The Role of Thrombo-inflammation in Ischemic Stroke: Focus on the Manipulation and Clinical Application.

Stroke leaves a great economic burden due to its high morbidity and mortality. Rapid revascularization of targeted vessel(s) is the effective treatment for ischemic stroke, but subsequent ischemia-reperfusion (I/R) injury is a common complication following revascularization, leading to microcirculation dysfunction and infarct volume increase. Thrombo-inflammation, the interaction between thrombosis and inflammation, plays a critical role in the pathophysiology of ischemic stroke. In the context of I/R injury, thrombo-inflammation consists of platelet activation, endothelial injury, and inflammatory cell infiltration. Numerous studies are devoted to exploring methods of regulating thrombo-inflammation to mitigate I/R injury post-stroke, including blocking activations of platelets and neutrophils. Drugs such as antiplatelet medications, anticoagulants, and glucocorticoids have been confirmed to have the potential to regulate thrombo-inflammation. Furthermore, several recently developed drugs have also shown promises in relieving I/R injury by manipulating thrombo-inflammation. However, the majority of these studies are still in the preclinical stage. Herein, in this review, we will address the mechanisms of thrombo-inflammation in ischemic stroke, related research advances, and particularly the clinical feasibility of thrombo-inflammation as a therapeutic strategy against I/R injury.

Regulation of the hematopoietic stem cell pool by C-Kit-associated trogocytosis.

Hematopoietic stem cells (HSCs) are routinely mobilized from the bone marrow (BM) to the blood circulation for clinical transplantation. However, the precise mechanisms by which individual stem cells exit the marrow are not understood. This study identified cell-extrinsic and molecular determinants of a mobilizable pool of blood-forming stem cells. We found that a subset of HSCs displays macrophage-associated markers on their cell surface. Although fully functional, these HSCs are selectively niche-retained as opposed to stem cells lacking macrophage markers, which exit the BM upon forced mobilization. Macrophage markers on HSCs could be acquired through direct transfer by trogocytosis, regulated by receptor tyrosine-protein kinase C-Kit (CD117), from BM-resident macrophages in mouse and human settings. Our study provides proof of concept that adult stem cells utilize trogocytosis to rapidly establish and activate function-modulating molecular mechanisms.

Novel GPIb-independent platelet aggregation induced by botrocetin: Implications for diagnosis and antithrombotic therapy.

BACKGROUND: Snake venom botrocetin facilitates von Willebrand factor (VWF) binding to platelet GPIbα and has been widely used for the diagnosis of von Willebrand diseases and GPIb-related disorders. Botrocetin is also commonly employed for the development/characterization of antithrombotics targeting the GPIb-VWF axis. OBJECTIVE: To explore the alternative receptor(s)/mechanisms participate in botrocetin-induced platelet aggregation. METHODS: The effects of botrocetin on platelet aggregation were examined using platelets from wild-type, VWF and fibrinogen-deficient, GPIbα-deficient, IL4Rα/GPIbα-transgenic and αIIbß3-deficient mice, Bernard-Soulier syndrome (BSS) and healthy human samples. Platelet-fibrinogen and platelet-VWF interaction were measured using flow cytometry. GPIbα-VWF binding was evaluated utilizing ELISA. Botrocetin-αIIbß3 and botrocetin-GPIbα interactions were measured using ELISA and fluorescence anisotropy assays. Heparinized whole blood from healthy donors was examined for thrombus formation and growth in a perfusion chamber. RESULTS: Botrocetin could induce aggregation of platelets from a BSS patient and GPIbα-deficient mice as well as platelets lacking the N-terminal extracellular domain of GPIbα. Botrocetin could interact with αIIbß3 and facilitated αIIbß3-VWF interaction independent of GPIb. Botrocetin competitively bound to the ligand-binding domain of activated rather than resting αIIbß3. Although botrocetin-induced platelet aggregation requires VWF, strikingly, in the absence of VWF, botrocetin blocked fibrinogen and other ligand binding to αIIbß3, and inhibited platelet aggregation and thrombus formation. Consistently, recombinant botrocetin defective in VWF binding inhibited αIIbß3 and GPIb-mediated platelet aggregation, spreading and thrombus formation. CONCLUSION: Our study provides insights into avoiding the misdiagnosis of GPIb-related disorders and developing botrocetin mutants as potential new antithrombotics that may simultaneously target both αIIbß3 and GPIbα.

Photocontrolled Reversible Solid-Fluid Transitions of Azopolymer Nanocomposites for Intelligent Nanomaterials.

Intelligent polymer nanocomposites are multicomponent and multifunctional materials that show immense potential across diverse applications. However, to exhibit intelligent traits such as adaptability, reconfigurability and dynamic properties, these materials often require a solvent or heating environment to facilitate the mobility of polymer chains and nanoparticles, rendering their applications in everyday settings impractical. Here intelligent azopolymer nanocomposites that function effectively in a solvent-free, room-temperature environment based on photocontrolled reversible solid-fluid transitions via switching flow temperatures (Tfs) are shown. A range of nanocomposites is synthesized through the grafting of Au nanoparticles, Au nanorods, quantum dots, or superparamagnetic nanoparticles with photoresponsive azopolymers. Leveraging the reversible cis-trans photoisomerization of azo groups, the azopolymer nanocomposites transition between solid (Tf above room temperature) and fluid (Tf below room temperature) states. Such photocontrolled reversible solid-fluid transitions empower the rewriting of nanopatterns, correction of nanoscale defects, reconfiguration of complex multiscale structures, and design of intelligent optical devices. These findings highlight Tf-switchable polymer nanocomposites as promising candidates for the development of intelligent nanomaterials operative in solvent-free, room-temperature conditions.

Trafficking circuit of CD8+ T cells between the intestine and bone marrow governs antitumour immunity.

Immunotherapy elicits a systemic antitumour immune response in peripheral circulating T cells. However, the T cell trafficking circuit between organs and their contributions to antitumour immunity remain largely unknown. Here we show in multiple mouse leukaemia models that high infiltration of leukaemic cells in bone marrow (BM) stimulates the transition of CD8+CD44+CD62L+ central memory T cells into CD8+CD44-CD62L- T cells, designated as inter-organ migratory T cells (TIM cells). TIM cells move from the BM to the intestine by upregulating integrin ß7 and downregulating C-X-C motif chemokine receptor 3 during leukaemogenesis. Upon immunogenic chemotherapy, these BM-derived TIM cells return from the intestine to the BM through integrin α4-vascular cell adhesion molecule 1 interaction. Blocking C-X-C motif chemokine receptor 3 function boosts the immune response against leukaemia by enhancing T cell trafficking. This phenomenon can also be observed in patients with leukaemia. In summary, we identify an unrecognized intestine-BM trafficking circuit of T cells that contributes to the antitumour effects of immunogenic chemotherapy.

Comparative study on the structure characterization and activity of RS5 made from Canna edulis native starch and high-amylose corn starch.

In this study, the high amylose corn starch and Canna edulis native starch were compounded with lauric acid and fermented by human fecal inoculation in vitro. Changes in beneficial metabolite profile and microbiota composition were evaluated. The structural properties showed that both NS-12C and HAMS-12C formed V-shaped crystals under the same preparation method, but NS-12C had a higher composite index and resistance content than HAMS-12C. At the end of fermentation, the starch-lauric acid complexes prepared from the two types of starch significantly promoted the formation of short-chain fatty acids and the contents of acetic acid, butyric acid and valeric acid produced by NS-12C were higher than those of HAMS-12C(p>0.05). HAMS-12C and NS-12C both increased the relative abundance of Blautia. Notably, NS-12C also increased the relative abundance of beneficial bacteria Bifidobacterium and Meganomas, while HAMS-12C did not. These results suggested that this effect may be related to starch type and provide a basis for designing and producing functional foods to improve intestinal health in Canna edulis native starch.

CircHIF1A induces cetuximab resistance in colorectal cancer by promoting HIF1α-mediated glycometabolism alteration.

Epidermal growth factor receptor (EGFR)-targeted therapy is an important treatment for RAS wild-type metastatic colorectal cancer (mCRC), but the resistance mechanism remains unclear. Here, the differential expression of circRNAs between Cetuximab sensitive and resistant cell lines was analyzed using whole-transcriptome sequencing. We identified that the expression of circHIF1A was significantly higher in LIM1215-R than in LIM1215. When treated with Cetuximab, downregulation of circHIF1A level weakened the proliferation and clonal formation ability of LIM1215-R, caused more cells to enter G0-G1 phase, and significantly reduced the basal respiration, ATP production, and maximal respiration, as well as the glycolytic capacity and glycolytic reserve. The response rate and prognosis of circHIF1A-positive patients were inferior to those of negative patients. Mechanistically, circHIF1A can upregulate the level of hypoxia-inducible factor 1 A (HIF1A) by competitively binding to miR-361-5p, inducing the overexpression of enzymes such as glucose transporter 1 (GLUT1) and lactate dehydrogenase A (LDHA). In a xenograft model, inhibition of circHIF1A expression increased the sensitivity to Cetuximab treatment. In conclusion, circHIF1A can promote HIF1α-mediated glycometabolism alteration to induce Cetuximab resistance in CRC. It has the potential to become a screening indicator for the Cetuximab beneficial population in mCRC and a new therapeutic target for enhancing treatment efficacy.

Unveiling the gastric microbiota: implications for gastric carcinogenesis, immune responses, and clinical prospects.

High-throughput sequencing has ushered in a paradigm shift in gastric microbiota, breaking the stereotype that the stomach is hostile to microorganisms beyond H. pylori. Recent attention directed toward the composition and functionality of this 'community' has shed light on its potential relevance in cancer. The microbial composition in the stomach of health displays host specificity which changes throughout a person's lifespan and is subject to both external and internal factors. Distinctive alterations in gastric microbiome signature are discernible at different stages of gastric precancerous lesions and malignancy. The robust microbes that dominate in gastric malignant tissue are intricately implicated in gastric cancer susceptibility, carcinogenesis, and the modulation of immunosurveillance and immune escape. These revelations offer fresh avenues for utilizing gastric microbiota as predictive biomarkers in clinical settings. Furthermore, inter-individual microbiota variations partially account for differential responses to cancer immunotherapy. In this review, we summarize current literature on the influence of the gastric microbiota on gastric carcinogenesis, anti-tumor immunity and immunotherapy, providing insights into potential clinical applications.

Apolipoprotein A-IV polymorphisms Q360H and T347S attenuate its endogenous inhibition of thrombosis.

Platelets are small anucleate cells that play a key role in thrombosis and hemostasis. Our group previously identified apolipoprotein A-IV (apoA-IV) as an endogenous inhibitor of thrombosis by competitive blockade of the αIIbß3 integrin on platelets. ApoA-IV inhibition of platelets was dependent on the N-terminal D5/D13 residues, and enhanced with absence of the C-terminus, suggesting it sterically hinders its N-terminal platelet binding site. The C-terminus is also the site of common apoA-IV polymorphisms apoA-IV-1a (T347S) and apoA-IV-2 (Q360H). Interestingly, both are linked with an increased risk of cardiovascular disease, however, the underlying mechanism remains unclear. Here, we generated recombinant apoA-IV and found that the Q360H or T347S polymorphisms dampened its inhibition of platelet aggregation in human platelet-rich plasma and gel-filtered platelets, reduced its inhibition of platelet spreading, and its inhibition of P-selectin on activated platelets. Using an ex vivo thrombosis assay, we found that Q360H and T347S attenuated its inhibition of thrombosis at both high (1800s-1) and low (300s-1) shear rates. We then demonstrate a conserved monomer-dimer distribution among apoA-IV WT, Q360H, and T347S and use protein structure modelling software to show Q360H and T347S enhance C-terminal steric hindrance over the N-terminal platelet-binding site. These data provide critical insight into increased cardiovascular risk for individuals with Q360H or T347S polymorphisms.

Reconfiguring hydrogel assemblies using a photocontrolled metallopolymer adhesive for multiple customized functions.

Stimuli-responsive hydrogels with programmable shape changes are promising materials for soft robots, four-dimensional printing, biomedical devices and artificial intelligence systems. However, these applications require the fabrication of hydrogels with complex, heterogeneous and reconfigurable structures and customizable functions. Here we report the fabrication of hydrogel assemblies with these features by reversibly gluing hydrogel units using a photocontrolled metallopolymer adhesive. The metallopolymer adhesive firmly attached individual hydrogel units via metal-ligand coordination and polymer chain entanglement. Hydrogel assemblies containing temperature- and pH-responsive hydrogel units showed controllable shape changes and motions in response to these external stimuli. To reconfigure their structures, the hydrogel assemblies were disassembled by irradiating the metallopolymer adhesive with light; the disassembled hydrogel units were then reassembled using the metallopolymer adhesive with heating. The shape change and structure reconfiguration abilities allow us to reprogramme the functions of hydrogel assemblies. The development of reconfigurable hydrogel assemblies using reversible adhesives provides a strategy for designing intelligent materials and soft robots with user-defined functions.

High-throughput prediction of enzyme promiscuity based on substrate-product pairs.

The screening of enzymes for catalyzing specific substrate-product pairs is often constrained in the realms of metabolic engineering and synthetic biology. Existing tools based on substrate and reaction similarity predominantly rely on prior knowledge, demonstrating limited extrapolative capabilities and an inability to incorporate custom candidate-enzyme libraries. Addressing these limitations, we have developed the Substrate-product Pair-based Enzyme Promiscuity Prediction (SPEPP) model. This innovative approach utilizes transfer learning and transformer architecture to predict enzyme promiscuity, thereby elucidating the intricate interplay between enzymes and substrate-product pairs. SPEPP exhibited robust predictive ability, eliminating the need for prior knowledge of reactions and allowing users to define their own candidate-enzyme libraries. It can be seamlessly integrated into various applications, including metabolic engineering, de novo pathway design, and hazardous material degradation. To better assist metabolic engineers in designing and refining biochemical pathways, particularly those without programming skills, we also designed EnzyPick, an easy-to-use web server for enzyme screening based on SPEPP. EnzyPick is accessible at http://www.biosynther.com/enzypick/.

Structure properties of Canna edulis RS3 (double enzyme hydrolysis) and RS4 (OS-starch and cross-linked starch): Influence on fermentation products and human gut microbiota.

This study investigated the in vitro fermentation characteristics of different structural types of Canna edulis resistant starch (RS). RS3 was prepared through a double enzyme hydrolysis method, and RS4 (OS-starch and cross-linked starch) was prepared using octenyl succinic anhydride and sodium trimetaphosphate/sodium tripolyphosphate, respectively. The RS3 and RS4 samples were structurally analyzed using scanning electron microscopy, Fourier-transform infrared spectroscopy, differential scanning calorimetry, and X-ray diffraction analysis. This was followed by in vitro fermentation experiments. The results revealed microstructure differences in the two groups of starch samples. Compared to native starch, RS3 and RS4 exhibited a lower degree of order and endothermic energy, with lower crystallinity (RS3: 29.59 ± 1.11 %; RS4 [OS-starch]: 28.01 ± 1.32 %; RS4 [cross-linked starch]: 30.44 ± 1.73 %) than that in native starch (36.29 ± 0.89 %). The RS content was higher in RS3 (63.40 ± 2.85 %) and RS4 (OS-starch: 71.21 ± 1.28 %; cross-linked starch: 74.33 ± 0.643 %) than in native starch (57.71 ± 2.95 %). RS3 and RS4 exhibited slow fermentation rates, promoting the production of short-chain fatty acids. RS3 and cross-linked starch significantly increased the production of acetate and butyrate. Moreover, RS3 significantly promoted the abundance of Lactobacillus, while OS-starch and cross-linked starch significantly enhanced the abundance of Dorea and Coprococcus, respectively. Hence, the morphological structure and RS content of the samples greatly influenced the fermentation rate. Moreover, the different varieties of RS induced specific gut microbial regulation. Hence, they show potential applications in functional foods for tailored gut microbiota management.

Enhanced Deep-Learning Model for Carbon Footprints of Chemicals.

Millions of chemicals have been designed; however, their product carbon footprints (PCFs) are largely unknown, leaving questions about their sustainability. This general lack of PCF data is because the data needed for comprehensive environmental analyses are typically not available in the early molecular design stages. Several predictive tools have been developed to estimate the PCF of chemicals, which are applicable to only a narrow range of common chemicals and have limited predictive ability. Here, we propose FineChem 2, which is based on a novel transformer framework and first-hand industry data, for accurately predicting the PCF of chemicals. Compared to previous tools, FineChem 2 demonstrates significantly better predictive power, and its applicability domains are improved by ∼75% on a diverse set of chemicals on the global market, including the high-production-volume chemicals identified by regulators, daily chemicals, and chemical additives in food and plastics. In addition, through better interpretability from the attention mechanism, FineChem 2 may successfully identify PCF-intensive substructures and critical raw materials of chemicals, providing insights into the design of more sustainable molecules and processes. Therefore, we highlight FineChem 2 for estimating the PCF of chemicals, contributing to advancements in the sustainable transition of the global chemical industry.

Longitudinal Profiling of Fasting Plasma Metabolome in Response to Weight-Loss Interventions in Patients with Morbid Obesity.

It is well recognized that patients with severe obesity exhibit remarkable heterogeneity in response to different types of weight-loss interventions. Those who undergo Roux-en-Y gastric bypass (RYGB) usually exhibit more favorable glycemic outcomes than those who receive adjustable gastric banding (BAND) or intensive medical intervention (IMI). The molecular mechanisms behind these observations, however, remain largely unknown. To identify the plasma metabolites associated with differential glycemic outcomes induced by weight-loss intervention, we studied 75 patients with severe obesity (25 each in RYGB, BAND, or IMI). Using untargeted metabolomics, we repeatedly measured 364 metabolites in plasma samples at baseline and 1-year after intervention. Linear regression was used to examine whether baseline metabolites or changes in metabolites are associated with differential glycemic outcomes in response to different types of weight-loss intervention, adjusting for sex, baseline age, and BMI as well as weight loss. Network analyses were performed to identify differential metabolic pathways involved in the observed associations. After correction for multiple testing (q < 0.05), 33 (RYGB vs. IMI) and 28 (RYGB vs. BAND) baseline metabolites were associated with changes in fasting plasma glucose (FPG) or glycated hemoglobin (HbA1c). Longitudinal changes in 38 (RYGB vs. IMI) and 38 metabolites (RYGB vs. BAND) were significantly associated with changes in FPG or HbA1c. The identified metabolites are enriched in pathways involved in the biosynthesis of aminoacyl-tRNA and branched-chain amino acids. Weight-loss intervention evokes extensive changes in plasma metabolites, and the altered metabolome may underlie the differential glycemic outcomes in response to different types of weight-loss intervention, independent of weight loss itself.

Study of the self-assembly, drug encapsulating and delivering characteristics of short chain amylose-based type 3 resistant starch nanoparticles from Canna edulis.

In developing type 3 resistant starch (RS3) from Canna edulis for use as functional food ingredients, we investigated the synthesis of C. edulis RS3 nanoparticles. Simultaneously, we explored the potential of C. edulis short-chain amylose (SCA)-based RS3 nanoparticles (RS3N) as a targeted delivery system, with a specific focus on colon targeting, yielding promising insights. Our study revealed that the degree of polymerization (DP) of C. edulis SCA, particularly the chains of DP 36- 100, exhibited a robust correlation with the particle size and physicochemical characteristics of C. edulis SCA-based RS3N. Additionally, recrystallization temperature variation (4, 25, and 45 °C) significantly influenced the self-assembly behavior of C. edulis SCA, with the preparation at 4 °C resulting in more uniform particle size distributions. In further expanding the scope of applications for C. edulis SCA-based RS3N, we harnessed the potential of Fe3O4 and curcumin (CUR) as guest molecules to assess drug encapsulation and colon-targeting capabilities. Incorporating Fe3O4 into the self-assembly system led to the production of magnetic RS3N, confirming the successful encapsulation of Fe3O4 within C. edulis SCA-based RS3N. Furthermore, in vitro experiments have demonstrated that CUR-RS3N was stable in the gastrointestinal tract and gradually released curcumin with fermentation in the colonic environment. Collectively, these findings provide invaluable insights into the intricate self-assembly behavior of C. edulis SCA with varying fine structures and recrystallization temperatures during RS3N formation. Moreover, they underscore the colon-targeted properties of C. edulis SCA-based RS3N, opening promising avenues for its application within the food industry, particularly in advanced controlled drug delivery systems.

Addition of Canna edulis starch and starch nanoparticles to stabilized Pickering emulsions: In vitro digestion and fecal fermentation.

Starch nanoparticles (SNPs) were prepared through acid hydrolysis of Canna edulis native starch and modified with octenyl succinic anhydride (OSA) to yield OS-starch and OS-SNPs. These modified particles were used to stabilize curcumin-loaded Pickering emulsions. Effects on gut microbiota during in vitro fecal fermentation were examined. The surface of OS-starch exhibits a porous structure, while OS-SNPs display layered grooves. OSA modification was confirmed by Fourier transform infrared spectroscopy (with peaks at 1728 cm-1 and 1573 cm-1) and proton nuclear magnetic resonance spectra (0.5-2 ppm). The degree of substitution for OS-starch and OS-SNPs is 0.0106 ± 0.0004 and 0.0079 ± 0.0003, respectively. Following modification, the crystallinity decreased from 35.69 ± 0.46 % (native starch) to 30.17 ± 0.70 % (OS-starch), SNPs decreased from 45.87 ± 0.89 % to 43.63 ± 0.64 % (OS-SNPs). Contact angles for OS-starch and OS-SNPs are 77.47 ± 1.78 and 55.57 ± 0.21, respectively. OS-SNPs exhibited superior emulsification properties compared to OS-starch, forming stable Pickering emulsions with pseudoplastic fluid behavior and enhanced curcumin storage protection over 14 days (60.88 ± 4.26 %) with controlled release. Stabilizing Pickering emulsions with OS-starch and OS-SNPs positively affected on gut microbiota and improved the intestinal environment, showing promise for their application in transportation systems and innovative prebiotic food formulations.

Carboxymethyl chitosan and octadecylamine-coated liposome-containing WPTS: design, optimization, and evaluation.

Liposomes (LPs) are a delivery system for stabilizing pharmaceuticals with limited use due to their propensity to congregate and fuse. A proposed method of addressing these problems is polymer coating. In this study, the potential of octadecylamine (ODA)-coated liposomes and carboxymethyl chitosan (CMCS/ODA-LPs) for enhancing Wacao pentacyclic triterpene saponin (WPTS) transport capacity was investigated. CMCS/ODA-LPs were produced by electrostatic adsorption and thin-film hydration. Response surface methodology (RSM) was employed to enhance the process and encapsulation efficiency (EE) for optimum drug encapsulation efficiency. The synthesized WPTS-CMCS/ODA-LPs were uniformly dispersed in a circular shape, and during 14 days of storage at 4 °C, the particle size and morphology did not significantly change. Vesicle size, zeta potential, polydispersity index (PDI), and entrapment efficiency (%) were 179.1 ± 7.31 nm, -29.6 ± 1.35 mV, 0.188 ± 0.052, and 75.62 ± 0.43, respectively. The hemolysis test revealed that WPTS-CMCS/ODA-LPs were sufficiently biocompatible. Compared to WPTS-LPs, WPTS-CMCS/ODA-LPs consistently showed a much more significant cytotoxic effect on cancer cells. Early and WPTS-CMCS/ODA-LPs-induced apoptosis resulted in almost seven times more cell death than the control. Compared to physiological pH 7.3, the pH-sensitive CMCS coupled LPs increased drug release at acidic pH 6.5. These findings suggest the efficacy of pH-sensitive CMCS/ODA-LPs as a medication delivery method for WPTS.

MCF2Chem: A manually curated knowledge base of biosynthetic compound production.

BACKGROUND: Microbes have been used as cell factories to synthesize various chemical compounds. Recent advances in synthetic biological technologies have accelerated the increase in the number and capacity of microbial cell factories; the variety and number of synthetic compounds produced via these cell factories have also grown substantially. However, no database is available that provides detailed information on the microbial cell factories and the synthesized compounds. RESULTS: In this study, we established MCF2Chem, a manually curated knowledge base on the production of biosynthetic compounds using microbial cell factories. It contains 8888 items of production records related to 1231 compounds that were synthesizable by 590 microbial cell factories, including the production data of compounds (titer, yield, productivity, and content), strain culture information (culture medium, carbon source/precursor/substrate), fermentation information (mode, vessel, scale, and condition), and other information (e.g., strain modification method). The database contains statistical analyses data of compounds and microbial species. The data statistics of MCF2Chem showed that bacteria accounted for 60% of the species and that "fatty acids", "terpenoids", and "shikimates and phenylpropanoids" accounted for the top three chemical products. Escherichia coli, Saccharomyces cerevisiae, Yarrowia lipolytica, and Corynebacterium glutamicum synthesized 78% of these chemical compounds. Furthermore, we constructed a system to recommend microbial cell factories suitable for synthesizing target compounds and vice versa by combining MCF2Chem data, additional strain- and compound-related data, the phylogenetic relationships between strains, and compound similarities. CONCLUSIONS: MCF2Chem provides a user-friendly interface for querying, browsing, and visualizing detailed statistical information on microbial cell factories and their synthesizable compounds. It is publicly available at https://mcf.lifesynther.com . This database may serve as a useful resource for synthetic biologists.

Local membrane source gathering by p62 body drives autophagosome formation.

Autophagosomes are double-membrane vesicles generated intracellularly to encapsulate substrates for lysosomal degradation during autophagy. Phase separated p62 body plays pivotal roles during autophagosome formation, however, the underlying mechanisms are still not fully understood. Here we describe a spatial membrane gathering mode by which p62 body functions in autophagosome formation. Mass spectrometry-based proteomics reveals significant enrichment of vesicle trafficking components within p62 body. Combining cellular experiments and biochemical reconstitution assays, we confirm the gathering of ATG9 and ATG16L1-positive vesicles around p62 body, especially in Atg2ab DKO cells with blocked lipid transfer and vesicle fusion. Interestingly, p62 body also regulates ATG9 and ATG16L vesicle trafficking flux intracellularly. We further determine the lipid contents associated with p62 body via lipidomic profiling. Moreover, with in vitro kinase assay, we uncover the functions of p62 body as a platform to assemble ULK1 complex and invigorate PI3KC3-C1 kinase cascade for PI3P generation. Collectively, our study raises a membrane-based working model for multifaceted p62 body in controlling autophagosome biogenesis, and highlights the interplay between membraneless condensates and membrane vesicles in regulating cellular functions.