eLife

Cell cycle arrest and polarized cell growth are commonly used to qualitatively characterize the fate of yeast in response to pheromone. However, the quantitative decision-making process underlying the time-dependent changes in cell fate remains unclear. Here, by observing the multi-dimensional responses at the single-cell level experimentally, we find that yeast cells have various fates. Multiple states are revealed, along with the kinetic switching rates and pathways among them, giving rise to a quantitative landscape of mating response. We developed a theoretical framework using a nonequilibrium landscape and flux theory to account for the cell morphology observed experimentally and performed a stochastic simulation of biochemical reactions to explain the signal transduction and cell growth. Our experimental results established the first global quantitative demonstration of the real-time synchronization of intracellular signaling with their physiological growth and morphological functions which reveals the underlying physical mechanism. This study provides an emerging mechanistic approach for understanding the nonequilibrium global pheromone-regulated cell fate decision-making in growth and morphology.

The Early Cretaceous diversification of birds was a major event in the history of terrestrial ecosystems, occurring during the earliest phase of the Cretaceous Terrestrial Revolution. Frugivorous birds play an important role in seed dispersal today, and may have done so since their origins. However, evidence of this has been lacking. Jeholornis is one of the earliest-diverging birds, only slightly more derived than Archaeopteryx, but its cranial anatomy has been poorly understood, obscuring diet-related functional interpretations. Originally hypothesised to be granivorous based on seeds preserved as gut contents, this interpretation has become controversial. We conducted high-resolution synchrotron tomography on an exquisitely preserved new skull of Jeholornis, revealing remarkable cranial plesiomorphies combined with a specialised rostrum. We use this to provide a near-complete cranial reconstruction of Jeholornis, and exclude the possibility that Jeholornis was granivorous, based on morphometric analyses of the mandible (3D) and cranium (2D), and comparisons with the 3D alimentary contents of extant birds. We show that Jeholornis was at least seasonally frugivorous, providing the earliest evidence for fruit consumption in birds, and indicating that seed dispersal was present from early in the avian radiation. As highly-mobile seed dispersers, early frugivorous birds could expand the scope for biotic dispersal in plants, and may explain, in part, the subsequent evolutionary expansion of fruits, indicating a potential role of bird-plant interactions in the Cretaceous Terrestrial Revolution.

It is estimated that the evolution of segmented bilaterians occurred during the Ediacaran, whereas most of their unambiguous body fossils did not appear until Cambrian Stage 3. This fossil gap hampers our understanding of the early history of body segmentation, which is a crucial evolutionary innovation for bilaterians. Trace fossils from the late Ediacaran and basal Cambrian suggest this gap is likely to represent a taphonomic bias, implying that the progenitors of segmented bilaterians that existed within this temporal span were hardly preserved. Here, we report a variety of segmented bilaterians from the lowermost Cambrian of South China. These fossils are preserved as microbial pseudomorphs, rather than as ordinary phosphatization. These findings demonstrate that microbial pseudomorphs represent a major pathway for the preservation of segmented bilaterians during this period, as well as an effective mechanism for overcoming the taphonomic bias that affects micro-animals with delicate, non-biomineralized bodies. Moreover, the newly described animals, among the earliest segmented bilaterians, reveal a high diversity of segmented bilaterians during Ediacaran-Cambrian transition, shedding new light on the evolution of body segmentation.

How myeloid cells evolved from invertebrate to vertebrate is still a mystery. Here we collected circulating hemocytes from a marine invertebrate-Penaeus vannamei via gradient centrifugation and identified prohemocyte, monocytic hemocyte and granulocyte as three major types of cells in shrimp hemolymph by single-cell mRNA sequencing. Additional pseudotime trajectory analysis revealed that shrimp monocytic hemocytes and granulocytes were differentiated from a common progenitor which was similar with that of human myeloid cells. More interestingly, we identified that MH2, a terminal differentiated monocytic hemocyte, was a macrophage-like phagocytic cell which could engulf fluorescein labelled Vibrio parahaemolyticus and shared nine marker genes including inflammasome components Nlrp3 and Casp1 with human macrophage. After that, we compared our classification with traditional shrimp hemocytes classification and found that hyalinocyte included both prohemocyte and monocytic hemocyte while semi-granulocyte included both monocytic hemocyte and granulocyte. In general, our results redefine shrimp hemocyte classification based on functional marker genes and unveil evolutionary trace of myeloid cells in marine invertebrate.

The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel that plays a vital role in water and ion secretion on epithelial surfaces. Loss of function in CFTR causes the life-threatening disease cystic fibrosis (CF). The functionally open state of CFTR has so far eluded detailed structural characterization. Although multiple near-atomic resolution structures of CFTR have been solved under conditions that promote channel opening, they all lack a continuous ion conduction pathway. In recent molecular dynamics (MD) simulations, structural fluctuations of human CFTR in a hydrated lipid bilayer led to the observation of transient Cl- conducting states, but the stability and conduction properties of these putative open states were not established. Here, we conduct massively repeated simulations initiated from these Cl- permeable conformations. Reproducible structural relaxation of the pore leads to a stable open conformation featuring five symmetrically arranged pore-lining helices. Unlike previously reported structures, this novel penta-helical arrangement reproduces experimentally determined properties of the open pore, including a Cl- conductance close to that measured at physiological voltages. Together, our results support the validity of this newly identified pore conformation as a model of the fully open channel. Detailed analysis highlights the role of cationic pore-lining residues in the Cl- permeation mechanism and suggests that the kinks observed in several transmembrane helices play a role in channel gating.

Before Cambrian Stage 3, unambiguous body fossils of segmented bilaterians were rare, severely hampering our understanding of the early history of such important animals. Here we report a variety of microfossils with quintessential features such as paired appendages, dorsoventral and anteroposterior differentiations from the basal Cambrian Fortunian of South China, representing the earliest known three-dimensional body fossils of segmented bilaterians. These fossils were all microbial pseudomorphs built up by secondarily phosphatized bacteria aggregations, testifying microbial pseudomorph could serve as a novel and important pathway to preserve tiny, fragile bilaterian progenitors. This finding unveils a diversified segmented bilaterian world at the very beginning of Cambrian and would arouse a more comprehensive perspective on the early evolution of bilaterian body plans.

PTEN dysfunction, caused by loss of lipid phosphatase activity or deletion, promotes pathologies, cancer, benign tumors, and neurodevelopmental disorders (NDDs). Despite efforts, exactly how the mutations trigger distinct phenotypic outcomes, cancer or NDD, has been puzzling. It has also been unclear how to distinguish between mutations harbored by isoforms, are they cancer or NDDs-related. Here we address both. We demonstrate that PTEN mutations differentially allosterically bias P-loop dynamics and its connection to the catalytic site, affecting catalytic activity. NDD-related mutations are likely to sample conformations present in the wild-type, while sampled conformations sheltering cancer-related hotspots favor catalysis-prone conformations, suggesting that NDD mutations are weaker. Analysis of isoform expression data indicates that if the transcript has NDD-related mutations, alone or in combination with cancer hotspots, there is high prenatal expression. If no mutations within the measured days, low expression levels. Cancer mutations promote stronger signaling and cell proliferation; NDDs are weaker, influencing brain cell differentiation. Further, exon 5 is impacted by NDD or non-NDD mutations, while exon 7 is exclusively impacted by NDD mutations. Our comprehensive conformational and genomic analysis helps discover how same allele mutations can foster different clinical manifestations and uncovers correlations of splicing isoform expression to life expectancy.

Individual neuron or muscle cells express many G protein coupled receptors (GPCRs) for neurotransmitters and neuropeptides. It remains unclear how these cells integrate multiple GPCR signals that all must act through the same few G proteins. We investigated how two serotonin GPCRs, Gq-coupled SER-1 and Gs-coupled SER-7, function together on the C. elegans egg-laying muscles to promote contraction and thus cause eggs to be laid. Using receptor null mutations and cell-specific knockdowns, we found that serotonin signaling through either SER-1/Gq or SER-7/Gs alone does not induce egg laying, but these subthreshold signals can combine to promote egg laying. However, using designer receptors or optogenetics to artificially induce high levels of either Gq signaling or Gs signaling in the muscles was sufficient to induce egg laying. Conversely, knocking down both Gq and Gs in the egg-laying muscle cells induced egg-laying defects stronger than those of a ser-7 ser-1 double knockout. These results suggest that, in the egg-laying muscles, multiple GPCRs for serotonin and other signals each produce weak effects that individually do not result in strong behavioral outcomes. However, they can combine to produce sufficient levels of Gq and Gs signaling to promote muscle activity and egg laying.

The ability to sense and adapt to adverse food conditions is essential for survival across species, but the detailed mechanisms of neuron-digestive crosstalk in food sensing and adaptation remain poorly understood. This study identifies a novel mechanism by which animals detect unfavorable food sources through neurons and initiate a systemic response to shut down digestion, thus safeguarding against potential harm. Specifically, we demonstrate that NSY-1, expressed in AWC neurons, detects Staphylococcus saprophyticus (SS) as an unfavorable food source, prompting the animal to avoid and halt digestion of SS. Upon detection, the animals activate the AWCOFF neural circuit, leading to a systemic digestive shutdown, which is mediated by NSY-1-dependent STR-130. Additionally, NSY-1 mutation triggers the production of insulin peptides, including INS-23, which interact with the DAF-2 receptor to modulate SS digestion and affects the expression of intestinal BCF-1. These findings uncover a crucial survival strategy through neuron-digestive crosstalk, where the NSY-1 pathway in AWC neurons orchestrates food evaluation and initiates digestive shutdown to adapt effectively to harmful food sources.

Homeostatic (anti-Hebbian) forms of synaptic are effective at eliminating "prediction errors" that signal the differences between predicted and actual sensory input. However, such mechanisms appear to preclude the possibility of transmitting the resulting predictions to downstream circuits, severely limiting their utility. Using modeling and recordings from the electrosensory lobe of mormyrid fish, we reveal interactions between axonal and dendritic spikes that support both the learning and transmission of predictions. We find that sensory input modulates the rate of dendritic spikes by adjusting the amplitude of backpropagating axonal action potentials. Homeostatic plasticity counteracts these effects through changes in the underlying membrane potential, allowing the dendritic spike rate to be restored to equilibrium while simultaneously transmitting predictions through modulation of the axonal spike rate. These results reveal how two types of spikes dramatically enhance the computational power of single neurons in support of an ethologically relevant multi-layer computation.

Long-term memory (LTM) requires learning-induced synthesis of new proteins allocated to specific neurons and synapses in a neural circuit. Not all learned information, however, becomes permanent memory. How the brain gates relevant information into LTM remains unclear. In Drosophila adults, a single training session in an olfactory aversive task is not sufficient to induce protein synthesis-dependent LTM. Instead, multiple spaced training sessions are required. Here, we report that initial learning induces neural activity in the early /{beta} subset of Kenyon cells of the mushroom body (MB), and output from these neurons inhibits LTM formation. Specifically in response to spaced training, Schnurri activates CREBB expression which then appears to suppress the inhibitory output from MB. One training session can enhance LTM formation when this inhibitory effect is relieved. We propose that learning-induced protein synthesis and spaced training-induced CREBB act antagonistically to modulate output from early /{beta} MB neurons during LTM formation.

The apoptosome is involved in the mitochondrial pathway of apoptosis, consisting of APAF-1, caspase 9 and cytochrome c, forming a heptamer that activates effector caspases, causing cell death. This protein complex has also been characterized in Drosophila melanogaster (DARK) and Caenorhabditis elegans (CED-4). Here we present an evolutionary guided in silico characterization of the APAF-1/apoptosome. The evolutionary history of the apoptosome was determined, taking the possible orthologs of the APAF-1 version, and executing a protein coevolution and a positive selection analysis, to make structural and functional inferences and identify residues under destabilizing changes, respectively. Results suggests that the APAF-1/apoptosome is not unique to vertebrates, but also some basal invertebrates could possess orthologous copies. New possible versions were also detected in other taxa. Not all insects and other arthropods have the DARK version, just as not all nematodes have the CED-4 version. In the APAF-1 version, amino acid clusters with coevolution signal located in the interior, gave more insights on new potential interactions, allowing us to infer a more detailed model that includes allosterism, of how cytochrome c associates with {beta} propellers during APAF-1 activation, as well as interactions essential for nucleotide exchange, activation of CASP9, the molecular timer and other pathways in mitochondria to induce apoptosis. Residues on the surface under destabilizing changes have guided the protein complex in adaptations necessary for conformational changes, interactions and folding.

Competition in sports does not involve a single solution because individuals aim to behave unpredictably, thereby preventing others from predicting their actions. This study determined how individuals in court net sports tried to control others unpredictable behavior, thereby addressing the gap of the lack of clarity about strategies employed by individuals in competitive situations. We employed a switching hybrid dynamics model, considering external inputs when analyzing individual behaviors. The study shows that skilled individuals, unlike intermediate players, exhibit greater regularity in their behavior, lead others to anticipate this regularity, and employ strategies to disrupt these expectations. This strategy exploits the principles of active human inference, implying that competition involves cooperation. We revealed this by analyzing both human decision-making and behavior in actual matches as discrete and continuous dynamical systems. This strategy helps policymakers adopt a new policy targeting cooperation with competitors, which would increase competitiveness in our daily lives.

Conditional loss and restoration of function are becoming important approaches for investigating gene function. Given that reversible conditional gene knockouts in cells required complicated manipulation, conditional inactivation and reactivation of a gene in primary somatic cells with limited proliferative capacity and in animal models remain difficult to achieve. Here, we first developed a reportable and reversible conditional intronic cassette (ReCOIN), wherein inactivation and reactivation of the gene are mediated via sequential expression of Cre and Flp recombinases, respectively. The expression pattern of the target gene can be monitored by direct visualization. To simply and tightly control temporal expression of the recombinases, on the basis of ReCOIN, we further presented a dual chemical-induced reversible gene knockout system (CIRKO) by insertion of reverse tetracycline transcriptional activator (rtTA) and tetracycline response element (TRE)-controlled Cre and FlpoERT2 recombinases cassettes into Rosa26 and Hipp11 loci of cells, respectively, in which transcription termination of the target gene can be induced at a specific stage in the presence of doxycycline, while gene restoration is achieved in the presence of doxycycline and tamoxifen simultaneously. This system provides a simple, rapid, and flexible gene switch for studying gene function in situ both in vitro and in vivo. Impact statementA novel chemical-induced reversible gene knockout system provides a simple, rapid, and flexible gene switch to facilitate the study of gene function in primary somatic cells in vitro, embryos in vitro or in vivo, and animals in vivo.

Multiciliogenesis is an evolutionarily conserved process required a unique transcriptional program. The mechanisms governing multiciliogenesis are incompletely understood. Here we show that an ancient transcription activator, Edf1, is essential for the multiciliogenesis program. Mice lacking Edf1 exhibit postnatal hydrocephalus and delayed multiciliated cells (MCCs) differentiation. Functional studies reveal that MCCs in Edf1-/- mice have defects in tissue-level polarity and reduced motility. These defects result in abnormal cerebrospinal fluid (CSF) dynamics in vivo, potentially contributing to the development of hydrocephalus. Intriguingly, we found that the expression of pivotal ciliary transcription factors was decreased in Edf1-/- mice. Collectively, our data suggest that Edf1 modulates the multiciliogenesis by regulating the transcription of important ciliary transcription factors required for ciliary gene expression.

Encapsulated ferritins belong to the universally distributed ferritin superfamily, which function as iron detoxification and storage systems. Encapsulated ferritins have a distinct annular structure and must associate with an encapsulin nanocage to form a competent iron store that is capable of holding significantly more iron than classical ferritins. The catalytic mechanism of iron oxidation in the ferritin family is still an open question, due to differences in organization of the ferroxidase catalytic site and secondary metal binding sites vicinal to this. We have previously identified a metal binding site on the inner surface of the Rhodospirillum rubrum encapsulated ferritin at the interface between the two-helix subunits and proximal to the ferroxidase center. Here we present a comprehensive structural and functional study to investigate the functional relevance of this proposed iron entry site by means of enzymatic assays, mass-spectrometry, and X-ray crystallography. We show that catalysis occurs in the ferroxidase center and suggest a dual role for the secondary site, which both serves to attract metal ions to the ferroxidase center and acts as a flow-restricting valve to limit the activity of the ferroxidase center. Moreover, confinement of encapsulated ferritins within the encapsulin nanocage, while enhancing the ability of the encapsulated ferritin to undergo catalysis, does not influence the function of the secondary site.

Emerging evidence demonstrates the important role of circular RNAs (circRNAs) in regulating pathological processes in various diseases including organ fibrosis. Endometrium fibrosis is the leading cause of uterine infertility, but the role of circRNAs in its pathogenesis is largely unknown. Here, we provide the evidence that upregulation of circPTPN12 in endometrial epithelial cells (EECs) of fibrotic endometrium functions as endogenous sponge of miR-21-5p to inhibit miR-21-5p expression and activity, which in turn results in upregulation of {Delta}Np63 to induce the epithelial mesenchymal transition (EMT) of EECs (EEC-EMT). In a mouse model of endometrium fibrosis, circPTPN12 appears to be a cofactor of driving EEC-EMT. Our findings reveal the novel mechanism in the pathogenesis of endometrium fibrosis and the potential therapeutic strategy for endometrium fibrosis via targeting circPTPN12/miR-21-5p/{Delta}Np63 pathway.

Ketamine (KET) and isoflurane (ISO) are two widely used general anesthetics, yet their distinct and shared neurophysiological mechanisms remain elusive. In this study, we conducted a comparative analysis of the effects of KET and ISO on c-Fos expression across the brain, utilizing hierarchical clustering and c-Fos-based functional network analysis to evaluate the responses of individual brain regions to each anesthetic. Our findings reveal that KET activates a wide range of brain regions, notably in the cortical and subcortical nuclei involved in sensory, motor, emotional, and reward processing, with the temporal association areas (TEa) as a strong hub, suggesting a top-down mechanism affecting consciousness by primarily targeting higher-order cortical networks. In contrast, ISO predominantly influences brain regions in the hypothalamus, impacting neuroendocrine control, autonomic function, and homeostasis, with the locus coeruleus (LC) as a connector hub, indicating a bottom-up mechanism in anesthetic-induced unconsciousness. KET and ISO both activate brain areas involved in sensory processing, memory and cognition, reward and motivation, as well as autonomic and homeostatic control, highlighting their shared effects on various neural pathways. In conclusion, our results highlight the distinct but overlapping effects of KET and ISO, enriching our understanding of the mechanisms underlying general anesthesia.

A central principle of synaptic transmission is that action potential-induced presynaptic neurotransmitter release occurs exclusively via Ca2+-dependent secretion (CDS). The discovery and mechanistic investigations of Ca2+-independent but voltage-dependent secretion (CiVDS) have demonstrated that the action potential per se is sufficient to trigger neurotransmission in the somata of primary sensory and sympathetic neurons in mammals. One key question remains, however, whether CiVDS contributes to central synaptic transmission. Here we report, in the central transmission from presynaptic (dorsal root ganglion) to postsynaptic (spinal dorsal horn) neurons, (1) excitatory postsynaptic currents (EPSCs) are mediated by glutamate transmission through both CiVDS (up to 87%) and CDS; (2) CiVDS-EPSCs are independent of extracellular and intracellular Ca2+; (3) CiVDS is >100 times faster than CDS in vesicle recycling with much less short-term depression; (4) the fusion machinery of CiVDS includes Cav2.2 (voltage sensor) and SNARE (fusion pore). Together, an essential component of activity-induced EPSCs is mediated by CiVDS in a central synapse.

Diverse subpopulations of mechanosensory neurons detect different mechanical forces and influence behavior. How these subpopulations connect with central circuits to influence behavior remains an important area of study. We previously discovered a neural circuit that elicits grooming of the Drosophila melanogaster antennae that is activated by an antennal mechanosensory chordotonal organ, the Johnstons organ (JO) (Hampel et al., 2015). Here, we describe anatomically and physiologically distinct JO mechanosensory neuron subpopulations and define how they interface with the circuit that elicits antennal grooming. We show that the subpopulations project to distinct zones in the brain and differ in their responses to mechanical stimulation of the antennae. Each subpopulation elicits grooming through direct synaptic connections with a single interneuron in the circuit, the dendrites of which span the different mechanosensory afferent projection zones. Thus, distinct JO subpopulations converge onto the same neural circuit to elicit a common behavioral response.