Negative Regulatory Mechanism Research Articles

African Swine Fever Virus L83L Negatively Regulates the cGAS-STING-Mediated IFN-I Pathway by Recruiting Tollip To Promote STING Autophagic Degradation.

African swine fever (ASF) is a devastating infectious disease of pigs caused by the African swine fever virus (ASFV), which poses a great danger to the global pig industry. Many viral proteins can suppress with interferon signaling to evade the host's innate immune responses. Therefore, the development of an effective vaccine against ASFV has been dampened. Recent studies have suggested that the L83L gene may be integrated into the host genome, weakening the host immune system, but the underlying mechanism is unknown. Our study found that L83L negatively regulates the cGAS-STING-mediated type I interferon (IFN-I) signaling pathway. Overexpression of L83L inhibited IFN-β promoter and ISRE activity, and knockdown of L83L induced higher transcriptional levels of interferon-stimulated genes (ISGs) and phosphorylation levels of IRF3 in primary porcine alveolar macrophages. Mechanistically, L83L interacted with cGAS and STING to promote autophagy-lysosomal degradation of STING by recruiting Tollip, thereby blocking the phosphorylation of the downstream signaling molecules TBK1, IRF3, and IκBα and reducing IFN-I production. Altogether, our study reveals a negative regulatory mechanism involving the L83L-cGAS-STING-IFN-I axis and provides insights into an evasion strategy involving autophagy and innate signaling pathways employed by ASFV. IMPORTANCE African swine fever virus (ASFV) is a large double-stranded DNA virus that primarily infects porcine macrophages. The ASFV genome encodes a large number of immunosuppressive proteins. Current options for the prevention and control of this pathogen remain pretty limited. Our study showed that overexpression of L83L inhibited the cGAS-STING-mediated type I interferon (IFN-I) signaling pathway. In contrast, the knockdown of L83L during ASFV infection enhanced IFN-I production in porcine alveolar macrophages. Additional analysis revealed that L83L protein downregulated IFN-I signaling by recruiting Tollip to promote STING autophagic degradation. Although L83L deletion has been reported to have little effect on viral replication, its immune evade mechanism has not been elucidated. The present study extends our understanding of the functions of ASFV-encoded pL83L and its immune evasion strategy, which may provide a new basis for developing a live attenuated vaccine for ASF.

IL-10 Negatively Controls the Primary T Cell Response of Tilapia by Triggering the JAK1/STAT3/SOCS3 Axis That Suppresses NF-κB and MAPK/ERK Signaling.

The braking mechanisms to protect the host from tissue damage and inflammatory disease caused by an overexuberant immune response are common in many T cell subsets. However, the negative regulation of T cell responses and detailed mechanisms are not well understood in early vertebrates. In the current study, using a Nile tilapia (Oreochromis niloticus) model, we investigated the suppression of T cell immunity by IL-10. Tilapia encodes an evolutionarily conserved IL-10, whose expression in lymphocytes is markedly induced during the primary adaptive immune response against Aeromonas hydrophila infection. Activated T cells of tilapia produce IL-10, which in turn inhibits proinflammatory cytokine expression and suppresses PHA-induced T cell activation. Moreover, administration of IL-10 impairs the proliferation of tilapia T cells, reduces their potential to differentiate into Th subsets, and cripples the cytotoxic function, rendering the animals more vulnerable to pathogen attack. After binding to its receptor IL-10Ra, IL-10 activates the JAK1/STAT3 axis by phosphorylation and enhances the expression of the suppressor of cytokine signaling 3 (SOCS3), which in turn attenuates the activation of the NF-κB and MAPK/ERK signaling pathways, thus suppressing the T cell response of tilapia. Our findings elucidate a negative regulatory mechanism of T cell immunity in a fish species and support the notion that the braking mechanism of T cells executed through IL-10 existed prior to the divergence of the tetrapod lineage from teleosts. Therefore, this study, to our knowledge, provides a novel perspective on the evolution of the adaptive immune system.

Regulation of EGFR phase transition through Grb2-Grb2 interactions.

Assembly of cellular receptors into condensed phases is emerging as a common theme in many cellular systems. Upon activation, multivalent interactions between proteins cause the formation of a condensate enriched in signaling molecules. One such receptor is epidermal growth factor receptor (EGFR), and it can form an extended network upon activation through the recruitment of growth factor receptor-bound protein 2 (Grb2) and guanine exchange factor Son of Sevenless (SOS). We previously demonstrated that EGFR phase transition is mediated by a Grb2-Grb2 interaction and that Grb2 phosphorylation at Y160 blocks the condensation. Here we show how kinase activity can regulate the extent of the phase transition by modulating the phosphorylation state of Grb2. Furthermore, since EGFR condensation promotes downstream signaling through Ras/MAPK, Grb2 phosphorylation represents a negative regulatory mechanism. However, kinase inhibitors, which are regularly used as cancer therapeutics intended to block EGFR-driven Ras/MAPK signaling, may inhibit this negative regulatory step, possibly enhancing the very signal they were intended to block. We demonstrate kinase inhibitors can rescue EGFR phase transition even under high kinase activity conditions. We later explore how kinase activity and kinase inhibitors affect downstream Ras signaling. These results identify a novel mechanism regulating the EGFR phase transition and how kinase inhibitors disrupt this inhibitory mechanism.

Toward dynamic regulation of bidirectional automatic fare gates: A macro-to-micro simulation approach

While bidirectional automatic fare gates (BAFGs) serve as important tools for mitigating the congestion of passengers in subway stations, most of BAFGs function merely as single-directional automatic fare gates (AFGs) in most cities of China and other countries. This paper proposes a pioneering work on the dynamic regulation problem of BAFGs. We build a macro-to-micro model which simulates the movement of passengers in stations from both the macroscopic and microscopic perspectives. The system dynamics based macromodel simulates the macroscopic movement of passengers in stations, while the social force based micromodel simulates the microscopic movement of passengers. Benefitting from the negative feedback regulation mechanism of the system dynamics, we adjust different number of BAFGs according to the congestion extent of the passenger flow on the platform in the macromodel, and change the pedestrian flowline in the micromodel to ensure that there is no new conflict produced by the regulation scheme. We conduct case studies on Dawanglu station and Jiangtai station, Beijing, China, and propose optimized configurations and dynamic regulation scheme of BAFGs accordingly. The simulation results show that the macro-to-micro model not only significantly improves both the BAFGs’ efficiency and the passengers’ efficiency, but also exhibits a high generalization ability towards different types of subway stations. Our study benefits the subway operation and management, and is conducive to sustainable urban development.

Protectin Conjugates in Tissue Regeneration 1 Inhibits Macrophage Pyroptosis by Restricting NLRP3 Inflammasome Assembly to Mitigate Sepsis via the cAMP-PKA Pathway

Protectin conjugates in tissue regeneration 1 (PCTR1) is a novel anti-inflammatory and proresolving lipid mediator biosynthesized from docosahexaenoic acid. Excessive activation of NLR family pyrin domain containing 3 (NLRP3) inflammasome and consequent pyroptosis are involved in diverse inflammatory diseases. However, how PCTR1 affects NLRP3 inflammasome activation and pyroptosis are still unclear. Here, we demonstrated that PCTR1 inhibited NLRP3 inflammasome activation and pyroptosis. These results show that PCTR1 dose-dependently inhibited gasdermin D cleavage in lipopolysaccharide (LPS)-primed murine primary macrophages upon nigericin stimulation. Additionally, PCTR1 treatment after LPS priming inhibited caspase-1 activation and subsequent mature interleukin-1β release independent of the nuclear factor-kappa B pathway. PCTR1 exerted its inhibitory effects by blocking NLRP3-apoptosis-associated speck-like protein containing a CARD (ASC) interaction and ASC oligomerization, thereby restricting NLRP3 inflammasome assembly. However, the inhibitory effect of PCTR1 could be reversed by KH7 and H89, which are the inhibitors of the cyclic adenosine monophosphate (cAMP)-protein kinase A (PKA) signaling pathway. Moreover, PCTR1 treatment alleviated lung tissue damage and improved mouse survival in LPS-induced sepsis. Our study unveils the molecular mechanism of negative regulation of NLRP3 inflammasome activation and pyroptosis by a novel lipid mediator and suggests that PCTR1 may serve as a potential treatment option for NLRP3-inflammasome driven diseases.

Targeting peroxisomal fatty acid oxidation improves hepatic steatosis and insulin resistance in obese mice

Obesity and diabetes normally cause mitochondrial dysfunction and hepatic lipid accumulation, while fatty acid synthesis is suppressed and malonyl-CoA is depleted in the liver of severe obese or diabetic animals. Therefore, a negative regulatory mechanism might work for the control of mitochondrial fatty acid metabolism that is independent of malonyl-CoA in the diabetic animals. As mitochondrial β-oxidation is controlled by the acetyl-CoA/CoA ratio, and the acetyl-CoA generated in peroxisomal β-oxidation could be transported into mitochondria via carnitine shuttles, we hypothesize that peroxisomal β-oxidation might play a role in regulating mitochondrial fatty acid oxidation and inducing hepatic steatosis under the condition of obesity or diabetes. This study reveals a novel mechanism by which peroxisomal β-oxidation controls mitochondrial fatty acid oxidation in diabetic animals. We determined that excessive oxidation of fatty acids by peroxisomes generates considerable acetyl-carnitine in the liver of diabetic mice, which significantly elevates the mitochondrial acetyl-CoA/CoA ratio and causes feedback suppression of mitochondrial β-oxidation. Additionally, we found that specific suppression of peroxisomal β-oxidation enhances mitochondrial fatty acid oxidation by reducing acetyl-carnitine formation in the liver of obese mice. In conclusion, we suggest that induction of peroxisomal fatty acid oxidation serves as a mechanism for diabetes-induced hepatic lipid accumulation. Targeting peroxisomal β-oxidation might be a promising pathway in improving hepatic steatosis and insulin resistance as induced by obesity or diabetes.

Serpentine Enhances Insulin Regulation of Blood Glucose through Insulin Receptor Signaling Pathway

Insulin sensitizers targeting insulin receptors (IR) are a potential drug for the treatment of diabetes. Serpentine is an alkaloid component in the root of Catharanthus roseus (L.) G. Don. Serpentine screened by surface plasmon resonance (SPR) technology has the ability to target IR. The objective of this study was to investigate whether serpentine could modulate the role of insulin in regulating blood glucose through insulin receptors in cells and in animal models of diabetes. SPR technology was used to detect the affinity of different concentrations of serpentine with insulin receptors. The Western blotting method was used to detect the expression levels of key proteins of the insulin signaling pathway in C2C12 cells and 3T3-L1 cells as well as in muscle and subcutaneous adipose tissue of diabetic mice after serpentine and insulin treatment. Diabetic mice were divided into four groups and simultaneously injected with insulin or serpentine, and the blood glucose concentration and serum levels of insulin, glucagon, and C-peptide were measured 150 min later. mRNA levels of genes related to lipid metabolism and glucose metabolism in liver, muscle, and subcutaneous adipose tissue were detected by RT-PCR. Serpentine was able to bind to the extracellular domain of IR with an affinity of 2.883 × 10-6 M. Serpentine combined with insulin significantly enhanced the ability of insulin to activate the insulin signaling pathway and significantly enhanced the glucose uptake capacity of C2C12 cells. Serpentine enhanced the ability of low-dose insulin (1 nM) and normal-dose insulin (100 nM) to activate the insulin signaling pathway. Serpentine also independently activated AMPK phosphorylation, thus stimulating glucose uptake by C2C12 cells. In high-fat-diet/streptozotocin (HFD/STZ)-induced diabetic mice, serpentine significantly prolonged the hypoglycemic time of insulin, significantly reduced the use of exogenous insulin, and inhibited endogenous insulin secretion. In addition, serpentine alone significantly increased the expression of GSK-3β mRNA in muscle tissue, thus enhancing glucose uptake, and at the same time, serpentine significantly increased glucagon secretion and liver gluconeogenesis. Serpentine enhances the ability of insulin to regulate blood glucose through the insulin receptor, and can also regulate blood glucose alone, but it has a negative regulation mechanism and cannot produce a hypoglycemic effect. Therefore, serpentine may be useful as an insulin sensitizer to assist insulin to lower blood glucose.

Tumor necrosis factor is a necroptosis-associated alarmin.

Necroptosis is a form of regulated cell death that can occur downstream of several immune pathways. While previous studies have shown that dysregulated necroptosis can lead to strong inflammatory responses, little is known about the identity of the endogenous molecules that trigger these responses. Using a reductionist in vitro model, we found that soluble TNF is strongly released in the context of necroptosis. On the one hand, necroptosis promotes TNF translation by inhibiting negative regulatory mechanisms acting at the post-transcriptional level. On the other hand, necroptosis markedly enhances TNF release by activating ADAM proteases. In studying TNF release at single-cell resolution, we found that TNF release triggered by necroptosis is activated in a switch-like manner that exceeds steady-state TNF processing in magnitude and speed. Although this shedding response precedes massive membrane damage, it is closely associated with lytic cell death. Further, we found that lytic cell death induction using a pore-forming toxin also triggers TNF shedding, indicating that the activation of ADAM proteases is not strictly related to the necroptotic pathway but likely associated with biophysical changes of the cell membrane upon lytic cell death. These results demonstrate that lytic cell death, particularly necroptosis, is a critical trigger for TNF release and thus qualify TNF as a necroptosis-associated alarmin.

Toll-interacting protein negatively regulated innate immune response via NF-κB signal pathway in blunt snout bream, Megalobrama amblycephala

Toll-interacting protein (Tollip) is an important negative regulator of Toll-like receptor-mediated innate immunity by preventing excessive proinflammatory responses. The structure and function of Tollip have been well identified in mammals, but the piscine Tollip remains poorly understood. In the present study, a homologue of Tollip was identified and characterized from blunt snout bream (named MaTollip), which was composed of an 831 bp open reading frame encoding a protein of 276 amino acids. Phylogenetic analysis indicated that MaTollip is a novel member of Tollip family and possessed the highest similarity to that of grass carp (99.28%). Multiple alignment of amino acid sequence showed that MaTOLLIP shared a high degree of structural conservation, including a TBD domain, a C2 domain and a CUE domain, with its counterparts from other vertebrates. With regard to tissue-specific expression without immune challenge, MaTollip was constitutively expressed in a wide range of normal tissues, with the highest in the head-kidney and the lowest in the intestine. MaTollip expression in the head-kidney was strongly upregulated upon LPS stimulation and A. hydrophila infection. Fluorescence microscopic analysis revealed that the green fluorescent protein-TOLLIP was localized predominantly in the cytoplasm of EPC cells in a dot-like state. When MaTollip was overexpressed in HEK-293T and EPC cells, it could significantly inhibit the activity of nuclear factor-κB (NF-κB) promoter in a dose dependent manner. MaTollip overexpression in MAF cells lowered drastically the transcriptional expression level of lipopolysaccharide-induced proinflammatory cytokines (IL-1β, IL-6 and IL-8), whereas they were dramatically promoted by MaTollip knock down with siRNA. Taken together, this study demonstrated that MaTollip played a pivotal role in mediating host innate immune response to pathogen invasion, and unveiled the involvement of MaTollip in NF-κB-mediated transcription of inflammation genes, which paved the way for further studies of immune negative regulation mechanisms mediated by Tollip in fish.

The Characteristics of AML1-ETO Fusion Gene Induced Pre-Leukemia Immune Microenvironment

Objective: The immune-privileged microenvironment plays a critical role in immune escape of acute myeloid leukemia (AML), however the characteristics of the immune micro-environment in pre-leukemia states have not yet been clarified. In this study, the Aml1Eto/+; Mx1-Cre mouse model was employed to explore the remodeling of the immune microenvironment by leukemic precursor cells, and to elucidate the characteristics of the immune microenvironment in the pre-leukemic state. Methods: Four weeks after PIPC induction (5mg/kg), bone marrow-derived immune cells such as T cells, B cells and macrophages(Mφ) that do not express the AML1-ETO (AE) fusion gene were sorted from Aml1Eto/+; Mx1-Cre mice (experimental group) and Aml1Eto/+;w/o Mx1-Cre mice (control group), respectively. The immune cell subsets were analyzed using CIBERSORT after bulk RNA-sequence, and TCR and BCR information was reconstructed by TRUST4. Results: After PIPC induction, the proportion of the AE fusion gene expressed hematopoietic precursors cells expanded significantly in the experiment group. The absolute counts of T cells and dendritic cells that did not express the fusion gene showed a considerable increment (p<0.0001; p=0.0067), and the monocyte-macrophage cells decreased (p<0.0001; p=0.0009). In addition, the expressions of Gzma and other cytotoxicity-related genes were significantly up-regulated in the T cells of experiment group. As for reconstructed TCR, the clonal diversity of TCR expanded. Although the proportion and absolute count of T cell increased when AE fusion protein induced, there didn't appear some hyperexpanded clones. The clonotype relative abundance and gene usage preference of TCR & BCR are similar between experiment and control group. There were 11 pre-leukemia-specific TCR amino acid sequences appeared, though no dominant clone was formed, suggesting that T cells produced relevant but not strong enough immune responses to pre-leukemia precursor cells. Further analysis found that the T cells in experiment group were composed of more Treg cells and expressed higher exhaustion-related genes such as PD-1, indicated that T cells began to accumulate negative immune regulation pathways in the bone marrow microenvironment of pre-leukemic state. For the antigen presentation, the expression of MHC-I molecules on AE fusion gene expressed LT-HSC and GMP in the experimental group was up-regulated, while the expressions of MHC-I and MHC-II molecules in dendritic cells were not significantly different from those in the control group. Meanwhile, CIBERSORT and flow cytometry analysis showed more classically activated M1-Mφ in the experiment group, in which the expressions of INF-γ, IL-1, and other genes were up-regulated. In terms of B cells, the production of immunoglobulins related genes and antigen processing and presenting genes were up-regulated. The BCR clonal diversity expanded, and 73 pre-leukemia-specific BCR amino acid sequences appeared, but no dominant clones were formed. Among the heavy chain sequences, the clonal diversity of IgD and IgM in the experimental group increased, the relative abundance of IgM increased, and the relative abundance of IgA decreased. Conclusion: We performed a comprehensive cell-type based dissection of the AML1-ETO fusion gene induced pre-leukemia immune microenvironment. The results demonstrates that in pre-leukemia stage, activated immune microenvironment is involved in the fight with AML1-ETO expressed cells. And there is also an accumulation of negative immune regulation mechanisms which may potentially contribute to weaken "the power" of immune surveillance. Although further validation is required, restoring dysfunctional immune cells or enhance the AML1-ETO specific immune response might be a potential early therapeutic approach for patients.

Sinusoidal and lymphatic vessel growth is controlled by reciprocal VEGF-C-CDH5 inhibition.

Sinusoids are specialized, low pressure blood vessels in the liver, bone marrow, and spleen required for definitive hematopoiesis. Unlike other blood endothelial cells (ECs), sinusoidal ECs express high levels of VEGFR3. VEGFR3 and its ligand VEGF-C are known to support lymphatic growth, but their function in sinusoidal vessels is unknown. In this study, we define a reciprocal VEGF-C/VEGFR3-CDH5 (VE-cadherin) signaling axis that controls growth of both sinusoidal and lymphatic vessels. Loss of VEGF-C or VEGFR3 resulted in cutaneous edema, reduced fetal liver size, and bloodless bone marrow due to impaired lymphatic and sinusoidal vessel growth. Mice with membrane-retained VE-cadherin conferred identical lymphatic and sinusoidal defects, suggesting that VE-cadherin opposes VEGF-C/VEGFR3 signaling. In developing mice, loss of VE-cadherin rescued defects in sinusoidal and lymphatic growth caused by loss of VEGFR3 but not loss of VEGF-C, findings explained by potentiated VEGF-C/VEGFR2 signaling in VEGFR3-deficient lymphatic ECs. Mechanistically, VEGF-C/VEGFR3 signaling induces VE-cadherin endocytosis and loss of function via SRC-mediated phosphorylation, while VE-cadherin prevents VEGFR3 endocytosis required for optimal receptor signaling. These findings establish an essential role for VEGF-C/VEGFR3 signaling during sinusoidal vascular growth, identify VE-cadherin as a powerful negative regulator of VEGF-C signaling that acts through both VEGFR3 and VEGFR2 receptors, and suggest that negative regulation of VE-cadherin is required for effective VEGF-C/VEGFR3 signaling during growth of sinusoidal and lymphatic vessels. Manipulation of this reciprocal negative regulatory mechanism, e.g. by reducing VE-cadherin function, may be used to stimulate therapeutic sinusoidal or lymphatic vessel growth.

Transcriptome analysis of response strategy in Hemerocallis fulva under drought stress.

Hemerocallis fulva is an important ground cover plant widely used in urban greening. The analysis of the molecular mechanism underlying the drought response of H. fulva can lay a foundation for improving its adaptability and expanding its planting area. To reveal the drought response mechanisms of H. fulva, identify candidate unigenes associated with drought response, and lay a foundation for further unigenes functional study and drought resistance improvement of H. fulva via genetic engineering. RNA was isolated from H. fulva under different experimental conditions. De novo transcriptomic analysis of the samples was performed to screen drought response unigenes. The transcriptional changes of candidate drought response unigenes were verified by quantitative real-time PCR. The differentially expressed unigenes and their functions were analyzed after H. fulva treated by PEG-simulated drought stress and rewatering. The candidate unigenes, associated with H. fulva drought response, were identified after transcriptome analysis. Then, the transcription level of drought response unigenes of H. fulva under different conditions was further verified. Abscisic acid, protein phosphorylation, sterol biosynthesis and ion transport were involved in drought response with quick restore in H. fulva. The response unigenes, involved in hormone (ABA, JA, CK and GA) signaling pathways, defense response, high light response, karrikin response and leaf shaping, can maintain at changed expression levels even after stress withdraw. Hemerocallis fulva has unique drought response mechanism. Negative regulation mechanism may play more important roles in drought response of H. fulva. The analysis of candidate unigenes, associated with drought response, lays a foundation for further drought resistance improvement of H. fulva.

The influenza virus PB2 protein evades antiviral innate immunity by inhibiting JAK1/STAT signalling

Influenza A virus (IAV) polymerase protein PB2 has been shown to partially inhibit the host immune response by blocking the induction of interferons (IFNs). However, the IAV PB2 protein that regulates the downstream signaling pathway of IFNs is not well characterized. Here, we report that IAV PB2 protein reduces cellular sensitivity to IFNs, suppressing the activation of STAT1/STAT2 and ISGs. Furthermore, IAV PB2 protein targets mammalian JAK1 at lysine 859 and 860 for ubiquitination and degradation. Notably, the H5 subtype of highly pathogenic avian influenza virus with I283M/K526R mutations on PB2 increases the ability to degrade mammalian JAK1 and exhibits higher replicate efficiency in mammalian (but not avian) cells and mouse lung tissues, and causes greater mortality in infected mice. Altogether, these data describe a negative regulatory mechanism involving PB2-JAK1 and provide insights into an evasion strategy from host antiviral immunity employed by IAV.

Clathrin-associated AP-1 controls termination of STING signalling

Stimulator of interferon genes (STING) functions downstream of cyclic GMP-AMP synthase in DNA sensing or as a direct receptor for bacterial cyclic dinucleotides and small molecules to activate immunity during infection, cancer and immunotherapy1–10. Precise regulation of STING is essential to ensure balanced immune responses and prevent detrimental autoinflammation11–16. After activation, STING, a transmembrane protein, traffics from the endoplasmic reticulum to the Golgi, where its phosphorylation by the protein kinase TBK1 enables signal transduction17–20. The mechanism that ends STING signalling at the Golgi remains unknown. Here we show that adaptor protein complex 1 (AP-1) controls the termination of STING-dependent immune activation. We find that AP-1 sorts phosphorylated STING into clathrin-coated transport vesicles for delivery to the endolysosomal system, where STING is degraded21. We identify a highly conserved dileucine motif in the cytosolic C-terminal tail (CTT) of STING that, together with TBK1-dependent CTT phosphorylation, dictates the AP-1 engagement of STING. A cryo-electron microscopy structure of AP-1 in complex with phosphorylated STING explains the enhanced recognition of TBK1-activated STING. We show that suppression of AP-1 exacerbates STING-induced immune responses. Our results reveal a structural mechanism of negative regulation of STING and establish that the initiation of signalling is inextricably associated with its termination to enable transient activation of immunity.

Mutation of the RelA(p65) Thr505 phosphosite disrupts the DNA replication stress response leading to CHK1 inhibitor resistance.

Mutation of the RelA(p65) Thr505 phosphosite disrupts the DNA replication stress response leading to CHK1 inhibitor resistance.

Precision Terminology: Why to Avoid the Term "Atypical Optic Neuritis".

Tuberculosis, one of the leading causes of death worldwide, stimulates inflammatory responses with beneficial and pathologic consequences. The regulation and nature of an optimal inflammatory response to <i>Mycobacterium tuberculosis</i> remains poorly understood in humans. Insight into mechanisms of negative regulation of the TLR-mediated innate immune response to <i>M. tuberculosis</i> could provide significant breakthroughs in the design of new vaccines and drugs. We hypothesized that TOLLIP and its common variants negatively regulate TLR signaling in human monocytes and are associated with susceptibility to tuberculosis. Using short hairpin RNA knockdown of TOLLIP in peripheral blood human monocytes, we found that TOLLIP suppresses TNF and IL-6 production after stimulation with TLR2 and TLR4 ligands. In contrast, secretion of the anti-inflammatory cytokine IL-10 was induced by TOLLIP. We also discovered two common polymorphisms that are associated with either decreased levels of mRNA expression (rs3750920) or increased IL-6 production (rs5743899) in a sample of 56 healthy volunteers. Furthermore, in a case-population study in Vietnam with 760 cord blood samples and 671 TB case patients, we found that SNPs rs3750920 and rs5743899 were associated with susceptibility to tuberculosis (<i>p</i> = 7.03 × 10⁻¹⁶ and 6.97 × 10⁻⁷, respectively). These data demonstrate that TOLLIP has an anti-inflammatory effect on TLR signaling in humans and that TOLLIP deficiency is associated with an increased risk of tuberculosis. To our knowledge, these data also show the first associations of TOLLIP polymorphisms with any infectious disease. These data also implicate an unexpected mechanism of negative regulation of TLR signaling in human tuberculosis pathogenesis.

A self-adaptive gradient-based particle swarm optimization algorithm with dynamic population topology

The aggregation of individuals facilitates local information exchange, and the migration of individuals from one population to another leads to a dynamic community structure. In addition, the negative feedback regulation mechanism of organisms helps them in good living conditions. Based on the above knowledge, a novel particle swarm optimization algorithm with a self-organizing topology structure and self-adaptive adjustable parameters is proposed (KGPSO). During the optimization process, the K-Means clustering method periodically divides the particle swarm into multiple distance-based sub-swarms, and the optimal number of sub-swarms is determined by maximizing the Calinski-Harabasz index. This strategy helps maintain the population diversity and gives particles the ability to perceive the surrounding environment. The parameters used to update the particle velocity are adjusted based on the gradient descent of its fitness error, ensuring a dynamic balance between exploration and exploitation. The hyperparameters of KGPSO are tuned by Bayesian optimization method to improve the algorithm performance further. Two benchmark suites are used to evaluate the performance of KGPSO. Both ranking results and Wilcoxon signed-rank tests show that KGPSO performs best among the PSO algorithms tested. Moreover, the excellent optimization capability of KGPSO are proven in the process of X-ray CT image enhancement, making it possible to analyze the structure and motion of heterogeneous granular materials efficiently and robustly. In conclusion, the proposed KGPSO can provide a stable and powerful support for the frontier experimental research of granular materials and expand the research scope.

Structural insights into the pSer/pThr dependent regulation of the SHP2 tyrosine phosphatase in insulin and CD28 signaling

Serine/threonine phosphorylation of insulin receptor substrate (IRS) proteins is well known to modulate insulin signaling. However, the molecular details of this process have mostly been elusive. While exploring the role of phosphoserines, we have detected a direct link between Tyr-flanking Ser/Thr phosphorylation sites and regulation of specific phosphotyrosine phosphatases. Here we present a concise structural study on how the activity of SHP2 phosphatase is controlled by an asymmetric, dual phosphorylation of its substrates. The structure of SHP2 has been determined with three different substrate peptides, unveiling the versatile and highly dynamic nature of substrate recruitment. What is more, the relatively stable pre-catalytic state of SHP2 could potentially be useful for inhibitor design. Our findings not only show an unusual dependence of SHP2 catalytic activity on Ser/Thr phosphorylation sites in IRS1 and CD28, but also suggest a negative regulatory mechanism that may also apply to other tyrosine kinase pathways as well.

Intelligent control of the electrochemical nitrate removal basing on artificial neural network (ANN)

Artificial intelligence technologies were confirmed as a useful tool for wastewater treatment, but its application in the electrochemical nitrate removal had less been reported. In this work, the artificial neural network in machine learning was used to construct the model, which combines the methods of electrochemistry and artificial intelligence to achieve the prediction and intelligent control of nitrate removal. The control system consists of a prediction module with an artificial neural network (ANN) algorithm model and a control module. First, initial nitrate concentration, pH, time and current density were considered as input. An ANN algorithm using 7 hidden layers and a negative feedback regulation mechanism was developed to optimize the model and predict the nitrate removal rate. Results indicates that the proposed prediction model (4–7–1) yields a better coefficient of determination and lower root mean square error. The optimal set-points of the current density in the electrochemical process can be obtained according to the water quality change and qualified effluent quality using the ANN model. Also, the proposed intelligent control strategy can eliminate the influence of water quality change on nitrate removal and reduce energy consumption by 15.0 % compared to the post strategy. This work demonstrated the potential of artificial intelligence in the electrochemical process of nitrate removal.

Arabidopsis TIE1 and TIE2 transcriptional repressors dampen cytokinin response during root development.

Cytokinin plays critical roles in root development. Cytokinin signaling depends on activation of key transcription factors known as type B Arabidopsis response regulators (ARRs). However, the mechanisms underlying the finely tuned regulation of type B ARR activity remain unclear. In this study, we demonstrate that the ERF-associated amphiphilic repression (EAR) motif–containing protein TCP interactor containing ear motif protein2 (TIE2) forms a negative feedback loop to finely tune the activity of type B ARRs during root development. Disruption of TIE2 and its close homolog TIE1 causes severely shortened roots. TIE2 interacts with type B ARR1 and represses transcription of ARR1 targets. The cytokinin response is correspondingly enhanced in tie1-1 tie2-1. We further show that ARR1 positively regulates TIE1 and TIE2 by directly binding to their promoters. Our findings demonstrate that TIEs play key roles in controlling plant development and reveal an important negative feedback regulation mechanism for cytokinin signaling.