regulates its growth and metabolism at acidic pH. Additionally, we consider the therapeutic potential of disrupting pH-driven adaptations in Mtb and review the growing class of compounds that exhibit pH-dependent activity or target pathways important for adaptation to acidic pH.

TARGET OF MONOPTEROS: key transcription factors orchestrating plant development and environmental response.

Plants have an incredible ability to sustain root and vascular growth after initiation of the embryonic root and the specification of vascular tissue in early embryos. Microarray assays have revealed that a group of transcription factors, TARGET OF MONOPTEROS (TMO), are important for embryonic root initiation in Arabidopsis. Despite the discovery of their auxin responsiveness early on, their function and mode of action remained unknown for many years. The advent of genome editing has accelerated the study of TMO transcription factors, revealing novel functions for biological processes such as vascular development, root system architecture, and response to environmental cues. This review covers recent achievements in understanding the developmental function and the genetic mode of action of TMO transcription factors in Arabidopsis and other plant species. We highlight the transcriptional and post-transcriptional regulation of TMO transcription factors in relation to their function, mainly in Arabidopsis. Finally, we provide suggestions for further research and potential applications in plant genetic engineering.

Central and peripheral neuropeptide RFRP-3: A bridge linking reproduction, nutrition, and stress response.

This article is an amalgamation of the current status of RFRP-3 (GnIH) in reproduction and its association with the nutrition and stress-mediated changes in the reproductive activities. GnIH has been demonstrated in the hypothalamus of all the vertebrates studied so far and is a well-known inhibitor of GnRH mediated reproduction. The RFRP-3 neurons interact with the other hypothalamic neurons and the hormonal signals from peripheral organs for coordinating the nutritional, stress, and environmental associated changes to regulate reproduction. RFRP-3 has also been shown to regulate puberty, reproductive cyclicity and senescence depending upon the nutritional status. A favourable nutritional status and the environmental cues which are permissive for the successful breeding and pregnancy outcome keep RFRP-3 level low, whereas unfavourable nutritional status and stressful conditions increase the expression of RFRP-3 which impairs the reproduction. Still our knowledge about RFRP-3 is incomplete regarding its therapeutic application for nutritional or stress-related reproductive disorders.

Migration timing and tributary use of spawning flannelmouth sucker (Catostomus latipinnis).

Spawning phenology and associated migrations of fishes are often regulated by factors such as temperature and stream discharge, but flow regulation of mainstem rivers coupled with climate change might disrupt these cues and affect fitness. Flannelmouth sucker (Catostomus latipinnis) persisting in heavily modified river networks are known to spawn in tributaries that might provide better spawning habitat than neighboring mainstem rivers subject to habitat degradation (e.g., embedded sediments, altered thermal regimes, and disconnected floodplains). PIT tag data and radio telemetry were used to quantify the timing and duration of flannelmouth sucker tributary spawning migrations in relation to environmental cues in McElmo Creek, a tributary of the San Juan River in the American Southwest. We also tested the extent of the tributary migration and assessed mainstem movements prior to and after tributary migrations. Additionally, multiyear data sets of PIT detections from other tributaries in the Colorado River basin were used to quantify interannual and cross-site variation in the timing of flannelmouth sucker spawning migrations in relation to environmental cues. The arrival and residence times of fish spawning in McElmo Creek varied among years, with earlier migration and a 3-week increase in residence time in relatively wet years compared to drier years. Classification tree analysis suggested a combination of discharge- and temperature-determined arrival timing. Of fish PIT tagged in the fall, 56% tagged within 10 km of McElmo Creek spawned in the tributary the following spring, as did 60% of radio-tagged fish, with a decline in its use corresponding to increased distance of tagging location. A broader analysis of four tributaries in the Colorado River basin, including McElmo Creek, found photoperiod and temperature of tributary and mainstem rivers were the most important variables in determining migration timing, but tributary and mainstem discharge also aided in classification success. The largest tributary, the Little Colorado River, had more residential fish or fish that stayed for longer periods (median = 30 days), whereas McElmo Creek fish stayed an average of just 10 days in 2022. Our results generally suggest that higher discharge, across years or across sites, results in extended use of tributaries by flannelmouth suckers. Conservation actions that limit water extraction and maintain natural flow regimes in tributaries, while maintaining open connection with mainstem rivers, may benefit migratory species, including flannelmouth suckers.

How the environment evokes actions that lead to different goals: the role of object multi-functionality in pavlovian-to-instrumental transfer.

Research shows that stimuli in the environment can trigger behavior via the activation of goal representations. This process can be tested in the Pavlovian-to-Instrumental Transfer (PIT) paradigm, where stimuli can only affect behavior through the activation of the representation of its desired outcome (i.e., the PIT effect). Previous research has demonstrated that the PIT effect is stronger when the goal is more desirable. While this research only looked at actions that have single outcomes (e.g., obtaining a snack to satisfy appetite), in the present paper, we reason that actions that are instrumental in obtaining outcomes that are desirable in multiple ways (e.g., obtaining a snack to satisfy one's appetite, giving it to a friend, trading it for money) should produce stronger PIT effects. In two experiments, participants learned to perform left and right key presses to earn a snack, either framed as having a single function or multiple functions. Participants also learned to associate the two differently framed snacks with two cues. In a PIT test, they were required to press the keys as fast as possible upon exposure to the cues (i.e., the PIT effect). We found that cues associated with the multi-functional snack facilitated the actions that earned those snacks before, while cues associated with the single-functional snack did not facilitate such actions. We discuss these findings in the context of research on free choice and personal autonomy and how people appreciate the multi-functional nature of their goal-directed behavior in the environment. Supplementary Information: The online version contains supplementary material available at 10.1007/s12144-023-04612-2.

From skinner box to daily life: Sign-tracker phenotype co-segregates with impulsivity, compulsivity, and addiction tendencies in humans.

Pavlovian conditioning holds the potential to incentivize environmental cues, leading to approach behavior toward them, even outside our awareness. Animal models suggest that this is particularly true for the so-called sign-tracker (ST) phenotype, which is considered to reflect a predisposition toward developing addiction-related behaviours. Despite its potential clinical relevance, few studies have demonstrated the translational validity of this model, likely due to difficulties in studying Pavlovian processes in humans. To fill this gap, we combined an ecological momentary assessment with ambulatory peripheral autonomic monitoring to test the hypothesis that traits associated with ST in preclinical studies would be associated with attribution of high incentive salience to reward-related cues. Several times for 2 days, participants were asked to rate the attractiveness of several preselected ecological rewards (e.g., coffee) and the preceding cues (the smell of coffee) while their electrocardiogram was recorded. While no absolute difference in subjective and physiological measures of motivational approach to daily cues compared with rewards emerged, individuals with high levels of impulsivity, obsessive-compulsive, and addiction-prone behaviors rated as more attractive and showed a greater increase in sympathetic arousal to cues versus rewards. The opposite pattern emerged for those with low levels in those dispositional traits, who responded more (both subjectively and physiologically) to rewards compared with their preceding cues. This study represents an attempt to answer the call to parcel complex behaviors into smaller constructs, improving the early detection of those who are vulnerable to develop psychopathological disorders, particularly in the domain of impulse control such as addiction.

Seed dormancy in space and time: global distribution, paleoclimatic and present climatic drivers, and evolutionary adaptations.

Seed dormancy is an important life history state that increases survival and fitness of seed plants, and thus it has attracted much attention. However, global biogeography, effects of paleoenvironment, evolutionary roles of dormancy transitions, and differences in adaptations of seed dormancy between life-forms are poorly understood. We compiled global distribution records for seed dormancy of 12 743 species and their phylogeny to explore the biogeographic patterns, environmental drivers, and evolutionary transitions between seed dormancy and nondormancy. Biogeographic patterns reveal a low proportion of dormancy in tropical rainforest regions and arctic regions and a high proportion of dormancy in remaining tropical, subtropical, and temperate regions for all species and woody species. Herbaceous plants show a greater proportion of dormancy in most global regions except arctic regions. Seasonal environments have a consistent positive influence on the dormancy pattern for both life-forms, but precipitation and temperature were important driving factors for woody and herbaceous plants, respectively. Seed dormancy was the dominating state during the evolutionary history of seed plants, and dormancy transitions had a significant relationship with paleotemperatures. Dormancy and nondormancy transitions in response to fluctuating environments during long-term evolutionary history may have played important roles in the diversification of seed plants. Our results add to the current knowledge about seed dormancy from macro-adaptive perspectives and the potential adaptive mechanisms of seed plants.

Insights into the molecular basis of c-di-GMP signalling in Pseudomonas aeruginosa.

The opportunistic human pathogen Pseudomonas aeruginosa can cause severe infections in immunocompromized people or cystic fibrosis (CF) patients. Because of its remarkable ability to invade the host and withstand the bacteriocidal effect of most conventional antibiotics, the infection caused by P. aeruginosa has become a major concern for human health. The switch from acute to chronic infection is governed by the second messenger bis-(3'-5')-cyclic dimeric guanosine mono-phosphate (c-di-GMP) in P. aeruginosa, and c-di-GMP is now recognized to regulate many important biological processes in pathogenesis. The c-di-GMP signalling mechanisms in P. aeruginosa have been studied extensively in the past decade, revealing complicated c-di-GMP metabolism and signalling network. In this review, the underlying mechanisms of this signalling network will be discussed, mainly focussing on how environmental cues regulate c-di-GMP signalling, protein-protein interaction mediated functional regulation, heterogeneity of c-di-GMP and cross talk between c-di-GMP signalling and other signalling systems. Understanding the molecular mechanism underlying the complex c-di-GMP signalling network would be beneficial for developing therapeutic approaches and antibacterial agents to combat the threat from P. aeruginosa.

Sexual differences in responses of meadow voles to environmental cues in the presence of mink odor.

In rodents, defensive behaviors increase the chances of survival during a predator encounter. Observable rodent defensive behaviors have been shown to be influenced by the presence of predator odors and nearby environmental cues such as cover, odors from conspecifics and food availability. Our experiment tested whether a predator scent cue influenced refuge preference in meadow voles within a laboratory setting. We placed voles in an experimental apparatus with bedding soaked in mink scent versus olive oil as a control across from four tubes that either contained (a) a dark plastic covering, (b) opposite-sex conspecific odor, (c) a food pellet, or (d) an empty, unscented space. A three-way interaction of tube contents, subject sex, and the presence of mink or olive oil on the preference of meadow voles to spend time in each area of the experimental apparatus and their latency to enter each area of the apparatus revealed sex differences in the environmental preference of meadow voles facing the risk of predation. The environmental preference of female, but not male, meadow voles was altered by the presence of mink urine or olive oil. A similar trend was found in the latency of males and females to enter each area of the experimental apparatus. These differences suggest that each sex utilizes different methods to increase their fitness when experiencing a predation risk. The observed sex differences may be explained by the natural history of voles owing to the differences in territorial range and the dynamics of evasion of terrestrial predators.

Characterization, costs, cues and future perspectives of phenotypic plasticity.

BACKGROUND: Plastic responses of plants to the environment are ubiquitous. Phenotypic plasticity occurs in many forms and at many biological scales, and its adaptive value depends on the specific environment and interactions with other plant traits and organisms. Even though plasticity is the norm rather than the exception, its complex nature has been a challenge in characterizing the expression of plasticity, its adaptive value for fitness and the environmental cues that regulate its expression. SCOPE: This review discusses the characterization and costs of plasticity and approaches, considerations, and promising research directions in studying plasticity. Phenotypic plasticity is genetically controlled and heritable; however, little is known about how organisms perceive, interpret and respond to environmental cues, and the genes and pathways associated with plasticity. Not every genotype is plastic for every trait, and plasticity is not infinite, suggesting trade-offs, costs and limits to expression of plasticity. The timing, specificity and duration of plasticity are critical to their adaptive value for plant fitness. CONCLUSIONS: There are many research opportunities to advance our understanding of plant phenotypic plasticity. New methodology and technological breakthroughs enable the study of phenotypic responses across biological scales and in multiple environments. Understanding the mechanisms of plasticity and how the expression of specific phenotypes influences fitness in many environmental ranges would benefit many areas of plant science ranging from basic research to applied breeding for crop improvement.

Getting leaves into shape: a molecular, cellular, environmental and evolutionary view.

Leaves arise from groups of undifferentiated cells as small primordia that go through overlapping phases of morphogenesis, growth and differentiation. These phases are genetically controlled and modulated by environmental cues to generate a stereotyped, yet plastic, mature organ. Over the past couple of decades, studies have revealed that hormonal signals, transcription factors and miRNAs play major roles during leaf development, and more recent findings have highlighted the contribution of mechanical signals to leaf growth. In this Review, we discuss how modulating the activity of some of these regulators can generate diverse leaf shapes during development, in response to a varying environment, or between species during evolution.

Sensory perception of environmental cues as a modulator of aging and neurodegeneration: Insights from Caenorhabditis elegans.

Environmental stimuli such as temperature, food, and smell significantly influence the physiology and behavior of animals. Animals are differentially adapted to maintain their internal body functions in response to varied environmental conditions. These external cues are sensed by specialized neurons which are a part of the chemosensory and thermosensory systems. The inability to respond correctly to varied environmental conditions may result in compromised bodily functions and reduced longevity. For example, the ability to sense food is derived from the integrated action of olfactory and gustatory systems. The damage to the olfactory system will affect our decision of palatable food items which in turn can affect the response of the gustatory system, ultimately causing abnormal feeding habits. Recent studies have provided evidence that aging is regulated by sensory perception of environment. Aging is one of the most common causes of various neurodegenerative diseases and the perception of environmental cues is also found to regulate the development of neurodegenerative phenotype in several animal models. However, specific molecular signaling pathways involved in the process are not completely understood. The research conducted on one of the best-studied animal models of aging, Caenorhabditis elegans, has demonstrated multiple examples of gene-environment interaction at the neuronal level which affects life span. The findings may be useful to identify the key neuronal regulators of aging and age-related diseases in humans owing to conserved core metabolic and aging pathways from worms to humans.

Bee phenology is predicted by climatic variation and functional traits.

Climate change is shifting the environmental cues that determine the phenology of interacting species. Plant-pollinator systems may be susceptible to temporal mismatch if bees and flowering plants differ in their phenological responses to warming temperatures. While the cues that trigger flowering are well-understood, little is known about what determines bee phenology. Using generalised additive models, we analyzed time-series data representing 67 bee species collected over 9 years in the Colorado Rocky Mountains to perform the first community-wide quantification of the drivers of bee phenology. Bee emergence was sensitive to climatic variation, advancing with earlier snowmelt timing, whereas later phenophases were best explained by functional traits including overwintering stage and nest location. Comparison of these findings to a long-term flower study showed that bee phenology is less sensitive than flower phenology to climatic variation, indicating potential for reduced synchrony of flowers and pollinators under climate change.

A matter of life and death: Molecular, physiological, and environmental regulation of seed longevity.

Both seed germination and early seedling establishment are important biological processes in a plant's lifecycle. Seed longevity is a key trait in agriculture, which directly influences seed germination and ultimately determines crop productivity and hence food security. Numerous studies have demonstrated that seed deterioration is regulated by complex interactions between diverse endogenous genetically controlled factors and exogenous environmental cues, including temperature, relative humidity, and oxygen partial pressure during seed storage. The endogenous factors, including the chlorophyll concentration, the structure of the seed coat, the balance of phytohormones, the concentration of reactive oxygen species, the integrity of nucleic acids and proteins and their associated repair systems, are also involved in the control of seed longevity. A precise understanding of the regulatory mechanisms underlying seed longevity is becoming a hot topic in plant molecular biology. In this review, we describe recent research into the regulation of seed longevity and the interactions between the various environmental and genetic factors. Based on this, the current state-of-play regarding seed longevity regulatory networks will be presented, particularly with respect to agricultural seed storage, and the research challenges to be faced in the future will be discussed.

When mother knows best: A population genetic model of transgenerational versus intragenerational plasticity.

Many organisms exhibit phenotypic plasticity; producing alternate phenotypes depending on the environment. Individuals can be plastic (intragenerational or direct plasticity), wherein individuals of the same genotype produce different phenotypes in response to the environments they experience. Alternatively, an individual's phenotype may be under the control of its parents, usually the mother (transgenerational or indirect plasticity), so that mother's genotype determines the phenotype produced by a given genotype of her offspring. Under what conditions does plasticity evolve to have intragenerational as opposed to transgenerational genetic control? To explore this question, we present a population genetic model for the evolution of transgenerational and intragenerational plasticity. We hypothesize that the capacity for plasticity incurs a fitness cost, which is borne either by the individual developing the plastic phenotype or by its mother. We also hypothesize that individuals are imperfect predictors of future environments and their capacity for plasticity can lead them occasionally to make a low-fitness phenotype for a particular environment. When the cost, benefit and error parameters are equal, we show that there is no evolutionary advantage to intragenerational over transgenerational plasticity, although the rate of evolution of transgenerational plasticity is half the rate for intragenerational plasticity, as predicted by theory on indirect genetic effects. We find that transgenerational plasticity evolves when mothers are better predictors of future environments than offspring or when the fitness cost of the capacity for plasticity is more readily borne by a mother than by her developing offspring. We discuss different natural systems with either direct intragenerational plasticity or indirect transgenerational plasticity and find a pattern qualitatively in accord with the predictions of our model.

Epigenetic Regulation of Vascular Diseases.

Epigenetic regulatory mechanisms, encompassing diverse molecular processes including DNA methylation, histone post-translational modifications, and noncoding RNAs, are essential to numerous processes such as cell differentiation, growth and development, environmental adaptation, aging, and disease states. In many cases, epigenetic changes occur in response to environmental cues and lifestyle factors, resulting in persistent changes in gene expression that affect vascular disease risk during the lifetime of the individual. Biological aging-a powerful cardiovascular risk factor-is partly genetically determined yet strongly influenced by traditional risk factors, reflecting epigenetic modulation. Quantification of specific DNA methylation patterns may serve as an accurate predictor of biological age-a concept known as the epigenetic clock, which could help to refine cardiovascular risk assessment. Epigenetic reprogramming of monocytes rewires cellular immune signaling and induces a metabolic shift toward aerobic glycolysis, thereby increasing innate immune responses. This form of trained epigenetic memory can be maladaptive, thus augmenting vascular inflammation. Somatic mutations in epigenetic regulatory enzymes lead to clonal hematopoiesis of indeterminate potential, a precursor of hematologic malignancies and a recently recognized cardiovascular risk factor; moreover, epigenetic regulators are increasingly being targeted in cancer therapeutics. Thus, understanding epigenetic regulatory mechanisms lies at the intersection between cancer and cardiovascular disease and is of paramount importance to the burgeoning field of cardio-oncology (Graphic Abstract).

Body Mass Index and stimulus control: Results from a real-world study of eating behaviour.

BACKGROUND: Evidence suggests decisions about when, what, and how much to eat can be influenced by external (location, food outlet presence, food availability) and internal (affect) cues. Although the relationship between stimulus control and obesity is debated, it is suggested that individuals with higher BMIs are more driven by cues to eating than individuals in the healthy-weight range (HWR). This study investigates the influence of stimulus control on real-world food intake, and whether stimulus control differs by BMI. It was hypothesised that, compared to those in the HWR, eating among individuals with higher BMIs would be under greater stimulus control. METHOD: 74 participants (n = 34 BMI < 24.9, n = 40 BMI > 24.9) recorded food intake for 14 days using Ecological Momentary Assessment. Participants also responded to 4-5 randomly-timed assessments per day. Known external and internal eating cues were assessed during both assessment types. Within-person logistic regression analyses were used to predict eating vs. non-eating occasions from stimulus control domains. FINDINGS: Results support the hypothesis that eating was influenced by stimulus control: food availability, affect, time of day, and location significantly distinguished between eating and non-eating instances (AUC-ROC = 0.56-0.69, all p's < 0.001). The presence of food outlets was significantly better at distinguishing between eating and non-eating instances for those with higher BMIs (compared to individuals in the HWR). DISCUSSION: Results support the notion of stimulus control in shaping eating decisions. Differences in levels of stimulus control between participants in the HWR compared to those with a high BMI suggest that dietary improvement interventions may be more effective when they are tailored to the individual and consider environmental influences on eating behaviour.

Characterization of S40-like proteins and their roles in response to environmental cues and leaf senescence in rice.

BACKGROUND: Senescence affects the quality and yield of plants by regulating different traits of plants. A few members of S40 gene family, the barley HvS40 and the Arabidopsis AtS40-3, have been shown to play a role in leaf senescence in Barley and Arabidopsis. Although we previously reported that S40 family exist in most of plants, up to now, no more function of S40 members in plant has been demonstrated. The aim of this study was to provide the senescence related information of S40 gene family in rice as rice is a major crop that feeds about half of the human population in the world. RESULTS: A total of 16 OsS40 genes were identified from the genome database of Oryza sativa L. japonica by bioinformatics analysis. Phylogenetic analysis reveals that the 16 OsS40 proteins are classified into five groups, and 4 of the 16 members belong to group I to which also the HvS40 and AtS40-3 is assigned. S40 genes of rice show high structural similarities, as 13 out of the 16 genes have no intron and the other 3 genes have only 1 or 2 introns. The expression patterns of OsS40 genes were analyzed during natural as well as stress-induced leaf senescence in correspondence with senescence marker genes. We found that 6 of them displayed differential but clearly up-regulated transcript profiles under diverse situations of senescence, including darkness, nitrogen deficiency, hormone treatments as well as pathogen infection. Furthermore, three OsS40 proteins were identified as nuclear located proteins by transient protoplast transformation assay. CONCLUSIONS: Taking all findings together, we concluded that OsS40-1, OsS40-2, OsS40-12 and OsS40-14 genes have potential regulatory function of crosstalk among abiotic, biotic and developmental senescence in rice. Our results provide valuable baseline for functional validation studies of the rice S40 genes in rice leaf senescence.

Fire cues trigger germination and stimulate seedling growth of grass species from Brazilian savannas.

PREMISE: Although fire cues (high temperatures and smoke) influence seed germination in numerous species from fire-prone environments, their effects on seed germination of species from neotropical savannas are poorly understood. METHODS: We exposed seeds of eight grass species from the Cerrado, the Brazilian savanna to heat-shock (80°C or 110°C for 5 min) and/or smoke water, and then set them to germinate in light or dark, at either summer (28°C/18°C) or winter (27°C/14°C) temperature regimes in an incubator. In addition, we evaluated the effects of smoke water on seedling root and shoot growth for four of the species. RESULTS: Smoke interacted with the dark treatment to increase germination from 28% to 93% in Aristida recurvata and 77% to 95% in Aristida riparia. Smoke had no effect on germination of either of these species in the light. Heat-shock alone also promoted seed germination in A. recurvata. For Digitaria lehmanniana, smoke interacted with heat-shock to improve germination from 5% to 16%. In contrast, the fire treatments did not have any effect on the seed germination of the remaining five species. Smoke water stimulated root growth for A. riparia, A. recurvata, and Ctenium cirrosum but had no effect on their shoot growth. CONCLUSIONS: The strong promotive effect of smoke on Aristida germination suggests that these species are fire-adapted. Aristida species have an active awn system, which facilitates seed burial, and the smoke and dark interaction would ensure buried seeds germinated post-fire. The species that showed no response to fire cues may either have adapted via alternative strategies or require different concentrations of smoke or levels of heat. This study is one of very few examples showing a positive germination and seedling growth response to smoke for species from neotropical savannas.