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1.
Res Sq ; 2024 Jun 03.
Article in English | MEDLINE | ID: mdl-38883721

ABSTRACT

The mechanisms through which systemic inflammation exerts its effect on the CNS are still not completely understood. Exosomes are small (30 to 100 nanometers) membrane-bound extracellular vesicles released by most of the mammalian cells. Exosomes play a vital role in cell-to-cell communication. This includes regulation of inflammatory responses by shuttling mRNAs, miRNAs, and cytokines both locally and systemically to the neighboring as well as distant cells to further modulate their transcriptional and/or translational states and affect the functional phenotype of those cells that have taken up these exosomes. The role of circulating blood exosomes leading to neuroinflammation during systemic inflammatory conditions was further characterized. Serum-derived exosomes from LPS-challenged mice (SDEL) were freshly isolated from the sera of the mice that were earlier treated with LPS and used to study SDEL effects on neuroinflammation. Exosomes isolated from the sera of the mice injected with saline were used as a control. In-vitro studies showed that the SDEL upregulate pro-inflammatory cytokine gene expression in the murine cell lines of microglia (BV-2), astrocytes (C8-D1A), and cerebral microvascular endothelial cells (bEnd.3). To further study their effects in-vivo, SDEL were intravenously injected into normal adult mice. Elevated mRNA expression of pro-inflammatory cytokines was observed in the brains of SDEL recipient mice. Proteomic analysis of the SDEL confirmed the increased expression of inflammatory cytokines in them. Together, these results further demonstrate and strengthen the novel role of peripheral circulating exosomes in causing neuroinflammation during systemic inflammatory conditions.

2.
Polymers (Basel) ; 16(7)2024 Mar 22.
Article in English | MEDLINE | ID: mdl-38611132

ABSTRACT

In low-pressure wax injection molding, cooling time refers to the period during which the molten plastic inside the mold solidifies and cools down to a temperature where it can be safely ejected without deformation. However, cooling efficiency for the mass production of injection-molded wax patterns is crucial. This work aims to investigate the impact of varying surface roughness on the inner walls of the cooling channel on the cooling efficiency of an aluminum-filled epoxy resin rapid tool. It was found that the cooling time for the injection-molded products can be determined by the surface roughness according to the proposed prediction equation. Employing fiber laser processing on high-speed steel rods allows for the creation of microstructures with different surface roughness levels. Results demonstrate a clear link between the surface roughness of cooling channel walls and cooling time for molded wax patterns. Employing an aluminum-filled epoxy resin rapid tool with a surface roughness of 4.9 µm for low-pressure wax injection molding can save time, with a cooling efficiency improvement of approximately 34%. Utilizing an aluminum-filled epoxy resin rapid tool with a surface roughness of 4.9 µm on the inner walls of the cooling channel can save the cooling time by up to approximately 60%. These findings underscore the significant role of cooling channel surface roughness in optimizing injection molding processes for enhanced efficiency.

3.
Eur J Pharmacol ; 965: 176331, 2024 Feb 15.
Article in English | MEDLINE | ID: mdl-38220140

ABSTRACT

Inflammatory bowel disease (IBD) is a condition characterized by inflammation in the gastrointestinal tract. Reducing intestinal inflammation is a promising approach for treating IBD. The nucleotide-binding oligomerization domain-like receptor family pyrin domain-containing protein 3 (NLRP3) inflammasome, a critical component of the innate immune system, is implicated in the pathogenesis of IBD. Therefore, inhibiting NLRP3 inflammasome activation is a potential therapeutic strategy for IBD. In this study, we investigated the effects of the interleukin-5 (IL-5) receptor antagonist YM-90709 on dextran sulfate sodium-induced experimental colitis in mice. We found that YM-90709 reduced the expressions of IL-1ß and caspase-1 p20 in the colon and ameliorated colitis. Furthermore, we identified YM-90709 as an effective agent for inhibiting NLRP3 inflammasome activation. Knockdown of IL-5 receptor or using an inhibitor of STAT5, a key transcription factor downstream of the IL-5/IL-5 receptor signal pathway, also reduced NLRP3 inflammasome-dependent IL-1ß release and ASC speck formation. Our study is the first to demonstrate that the NLRP3 inflammasome may be a downstream signal of IL-5/IL-5 receptor and that YM-90709 protects against IBD by inhibiting IL-5 receptor. These findings suggest a new strategy for regulating intestinal inflammation and managing IBD.


Subject(s)
Colitis , Inflammatory Bowel Diseases , Animals , Mice , Inflammasomes/metabolism , NLR Family, Pyrin Domain-Containing 3 Protein/metabolism , Dextran Sulfate/toxicity , Receptors, Interleukin-5 , Interleukin-5/adverse effects , Colitis/chemically induced , Colitis/drug therapy , Inflammation , Caspase 1/metabolism , Interleukin-1beta/metabolism , Mice, Inbred C57BL
4.
Nucleic Acids Res ; 52(D1): D483-D493, 2024 Jan 05.
Article in English | MEDLINE | ID: mdl-37941148

ABSTRACT

MESPEUS is a freely accessible database which uses carefully selected metal coordination groups found in metalloprotein structures taken from the Protein Data Bank. The database contains geometrical information of metal sites within proteins, including 40 metal types. In order to completely determine the metal coordination, the symmetry-related units of a given protein structure are taken into account and are generated using the appropriate space group symmetry operations. This permits a more complete description of the metal coordination geometry by including all coordinating atoms. The user-friendly web interface allows users to directly search for a metal site of interest using several useful options, including searching for metal elements, metal-donor distances, coordination number, donor residue group, and structural resolution. These searches can be carried out singly or in combination. The details of a metal site and the metal site(s) in the whole structure can be graphically displayed using the interactive web interface. MESPEUS is automatically updated monthly by synchronizing with the PDB database. An investigation for the Mg-ATP interaction is given to demonstrate how MESPEUS can be used to extract information about metal sites by selecting structure and coordination features. MESPEUS is available at http://mespeus.nchu.edu.tw/.


Subject(s)
Metalloproteins , Metalloproteins/chemistry , Metals/chemistry , Databases, Protein , User-Computer Interface , Internet
5.
Article in English | MEDLINE | ID: mdl-37672376

ABSTRACT

Learning probabilistic models that can estimate the density of a given set of samples, and generate samples from that density, is one of the fundamental challenges in unsupervised machine learning. We introduce a new generative model based on denoising density estimators (DDEs), which are scalar functions parametrized by neural networks, that are efficiently trained to represent kernel density estimators of the data. Leveraging DDEs, our main contribution is a novel technique to obtain generative models by minimizing the Kullback-Leibler (KL)-divergence directly. We prove that our algorithm for obtaining generative models is guaranteed to converge consistently to the correct solution. Our approach does not require specific network architecture as in normalizing flows (NFs), nor use ordinary differential equation (ODE) solvers as in continuous NFs. Experimental results demonstrate substantial improvement in density estimation and competitive performance in generative model training.

6.
Cancer Nurs ; 2023 Aug 08.
Article in English | MEDLINE | ID: mdl-37552228

ABSTRACT

BACKGROUND: Chimeric antigen receptor T-cell therapy-related severe cytokine release syndrome (sCRS) has seriously affected the life safety of patients. OBJECTIVE: To explore the influencing factors of sCRS in children with B-cell hematological malignancies and build a risk prediction model. METHODS: The study recruited 115 children with B-cell hematological malignancies who received CD19- and CD22-targeted chimeric antigen receptor T-cell therapy. A nomogram model was established based on symptomatic adverse events and highly accessible clinical variables. The model discrimination was evaluated by the area under the receiver operating characteristic curve. The calibration of our model was evaluated by the calibration curve and Hosmer-Lemeshow test. The bootstrap self-sampling method was used to internally validate. RESULTS: Thirty-seven percent of the children experienced sCRS. Indicators included in the nomogram were tumor burden before treatment, thrombocytopenia before pretreatment, and the mean value of generalized muscle weakness and headache scores. The results showed that the area under the receiver operating characteristic curve was 0.841, and the calibration curve showed that the probability of sCRS predicted by the nomogram was in good agreement with the actual probability of sCRS. The Hosmer-Lemeshow test indicated that the model fit the data well (χ2 = 5.759, P = .674). The concordance index (C-index) obtained by internal validation was 0.841 (0.770, 0.912). CONCLUSIONS: The nomogram model constructed has a good degree of discrimination and calibration, which provides a more convenient and visual evaluation tool for identifying the sCRS. IMPLICATIONS FOR PRACTICE: Incorporation of patient-reported outcomes into risk prediction models enables early identification of sCRS.

7.
IEEE Trans Pattern Anal Mach Intell ; 45(11): 13152-13169, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37399165

ABSTRACT

As a task that aims to assess the trustworthiness of the model's prediction output during deployment, confidence estimation has received much research attention recently, due to its importance for the safe deployment of deep models. Previous works have outlined two important characteristics that a reliable confidence estimation model should possess, i.e., the ability to perform well under label imbalance and the ability to handle various out-of-distribution data inputs. In this work, we propose a meta-learning framework that can simultaneously improve upon both characteristics in a confidence estimation model. Specifically, we first construct virtual training and testing sets with some intentionally designed distribution differences between them. Our framework then uses the constructed sets to train the confidence estimation model through a virtual training and testing scheme leading it to learn knowledge that generalizes to diverse distributions. Besides, we also incorporate our framework with a modified meta optimization rule, which converges the confidence estimator to flat meta minima. We show the effectiveness of our framework through extensive experiments on various tasks including monocular depth estimation, image classification, and semantic segmentation.

8.
J Therm Biol ; 116: 103649, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37478582

ABSTRACT

Abnormal temperature has important effects on the occurrence of ischemic stroke (IS). However, relatively less efforts have been taken to systematically unravel the association between various abnormal temperature and IS hospital admission. Focusing on three temperature indicators (i.e., mean temperature, maximum temperature, and minimum temperature), this study attempts to analyse how their abnormal values affect IS hospital admission. The dataset covers the period between September 17, 2012 and August 28, 2018, and includes a total of 1464 cases who were admitted to the hospital for the first onset of IS and lived in the main urban area of Guangzhou. The study adopts the time-stratified case-crossover analysis. Abnormal values of temperature were measured using the 2.5th and 97.5th quantile values of each temperature indicator, with the former refers to a low value whereas the latter a high one. The effects of abnormal temperature on IS hospital admission were assessed through calculating the relative risks induced by the low and high values (the median values of each temperature indicators were taken as the references). The results show that the risk window periods for IS hospital admission associated with the low values of the temperature indicators are the lags of 3-7 days and 18-19 days. The risks of high temperature values on IS admission, however, are insignificant with either one-day lag or cumulative lag. As to different population groups, females show higher risks of IS hospital admission at low temperature values than males; and elderly people, compared with young people, are more vulnerable to low temperature values. To cities with similar climate of Guangzhou, particular attention should be paid to the impact of low temperature values, especially the low value of minimum temperature, on IS admission, and to females and elderly people who are more sensitive to abnormal temperatures.


Subject(s)
Air Pollution , Ischemic Stroke , Male , Female , Humans , Aged , Adolescent , Temperature , China/epidemiology , Hospitals
9.
Cell Mol Life Sci ; 80(8): 230, 2023 Jul 27.
Article in English | MEDLINE | ID: mdl-37498355

ABSTRACT

The aberrant activation of the nucleotide-binding oligomerization domain-like receptor family pyrin domain containing 3 (NLRP3) inflammasome is known to contribute to the pathogenesis of various human inflammation-related diseases. However, to date, no small-molecule NLRP3 inhibitor has been used in clinical settings. In this study, we have identified SB-222200 as a novel direct NLRP3 inhibitor through the use of drug affinity responsive target stability assay, cellular thermal shift assay, and surface plasmon resonance analysis. SB-222200 effectively inhibits the activation of the NLRP3 inflammasome in macrophages, while having no impact on the activation of NLRC4 or AIM2 inflammasome. Furthermore, SB-222200 directly binds to the NLRP3 protein, inhibiting NLRP3 inflammasome assembly by blocking the NEK7 - NLRP3 interaction and NLRP3 oligomerization. Importantly, treatment with SB-222200 demonstrates alleviation of NLRP3-dependent inflammatory diseases in mouse models, such as monosodium urate crystal-induced peritonitis and dextran sulfate sodium-induced acute intestinal inflammation. Therefore, SB-222200 holds promise as a lead compound for the development of NLRP3 inhibitors to combat NLRP3-driven disease and serves as a versatile tool for pharmacologically investigating NLRP3 biology.


Subject(s)
NLR Family, Pyrin Domain-Containing 3 Protein , Peritonitis , Mice , Animals , Humans , NLR Family, Pyrin Domain-Containing 3 Protein/metabolism , Inflammasomes/metabolism , Peritonitis/chemically induced , Peritonitis/drug therapy , Peritonitis/metabolism , Macrophages/metabolism , Inflammation/metabolism , Mice, Inbred C57BL , Interleukin-1beta/metabolism
10.
Int J Hyg Environ Health ; 251: 114193, 2023 Jun.
Article in English | MEDLINE | ID: mdl-37247607

ABSTRACT

BACKGROUND: Extreme temperatures have an adverse effect on the occurrence of cardiovascular diseases (CVDs). Previous literatures tend to discuss the modification of CVDs occurrence by green space under high temperature. Relatively less attention is paid to the modification under low temperature. The variation of different attributes and spatial scales of green space in affecting CVDs occurrence are also overlooked. METHODS: This study collected a total of 4364 first-time admission cases due to CVDs in a tertiary hospital in Guangzhou from 2012 to 2018, measured the scale of green space by greening rate (GR) and percentage of landscape (PLAND), the distribution of green space by patch density (PD), mean nearest neighbor distance (ENN_MN) and largest patch index (LPI), and the accessibility of green space by green patch accessibility index (GPAI). Using the time stratified case crossover design method, the modification of low temperature-related CVDs occurrence by the above green space indicators is evaluated in an area with a radius of 100-1000 m which is further divided at an interval of 100 m. RESULTS: We found high GR, high PLAND, high PD, low ENN_MN, high LPI, and low GPAI corresponds to low risk of CVDs occurrence, the optimal modification scale of each green space indicator, which is radius corresponding to the maximum risk difference between high and low indicator subgroups, is around 800 m (GR), 600 m (PLAND and PD), 500 m (GPAI), and 300 m (LPI and ENN_MN), respectively. As the temperature decreases further, the health benefit from low GPAI at the optimal scale is weakened, whereas the benefits from the others are strengthened. CONCLUSIONS: Low temperature related CVDs occurrence risk can be modified by multiple green space indicators, and these modifications have spatial scale effect. Our findings have important theoretical and practical significance for the formulation and implementation of local green space policies.


Subject(s)
Cardiovascular Diseases , Humans , Cardiovascular Diseases/epidemiology , China/epidemiology , Hospitals , Parks, Recreational , Temperature , Cross-Over Studies
11.
IEEE Trans Pattern Anal Mach Intell ; 45(9): 11374-11381, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37015128

ABSTRACT

Dynamic neural networks can greatly reduce computation redundancy without compromising accuracy by adapting their structures based on the input. In this paper, we explore the robustness of dynamic neural networks against energy-oriented attacks targeted at reducing their efficiency. Specifically, we attack dynamic models with our novel algorithm GradMDM. GradMDM is a technique that adjusts the direction and the magnitude of the gradients to effectively find a small perturbation for each input, that will activate more computational units of dynamic models during inference. We evaluate GradMDM on multiple datasets and dynamic models, where it outperforms previous energy-oriented attack techniques, significantly increasing computation complexity while reducing the perceptibility of the perturbations https://github.com/lingengfoo/GradMDM.

12.
Sci Rep ; 13(1): 6911, 2023 04 27.
Article in English | MEDLINE | ID: mdl-37106073

ABSTRACT

Sarcopenia has been associated with conventional chemotherapy-related toxicity, postoperative complications and poor overall survival in patients with genotype-unselected metastatic colorectal cancer (mCRC). This study aimed to evaluate the prognostic implications of sarcopenia and its change after perioperative cetuximab plus doublet chemotherapy and hepatectomy in patients with RAS wild-type colorectal liver metastasis (CRLM). Patients with CRLM from 2007 to 2018 in Chang Gung Research Database were retrospectively analyzed. Baseline characteristics as well as skeletal muscle index (SMI) at baseline and dynamic changes after interventions were collected. A multivariate Cox proportional hazard model was used to evaluate the effect of each parameter on overall survival (OS), and the Kaplan-Meier method was used to establish survival curves. A two-sided p value < 0.05 was considered statistically significance. Of 214 RAS wild-type mCRC patients who received both cetuximab and doublet chemotherapy, 77 who received upfront or subsequent hepatectomy were included in this study. The median follow-up time was 2.3 years. The rate of sarcopenia was higher in the patients who received neoadjuvant cetuximab-containing regimens than in those who received upfront hepatectomy (95% versus 63%, p = 0.001). Increased SMI after perioperative systemic therapy remained independently associated with better OS in multivariate analysis [hazard ratio (HR) = 0.27/10% increase, p = 0.013). The patients with sarcopenia had a trend of worse OS than those without sarcopenia (median OS: 4.5 versus 3.6 years, log-rank p = 0.282). Improvement in sarcopenia ([SMI after intervention - initial SMI]/initial SMI × 100%) is an important prognostic factor for OS. Future research is warranted to investigate direct interventions for sarcopenia and the impact on OS.


Subject(s)
Colorectal Neoplasms , Liver Neoplasms , Sarcopenia , Humans , Sarcopenia/etiology , Hepatectomy/adverse effects , Cetuximab/therapeutic use , Retrospective Studies , Colorectal Neoplasms/complications , Colorectal Neoplasms/drug therapy , Colorectal Neoplasms/genetics , Liver Neoplasms/genetics , Liver Neoplasms/surgery , Liver Neoplasms/drug therapy , Prognosis , Antineoplastic Combined Chemotherapy Protocols/adverse effects
13.
J Orthop Surg Res ; 18(1): 222, 2023 Mar 21.
Article in English | MEDLINE | ID: mdl-36944974

ABSTRACT

BACKGROUND: Due to the poor specificity of D-dimer, more accurate thrombus biomarkers are clinically needed to improve the diagnostic power of VTE. METHODS: The plasma samples were classified into low-risk group (n = 6) and high-risk group (n = 6) according to the Caprini Thrombosis Risk Assessment Scale score. Data-independent acquisition mass spectrometry (DIA-MS) was performed to identify the proteins in the 12 plasma samples. Bioinformatics analysis including volcano plot, heatmap, KEGG pathways and chord diagram analysis were drawn to analyze the significantly differentially expressed proteins (DEPs) between the two groups. Then, another 26 plasma samples were collected to verify the key proteins as potential biomarkers of VTE in orthopedic surgery patients. RESULTS: A total of 371 proteins were identified by DIA-MS in 12 plasma samples. Volcano plotting showed that there were 30 DEPs. KEGG pathway enrichment analysis revealed that the DEPs were majorly involved in the blood coagulation pathway. The chord diagram analysis demonstrated that proteins SAA1, VWF, FLNA, ACTB, VINC, F13B, F13A and IPSP in the DEPs were significantly related to blood coagulation. VWF and F13B were selected for validation experiments. ELISA test showed that, as compared with those in the low-risk group, the level of VWF in the high-risk sera was significantly increased. CONCLUSIONS: The level of VWF in the high-risk group of thrombosis after orthopedic surgery was significantly higher than that in the low-risk group of preoperative thrombosis, suggesting that VWF may be used as a potential thrombus biomarker in orthopedic surgery patients.


Subject(s)
Orthopedic Procedures , Thrombosis , Venous Thromboembolism , Humans , von Willebrand Factor/analysis , von Willebrand Factor/metabolism , Proteomics , Risk Assessment , Biomarkers , Thrombosis/diagnosis , Thrombosis/etiology , Orthopedic Procedures/adverse effects
14.
ACS Synth Biol ; 12(4): 1119-1132, 2023 04 21.
Article in English | MEDLINE | ID: mdl-36943773

ABSTRACT

The optimization of cellular functions often requires the balancing of gene expression, but the physical construction and screening of alternative designs are costly and time-consuming. Here, we construct a strain of Saccharomyces cerevisiae that contains a "sensor array" containing bacterial regulators that respond to four small-molecule inducers (vanillic acid, xylose, aTc, IPTG). Four promoters can be independently controlled with low background and a 40- to 5000-fold dynamic range. These systems can be used to study the impact of changing the level and timing of gene expression without requiring the construction of multiple strains. We apply this approach to the optimization of a four-gene heterologous pathway to the terpene linalool, which is a flavor and precursor to energetic materials. Using this approach, we identify bottlenecks in the metabolic pathway. This work can aid the rapid automated strain development of yeasts for the bio-manufacturing of diverse products, including chemicals, materials, fuels, and food ingredients.


Subject(s)
Chromosomes, Fungal , Saccharomyces cerevisiae , Xylose , Chromosomes , Metabolic Engineering , Promoter Regions, Genetic/genetics , Saccharomyces cerevisiae/metabolism , Xylose/metabolism , Terpenes/metabolism
15.
Neurobiol Dis ; 181: 106096, 2023 06 01.
Article in English | MEDLINE | ID: mdl-37001611

ABSTRACT

Striatal medium spiny neurons (MSNs) and striatal dopamine (DA) innervation are profoundly important for brain function such as motor control and cognition. A widely accepted theory posits that striatal DA loss causes (or leads to) MSN dendritic atrophy. However, examination of the literature indicates that the data from Parkinson's disease (PD) patients and animal PD models were contradictory among studies and hard to interpret. Here we have re-examined the potential effects of DA activity on MSN morphology or lack thereof. We found that in 15-day, 4- and 12-month old Pitx3 null mutant mice that have severe DA denervation in the dorsal striatum while having substantial residual DA innervation in the ventral striatum, MSN dendrites and spine numbers were similar in dorsal and ventral striatum, and also similar to those in normal mice. In 15-day, 4- and 12-month old tyrosine hydroxylase knockout mice that cannot synthesize L-dopa and thus have no endogenous DA in the entire brain, MSN dendrites and spine numbers were also indistinguishable from age-matched wild-type (WT) mice. Furthermore, in adult WT mice, unilateral 6-OHDA lesion at 12 months of age caused an almost complete striatal DA denervation in the lesioned side, but MSN dendrites and spine numbers were similar in the lesioned and control sides. Taken together, our data indicate that in mice, the development and maintenance of MSN dendrites and spines are DA-independent such that DA depletion does not trigger MSN dendritic atrophy; our data also suggest that the reported MSN dendritic atrophy in PD may be a component of neurodegeneration in PD rather than a consequence of DA denervation.


Subject(s)
Dopamine , Parkinson Disease , Mice , Animals , Dopamine/physiology , Neurons/pathology , Dendritic Spines/pathology , Medium Spiny Neurons , Levodopa/pharmacology , Parkinson Disease/pathology , Corpus Striatum/pathology
16.
Front Public Health ; 11: 1060714, 2023.
Article in English | MEDLINE | ID: mdl-36794065

ABSTRACT

Background: Epidemiological studies have widely proven the impact of ozone (O3) on respiratory mortality, while only a few studies compared the association between different O3 indicators and health. Methods: This study explores the relationship between daily respiratory hospitalization and multiple ozone indicators in Guangzhou, China, from 2014 to 2018. It uses a time-stratified case-crossover design. Sensitivities of different age and gender groups were analyzed for the whole year, the warm and the cold periods. We compared the results from the single-day lag model and the moving average lag model. Results: The results showed that the maximum daily 8 h average ozone concentration (MDA8 O3) had a significant effect on the daily respiratory hospitalization. This effect was stronger than for the maximum daily 1 h average ozone concentration (MDA1 O3). The results further showed that O3 was positively associated with daily respiratory hospitalization in the warm season, while there was a significantly negative association in the cold season. Specifically, in the warm season, O3 has the most significant effect at lag 4 day, with the odds ratio (OR) equal to 1.0096 [95% confidence intervals (CI): 1.0032, 1.0161]. Moreover, at the lag 5 day, the effect of O3 on the 15-60 age group was less than that on people older than 60 years, with the OR value of 1.0135 (95% CI: 1.0041, 1.0231) for the 60+ age group; women were more sensitive than men to O3 exposure, with an OR value equal to 1.0094 (95% CI: 0.9992, 1.0196) for the female group. Conclusion: These results show that different O3 indicators measure different impacts on respiratory hospitalization admission. Their comparative analysis provided a more comprehensive insight into exploring associations between O3 exposure and respiratory health.


Subject(s)
Air Pollutants , Air Pollution , Ozone , Male , Humans , Female , Middle Aged , Air Pollution/analysis , Air Pollutants/analysis , Hospitalization , China/epidemiology
17.
Nucleic Acids Res ; 51(D1): D603-D610, 2023 01 06.
Article in English | MEDLINE | ID: mdl-36399496

ABSTRACT

With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.


Subject(s)
Genome , Genomics , Multigene Family , Biosynthetic Pathways/genetics
18.
Chem Biol Interact ; 365: 110122, 2022 Sep 25.
Article in English | MEDLINE | ID: mdl-36002070

ABSTRACT

Psoriasis is a common chronic autoinflammatory/autoimmune skin disease associated with elevated pro-inflammatory cytokines. The pivotal role of interleukin (IL)-1ß and nucleotide-binding oligomerization domain-like receptor family pyrin domain-containing protein 3 (NLRP3) inflammasome in the pathogenesis of psoriasis has been widely described. Accordingly, the suppression of NLRP3-dependent IL-1ß release is a potential therapy for psoriasis. Repurposing marketed drugs is a strategy for identifying new inhibitors of NLRP3 inflammasome activation. Herein, chlorquinaldol (CQD), a historic antimicrobial agent used as a topical treatment for skin and vaginal infections, was found to have a distinct effect by inhibiting NLRP3 inflammasome activation at concentrations ranging from 2 to 6 µM. CQD significantly suppressed apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC) oligomerization, NLRP3-ASC interaction, and pyroptosis in macrophages. The levels of cleaved IL-1ß and caspase-1 were reduced by CQD in the cell lysates of macrophages, suggesting that CQD acted on upstream of pore formation in the cell membrane. Mechanistically, CQD reduced mitochondrial reactive oxygen species production but did not affect the nuclear factor-κB (NF-κB) pathway. Intraperitoneal administration of CQD (15 mg/kg) for 6 days was found to improve the skin lesions in the imiquimod-induced psoriatic mouse model (male C57BL/6 mice), while secretion of pro-inflammatory cytokines (IL-17 and IL-1ß) and keratinocyte proliferation were significantly suppressed by CQD. In conclusion, CQD exerted inhibitory effects on NLRP3 inflammasome activation in macrophages and decreased the severity of psoriatic response in vivo. Such findings indicate that the repurposing of the old drug, CQD, is a potential pharmacological approach for the treatment of psoriasis and other NLRP3-driven diseases.


Subject(s)
Chlorquinaldol , Dermatitis , Psoriasis , Animals , Carrier Proteins/metabolism , Caspase 1/metabolism , Chlorquinaldol/adverse effects , Cytokines/metabolism , Female , Imiquimod/toxicity , Inflammasomes/metabolism , Interleukin-1beta/metabolism , Male , Mice , Mice, Inbred C57BL , NLR Family, Pyrin Domain-Containing 3 Protein/metabolism , Nucleotides/adverse effects , Nucleotides/metabolism , Psoriasis/chemically induced , Psoriasis/drug therapy , Pyrin Domain
19.
Mol Psychiatry ; 27(11): 4754-4769, 2022 Nov.
Article in English | MEDLINE | ID: mdl-35948662

ABSTRACT

Vascular cognitive impairment and dementia (VCID) is the second most common form of dementia after Alzheimer's disease (AD). Currently, the mechanistic insights into the evolution and progression of VCID remain elusive. White matter change represents an invariant feature. Compelling clinical neuroimaging and pathological evidence suggest a link between white matter changes and neurodegeneration. Our prior study detected hypoperfused lesions in mice with partial deficiency of endothelial nitric oxide (eNOS) at very young age, precisely matching to those hypoperfused areas identified in preclinical AD patients. White matter tracts are particularly susceptible to the vascular damage induced by chronic hypoperfusion. Using immunohistochemistry, we detected severe demyelination in the middle-aged eNOS-deficient mice. The demyelinated areas were confined to cortical and subcortical areas including the corpus callosum and hippocampus. The intensity of demyelination correlated with behavioral deficits of gait and associative recognition memory performances. By Evans blue angiography, we detected blood-brain barrier (BBB) leakage as another early pathological change affecting frontal and parietal cortex in eNOS-deficient mice. Sodium nitrate fortified drinking water provided to young and middle-aged eNOS-deficient mice completely prevented non-perfusion, BBB leakage, and white matter pathology, indicating that impaired endothelium-derived NO signaling may have caused these pathological events. Furthermore, genome-wide transcriptomic analysis revealed altered gene clusters most related to mitochondrial respiratory pathways selectively in the white matter of young eNOS-deficient mice. Using eNOS-deficient mice, we identified BBB breakdown and hypoperfusion as the two earliest pathological events, resulting from insufficient vascular NO signaling. We speculate that the compromised BBB and mild chronic hypoperfusion trigger vascular damage, along with oxidative stress and astrogliosis, accounting for the white matter pathological changes in the eNOS-deficient mouse model. We conclude that eNOS-deficient mice represent an ideal spontaneous evolving model for studying the earliest events leading to white matter changes, which will be instrumental to future therapeutic testing of drug candidates and for targeting novel/specific vascular mechanisms contributing to VCID and AD.


Subject(s)
Alzheimer Disease , Cognitive Dysfunction , Dementia, Vascular , White Matter , Animals , Mice , White Matter/pathology , Nitric Oxide/metabolism , Cerebrovascular Circulation , Dementia, Vascular/pathology , Dementia, Vascular/psychology , Disease Models, Animal , Cognitive Dysfunction/metabolism , Alzheimer Disease/metabolism
20.
ACS Appl Bio Mater ; 5(6): 2819-2833, 2022 06 20.
Article in English | MEDLINE | ID: mdl-35616917

ABSTRACT

The facile and straightforward fabrication of NIR-responsive theranostic materials with high biocompatibility is still an unmet need for nanomedicine applications. Here, we used a natural photosensitizer, iron chlorophyll (Chl/Fe), for the J-aggregate template-assisted synthesis of Au@Chl/Fe nanorods with high stability. The assembly of a high amount of Chl/Fe J-aggregate onto the Au surface enabled red-NIR fluorescence for monitoring and tracking residential tumor lesions. The Chl/Fe moieties condensed on the nanorods could change the redox balance by the photon induction of reactive oxygen species and attenuate iron-mediated lipid peroxidation by inducing a Fenton-like reaction. After conjugation with carboxyphenylboronic acid (CPBA) to target the glycoprotein receptor on T24 bladder cancer (BC) cells, the enhanced delivery of Au@Chl/Fe-CPBA nanorods could induce over 85% cell death at extremely low concentrations of 0.16 ppm[Au] at 660 nm and 1.6 ppm[Au] at 785 nm. High lipid peroxidation, as shown by BODIPY staining and GSH depletion, was observed when treated T24 cells were exposed to laser irradiation, suggesting that preliminary photodynamic therapy (PDT) can revitalize Fenton-like reaction-mediated chemodynamic ferroptosis in T24 cells. We also manipulated the localized administration of Au@Chl-Fe combined with PDT at restricted regions in orthotopic tumor-bearing mice to cure malignant BC successfully without recurrence. By intravesical instillation of the Au@Chl/Fe-CPBA nanorods, this localized treatment could prevent the material from entering the systemic circulation, thus minimizing systemic toxicity. Upon activating NIR-PDT-elicited chemodynamic therapy, ultrasound imaging revealed almost complete tumor remission. Anti-tumor efficacy and survival benefit were achieved with a green photosensitizer.


Subject(s)
Nanotubes , Photochemotherapy , Urinary Bladder Neoplasms , Animals , Chlorophyll/pharmacology , Gold , Iron , Mice , Photochemotherapy/methods , Photosensitizing Agents/pharmacology , Surface-Active Agents , Triazenes , Urinary Bladder Neoplasms/drug therapy
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