A census of baryons in the Universe from localized fast radio bursts.

More than three-quarters of the baryonic content of the Universe resides in a highly diffuse state that is difficult to detect, with only a small fraction directly observed in galaxies and galaxy clusters1,2. Censuses of the nearby Universe have used absorption line spectroscopy3,4 to observe the 'invisible' baryons, but these measurements rely on large and uncertain corrections and are insensitive to most of the Universe's volume and probably most of its mass. In particular, quasar spectroscopy is sensitive either to the very small amounts of hydrogen that exist in the atomic state, or to highly ionized and enriched gas4-6 in denser regions near galaxies7. Other techniques to observe these invisible baryons also have limitations; Sunyaev-Zel'dovich analyses8,9 can provide evidence from gas within filamentary structures, and studies of X-ray emission are most sensitive to gas near galaxy clusters9,10. Here we report a measurement of the baryon content of the Universe using the dispersion of a sample of localized fast radio bursts; this technique determines the electron column density along each line of sight and accounts for every ionized baryon11-13. We augment the sample of reported arcsecond-localized14-18 fast radio bursts with four new localizations in host galaxies that have measured redshifts of 0.291, 0.118, 0.378 and 0.522. This completes a sample sufficiently large to account for dispersion variations along the lines of sight and in the host-galaxy environments11, and we derive a cosmic baryon density of [Formula: see text] (95 per cent confidence; h70 = H0/(70 km s-1 Mpc-1) and H0 is Hubble's constant). This independent measurement is consistent with values derived from the cosmic microwave background and from Big Bang nucleosynthesis19,20.

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.

Prediction of photoperiodic regulators from quantitative gene circuit models.

Photoperiod sensors allow physiological adaptation to the changing seasons. The prevalent hypothesis is that day length perception is mediated through coupling of an endogenous rhythm with an external light signal. Sufficient molecular data are available to test this quantitatively in plants, though not yet in mammals. In Arabidopsis, the clock-regulated genes CONSTANS (CO) and FLAVIN, KELCH, F-BOX (FKF1) and their light-sensitive proteins are thought to form an external coincidence sensor. Here, we model the integration of light and timing information by CO, its target gene FLOWERING LOCUS T (FT), and the circadian clock. Among other predictions, our models show that FKF1 activates FT. We demonstrate experimentally that this effect is independent of the known activation of CO by FKF1, thus we locate a major, novel controller of photoperiodism. External coincidence is part of a complex photoperiod sensor: modeling makes this complexity explicit and may thus contribute to crop improvement.

The dispersion-brightness relation for fast radio bursts from a wide-field survey.

Despite considerable efforts over the past decade, only 34 fast radio bursts-intense bursts of radio emission from beyond our Galaxy-have been reported1,2. Attempts to understand the population as a whole have been hindered by the highly heterogeneous nature of the searches, which have been conducted with telescopes of different sensitivities, at a range of radio frequencies, and in environments corrupted by different levels of radio-frequency interference from human activity. Searches have been further complicated by uncertain burst positions and brightnesses-a consequence of the transient nature of the sources and the poor angular resolution of the detecting instruments. The discovery of repeating bursts from one source3, and its subsequent localization4 to a dwarf galaxy at a distance of 3.7 billion light years, confirmed that the population of fast radio bursts is located at cosmological distances. However, the nature of the emission remains elusive. Here we report a well controlled, wide-field radio survey for these bursts. We found 20, none of which repeated during follow-up observations between 185-1,097 hours after the initial detections. The sample includes both the nearest and the most energetic bursts detected so far. The survey demonstrates that there is a relationship between burst dispersion and brightness and that the high-fluence bursts are the nearby analogues of the more distant events found in higher-sensitivity, narrower-field surveys5.

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.

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.

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.

Coordinated circadian timing through the integration of local inputs in Arabidopsis thaliana.

Individual plant cells have a genetic circuit, the circadian clock, that times key processes to the day-night cycle. These clocks are aligned to the day-night cycle by multiple environmental signals that vary across the plant. How does the plant integrate clock rhythms, both within and between organs, to ensure coordinated timing? To address this question, we examined the clock at the sub-tissue level across Arabidopsis thaliana seedlings under multiple environmental conditions and genetic backgrounds. Our results show that the clock runs at different speeds (periods) in each organ, which causes the clock to peak at different times across the plant in both constant environmental conditions and light-dark (LD) cycles. Closer examination reveals that spatial waves of clock gene expression propagate both within and between organs. Using a combination of modeling and experiment, we reveal that these spatial waves are the result of the period differences between organs and local coupling, rather than long-distance signaling. With further experiments we show that the endogenous period differences, and thus the spatial waves, can be generated by the organ specificity of inputs into the clock. We demonstrate this by modulating periods using light and metabolic signals, as well as with genetic perturbations. Our results reveal that plant clocks can be set locally by organ-specific inputs but coordinated globally via spatial waves of clock gene expression.

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.

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.

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.

Cell size control driven by the circadian clock and environment in cyanobacteria.

How cells maintain their size has been extensively studied under constant conditions. In the wild, however, cells rarely experience constant environments. Here, we examine how the 24-h circadian clock and environmental cycles modulate cell size control and division timings in the cyanobacterium Synechococcus elongatus using single-cell time-lapse microscopy. Under constant light, wild-type cells follow an apparent sizer-like principle. Closer inspection reveals that the clock generates two subpopulations, with cells born in the subjective day following different division rules from cells born in subjective night. A stochastic model explains how this behavior emerges from the interaction of cell size control with the clock. We demonstrate that the clock continuously modulates the probability of cell division throughout day and night, rather than solely applying an on-off gate to division, as previously proposed. Iterating between modeling and experiments, we go on to identify an effective coupling of the division rate to time of day through the combined effects of the environment and the clock on cell division. Under naturally graded light-dark cycles, this coupling narrows the time window of cell divisions and shifts divisions away from when light levels are low and cell growth is reduced. Our analysis allows us to disentangle, and predict the effects of, the complex interactions between the environment, clock, and cell size control.

Nitrate modulates stem cell dynamics in Arabidopsis shoot meristems through cytokinins.

The shoot apical meristem (SAM) is responsible for the generation of all the aerial parts of plants. Given its critical role, dynamical changes in SAM activity should play a central role in the adaptation of plant architecture to the environment. Using quantitative microscopy, grafting experiments, and genetic perturbations, we connect the plant environment to the SAM by describing the molecular mechanism by which cytokinins signal the level of nutrient availability to the SAM. We show that a systemic signal of cytokinin precursors mediates the adaptation of SAM size and organogenesis rate to the availability of mineral nutrients by modulating the expression of WUSCHEL, a key regulator of stem cell homeostasis. In time-lapse experiments, we further show that this mechanism allows meristems to adapt to rapid changes in nitrate concentration, and thereby modulate their rate of organ production to the availability of mineral nutrients within a few days. Our work sheds light on the role of the stem cell regulatory network by showing that it not only maintains meristem homeostasis but also allows plants to adapt to rapid changes in the environment.

Unexpected Observations: Probiotic Administration Greatly Aggravates the Reproductive Toxicity of Perfluorobutanesulfonate in Zebrafish.

The present study exposed adult zebrafish to 0, 10, and 100 µg/L perfluorobutanesulfonate (PFBS) with or without dietary supplement of probiotic Lactobacillus rhamnosus. Interaction between probiotic and PFBS on sex endocrine and reproduction was investigated. It was striking to find that PFBS and probiotic coexposures almost ceased the fecundity, which was accompanied by disturbances in sex hormones and oocyte maturation in females. In contrast, probiotic additive efficiently antagonized the estrogenic activity of PFBS in males. For the first time, this study reported that probiotic heavily depended on sex to modulate the endocrine disruption and reproductive toxicity of aquatic pollutants.

Probiotic Modulation of Lipid Metabolism Disorders Caused by Perfluorobutanesulfonate Pollution in Zebrafish.

To determine whether and how probiotic supplement can alter gut microbiota dysbiosis and lipid metabolism disorders caused by perfluorobutanesulfonate (PFBS), the present study exposed adult zebrafish to 0, 10, and 100 µg/L PFBS for 28 days, with or without dietary administration of probiotic Lactobacillus rhamnosus. Regarding intestinal health and gut microbiota, probiotic supplement altered the innate toxicities of PFBS, depending on exposure concentration and the sex of the fish. Lactobacillus genus correlated positively (P < 0.001; r > 0.5) with other beneficial bacteria in the gut microbiota, thereby indirectly regulating host metabolic activities. In female fish, the PFBS and probiotic combination enhanced fatty acid synthesis and ß-oxidation, but mitigated the accumulation of cholesterol in the blood compared with PFBS single exposure, highlighting the benefits of the probiotic to host health. In male zebrafish, probiotic administration antagonized the PFBS-induced disturbances of bile acid metabolism, presumably via farnesoid X receptor signaling. However, coexposure to PFBS and probiotic caused significant accumulation of triglyceride in male livers (2.6-fold relative to the control), implying the induction of hepatic steatosis. Overall, the present study underlined the potential of probiotics to modulate gut microbial dysbiosis and lipid metabolism disorders caused by PFBS exposure, which could provide implications to the application of probiotics in aquaculture.

Reducing the complexity of mathematical models for the plant circadian clock by distributed delays.

A major bottleneck in the modelling of biological networks is the parameter explosion problem - the exponential increase in the number of parameters that need to be optimised to data as the size of the model increases. Here, we address this problem in the context of the plant circadian clock by applying the method of distributed delays. We show that using this approach, the system architecture can be simplified efficiently - reducing the number of parameters - whilst still preserving the core mechanistic dynamics of the gene regulatory network. Compared to models with discrete time-delays, which are governed by functional differential equations, the distributed delay models can be converted into sets of equivalent ordinary differential equations, enabling the use of standard methods for numerical integration, and for stability and bifurcation analyses. We demonstrate the efficiency of our modelling approach by applying it to three exemplar mathematical models of the Arabidopsis circadian clock of varying complexity, obtaining significant reductions in complexity in each case. Moreover, we revise one of the most up-to-date Arabidopsis models, updating the regulation of the PRR9 and PRR7 genes by LHY in accordance with recent experimental data. The revised model more accurately reproduces the LHY-induction experiments of core clock genes, compared with the original model. Our work thus shows that the method of distributed delays facilitates the optimisation and reformulation of genetic network models.

Occurrence and Distribution of Photoinitiator Additives in Paired Maternal and Cord Plasma in a South China Population.

Photoinitiators (PIs) are widely used in industrial polymerization and have been detected as emerging contaminants in environmental matrixes. It has been reported that humans are exposed to PIs, but the maternal-fetal transmission of PIs has not been documented. In this study, we analyzed 21 PIs (9 benzophenones, BZPs; 8 amine co-initiators, ACIs; and 4 thioxanthones, TXs) in matched maternal-cord plasma samples from 49 pregnant women in South China. Sixteen of the 21 target PIs were found in maternal plasma at concentrations of ∑PIs (sum of the detected PIs) from 303 to 3500 pg/mL. Meanwhile, 12 PIs were detected in cord plasma with ∑PIs from 104 to 988 pg/mL. The PIs detected in both maternal and cord plasma samples were dominated by BZPs, followed by ACIs and TXs. Different groups of PIs showed structure-dependent placental transfer efficiencies (PTEs). The PTEs were generally less than 100% for BZPs but greater than 100% for ACIs and TXs. By further theoretical calculation, we revealed the critical structural features of PIs that affect PTEs. This is the first study to investigate the occurrence and distribution of PIs in paired maternal and cord plasma, and it sheds light on the potential mechanism of structure-dependent placental transfer.

Perfluorobutanesulfonate Exposure Skews Sex Ratio in Fish and Transgenerationally Impairs Reproduction.

Perfluorobutanesulfonate (PFBS) is increasingly polluting aquatic environments due to worldwide manufacturing and application. However, toxicological knowledge regarding PFBS exposure remains scarce. Here, we showed that PFBS life-cycle exposure at environmentally realistic concentrations (0, 1.0, 2.9, and 9.5 µg/L) skewed the sex ratio in fish toward male dominance, while reproductive functions of female fish were greatly impaired, as characterized by extremely small ovaries, blocked oocyte development, and decreased egg production. Endocrine disruption through the hypothalamus-pituitary-gonad axis was induced by PFBS exposure, showing antiestrogenic activity in females but estrogenic activity in males. PFBS was found to gradually accumulate in F0 adults during continuous exposure but can be rapidly eliminated when depurated in clean water. Parental exposure also transferred PFBS pollutant to F1 offspring eggs. Although no trace of PFBS was detected in F1 adults and F2 eggs, adverse effects from parental exposure persisted in F1 and F2 offspring. These transgenerational effects implicate PFBS as an ongoing threat to the fitness and sustainability of fish populations. The dramatic impairment of fish reproduction highlights the urgency of re-evaluations of the ecological and evolutionary consequences of PFBS exposure.

Prevalence, Biotransformation, and Maternal Transfer of Synthetic Phenolic Antioxidants in Pregnant Women from South China.

Synthetic phenolic antioxidants (SPAs) have been identified as an emerging group of contaminants in recent years. However, there are significant gaps in our knowledge of human prenatal exposure to these synthetic chemicals. In this study, a set of eight SPAs and four major transformation products (TPs) were systematically analyzed in matched samples of maternal plasma, cord plasma, and placenta from a population of pregnant women. Five of the eight target SPAs and all four target TPs were frequently detected in the maternal-placental-fetal unit, indicating prenatal exposure to SPAs and the transfer of SPAs across the placenta. In the three matrices, 2,6-di-tert-butyl-hydroxytoluene (BHT), 2,4-di-tert-butylphenol (DBP), and 2,2'-methylenebis(4-methyl-6-tert-butylphenol) (AO 2246) were identified as the most abundant SPAs, while 2,6-di-tert-butyl-1,4-benzoquinone (BHT-Q) and 2,6-di-tert-butyl-4-hydroxy-4-methyl-2,5-cyclohexadienone (BHT-quinol) were identified as the predominant TPs of BHT. In the maternal plasma, concentrations of both BHT-Q and BHT-quinol were significantly correlated with BHT (p < 0.001), suggesting that the two TPs mainly originated from the biotransformation of BHT itself in pregnant women. The transplacental transfer efficiencies (TTEs) of the SPAs and TPs were structure-dependent and generally less than 1. Significantly higher TTEs for four target TPs than their parent BHT were identified. To our knowledge, this study provides the first evidence that SPAs and TPs transfer across the placenta in pregnant women.

Parental Exposure to Perfluorobutanesulfonate Impairs Offspring Development through Inheritance of Paternal Methylome.

Perfluorobutanesulfonate (PFBS), an environmental pollutant of emerging concern, significantly impairs offspring development and overall health after parental exposure. However, the true inducer of offspring developmental defects among the complexity of parental influences remains unknown. In the present study, marine medaka (Oryzias melastigma) were exposed to environmentally realistic concentrations of PFBS (0, 1, 3, and 10 µg/L) for an entire life cycle. By mixing and mating control and exposed medaka (male or female), a crossbreeding strategy was employed to produce offspring eggs from various crossbreeds, with the aim of differentiating the maternal and paternal influences. Measurements of swimming performance in larval offspring showed that larvae of exposed male parents swam hyperactively in comparison to the control larvae. Contrasting trends in PFBS transfer and maternal factor transfer (e.g., proteins and lipids) to that of swimming behavior eliminated these two factors as major inducers of offspring developmental impairment. Inheritance of the exposed paternal methylome marks in offspring may be partially responsible for abnormal swimming behavior, although different toxic mechanisms may be involved depending on the exposure concentration. Overall, these findings suggest that inheritance of epigenetic modifications implicates a long-lasting threat of PFBS to the fitness and sustainability of fish populations.