Bet-hedging and variability in plant development: seed germination and beyond.

When future conditions are unpredictable, bet-hedging strategies can be advantageous. This can involve isogenic individuals producing different phenotypes, under the same environmental conditions. Ecological studies provide evidence that variability in seed germination time has been selected for as a bet-hedging strategy. We demonstrate how variability in germination time found in Arabidopsis could function as a bet-hedging strategy in the face of unpredictable lethal stresses. Despite a body of knowledge on how the degree of seed dormancy versus germination is controlled, relatively little is known about how differences between isogenic seeds in a batch are generated. We review proposed mechanisms for generating variability in germination time and the current limitations and new possibilities for testing the model predictions. We then look beyond germination to the role of variability in seedling and adult plant growth and review new technologies for quantification of noisy gene expression dynamics. We discuss evidence for phenotypic variability in plant traits beyond germination being under genetic control and propose that variability in stress response gene expression could function as a bet-hedging strategy. We discuss open questions about how noisy gene expression could lead to between-plant heterogeneity in gene expression and phenotypes. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.

A luminous fast radio burst that probes the Universe at redshift 1.

Fast radio bursts (FRBs) are millisecond-duration pulses of radio emission originating from extragalactic distances. Radio dispersion is imparted on each burst by intervening plasma, mostly located in the intergalactic medium. In this work, we observe the burst FRB 20220610A and localize it to a morphologically complex host galaxy system at redshift 1.016 ± 0.002. The burst redshift and dispersion measure are consistent with passage through a substantial column of plasma in the intergalactic medium and extend the relationship between those quantities measured at lower redshift. The burst shows evidence for passage through additional turbulent magnetized plasma, potentially associated with the host galaxy. We use the burst energy of 2 × 1042 erg to revise the empirical maximum energy of an FRB.

The σB alternative sigma factor circuit modulates noise to generate different types of pulsing dynamics.

Single-cell approaches are revealing a high degree of heterogeneity, or noise, in gene expression in isogenic bacteria. How gene circuits modulate this noise in gene expression to generate robust output dynamics is unclear. Here we use the Bacillus subtilis alternative sigma factor σB as a model system for understanding the role of noise in generating circuit output dynamics. σB controls the general stress response in B. subtilis and is activated by a range of energy and environmental stresses. Recent single-cell studies have revealed that the circuit can generate two distinct outputs, stochastic pulsing and a single pulse response, but the conditions under which each response is generated are under debate. We implement a stochastic mathematical model of the σB circuit to investigate this and find that the system's core circuit can generate both response types. This is despite one response (stochastic pulsing) being stochastic in nature, and the other (single response pulse) being deterministic. We demonstrate that the main determinant for whichever response is generated is the degree with which the input pathway activates the core circuit, although the noise properties of the input pathway also biases the system towards one or the other type of output. Thus, our work shows how stochastic modelling can reveal the mechanisms behind non-intuitive gene circuit output dynamics.

Spatially specific mechanisms and functions of the plant circadian clock.

Like many organisms, plants have evolved a genetic network, the circadian clock, to coordinate processes with day/night cycles. In plants, the clock is a pervasive regulator of development and modulates many aspects of physiology. Clock-regulated processes range from the correct timing of growth and cell division to interactions with the root microbiome. Recently developed techniques, such as single-cell time-lapse microscopy and single-cell RNA-seq, are beginning to revolutionize our understanding of this clock regulation, revealing a surprising degree of organ, tissue, and cell-type specificity. In this review, we highlight recent advances in our spatial view of the clock across the plant, both in terms of how it is regulated and how it regulates a diversity of output processes. We outline how understanding these spatially specific functions will help reveal the range of ways that the clock provides a fitness benefit for the plant.

A spatial model of the plant circadian clock reveals design principles for coordinated timing.

Individual plant cells possess a genetic network, the circadian clock, that times internal processes to the day-night cycle. Mathematical models of the clock are typically either "whole-plant" that ignore tissue or cell type-specific clock behavior, or "phase-only" that do not include molecular components. To address the complex spatial coordination observed in experiments, here we implemented a clock network model on a template of a seedling. In our model, the sensitivity to light varies across the plant, and cells communicate their timing via local or long-distance sharing of clock components, causing their rhythms to couple. We found that both varied light sensitivity and long-distance coupling could generate period differences between organs, while local coupling was required to generate the spatial waves of clock gene expression observed experimentally. We then examined our model under noisy light-dark cycles and found that local coupling minimized timing errors caused by the noise while allowing each plant region to maintain a different clock phase. Thus, local sensitivity to environmental inputs combined with local coupling enables flexible yet robust circadian timing.

High Spatial Resolution Luciferase Imaging of the Arabidopsis thaliana Circadian Clock.

The A. thaliana circadian clock is an example of a gene network that generates rich temporal and spatial dynamics. Bioluminescent imaging has proven a powerful method to help dissect the genetic mechanisms that generate oscillations of gene expression over the course of the day. However, its use for the study of spatial regulation is often limited by resolution. Here, we describe a modified luciferase imaging method for the study of the Arabidopsis circadian clock across the plant at sub-tissue-level resolution.

Spatial distribution and accumulation profiles of volatile methylsiloxanes in Tokyo Bay, Japan: Mass loadings and historical trends.

We investigated mass loading and the spatial distribution of volatile methylsiloxanes (VMSs) including four cyclic VMSs (D3-D6; cVMSs, the number refers to the number of SiO bonds) and three linear VMSs (L3-L5; lVMSs) in Tokyo Bay, Japan, which is one of the most industrialized, urbanized, and populated areas in the world. Based on the VMS concentrations determined in eight main inflow rivers to the bay, the mass loading of VMSs via inflow rivers and sewage treatment plants located in Tokyo Bay was estimated at 2500 kg/y for total VMSs. Elevated mass loadings of VMSs were found in three of the rivers, inflowing to the inner west of Tokyo Bay. The distribution and deposition characteristics of VMSs were observed depending on the estuarine condition. Estuarine sediments were found to be efficient and effective traps for VMSs and the salting-out effect is one possible mechanism to explain this phenomenon. The overall profiles of D4, D5, and D6 in surface water and sediment were observed across Tokyo Bay; elevated concentrations were identified in the inner west bay with dispersed low concentrations in the outer bay, except for one hotspot of D4 in the sediment, indicating a major emission route of VMSs via inflow rivers. Additionally, the historical pollution profiles of VMSs in Tokyo Bay were reconstructed based on the VMS concentrations determined in a dated sediment core. VMSs were identified throughout the upper 40 cm of the sediment core (representing the mid 1980s); the profiles correspond with the historical use of VMSs in wash-off personal care-products. The noted decreasing trend of D4 might be a reflection of the early 2000s replacement of D4 with D5 in such products. The elevated VMS concentrations in the estuarine sediment raise concerns about the impact on the aquatic environment.

Cut the noise or couple up: Coordinating circadian and synthetic clocks.

Circadian clocks are important to much of life on Earth and are of inherent interest to humanity, implicated in fields ranging from agriculture and ecology to developmental biology and medicine. New techniques show that it is not simply the presence of clocks, but coordination between them that is critical for complex physiological processes across the kingdoms of life. Recent years have also seen impressive advances in synthetic biology to the point where parallels can be drawn between synthetic biological and circadian oscillators. This review will emphasize theoretical and experimental studies that have revealed a fascinating dichotomy of coupling and heterogeneity among circadian clocks. We will also consolidate the fields of chronobiology and synthetic biology, discussing key design principles of their respective oscillators.

Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit.

Genetically identical individuals in bacterial populations can display significant phenotypic variability. This variability can be functional, for example by allowing a fraction of stress prepared cells to survive an otherwise lethal stress. The optimal fraction of stress prepared cells depends on environmental conditions. However, how bacterial populations modulate their level of phenotypic variability remains unclear. Here we show that the alternative sigma factor σV circuit in Bacillus subtilis generates functional phenotypic variability that can be tuned by stress level, environmental history and genetic perturbations. Using single-cell time-lapse microscopy and microfluidics, we find the fraction of cells that immediately activate σV under lysozyme stress depends on stress level and on a transcriptional memory of previous stress. Iteration between model and experiment reveals that this tunability can be explained by the autoregulatory feedback structure of the sigV operon. As predicted by the model, genetic perturbations to the operon also modulate the response variability. The conserved sigma-anti-sigma autoregulation motif is thus a simple mechanism for bacterial populations to modulate their heterogeneity based on their environment.

Occurrence and Trophodynamics of Marine Lipophilic Phycotoxins in a Subtropical Marine Food Web.

Marine lipophilic phycotoxins (MLPs) are produced by toxigenic microalgae and cause foodborne illnesses. However, there is little information on the trophic transfer potential of MLPs in marine food webs. In this study, various food web components including 17 species of mollusks, crustaceans, and fishes were collected for an analysis of 17 representative MLPs, including azaspiracids (AZAs), brevetoxins (BTXs), gymnodimine (GYM), spirolides (SPXs), okadaic acid (OA), dinophysistoxins (DTXs), pectenotoxins (PTXs), yessotoxins (YTXs), and ciguatoxins (CTXs). Among the 17 target MLPs, 12, namely, AZAs1-3, BTX3, GYM, SPX1, OA, DTXs1-2, PTX2, YTX, and the YTX derivative homoYTX, were detected, and the total MLP concentrations ranged from 0.316 to 20.3 ng g-1 wet weight (ww). The mean total MLP concentrations generally decreased as follows: mollusks (8.54 ng g-1, ww) > crustaceans (1.38 ng g-1, ww) > fishes (0.914 ng g-1, ww). OA, DTXs, and YTXs were the predominant MLPs accumulated in the studied biota. Trophic dilution of the total MLPs was observed with a trophic magnification factor of 0.109. The studied MLPs might not pose health risks to residents who consume contaminated seafood; however, their potential risks to the ecosystem can be a cause for concern.

Antagonistic interaction between perfluorobutanesulfonate and probiotic on lipid and glucose metabolisms in the liver of zebrafish.

Perfluorobutanesulfonate (PFBS) and probiotic bacteria can interact to induce hepatic hypertrophy. However, the molecular events occurring in the hypertrophic liver are still unknown. Therefore, we performed this follow-up study using adult zebrafish that were exposed for 40 days to 0 and 10 µg/L PFBS, with or without dietary supplementation of probiotic Lactobacillus rhamnosus. After PFBS or/and probiotic exposures, proteome perturbation, histological pathogenesis and glucose metabolism were investigated in the livers. Proteomic analysis showed potent intervention of PFBS or/and probiotic with hepatic functions. PFBS single exposure caused marked disturbances in lipid metabolisms, which may underlie the severe vacuolization in male liver. The addition of probiotic alleviated the lipid metabolic disorders of PFBS. Furthermore, probiotic supplementation enhanced ATP energy production using glucose in mitochondrial respiratory chain of male fish. However, PFBS alone caused remarkable increase in blood glucose level (by 2.5-fold relative to the control), underlining the onset of hyperglycemia symptom. In contrast, the liver of male fish from the coexposure group functioned appropriately, which immediately increased insulin levels by 2.2-fold to reduce the glucose accumulation in blood. In female liver, PFBS alone significantly decreased the blood glucagon concentration by 2.9-fold. The deficiency of glucagon hormone consequently contributed to the accumulation of glycogen (3.2-fold) therein. Vigorous antagonistic interaction between PFBS and probiotic was noted with respect to glucose metabolism, which restored ATP, glucose, glycogen and glucagon to the control levels. Overall, the present study finds that probiotic L. rhamnosus is efficient to mitigate the metabolic disorders of PFBS on lipid and glucose, highlighting the potential values of probiotic bacteria to protect the aquatic ecosystem.

Target, Nontarget, and Suspect Screening and Temporal Trends of Per- and Polyfluoroalkyl Substances in Marine Mammals from the South China Sea.

Per- and polyfluoroalkyl substances (PFASs) have been manufactured and widely used for over 60 years. Currently, there are thousands of marketed PFASs, but only dozens of them are routinely monitored. This work involved target, nontarget, and suspect screening of PFASs in the liver of Indo-Pacific humpback dolphin (Sousa chinensis) and finless porpoise (Neophocaena phocaenoides), two resident marine mammals in the South China Sea, stranded between 2012 and 2018. Among the 21 target PFASs, perfluorooctane sulfonate and 6:2 chlorinated polyfluoroalkyl ether sulfonate (6:2 Cl-PFESA) predominated in the samples, accounting for 46 and 30% of the total PFASs, respectively. Significantly higher total target PFAS concentrations (p < 0.05) were found in dolphin liver samples [3.23 × 103 ± 2.63 × 103 ng/g dry weight (dw)] than in porpoise liver samples (2.63 × 103 ± 1.10 × 103 ng/g dw). Significant increasing temporal trends (p < 0.05) were found in the concentrations of two emerging PFASs, perfluoroethylcyclohexane sulfonate and 2,3,3,3-tetrafluoro-2-propanoate in porpoises, indicating increasing pollution by these emerging PFASs. Forty-four PFASs from 9 classes were additionally identified by nontarget and suspect screening, among which 15 compounds were reported for the first time in marine mammals. A primary risk assessment showed that the emerging PFAS 6:2 Cl-PFESA could have possible adverse effects in terms of reproductive injury potential on most of the investigated cetaceans.

Disturbances in Microbial and Metabolic Communication across the Gut-Liver Axis Induced by a Dioxin-like Pollutant: An Integrated Metagenomics and Metabolomics Analysis.

To determine how the aryl hydrocarbon receptor (AhR) signaling acts along the gut-liver axis, we employed an integrated metagenomic and metabolomic approach to comprehensively profile the microbial and metabolic networks. Adult zebrafish were exposed to a model agonist of the AhR: polychlorinated biphenyl (PCB) 126. The metagenomic analysis showed that PCB126 suppressed microbial activities related to primary bile acid metabolism in male intestines. Accordingly, a suite of primary bile acids consistently showed higher concentrations, suggesting that bacterial conversion of primary bile acids was blocked. PCB126 also disturbed bacterial metabolism of bile acids in female intestines, as revealed by higher concentrations of primary bile acids (e.g., chenodeoxycholic acid) and activation of the nuclear farnesoid X receptor signaling. In addition, PCB126 exposure impaired the metabolism of various essential vitamins (e.g., retinol, vitamin B6, and folate). Degradation of vitamin B6 by bacterial enzymes was inhibited in male intestines, resulting in its intestinal accumulation. However, PCB126 suppressed the bacterial metabolism of vitamins in female intestines, causing systematic deficiency of essential vitamins. Overall, we found that PCB126 exposure dysregulated gut microbial activities, consequently interrupting bile acid and vitamin metabolism along the gut-liver axis. The findings provided an insight of the AhR action in microbe-host metabolic communication related to PCBs.

Interpretation of morphogen gradients by a synthetic bistable circuit.

During development, cells gain positional information through the interpretation of dynamic morphogen gradients. A proposed mechanism for interpreting opposing morphogen gradients is mutual inhibition of downstream transcription factors, but isolating the role of this specific motif within a natural network remains a challenge. Here, we engineer a synthetic morphogen-induced mutual inhibition circuit in E. coli populations and show that mutual inhibition alone is sufficient to produce stable domains of gene expression in response to dynamic morphogen gradients, provided the spatial average of the morphogens falls within the region of bistability at the single cell level. When we add sender devices, the resulting patterning circuit produces theoretically predicted self-organised gene expression domains in response to a single gradient. We develop computational models of our synthetic circuits parameterised to timecourse fluorescence data, providing both a theoretical and experimental framework for engineering morphogen-induced spatial patterning in cell populations.

Binary exposure to hypoxia and perfluorobutane sulfonate disturbs sensory perception and chromatin topography in marine medaka embryos.

Perfluorobutane sulfonate (PFBS), an environmental pollutant of emerging concern, is previously shown to dynamically interact with hypoxia on aquatic developmental toxicities. However, the molecular mechanisms underlying the interaction remain unknown. In this follow-up study, marine medaka embryos were exposed to 0 and 3.3 mg/L of PFBS under normoxia (6.9 mg/L) or hypoxia (1.7 mg/L) condition till 15 days post-fertilization. High-throughput transcriptomic sequencing was employed to filter differentially expressed genes and provide mechanistic insight into interactive action between hypoxia and PFBS. The results showed that hypoxia alone and the coexposure paradigm were similarly potent to modify transcriptional profiles, with the majority of genes significantly down-regulated. In contrast, transcriptional toxicity of PFBS was relatively milder. Functional annotation analyses found that hypoxia and coexposure groups mainly impacted phototransduction signaling by decreasing the transcriptions of cyclic nucleotide-gated (CNG) cation channels and retinol transport genes. However, this study demonstrated the first toxicological evidence that toxic effects of PFBS targeted the perception of chemical stimulus through olfactory and gustatory receptors. The addition of PFBS moderately exacerbated the toxic actions of hypoxia, which largely shaped the transcriptional pattern of coexposure group. In addition, gene interactive networks were constructed for hypoxia and coexposure groups, underlining the increased chromatin deacetylation and methylation to epigenetically repress genome-wide transcriptional initiation. Overall, PFBS and hypoxia interact to interrupt the embryonic development of sensory systems, which may compromise the individual fitness and survival, especially during early life stages when precocious perception of food and escape from predators are essential.

Blood partitioning and whole-blood-based maternal transfer assessment of chlorinated paraffins in mother-infant pairs from South China.

As a new group of persistent organic pollutants of concern, chlorinated paraffins (CPs) have been widely detected in the environment and biota, but their occurrence, partitioning, and transfer in humans have been not well documented. In this study, 32 pairs of maternal blood, cord blood, and placenta samples were collected from pregnant women in South China, and the blood was further separated into plasma and red blood cells (RBCs) for blood partitioning study. Short- and medium-chain CPs (SCCPs and MCCPs, respectively) were detected in all the five human biological matrices, suggesting prevalent exposure and maternal transfer of CPs in the pregnant women. Discrepant congener group profiles of CPs were observed in different human biological matrices. Significant differences in the plasma-RBC partitioning of CPs in the maternal and cord bloods were identified (p < 0.001). CP partitioning to plasma was stronger than that to RBCs in maternal blood, but the converse was true for cord blood. Mass fractions in plasma (Fp) for SCCPs (mean, 0.78) and MCCPs (0.74) in maternal blood were significantly higher than the values in cord blood. Transplacental transfer efficiencies (TTEs) were evaluated based on the whole blood concentrations of CPs in the maternal and cord bloods, and the TTEs ranged from 0.50 to 0.69 (first to third quartiles) for SCCPs and MCCPs, indicating that the placenta can partially restrict maternal transfer. The extent of CP retention in the placenta was assessed by the concentration ratio (RPM) of matched placenta and maternal blood, and interestingly, a U-shaped trend for placental retention (RPM) with increasing chain length was observed for individual congener groups. Significant relationships of the CP concentrations among the maternal blood, cord blood, and placenta were observed (p < 0.001). To our knowledge, this is the first study to report the plasma-RBC partitioning of CPs in human maternal and cord bloods, as well as the first study to evaluate TTEs based on whole blood concentrations. Our study confirmed that whole blood is the preferred matrix for accurately assessing human internal exposure and transplacental transfer of CPs.

Probiotic modulation of perfluorobutanesulfonate toxicity in zebrafish: Disturbances in retinoid metabolism and visual physiology.

Perfluorobutanesulfonate (PFBS), an aquatic pollutant of emerging concern, is found to disturb gut microbiota, retinoid metabolism and visual signaling in teleosts, while probiotic supplementation can shape gut microbial community to improve retinoid absorption. However, it remains unknown whether probiotic bacteria can modulate the toxicities of PFBS on retinoid metabolism and visual physiology. In the present study, adult zebrafish were exposed for 28 days to 0, 10 and 100 µg/L PFBS, with or without dietary administration of probiotic Lactobacillus rhamnosus. Interaction between PFBS and probiotic was examined regarding retinoid dynamics (intestine, liver and eye) and visual stimuli transmission. PFBS single exposures remarkably inhibited the absorption of retinyl ester in female intestines, which were, however, restored by probiotic to normal status. Although coexposure scenarios markedly increased the hepatic storage of retinyl ester in females, mobilization of retinol was reduced in livers by single or combined exposures regardless of sex. In the eyes, transport and catalytic conversion of retinol to retinal and retinoic acid were interrupted by PFBS alone, which were efficiently antagonized by probiotic presumably through an indirect action. In response to the availability of retinal chromophore, transcriptions of opsins and arrestin genes were altered adaptively to control visual perception and termination. Neurotransmission across retina circuitry was changed accordingly, centering on epinephrine and norepinephrine. In summary, the present study found the efficient modulation of probiotic on retinoid metabolic disorders of PFBS pollution, which subsequently impacted visual signaling. A future work is warranted to provide mechanistic clues in retinoid interaction.

Parental exposure to perfluorobutane sulfonate disturbs the transfer of maternal transcripts and offspring embryonic development in zebrafish.

Parental exposure to perfluorobutane sulfonate (PFBS), an aquatic pollutant of emerging concern, is previously found to impair the embryonic development of offspring. However, the impairing mechanisms remain to clarify. In the present study, adult zebrafish were exposed to 0, 10 and 100 µg/L PFBS for 28 d, after which disturbances in maternal transcript transfer and offspring embryogenesis were investigated. Prior to zygotic genome activation, high-throughput transcriptomic sequencing revealed that parental PFBS exposure significantly altered the transcript profile of maternal origin in offspring eggs, while toxic actions varied as a function of PFBS concentrations. In offspring eggs derived from 10 µg/L exposure group, differential transcripts were mainly associated with the histone-DNA interaction of nucleosome, which would modify the compacted chromatin configuration and accessibility of transcriptional factors to DNA sequences. In this regard, the timing of zygotic genome activation was presumably disrupted. Parental exposure to 100 µg/L PFBS primarily interrupted the maternal transfer of adherens junction transcripts, which was supposed to dysregulate the cell-cell adhesion during early embryo formation. Development and growth of offspring embryos were significantly compromised by parental PFBS exposure, as exemplified by higher mortality, delayed hatching, slower heart rate, reduced body weight and neurobehavioral disorders. Overall, the present study presented the first toxicological evidence about the disturbances of PFBS in maternal transcript transfer, although the inherent linkage between maternal transcript modifications and offspring development defects still needs future works to construct.