Feedback loops shape cellular signals in space and time

Oscillatory Dynamics and Regulatory Mechanisms of the p53-Per2 Network in DNA-Damaged Cells

Circadian rhythm disruptions are linked to increased cancer risk and unfavorable prognosis in patients with cancer, highlighting the critical role of the interplay between the circadian rhythm factor Per2 and the tumor suppressor p53. This brief presents, for the first time, a mathematical model to capture the dynamics of the p53-Per2 network in DNA-damaged cells. The model accurately describes the different stages of the process from unstressed cells to cellular repair and finally to apoptosis as the degree of DNA damage increases. Furthermore, it is found that increasing the inhibition of Per2 by p53 leads to the phase advance of Per2 oscillations, whereas by modulating the inhibition of Mdm2 by Per2, an independent amplitude modulation of active p53 can be achieved, with the range of modulation increasing with the strength of the inhibition. Moreover, the effects of time delays inherent in the transcription, translation, and nuclear translocation of Per2 on the circadian rhythm of DNA-damaged cells are quantitatively investigated by theoretical analyses. It is found that time delays can induce stable oscillations through a supercritical Hopf bifurcation, thereby maintaining the circadian function of DNA-damaged cells and enhancing their DNA-damage repair capacity. This study proposes new insights into cancer prevention and treatment strategies.

Verticillium dahliae effector Vd06254 disrupts cotton defence response by interfering with GhMYC3-GhCCD8-mediated hormonal crosstalk between jasmonic acid and strigolactones

Verticillium dahliae is among the most destructive plant pathogens, posing a significant threat to global cotton production. Cotton plants have developed sophisticated immune networks to inhibit V. dahliae colonization. Ingeniously, V. dahliae employs numerous virulent effectors to surmount plant immune responses. However, the pathogenic mechanisms of V. dahliae-derived effectors remain elusive. In this study, we demonstrate that the Vd06254 effector from V. dahliae disrupts the synergistic interaction between jasmonic acid (JA) and strigolactones (SL), thereby suppressing cotton immunity. Ectopic expression of Vd06254 enhanced susceptibility to both viral and V. dahliae infections in Nicotiana benthamiana and cotton, respectively. Vd06254 directly interacts with the JA pathway regulator GhMYC3. The nuclear localization signal (NLS) was found to be essential for the virulence of Vd06254 and its interaction with GhMYC3. Additionally, overexpression and knockout of GhMYC3 in cotton modified the plant's resistance to V. dahliae. Our findings further reveal that GhMYC3 inhibits the expression of GhCCD8 by binding to its promoter, potentially regulating SL homeostasis in cotton through a negative feedback loop. This repression was enhanced by Vd06254, highlighting its crucial role in modulating cotton immunity and illustrating how V. dahliae effectors reprogram cotton transcription to disrupt this regulatory mechanism.

Catalysis-driven Active Transport Across a Liquid Membrane

Biology has mastered energy transduction, converting energy between various forms, and employing it to drive its vital processes. Central to this is the ability to use chemical energy for the active transport of substances, pumping ions and molecules across hydrophobic lipid membranes between aqueous (sub)cellular compartments. Biology employs information ratchet mechanisms, where kinetic asymmetry in the fuel-to-waste (i. e., substrate-to-product) conversion results in catalysis-driven active transport. Here, we report an artificial system for catalysis-driven active transport across a hydrophobic phase, pumping a maleic acid cargo between aqueous compartments. We employ two strategies to differentiate the conditions in either compartment, showing that active transport can be driven either by adding fuel to a single compartment, or by differentiating the rates of activation and/or hydrolysis when fuel is present in both compartments. We characterize the nonequilibrium system through complete kinetic analysis. Finally, we quantify the energy transduction achieved by the catalysis-driven active transport and establish the emergence of positive and negative feedback mechanisms within the system.

Finding the brakes on the Toxoplasma life cycle

Toxoplasma gondii motility is an all-or-nothing response. Claywell et al. identify negative-feedback loops in cyclic-nucleotide signaling that allow parasites to turn off motility and commit to intracellular replication. Feedback mechanisms and bistability are useful frameworks for describing, modeling, and testing T. gondii motility signaling pathways.

Dynamic Plasma Membrane Topography Linked With Arp2/3 Actin Network Induction During Cell Shape Change

Recent studies show the importance of mesoscale changes to plasma membrane (PM) topography during cell shape change. Local folding and flattening of the cell surface is mechanosensitive, changing in response to both microenvironment structural elements and intracellular cytoskeletal activities. These topography changes elicit local mechanical signaling events that act in conjunction with molecular signal transduction pathways to remodel the cell cortex. Experimental manipulations of local PM curvature show its sufficiency for recruiting Arp2/3 actin network induction pathways. Additionally, studies of diverse cell shape changes-ranging from neutrophil migration to early Drosophila embryo cleavage to neural stem cell asymmetric division-show that local generation of PM folding is linked with local Arp2/3 actin network induction, which then remodels the PM topography during dynamic control of cell structure. These examples are reviewed in detail, together with known and potential causes of PM topography changes, downstream effects, and higher-order feedback.

The putative forkhead transcription factor FhpA is necessary for development, aflatoxin production, and stress response in Aspergillus flavus

Forkhead transcription factors regulate several important biological processes in many eukaryotic species including fungi. Bioinformatic analysis of the Aspergillus flavus genome revealed four putative forkhead transcription factor genes. Genetic disruption of (AFLA_005634), a homolog of the Aspergillus nidulans fhpA/fkhA gene (AN4521), revealed that the fhpA gene is a negative regulator of both asexual spore production and aflatoxin B1 production in A. flavus. Furthermore, disruption of the fhpA gene caused a complete loss of sclerotial formation. Overexpression of the fhpA gene caused A. flavus to become more sensitive to sodium chloride whereas disruption of the fhpA gene did not change the ability of A. flavus to respond to any osmotic stress agent tested. Interestingly, both disruption and overexpression of the fhpA gene led to increases in sensitivity to the oxidative stress agent menadione. Overall, these results suggest that fhpA is an important regulator of morphological and chemical development in addition to stress response in A. flavus.

Phospho-relay feedback loops control egress vs. intracellular development in Toxoplasma gondii

The intracellular parasite Toxoplasma gondii alternates between a motile invasive and a quiescent intracellular replicative form, yet how these transitions are regulated is unknown. A positive feedback loop involving protein kinase G (PKG) and calcium-dependent PKs (CDPKs) controls motility, invasion, and egress by Toxoplasma gondii, while PKA isoform c1 (PKAc1) counteracts this pathway. Shortly after invasion, PKAc1 is activated by cyclic AMP (cAMP) produced by adenylate cyclases, leading to the suppression of the PKG/CDPK pathway. PKAc1 further activates phosphodiesterase 2, which selectively consumes cAMP, thus forming a negative feedback loop, causing transient activation of PKAc1. Perturbation of cyclic GMP (cGMP) vs. calcium demonstrates that PKAc1 acts on targets between guanylate cyclase and calcium release. The combined activation of PKG/CDPKs and inhibition by PKAc1, controlled by a transient negative feedback loop, ensures that the parasite is responsive to environmental signals needed to activate motility while also ensuring periods of long-term stable intracellular growth.

Host metabolism balances microbial regulation of bile acid signalling

Metabolites derived from the intestinal microbiota, including bile acids (BA), extensively modulate vertebrate physiology, including development1, metabolism2-4, immune responses5-7 and cognitive function8. However, to what extent host responses balance the physiological effects of microbiota-derived metabolites remains unclear9,10. Here, using untargeted metabolomics of mouse tissues, we identified a family of BA-methylcysteamine (BA-MCY) conjugates that are abundant in the intestine and dependent on vanin 1 (VNN1), a pantetheinase highly expressed in intestinal tissues. This host-dependent MCY conjugation inverts BA function in the hepatobiliary system. Whereas microbiota-derived free BAs function as agonists of the farnesoid X receptor (FXR) and negatively regulate BA production, BA-MCYs act as potent antagonists of FXR and promote expression of BA biosynthesis genes in vivo. Supplementation with stable-isotope-labelled BA-MCY increased BA production in an FXR-dependent manner, and BA-MCY supplementation in a mouse model of hypercholesteraemia decreased lipid accumulation in the liver, consistent with BA-MCYs acting as intestinal FXR antagonists. The levels of BA-MCY were reduced in microbiota-deficient mice and restored by transplantation of human faecal microbiota. Dietary intervention with inulin fibre further increased levels of both free BAs and BA-MCY levels, indicating that BA-MCY production by the host is regulated by levels of microbiota-derived free BAs. We further show that diverse BA-MCYs are also present in human serum. Together, our results indicate that BA-MCY conjugation by the host balances host-dependent and microbiota-dependent metabolic pathways that regulate FXR-dependent physiology.

SpMS1, a male sterility factor, interacts with SpAP1 to regulate unisexual flower development in dioecious spinach

The emergence of unisexual flower is an important event during plant evolution. The molecular mechanism underlying the formation of unisexual flowers remains unclear in dioecious spinach. In this study, we identified the spinach MALE STERILITY1 gene, SpMS1, which serves as a masculine factor to regulate male fertility and sex reversion. Silencing SpMS1 led to stamen sterility in male flowers and the development of masculine traits in female flowers. Overexpression of SpMS1 in wild-type Arabidopsis resulted in sterile stamens and irregular pollen exine. Notably, ectopic expression of SpMS1 in Arabidopsis ms1 mutants restored pollen viability and flower fertility. Furthermore, our findings demonstrate that SpMS1 interacts with MADS-box transcription factor SpAP1 to regulate unisexual flower development. Thus, SpMS1 exhibits a conserved function in pollen fertility akin to bisexual flowers, while also acting as a key regulator of unisexual flower development in spinach. This study sheds light on the mechanism of sex differentiation in dioecious plants and also provides valuable insights for manipulating male sterility in plant breeding programs.

CaMKK2: bridging the gap between Ca2+ signaling and energy-sensing

Calcium (Ca2+) ions are ubiquitous and indispensable signaling messengers that regulate virtually every cell function. The unique ability of Ca2+ to regulate so many different processes yet cause stimulus specific changes in cell function requires sensing and decoding of Ca2+ signals. Ca2+-sensing proteins, such as calmodulin, decode Ca2+ signals by binding and modifying the function of a diverse range of effector proteins. These effectors include the Ca2+-calmodulin dependent protein kinase kinase-2 (CaMKK2) enzyme, which is the core component of a signaling cascade that plays a key role in important physiological and pathophysiological processes, including brain function and cancer. In addition to its role as a Ca2+ signal decoder, CaMKK2 also serves as an important junction point that connects Ca2+ signaling with energy metabolism. By activating the metabolic regulator AMP-activated protein kinase (AMPK), CaMKK2 integrates Ca2+ signals with cellular energy status, enabling the synchronization of cellular activities regulated by Ca2+ with energy availability. Here, we review the structure, regulation, and function of CaMKK2 and discuss its potential as a treatment target for neurological disorders, metabolic disease, and cancer.

UCLN: Toward the Causal Understanding of Brain Disorders With Temporal Lag Dynamics

Resting-state functional magnetic resonance imaging (rs-fMRI) has emerged as a powerful tool for exploring interactions among brain regions. A growing body of research is actively investigating various computational approaches for estimating causal effects among brain regions. Compared to traditional methods, causal relationship reveals the causal influences among distinct brain regions, offering a deeper understanding of brain network dynamics. However, existing methods either neglect the concept of temporal lag across brain regions or set the temporal lag value to a fixed value. To address this limitation, we propose a Unified Causal and Temporal Lag Network (termed UCLN) that jointly learns the causal effects and temporal lag values among brain regions. Our method effectively captures variations in temporal lag between distant brain regions by avoiding the predefined lag value across the entire brain. The brain networks obtained are directed and weighted graphs, enabling a more comprehensive disentanglement of complex interactions. In addition, we also introduce three guiding mechanisms for efficient brain network modeling. The proposed method outperforms state-of-the-art approaches in classification accuracy on the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Our findings indicate that the method not only achieves superior classification but also successfully identifies crucial neuroimaging biomarkers associated with the disease.

Regulation of Glandular Size and Phytoalexin Biosynthesis by a Negative Feedback Loop in Cotton

Plants have evolved diverse defense mechanisms encompassing physical and chemical barriers. Cotton pigment glands are known for containing various defense metabolites, but the precise regulation of gland size to modulate defense compound levels remains enigmatic. Here, it is discovered that the VQ domain-containing protein JAVL negatively regulates pigment gland size and the biosynthesis of defense compounds, while the MYC2-like transcription factor GoPGF has the opposite effect. Notably, GoPGF directly activates the expression of JAVL, whereas JAVL suppresses GoPGF transcription, establishing a negative feedback loop that maintains the expression homeostasis between GoPGF and JAVL. Furthermore, it is observed that JAVL negatively regulates jasmonate levels by inhibiting the expression of jasmonate biosynthetic genes and interacting with GoPGF to attenuate its activation effects, thereby maintaining homeostatic regulation of jasmonate levels. The increased expression ratio of GoPGF to JAVL leads to enlarged pigment glands and elevated jasmonates and defense compounds, enhancing insect and pathogen resistance in cotton. These findings unveil a new mechanism for regulating gland size and secondary metabolites biosynthesis, providing innovative strategies for strengthening plant defense.

ERMA (TMEM94) is a P-type ATPase transporter for Mg2+ uptake in the endoplasmic reticulum

Intracellular Mg2+ (iMg2+) is bound with phosphometabolites, nucleic acids, and proteins in eukaryotes. Little is known about the intracellular compartmentalization and molecular details of Mg2+ transport into/from cellular organelles such as the endoplasmic reticulum (ER). We found that the ER is a major iMg2+ compartment refilled by a largely uncharacterized ER-localized protein, TMEM94. Conventional and AlphaFold2 predictions suggest that ERMA (TMEM94) is a multi-pass transmembrane protein with large cytosolic headpiece actuator, nucleotide, and phosphorylation domains, analogous to P-type ATPases. However, ERMA uniquely combines a P-type ATPase domain and a GMN motif for ERMg2+ uptake. Experiments reveal that a tyrosine residue is crucial for Mg2+ binding and activity in a mechanism conserved in both prokaryotic (mgtB and mgtA) and eukaryotic Mg2+ ATPases. Cardiac dysfunction by haploinsufficiency, abnormal Ca2+ cycling in mouse Erma+/- cardiomyocytes, and ERMA mRNA silencing in human iPSC-cardiomyocytes collectively define ERMA as an essential component of ERMg2+ uptake in eukaryotes.

Phosphorylation of the compartmentalized PKA substrate TAF15 regulates RNA-protein interactions

Spatiotemporal-controlled second messengers alter molecular interactions of central signaling nodes for ensuring physiological signal transmission. One prototypical second messenger molecule which modulates kinase signal transmission is the cyclic-adenosine monophosphate (cAMP). The main proteinogenic cellular effectors of cAMP are compartmentalized protein kinase A (PKA) complexes. Their cell-type specific compositions precisely coordinate substrate phosphorylation and proper signal propagation which is indispensable for numerous cell-type specific functions. Here we present evidence that TAF15, which is implicated in the etiology of amyotrophic lateral sclerosis, represents a novel nuclear PKA substrate. In cross-linking and immunoprecipitation experiments (iCLIP) we showed that TAF15 phosphorylation alters the binding to target transcripts related to mRNA maturation, splicing and protein-binding related functions. TAF15 appears to be one of multiple PKA substrates that undergo RNA-binding dynamics upon phosphorylation. We observed that the activation of the cAMP-PKA signaling axis caused a change in the composition of a collection of RNA species that interact with TAF15. This observation appears to be a broader principle in the regulation of molecular interactions, as we identified a significant enrichment of RNA-binding proteins within endogenous PKA complexes. We assume that phosphorylation of RNA-binding domains adds another layer of regulation to binary protein-RNAs interactions with consequences to RNA features including binding specificities, localization, abundance and composition.

Towards a Light-mediated Gene Therapy for the Eye using Caged Ethinylestradiol and the Inducible Cre/lox System

Increasingly, retinal pathologies are being treated with virus-mediated gene therapies. To be able to target viral transgene expression specifically to the pathological regions of the retina with light, we established an in vivo photoactivated gene expression paradigm for retinal tissue. Based on the inducible Cre/lox system, we discovered that ethinylestradiol is a suitable alternative to Tamoxifen as ethinylestradiol is more amenable to modification with photosensitive protecting compounds, i.e., "caging." Identification of ethinylestradiol as a ligand for the mutated human estradiol receptor was supported by in silico binding studies showing the reduced binding of caged ethinylestradiol. Caged ethinylestradiol was injected into the eyes of double transgenic GFAP-CreERT2 mice with a Cre-dependent tdTomato reporter transgene followed by irradiation with light of 450 nm. Photoactivation significantly increased retinal tdTomato expression compared to controls. We thus demonstrated a first step towards the development of a targeted, light-mediated gene therapy for the eyes.

SHR and SCR coordinate root patterning and growth early in the cell cycle

Precise control of cell division is essential for proper patterning and growth during the development of multicellular organisms. Coordination of formative divisions that generate new tissue patterns with proliferative divisions that promote growth is poorly understood. SHORTROOT (SHR) and SCARECROW (SCR) are transcription factors that are required for formative divisions in the stem cell niche of Arabidopsis roots1,2. Here we show that levels of SHR and SCR early in the cell cycle determine the orientation of the division plane, resulting in either formative or proliferative cell division. We used 4D quantitative, long-term and frequent (every 15 min for up to 48 h) light sheet and confocal microscopy to probe the dynamics of SHR and SCR in tandem within single cells of living roots. Directly controlling their dynamics with an SHR induction system enabled us to challenge an existing bistable model3 of the SHR-SCR gene-regulatory network and to identify key features that are essential for rescue of formative divisions in shr mutants. SHR and SCR kinetics do not align with the expected behaviour of a bistable system, and only low transient levels, present early in the cell cycle, are required for formative divisions. These results reveal an uncharacterized mechanism by which developmental regulators directly coordinate patterning and growth.

A critical signal for phenotype transition driven by negative feedback loops

The biological rhythms governed by negative feedback loops have undergone extensive investigation. However, developing reliable and versatile warning signals to predict periodic fluctuations in physiological processes and behaviors associated with these rhythms remains a challenge. Here, we monitored the heart rate and tracked ovulation dates of 91 fertile women. The finding strongly links the velocity (derivative) of heart rate with ovulation in menstrual cycles, providing a predictive warning signal. Similarly, an analysis of calcium signaling in the suprachiasmatic nucleus (SCN) of mice reveals that the maximum velocity of rising calcium signal aligns with locomotor activity offsets. To demonstrate the generality of derivative-transitions link, numerical simulations using a negative feedback loop model were conducted. Statistical analysis indicated that over 90% of the oscillations exhibited a correlation between maximum velocity and transition points. Consequently, the maximum velocity derived from oscillatory curves holds significant potential as an early warning signal for critical transitions.

MICA: a multi-omics method to predict gene regulatory networks in early human embryos

Recent advances in single-cell omics have transformed characterisation of cell types in challenging-to-study biological contexts. In contexts with limited single-cell samples, such as the early human embryo inference of transcription factor-gene regulatory network (GRN) interactions is especially difficult. Here, we assessed application of different linear or non-linear GRN predictions to single-cell simulated and human embryo transcriptome datasets. We also compared how expression normalisation impacts on GRN predictions, finding that transcripts per million reads outperformed alternative methods. GRN inferences were more reproducible using a non-linear method based on mutual information (MI) applied to single-cell transcriptome datasets refined with chromatin accessibility (CA) (called MICA), compared with alternative network prediction methods tested. MICA captures complex non-monotonic dependencies and feedback loops. Using MICA, we generated the first GRN inferences in early human development. MICA predicted co-localisation of the AP-1 transcription factor subunit proto-oncogene JUND and the TFAP2C transcription factor AP-2γ in early human embryos. Overall, our comparative analysis of GRN prediction methods defines a pipeline that can be applied to single-cell multi-omics datasets in especially challenging contexts to infer interactions between transcription factor expression and target gene regulation.

Mechanistic Model-Driven Biodesign in Mammalian Synthetic Biology

Mathematical modeling plays a vital role in mammalian synthetic biology by providing a framework to design and optimize design circuits and engineered bioprocesses, predict their behavior, and guide experimental design. Here, we review recent models used in the literature, considering mathematical frameworks at the molecular, cellular, and system levels. We report key challenges in the field and discuss opportunities for genome-scale models, machine learning, and cybergenetics to expand the capabilities of model-driven mammalian cell biodesign.

Single-neuron mechanical perturbation evokes calcium plateaus that excite and modulate the network

Mechanical stimulation is a promising means to non-invasively excite and modulate neuronal networks with a high spatial resolution. Despite the thorough characterization of the initiation mechanism, whether or how mechanical responses disperse into non-target areas remains to be discovered. Our in vitro study demonstrates that a single-neuron deformation evokes responses that propagate to about a third of the untouched neighbors. The responses develop via calcium influx through mechanosensitive channels and regeneratively propagate through the neuronal ensemble via gap junctions. Although independent of action potentials and synapses, mechanical responses reliably evoke membrane depolarizations capable of inducing action potentials both in the target and neighbors. Finally, we show that mechanical stimulation transiently potentiates the responding assembly for further inputs, as both gain and excitability are transiently increased exclusively in neurons that respond to a neighbor's mechanical stimulation. The findings indicate a biological component affecting the spatial resolution of mechanostimulation and point to a cross-talk in broad-network mechanical stimulations. Since giga-seal formation in patch-clamp produces a similar mechanical stimulus on the neuron, our findings inform which neuroscientific questions could be reliably tackled with patch-clamp and what recovery post-gigaseal formation is necessary.

A bifunctional kinase-phosphatase module balances mitotic checkpoint strength and kinetochore-microtubule attachment stability

Two major mechanisms safeguard genome stability during mitosis: the mitotic checkpoint delays mitosis until all chromosomes have attached to microtubules, and the kinetochore-microtubule error-correction pathway keeps this attachment process free from errors. We demonstrate here that the optimal strength and dynamics of these processes are set by a kinase-phosphatase pair (PLK1-PP2A) that engage in negative feedback from adjacent phospho-binding motifs on the BUB complex. Uncoupling this feedback to skew the balance towards PLK1 produces a strong checkpoint, hypostable microtubule attachments and mitotic delays. Conversely, skewing the balance towards PP2A causes a weak checkpoint, hyperstable microtubule attachments and chromosome segregation errors. These phenotypes are associated with altered BUB complex recruitment to KNL1-MELT motifs, implicating PLK1-PP2A in controlling auto-amplification of MELT phosphorylation. In support, KNL1-BUB disassembly becomes contingent on PLK1 inhibition when KNL1 is engineered to contain excess MELT motifs. This elevates BUB-PLK1/PP2A complex levels on metaphase kinetochores, stabilises kinetochore-microtubule attachments, induces chromosome segregation defects and prevents KNL1-BUB disassembly at anaphase. Together, these data demonstrate how a bifunctional PLK1/PP2A module has evolved together with the MELT motifs to optimise BUB complex dynamics and ensure accurate chromosome segregation.

MRPS6 modulates glucose-stimulated insulin secretion in mouse islet cells through mitochondrial unfolded protein response

Lack of efficient insulin secretion from the pancreas can lead to impaired glucose tolerance (IGT), prediabetes, and diabetes. We have previously identified two IGT-associated single nucleotide polymorphisms (SNPs) rs62212118 and rs13052524 located at two overlapping genes: MRPS6 and SLC5A3. In this study, we show that MRPS6 but not SLC5A3 regulates glucose-stimulated insulin secretion (GSIS) in primary human β-cell and a mouse pancreatic insulinoma β-cell line. Data mining and biochemical studies reveal that MRPS6 is positively regulated by the mitochondrial unfolded protein response (UPRmt), but feedback inhibits UPRmt. Disruption of such feedback by MRPS6 knockdown causes UPRmt hyperactivation in high glucose conditions, hence elevated ROS levels, increased apoptosis, and impaired GSIS. Conversely, MRPS6 overexpression reduces UPRmt, mitigates high glucose-induced ROS levels and apoptosis, and enhances GSIS in an ATF5-dependent manner. Consistently, UPRmt up-regulation or down-regulation by modulating ATF5 expression is sufficient to decrease or increase GSIS. The negative role of UPRmt in GSIS is further supported by analysis of public transcriptomic data from murine islets. In all, our studies identify MRPS6 and UPRmt as novel modulators of GSIS and apoptosis in β-cells, contributing to our understanding of the molecular and cellular mechanisms of IGT, prediabetes, and diabetes.

Cas phosphorylation regulates focal adhesion assembly

Integrin-mediated cell attachment rapidly induces tyrosine kinase signaling. Despite years of research, the role of this signaling in integrin activation and focal adhesion assembly is unclear. We provide evidence that the Src-family kinase (SFK) substrate Cas (Crk-associated substrate, p130Cas, BCAR1) is phosphorylated and associated with its Crk/CrkL effectors in clusters that are precursors of focal adhesions. The initial phospho-Cas clusters contain integrin β1 in its inactive, bent closed, conformation. Later, phospho-Cas and total Cas levels decrease as integrin β1 is activated and core focal adhesion proteins including vinculin, talin, kindlin, and paxillin are recruited. Cas is required for cell spreading and focal adhesion assembly in epithelial and fibroblast cells on collagen and fibronectin. Cas cluster formation requires Cas, Crk/CrkL, SFKs, and Rac1 but not vinculin. Rac1 provides positive feedback onto Cas through reactive oxygen, opposed by negative feedback from the ubiquitin proteasome system. The results suggest a two-step model for focal adhesion assembly in which clusters of phospho-Cas, effectors and inactive integrin β1 grow through positive feedback prior to integrin activation and recruitment of core focal adhesion proteins.

Feedback circuits are numerous in embryonic gene regulatory networks and offer a stabilizing influence on evolution of those networks

The developmental gene regulatory networks (dGRNs) of two sea urchin species, Lytechinus variegatus (Lv) and Strongylocentrotus purpuratus (Sp), have remained remarkably similar despite about 50 million years since a common ancestor. Hundreds of parallel experimental perturbations of transcription factors with similar outcomes support this conclusion. A recent scRNA-seq analysis suggested that the earliest expression of several genes within the dGRNs differs between Lv and Sp. Here, we present a careful reanalysis of the dGRNs in these two species, paying close attention to timing of first expression. We find that initial expression of genes critical for cell fate specification occurs during several compressed time periods in both species. Previously unrecognized feedback circuits are inferred from the temporally corrected dGRNs. Although many of these feedbacks differ in location within the respective GRNs, the overall number is similar between species. We identify several prominent differences in timing of first expression for key developmental regulatory genes; comparison with a third species indicates that these heterochronies likely originated in an unbiased manner with respect to embryonic cell lineage and evolutionary branch. Together, these results suggest that interactions can evolve even within highly conserved dGRNs and that feedback circuits may buffer the effects of heterochronies in the expression of key regulatory genes.

CHOP promotes coelomocyte apoptosis through p38-MAPK pathway in Vibrio splendidus-challenged sea cucumber Apostichopus japonicus

CCAAT/enhancer-binding protein (C/EBP) homologous protein (CHOP) belongs to the C/EBP family of transcription factors that has been proven to regulate apoptosis in many vertebrate species. However, the functional role of CHOP in invertebrates is largely unknown. In this paper, the open reading frame of CHOP was cloned and characterized in the sea cucumber Apostichopus japonicus (AjCHOP). The deuced amino acid of AjCHOP shared a conserved RTP801_C domain from 63 to 171 aa. Phylogenetic analysis indicated that AjCHOP clustered with CHOPs from Lytechinus variegatus and Strongylocentrotus purpuratus. To confirm the immune function of AjCHOP, the time-course expression profiles of AjCHOP were investigated, and the findings revealed AjCHOP was significantly induced in coelomocytes at mRNA and protein levels after Vibro splendidus challenge. Furthermore, knockdown of AjCHOP in coelomocyes by siRNA transfection significantly decreased the apoptosis level induced by V. splendidus. Mechanically, AjCHOP-mediated apoptosis was dependent on the activation of p38-MAPK pathway but not JNK/ERK-MAPK. Overall, our results supported that V. splendidus triggers apoptosis among the coelomocytes, whereas AjCHOP mediates through the p38-MAPK pathway in A. japonicus.

Dynamic model assuming mutually inhibitory biomarkers of frailty suggests bistability with contrasting mobility phenotypes

Bistability is a fundamental biological phenomenon associated with "switch-like" behavior reflecting the capacity of a system to exist in either of two stable states. It plays a role in gene regulation, cell fate switch, signal transduction and cell oscillation, with relevance for cognition, hearing, vision, sleep, gait and voiding. Here we consider a potential role for bistability in the existence of specific frailty states or phenotypes as part of disablement pathways. We use mathematical modeling with two frailty biomarkers (insulin growth factor-1, IGF-1 and interleukin-6, IL-6), which mutually inhibit each other. In our model, we demonstrate that small variations around critical IGF-1 or IL-6 blood levels lead to strikingly different mobility outcomes. We employ deterministic modeling of mobility outcomes, calculating the average trends in population health. Our model predicts the bistability of clinical outcomes: the deterministically-computed likelihood of an individual remaining mobile, becoming less mobile, or dying over time either increases to almost 100% or decreases to almost zero. Contrary to statistical models that attempt to estimate the likelihood of final outcomes based on probabilities and correlations, our model predicts functional outcomes over time based on specific hypothesized molecular mechanisms. Instead of estimating probabilities based on stochastic distributions and arbitrary priors, we deterministically simulate model outcomes over a wide range of physiological parameter values within experimentally derived boundaries. Our study is "a proof of principle" as it is based on a major assumption about mutual inhibition of pathways that is oversimplified. However, by making such an assumption, interesting effects can be described qualitatively. As our understanding of molecular mechanisms involved in aging deepens, we believe that such modeling will not only lead to more accurate predictions, but also help move the field from using mostly studies of associations to mechanistically guided approaches.

Multiomics reveals glutathione metabolism as a driver of bimodality during stem cell aging

With age, skeletal muscle stem cells (MuSCs) activate out of quiescence more slowly and with increased death, leading to defective muscle repair. To explore the molecular underpinnings of these defects, we combined multiomics, single-cell measurements, and functional testing of MuSCs from young and old mice. The multiomics approach allowed us to assess which changes are causal, which are compensatory, and which are simply correlative. We identified glutathione (GSH) metabolism as perturbed in old MuSCs, with both causal and compensatory components. Contrary to young MuSCs, old MuSCs exhibit a population dichotomy composed of GSHhigh cells (comparable with young MuSCs) and GSHlow cells with impaired functionality. Mechanistically, we show that antagonism between NRF2 and NF-κB maintains this bimodality. Experimental manipulation of GSH levels altered the functional dichotomy of aged MuSCs. These findings identify a novel mechanism of stem cell aging and highlight glutathione metabolism as an accessible target for reversing MuSC aging.

The context-dependent role of transforming growth factor-β/miR-378a-3p/connective tissue growth factor in vascular calcification: a translational study

BACKGROUND

Vascular calcification (VC) constitutes an important vascular pathology with prognostic importance. The pathogenic role of transforming growth factor-β (TGF-β) in VC remains unclear, with heterogeneous findings that we aimed to evaluate using experimental models and clinical specimens.

METHODS

Two approaches, exogenous administration and endogenous expression upon osteogenic media (OM) exposure, were adopted. Aortic smooth muscle cells (ASMCs) were subjected to TGF-β1 alone, OM alone, or both, with calcification severity determined. We evaluated miR-378a-3p and TGF-β1 effectors (connective tissue growth factor; CTGF) at different periods of calcification. Results were validated in an ex vivo model and further in sera from older adults without or with severe aortic arch calcification.

RESULTS

TGF-β1 treatment induced a significant dose-responsive increase in ASMC calcification without or with OM at the mature but not early or mid-term VC period. On the other hand, OM alone induced VC accompanied by suppressed TGF-β1 expressions over time; this phenomenon paralleled the declining miR-378a-3p and CTGF expressions since early VC. TGF-β1 treatment led to an upregulation of CTGF since early VC but not miR-378a-3p until mid-term VC, while miR-378a-3p overexpression suppressed CTGF expressions without altering TGF-β1 levels. The OM-induced down-regulation of TGF-β1 and CTGF was also observed in the ex vivo models, with compatible results identified from human sera.

CONCLUSIONS

We showed that TGF-β1 played a context-dependent role in VC, involving a time-dependent self-regulatory loop of TGF-β1/miR-378a-3p/CTGF signaling. Our findings may assist subsequent studies in devising potential therapeutics against VC.

Buffered EGFR signaling regulated by spitz-to-argos expression ratio is a critical factor for patterning the Drosophila eye

The Epidermal Growth Factor Receptor (EGFR) signaling pathway plays a critical role in regulating tissue patterning. Drosophila EGFR signaling achieves specificity through multiple ligands and feedback loops to finetune signaling outcomes spatiotemporally. The principal Drosophila EGF ligand, cleaved Spitz, and the negative feedback regulator, Argos are diffusible and can act both in a cell autonomous and non-autonomous manner. The expression dose of Spitz and Argos early in photoreceptor cell fate determination has been shown to be critical in patterning the Drosophila eye, but the exact identity of the cells expressing these genes in the larval eye disc has been elusive. Using single molecule RNA Fluorescence in situ Hybridization (smFISH), we reveal an intriguing differential expression of spitz and argos mRNA in the Drosophila third instar eye imaginal disc indicative of directional non-autonomous EGFR signaling. By genetically tuning EGFR signaling, we show that rather than absolute levels of expression, the ratio of expression of spitz-to-argos to be a critical determinant of the final adult eye phenotype. Proximate effects on EGFR signaling in terms of cell cycle and differentiation markers are affected differently in the different perturbations. Proper ommatidial patterning is robust to thresholds around a tightly maintained wildtype spitz-to-argos ratio, and breaks down beyond. This provides a powerful instance of developmental buffering against gene expression fluctuations.

Fabricating a multi-component microfluidic system for exercise-induced endothelial cell mechanobiology guided by hemodynamic similarity

Generating precise in vivo arterial endothelial hemodynamic microenvironments using microfluidics is essential for exploring endothelial mechanobiology. However, a hemodynamic principle guiding the fabrication of microfluidic systems is still lacking. We propose a hemodynamic similarity principle for quickly obtaining the input impedance of the microfluidic system in vitro derived from that of the arterial system in vivo to precisely generate the desired endothelial hemodynamic microenvironments. First, based on the equivalent of blood pressure (BP) and wall shear stress (WSS) waveforms, we establish a hemodynamic similarity principle to efficiently map the input impedance in vivo to that in vitro, after which the multi-component microfluidic system is designed and fabricated using a lumped parameter hemodynamic model. Second, numerical simulation and experimental studies are carried out to validate the performance of the designed microfluidic system. Finally, the intracellular Ca²⁺ responses after exposure to different intensities of exercise-induced BP and WSS waveforms are measured to improve the reliability of EC mechanobiological studies using the designed microfluidic system. Overall, the proposed hemodynamic similarity principle can guide the fabrication of a multi-component microfluidic system for endothelial cell mechanobiology.

Design principles of improving the dose-response alignment in coupled GTPase switches

"Dose-response alignment" (DoRA), where the downstream response of cellular signaling pathways closely matches the fraction of activated receptor, can improve the fidelity of dose information transmission. The negative feedback has been experimentally identified as a key component for DoRA, but numerical simulations indicate that negative feedback is not sufficient to achieve perfect DoRA, i.e., perfect match of downstream response and receptor activation level. Thus a natural question is whether there exist design principles for signaling motifs within only negative feedback loops to improve DoRA to near-perfect DoRA. Here, we investigated several model formulations of an experimentally validated circuit that couples two molecular switches-mGTPase (monomeric GTPase) and tGTPase (heterotrimeric GTPases) - with negative feedback loops. In the absence of feedback, the low and intermediate mGTPase activation levels benefit DoRA in mass action and Hill-function models, respectively. Adding negative feedback has versatile roles on DoRA: it may impair DoRA in the mass action model with low mGTPase activation level and Hill-function model with intermediate mGTPase activation level; in other cases, i.e., the mass action model with a high mGTPase activation level or the Hill-function model with a non-intermediate mGTPase activation level, it improves DoRA. Furthermore, we found that DoRA in a longer cascade (i.e., tGTPase) can be obtained using Hill-function kinetics under certain conditions. In summary, we show how ranges of activity of mGTPase, reaction kinetics, the negative feedback, and the cascade length affect DoRA. This work provides a framework for improving the DoRA performance in signaling motifs with negative feedback.

Chemically Driven Multimodal Locomotion of Active, Flexible Sheets

The inhibitor-promoter feedback loop is a vital component in regulatory pathways that controls functionality in living systems. In this loop, the production of chemical A at one site promotes the production of chemical B at another site, but B inhibits the production of A. In solution, differences in the volumes of the reactants and products of this reaction can generate buoyancy-driven fluid flows, which will deform neighboring soft material. To probe the intrinsic interrelationship among chemistry, hydrodynamics, and fluid-structure interactions, we model a bio-inspired system where a flexible sheet immersed in solution encompasses two spatially separated catalytic patches, which drive the A-B inhibitor-promotor reaction. The convective rolls of fluid generated above the patches can circulate inward or outward depending on the chemical environment. Within the regime displaying chemical oscillations, the dynamic fluid-structure interactions morph the shape of the sheet to periodically "fly", "crawl", or "swim" along the bottom of the confining chamber, revealing an intimate coupling between form and function in this system. The oscillations in the sheet's motion in turn affect the chemical oscillations in the solution. In the regime with non-oscillatory chemistry, the induced flow still morphs the shape of the sheet, but now, the fluid simply translates the sheet along the length of the chamber. The findings reveal the potential for enzymatic reactions in the body to generate hydrodynamic behavior that modifies the shape of neighboring soft tissue, which in turn modifies both the fluid dynamics and the enzymatic reaction. The findings indicate that this non-linear dynamic behavior can be playing a critical role in the functioning of regulatory pathways in living systems.

Stochastic Fluctuations Drive Non-genetic Evolution of Proliferation in Clonal Cancer Cell Populations

Evolutionary dynamics allows us to understand many changes happening in a broad variety of biological systems, ranging from individuals to complete ecosystems. It is also behind a number of remarkable organizational changes that happen during the natural history of cancers. These reflect tumour heterogeneity, which is present at all cellular levels, including the genome, proteome and phenome, shaping its development and interrelation with its environment. An intriguing observation in different cohorts of oncological patients is that tumours exhibit an increased proliferation as the disease progresses, while the timescales involved are apparently too short for the fixation of sufficient driver mutations to promote explosive growth. Here, we discuss how phenotypic plasticity, emerging from a single genotype, may play a key role and provide a ground for a continuous acceleration of the proliferation rate of clonal populations with time. We address this question by combining the analysis of real-time growth of non-small-cell lung carcinoma cells (N-H460) together with stochastic and deterministic mathematical models that capture proliferation trait heterogeneity in clonal populations to elucidate the contribution of phenotypic transitions on tumour growth dynamics.

Neomycin Interferes with Phosphatidylinositol-4,5-Bisphosphate at the Yeast Plasma Membrane and Activates the Cell Wall Integrity Pathway

The cell wall integrity pathway (CWI) is a MAPK-mediated signaling route essential for yeast cell response to cell wall damage, regulating distinct aspects of fungal physiology. We have recently proven that the incorporation of a genetic circuit that operates as a signal amplifier into this pathway allows for the identification of novel elements involved in CWI signaling. Here, we show that the strong growth inhibition triggered by pathway hyperactivation in cells carrying the “Integrity Pathway Activation Circuit” (IPAC) also allows the easy identification of new stimuli. By using the IPAC, we have found various chemical agents that activate the CWI pathway, including the aminoglycoside neomycin. Cells lacking key components of this pathway are sensitive to this antibiotic, due to the disruption of signaling upon neomycin stimulation. Neomycin reduces both phosphatidylinositol-4,5-bisphosphate (PIP₂) availability at the plasma membrane and myriocin-induced TORC2-dependent Ypk1 phosphorylation, suggesting a strong interference with plasma membrane homeostasis, specifically with PIP₂. The neomycin-induced transcriptional profile involves not only genes related to stress and cell wall biogenesis, but also to amino acid metabolism, reflecting the action of this antibiotic on the yeast ribosome.

Signal Transduction Network Principles Underlying Bacterial Collective Behaviors

Bacteria orchestrate collective behaviors and accomplish feats that would be unsuccessful if carried out by a lone bacterium. Processes undertaken by groups of bacteria include bioluminescence, biofilm formation, virulence factor production, and release of public goods that are shared by the community. Collective behaviors are controlled by signal transduction networks that integrate sensory information and transduce the information internally. Here, we discuss network features and mechanisms that, even in the face of dramatically changing environments, drive precise execution of bacterial group behaviors. We focus on representative quorum-sensing and second-messenger cyclic dimeric GMP (c-di-GMP) signal relays. We highlight ligand specificity versus sensitivity, how small-molecule ligands drive discrimination of kin versus nonkin, signal integration mechanisms, single-input sensory systems versus coincidence detectors, and tuning of input-output dynamics via feedback regulation. We summarize how different features of signal transduction systems allow groups of bacteria to successfully interpret and collectively react to dynamically changing environments.

Single-cell RNA sequencing uncovers the nuclear decoy lincRNA PIRAT as a regulator of systemic monocyte immunity during COVID-19

SARS-CoV-2–infected patients often display characteristic changes in the production of immune mediators that trigger life-threatening courses of COVID-19. The underlying molecular mechanisms are not yet fully understood. Here, we used single-cell RNA sequencing to investigate the involvement of the emerging class of long regulatory RNA in COVID-19. Our data reveal that a previously unknown regulatory RNA in the nucleus of immune cells is altered after SARS-CoV-2 infection. The degradation of this RNA removes a natural brake on the production of critical immune mediators that can promote the development of severe COVID-19. We believe that therapeutic intervention in this nuclear RNA circuit could counteract the overproduction of disease-causing immune mediators and protect against severe COVID-19.

The systemic immune response to viral infection is shaped by master transcription factors, such as NF-κB, STAT1, or PU.1. Although long noncoding RNAs (lncRNAs) have been suggested as important regulators of transcription factor activity, their contributions to the systemic immunopathologies observed during SARS-CoV-2 infection have remained unknown. Here, we employed a targeted single-cell RNA sequencing approach to reveal lncRNAs differentially expressed in blood leukocytes during severe COVID-19. Our results uncover the lncRNA PIRAT (PU.1-induced regulator of alarmin transcription) as a major PU.1 feedback-regulator in monocytes, governing the production of the alarmins S100A8/A9, key drivers of COVID-19 pathogenesis. Knockout and transgene expression, combined with chromatin-occupancy profiling, characterized PIRAT as a nuclear decoy RNA, keeping PU.1 from binding to alarmin promoters and promoting its binding to pseudogenes in naïve monocytes. NF-κB–dependent PIRAT down-regulation during COVID-19 consequently releases a transcriptional brake, fueling alarmin production. Alarmin expression is additionally enhanced by the up-regulation of the lncRNA LUCAT1, which promotes NF-κB–dependent gene expression at the expense of targets of the JAK-STAT pathway. Our results suggest a major role of nuclear noncoding RNA networks in systemic antiviral responses to SARS-CoV-2 in humans.

The need for speed: Migratory cells in tight spaces boost their molecular clock

Cells migrating in spatial confinement exhibit higher intracellular calcium levels, which increases the oscillation frequency of a "molecular clock" that synchronizes guanine nucleotide exchange factor GEF-H1 and microtubule polymerization for more frequent bursts of speed.

FL-DTD: an integrated pipeline to predict the drug interacting targets by feedback loop-based network analysis

Drug target discovery is an essential step to reveal the mechanism of action (MoA) underlying drug therapeutic effects and/or side effects. Most of the approaches are usually labor-intensive while unable to identify the tissue-specific interacting targets, especially the targets with weaker drug binding affinity. In this work, we proposed an integrated pipeline, FL-DTD, to predict the drug interacting targets of novel compounds in a tissue-specific manner. This method was built based on a hypothesis that cells under a status of homeostasis would take responses to drug perturbation by activating feedback loops. Therefore, the drug interacting targets can be predicted by analyzing the network responses after drug perturbation. We evaluated this method using the expression data of estrogen stimulation, gene manipulation and drug perturbation and validated its good performance to identify the annotated drug targets. Using STAT3 as a target protein, we applied this method to drug perturbation data of 500 natural compounds and predicted five compounds with STAT3 interacting activities. Experimental assay validated the STAT3-interacting activities of four compounds. Overall, our evaluation suggests that FL-DTD predicts the drug interacting targets with good accuracy and can be used for drug target discovery.

Human papillomavirus targets the YAP1-LATS2 feedback loop to drive cervical cancer development

Human papillomavirus (HPV) infection is very common in sexually active women, but cervical cancer only develops in a small fraction of HPV-infected women, suggesting that unknown intrinsic factors associated with the unique genetic/genomic background of the high-risk population play a critical role in cervical carcinogenesis. Although our previous studies have identified the hyperactivated YAP1 oncogene as a critical contributor to cervical cancer, the molecular mechanism by which YAP1 drives cervical cancer is unknown. In the present study, we found that although the hyperactivated YAP1 caused a malignant transformation of immortalized cervical epithelial cells, it induced cellular senescence in cultures of primary human cervical epithelial cells (HCvECs). However, the hyperactivated YAP1 induced malignant transformation of HCvECs in the presence of high-risk HPV E6/E7 proteins, suggesting that the hyperactivated YAP1 synergizes with HPV to initiate cervical cancer development. Our mechanistic studies demonstrate that YAP1, via up-regulating LATS2, formed a YAP1-LATS2 negative feedback loop in cervical epithelial cells to maintain homeostasis of cervical tissue. Intriguingly, we found that high-risk HPV targets LATS2 to disrupt the feedback loop leading to the malignant transformation of cervical epithelial cells. Finally, we report that mitomycin C, an FDA-approved drug that could upregulate LATS2 and drive cellular senescence in vitro and in vivo, induced a regression of cervical cancer in a pre-clinial animal model. Thus, high-risk HPV targeting the YAP1-LATS2 feedback loop represents a new mechanism of cervical cancer development.

Integrating knowledge and omics to decipher mechanisms via large-scale models of signaling networks

Signal transduction governs cellular behavior, and its dysregulation often leads to human disease. To understand this process, we can use network models based on prior knowledge, where nodes represent biomolecules, usually proteins, and edges indicate interactions between them. Several computational methods combine untargeted omics data with prior knowledge to estimate the state of signaling networks in specific biological scenarios. Here, we review, compare, and classify recent network approaches according to their characteristics in terms of input omics data, prior knowledge and underlying methodologies. We highlight existing challenges in the field, such as the general lack of ground truth and the limitations of prior knowledge. We also point out new omics developments that may have a profound impact, such as single-cell proteomics or large-scale profiling of protein conformational changes. We provide both an introduction for interested users seeking strategies to study cell signaling on a large scale and an update for seasoned modelers.

A mechanism for exocyst-mediated tethering via Arf6 and PIP5K1C-driven phosphoinositide conversion

Polarized trafficking is necessary for the development of eukaryotes and is regulated by a conserved molecular machinery. Late steps of cargo delivery are mediated by the exocyst complex, which integrates lipid and protein components to tether vesicles for plasma membrane fusion. However, the molecular mechanisms of this process are poorly defined. Here, we reconstitute functional octameric human exocyst, demonstrating the basis for holocomplex coalescence and biochemically stable subcomplexes. We determine that each subcomplex independently binds to phosphatidylinositol 4,5-bisphosphate (PI(4,5)P₂), which is minimally sufficient for membrane tethering. Through reconstitution and epithelial cell biology experiments, we show that Arf6-mediated recruitment of the lipid kinase PIP5K1C rapidly converts phosphatidylinositol 4-phosphate (PI(4)P) to PI(4,5)P₂, driving exocyst recruitment and membrane tethering. These results provide a molecular mechanism of exocyst-mediated tethering and a unique functional requirement for phosphoinositide signaling on late-stage vesicles in the vicinity of the plasma membrane.

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Complete reconstitution and subunit connectivity of the human exocyst complex

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Binding to PI(4,5)P₂ in trans by each subcomplex enables membrane tethering

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PI(4)P to PI(4,5)P2 conversion is sufficient for exocyst recruitment and tethering

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Arf6 controls phosphoinositide conversion by PIP5K1C in cells and in vitro

Fixed Point Attractor Theory Bridges Structure and Function in C. elegans Neuronal Network

Understanding the structure–function relationship in a neuronal network is one of the major challenges in neuroscience research. Despite increasing researches at circuit connectivity and neural network structure, their structure-based biological interpretability remains unclear. Based on the attractor theory, here we develop an analytical framework that links neural circuit structures and their functions together through fixed point attractor in Caenorhabditis elegans. In this framework, we successfully established the structural condition for the emergence of multiple fixed points in C. elegans connectome. Then we construct a finite state machine to explain how functions related to bistable phenomena at the neural activity and behavioral levels are encoded. By applying the proposed framework to the command circuit in C. elegans, we provide a circuit level interpretation for the forward-reverse switching behaviors. Interestingly, network properties of the command circuit and first layer amphid interneuron circuit can also be inferred from their functions in this framework. Our research indicates the reliability of the fixed point attractor bridging circuit structure and functions, suggesting its potential applicability to more complex neuronal circuits in other species.

A negative feedback loop of TOR signaling balances growth and stress-response trade-offs in plants

TOR kinase is a central coordinator of nutrient-dependent growth in eukaryotes. Maintaining optimal TOR signaling is critical for the normal development of organisms. In this study, we describe a negative feedback loop of TOR signaling helping in the adaptability of plants in changing environmental conditions. Using an interdisciplinary approach, we show that the plant-specific zinc finger protein FLZ8 acts as a regulator of TOR signaling in Arabidopsis. In sugar sufficiency, TOR-dependent and -independent histone modifications upregulate the expression of FLZ8. FLZ8 negatively regulates TOR signaling by promoting antagonistic SnRK1α1 signaling and bridging the interaction of SnRK1α1 with RAPTOR1B, a crucial accessory protein of TOR. This negative feedback loop moderates the TOR-growth signaling axis in the favorable condition and helps in the activation of stress signaling in unfavorable conditions, establishing its importance in the adaptability of plants.

Systematic inference identifies a major source of heterogeneity in cell signaling dynamics: The rate-limiting step number

Identifying the sources of cell-to-cell variability in signaling dynamics is essential to understand drug response variability and develop effective therapeutics. However, it is challenging because not all signaling intermediate reactions can be experimentally measured simultaneously. This can be overcome by replacing them with a single random time delay, but the resulting process is non-Markovian, making it difficult to infer cell-to-cell heterogeneity in reaction rates and time delays. To address this, we developed an efficient and scalable moment-based Bayesian inference method (MBI) with a user-friendly computational package that infers cell-to-cell heterogeneity in the non-Markovian signaling process. We applied MBI to single-cell expression profiles from promoters responding to antibiotics and discovered a major source of cell-to-cell variability in antibiotic stress response: the number of rate-limiting steps in signaling cascades. This knowledge can help identify effective therapies that destroy all pathogenic or cancer cells, and the approach can be applied to precision medicine.

A New Cell Signal Regulation Theory: Blocking the Signal from being Reactivated Before a New Activation

Currently, the concept of cell signal regulation has two basic steps: activation and deactivation. There are many activators of the signals in vivo (e.g., hormones, growth factors, signal cross-talk, etc.). According to the two step theory, cell signals are expected to keep activating, deactivating, activating, deactivating,……However, cell signals in vivo are usually quiescent for the most of the time. This indicates that, there is a mechanism that blocks the signal from being reactivated for a certain period of time after an activation is terminated. Here, we propose that cell's signal regulation consists of three basic steps: activation, deactivation, and blocking the signal from being reactivated for a certain period of time until cells are ready for a new activation. We explain the third step of regulation using GH/STAT5 and insulin/AKT signal pathways as examples, and discuss why the third step in regulation is important for cell homeostasis and the development of diseases.

Neural oscillation of single silicon nanowire neuron device with no external bias voltage

In this study, we perform simulations to demonstrate neural oscillations in a single silicon nanowire neuron device comprising a gated p–n–p–n diode structure with no external bias lines. The neuron device emulates a biological neuron using interlinked positive and negative feedback loops, enabling neural oscillations with a high firing frequency of ~ 8 MHz and a low energy consumption of ~ 4.5 × 10⁻¹⁵ J. The neuron device provides a high integration density and low energy consumption for neuromorphic hardware. The periodic and aperiodic patterns of the neural oscillations depend on the amplitudes of the analog and digital input signals. Furthermore, the device characteristics, energy band diagram, and leaky integrate-and-fire operation of the neuron device are discussed.

Multisite phosphorylation by Cdk1 initiates delayed negative feedback to control mitotic transcription

Cell-cycle progression is driven by the phosphorylation of cyclin-dependent kinase (Cdk) substrates.^1-3 The order of substrate phosphorylation depends in part on the general rise in Cdk activity during the cell cycle,^4-7 together with variations in substrate docking to sites on associated cyclin and Cks subunits.^3,6,8-10 Many substrates are modified at multiple sites to provide more complex regulation.^10-14 Here, we describe an elegant regulatory circuit based on multisite phosphorylation of Ndd1, a transcriptional co-activator of budding yeast genes required for mitotic progression.^11,12 As cells enter mitosis, Ndd1 phosphorylation by Cdk1 is known to promote mitotic cyclin (CLB2) gene transcription, resulting in positive feedback.^13-16 Consistent with these findings, we show that low Cdk1 activity promotes CLB2 expression at mitotic entry. We also find, however, that when high Cdk1 activity accumulates in a mitotic arrest, CLB2 expression is inhibited. Inhibition is accompanied by Ndd1 degradation, and we present evidence that degradation is triggered by multisite Ndd1 phosphorylation by high mitotic Cdk1-Clb2 activity. Complete Ndd1 phosphorylation by Clb2-Cdk1-Cks1 requires the phosphothreonine-binding site of Cks1, as well as a recently identified phosphate-binding pocket on the cyclin Clb2.¹⁷ We therefore propose that initial phosphorylation by Cdk1 primes Ndd1 for delayed secondary phosphorylation at suboptimal sites that promote degradation. Together, our results suggest that rising levels of mitotic Cdk1 activity act at multiple phosphorylation sites on Ndd1, first triggering rapid positive feedback and then promoting delayed negative feedback, resulting in a pulse of mitotic gene expression.

Signalling dynamics in embryonic development

In multicellular organisms, cellular behaviour is tightly regulated to allow proper embryonic development and maintenance of adult tissue. A critical component in this control is the communication between cells via signalling pathways, as errors in intercellular communication can induce developmental defects or diseases such as cancer. It has become clear over the last years that signalling is not static but varies in activity over time. Feedback mechanisms present in every signalling pathway lead to diverse dynamic phenotypes, such as transient activation, signal ramping or oscillations, occurring in a cell type- and stage-dependent manner. In cells, such dynamics can exert various functions that allow organisms to develop in a robust and reproducible way. Here, we focus on Erk, Wnt and Notch signalling pathways, which are dynamic in several tissue types and organisms, including the periodic segmentation of vertebrate embryos, and are often dysregulated in cancer. We will discuss how biochemical processes influence their dynamics and how these impact on cellular behaviour within multicellular systems.

Principles of synthetic biology

In synthetic biology, biological cells and processes are dismantled and reassembled to make novel systems that do useful things. Designs are encoded by deoxyribonucleic acid (DNA); DNA makes biological (bio-)parts; bioparts are combined to make devices; devices are built into biological systems. Computers are used at all stages of the Design-Build-Test-Learn cycle, from mathematical modelling through to the use of robots for the automation of assembly and experimentation. Synthetic biology applies engineering principles of standardisation, modularity, and abstraction, enabling fast prototyping and the ready exchange of designs between synthetic biologists working around the world. Like toy building blocks, compatible modular designs enable bioparts to be combined and optimised easily; biopart specifications are shared in open registries. Synthetic biology is made possible due to major advances in DNA sequencing and synthesis technologies, and through knowledge gleaned in the field of systems biology. Systems biology aims to understand biology across scales, from the molecular and cellular, up to tissues and organisms, and describes cells as complex information-processing systems. By contrast, synthetic biology seeks to design and build its own systems. Applications of synthetic biology are wide-ranging but include impacting healthcare to improve diagnosis and make better treatments for disease; it seeks to improve the environment by finding novel ways to clean up pollution, make industrial processes for chemical synthesis sustainable, and remove the need for damaging farming practices by making better fertilisers. Synthetic biology has the potential to change the way we live and help us to protect the future of our planet.