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1.
Water Res ; 261: 122043, 2024 Jul 03.
Article in English | MEDLINE | ID: mdl-38981351

ABSTRACT

The bioaccumulation and trophic transfer of organophosphate flame retardants (OPFRs) in marine ecosystems have attracted great attention in recent research, but our understanding of the trophic transfer mechanisms involved is limited. In this study, we investigated the trophodynamics of OPFRs and their metabolites in a subtropical coastal food web collected from the northern Beibu Gulf, China, and characterized their trophodynamics using fugacity- and biotransformation-based approaches. Eleven OPFRs and all seven metabolites were simultaneously quantified in the shellfish, crustacean, pelagic fish, and benthic fish samples, with total concentrations ranging from 164 to 4.11 × 104 and 4.56-4.28 × 103 ng/g lipid weight, respectively. Significant biomagnification was observed only for tris (phenyl) phosphate (TPHP) and tris (2-ethylhexyl) phosphate (TEHP), while other compounds except for tris(2-chloroethyl) phosphate (TCEP) displayed biomagnification trends based on Monte Carlo simulations. Using a fugacity-based approach to normalize the accumulation of OPFRs in biota to their relative biological phase composition, storage lipid is the predominant biological phase for the mass distribution of 2-ethylhexyl diphenyl phosphate (EHDPHP) and TPHP. The water content and structure protein are equally important for TCEP, whereas lipid and structure protein are the two most important phases for other OPFRs. The mass distribution of these OPFRs along with TLs can explain their trophodynamics in the food web. The organophosphate diesters (as OPFR metabolites) also displayed biomagnification trends based on bootstrapped estimation. The correlation analysis and Korganism-water results jointly suggested the metabolites accumulation in high-TL organisms was related to biotransformation processes. The metabolite-backtracked trophic magnification factors for tri-n­butyl phosphate (TNBP) and TPHP were both greater than the values that accounted for only the parent compounds. This study highlights the incorporation of fugacity and biotransformation analysis to characterize the trophodynamic processes of OPFRs and other emerging pollutants in food webs.

2.
Bioresour Technol ; 406: 131060, 2024 Jun 29.
Article in English | MEDLINE | ID: mdl-38950831

ABSTRACT

This study surveyed the fates of artificial sweeteners in influent, effluent, and sewage sludge (SS) in wastewater treatment plant, and investigated the effects of Micro-Kaolin (Micro-KL) and Nano-Kaolin (Nano-KL) on nitrogen transformation and sucralose (SUC) and acesulfame (ACE) degradation during SS composting. Results showed the cumulative rate of ACE and SUC in SS was ∼76 %. During SS composting, kaolin reduced NH3 emissions by 30.2-45.38 %, and N2O emissions by 38.4-38.9 %, while the Micro-KL and Nano-KL reduced nitrogen losses by 14.8 % and 12.5 %, respectively. Meanwhile, Micro-KL and Nano-KL increased ACE degradation by 76.8 % and 84.2 %, and SUC degradation by 75.3 % and 77.7 %, and significantly shifted microbial community structure. Furthermore, kaolin caused a positive association between Actinobacteria and sweetener degradation. Taken together, kaolin effectively inhibited nitrogen loss and promoted the degradation of ACE and SUC during the SS composting, which is of great significance for the removal of emerging organic pollutants in SS.

3.
Environ Int ; 190: 108882, 2024 Jul 08.
Article in English | MEDLINE | ID: mdl-38996798

ABSTRACT

The role of the gut microbiota in host physiology has been previously elucidated for some marine organisms, but little information is available on their metabolic activity involved in transformation of environmental pollutants. This study assessed the metabolic profiles of the gut microbial cultures from grouper (Epinephelus coioides), green mussel (Perna viridis) and giant tiger prawn (Penaeus monodon) and investigated their transformation mechanisms to typical plastic additives. Community-level physiological profiling analysis confirmed the utilization profiles of the microbial cultures including carbon sources of carbohydrates, amines, carboxylic acids, phenolic compounds, polymers and amino acids, and the plastic additives of organophosphate flame retardants, tetrabromobisphenol A derivates and bisphenols. Using in vitro incubation, triphenyl phosphate (TPHP) was found to be rapidly metabolized into diphenyl phosphate by the gut microbiota as a representative ester-containing plastic additive, whereas the transformation of BPA (a representative phenol) was relatively slower. Interestingly, all three kinds of microbial cultures efficiently transformed the hepatic metabolite of BPA (BPA-G) back to BPA, thereby increasing its bioavailability in the body. The specific enzyme analysis confirmed the ability of the gut microbiota to perform the metabolic reactions. The results of 16S rRNA sequencing and network analysis revealed that the genera Escherichia-Shigella, Citrobacter, and Anaerospora were functional microbes, and their collaboration with fermentative microbes played pivotal roles in the transformation of the plastic additives. The structure-specific transformations by the gut microbiota and their distinct bioavailability deserve more attention in the future.

5.
Pharmacol Res ; 204: 107221, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38768669

ABSTRACT

Based on the concept of "Evolutionary Traps", targeting survival essential genes obtained during tumor drug resistance can effectively eliminate resistant cells. While, it still faces limitations. In this study, lapatinib-resistant cells were used to test the concept of "Evolutionary Traps" and no suitable target stand out because of the identified genes without accessible drug. However, a membrane protein PDPN, which is low or non-expressed in normal tissues, is identified as highly expressed in lapatinib-resistant tumor cells. PDPN CAR-T cells were developed and showed high cytotoxicity against lapatinib-resistant tumor cells in vitro and in vivo, suggesting that CAR-T may be a feasible route for overcoming drug resistance of tumor based on "Evolutionary Trap". To test whether this concept is cell line or drug dependent, we analyzed 21 drug-resistant tumor cell expression profiles reveal that JAG1, GPC3, and L1CAM, which are suitable targets for CAR-T treatment, are significantly upregulated in various drug-resistant tumor cells. Our findings shed light on the feasibility of utilizing CAR-T therapy to treat drug-resistant tumors and broaden the concept of the "Evolutionary Trap".


Subject(s)
Antineoplastic Agents , Drug Resistance, Neoplasm , Immunotherapy, Adoptive , Humans , Animals , Cell Line, Tumor , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Immunotherapy, Adoptive/methods , Lapatinib/pharmacology , Lapatinib/therapeutic use , Neoplasms/drug therapy , Neoplasms/genetics , Neoplasms/therapy , Receptors, Chimeric Antigen/genetics , Receptors, Chimeric Antigen/immunology , Mice, Nude , Mice, Inbred BALB C , Mice , Female
6.
Int J Genomics ; 2024: 2439396, 2024.
Article in English | MEDLINE | ID: mdl-38716378

ABSTRACT

Pod dehiscence brings much loss for modern agricultural production, and multiple pod dehiscence components have been identified in many plant species. However, the pod dehiscence regulation factors in soybean are limited. In this study, we investigate the function of GmDIR26, a close homologues gene of pod dehiscence genes GmPdh1, PvPdh1, and CaPdh1, in the regulation of pod dehiscence in soybean. The secondary and tertiary structure analysis reveals that GmDIR26 protein has a similar structure with GmPdh1, PvPdh1, and CaPdh1 proteins. Synteny analysis of soybean and chickpea genomes shows that the genomic region surrounding GmDIR26 and CaPdh1 might be evolved from the same ancestor, and these two genes might have similar function. GmDIR26 shows an increased expression pattern during pod development and reaches a peak at beginning seed stage. Meanwhile, GmDIR26 exhibits high expression levels in dorsal suture and pod wall, but low expression pattern in ventral suture. In addition, GmDIR26 shows higher expression levels in pod dehiscence genotype than that in pod indehiscence accessions. Overexpression of GmDIR26 in soybean increases pod dehiscence in transgenic plants, of which the lignin layer in inner sclerenchyma pods is thicker and looser. The expression levels of several pod dehiscence genes are altered. Our study provides important information for further modification of pod dehiscence resistance soybean and characterization of soybean pod dehiscence regulation network.

7.
Arch Microbiol ; 206(5): 235, 2024 May 09.
Article in English | MEDLINE | ID: mdl-38722413

ABSTRACT

In recent years, blueberry root rot has been caused mainly by Fusarium commune, and there is an urgent need for a green and efficient method to control this disease. To date, research on Schizophyllum commune has focused on antioxidant mechanisms, reactive dye degradation, etc., but the mechanism underlying the inhibition of pathogenic microorganisms is still unclear. Here, the control effects of S. commune on F. commune and blueberry root rot were studied using adversarial culture, tissue culture, and greenhouse pot experiments. The results showed that S. commune can dissolve insoluble phosphorus and secrete various extracellular hydrolases. The results of hyphal confrontation and fermentation broth antagonism experiments showed that S. commune had a significant inhibitory effect on F. commune, with inhibition rates of 70.30% and 22.86%, respectively. Microscopy results showed distortion of F. commune hyphae, indicating that S. commune is strongly parasitic. S. commune had a significant growth-promoting effect on blueberry tissue-cultured seedlings. After inoculation with S. commune, inoculation with the pathogenic fungus, or inoculation at a later time, the strain significantly reduced the root rot disease index in the potted blueberry seedlings, with relative control effects of 79.14% and 62.57%, respectively. In addition, S. commune G18 significantly increased the antioxidant enzyme contents in the aboveground and underground parts of potted blueberry seedlings. We can conclude that S. commune is a potential biocontrol agent that can be used to effectively control blueberry root rot caused by F. commune in the field.


Subject(s)
Blueberry Plants , Fusarium , Plant Diseases , Plant Roots , Schizophyllum , Blueberry Plants/microbiology , Plant Diseases/microbiology , Plant Diseases/prevention & control , Plant Roots/microbiology , Fusarium/physiology , Schizophyllum/metabolism , Schizophyllum/growth & development , Antibiosis , Hyphae/growth & development , Biological Control Agents , Seedlings/microbiology , Seedlings/growth & development
8.
Int J Gen Med ; 17: 2311-2326, 2024.
Article in English | MEDLINE | ID: mdl-38799202

ABSTRACT

Purpose: Delayed onset of lactogenesis is a significant barrier to achieving the WHO-recommended 50% exclusive breastfeeding rate in the first six months. This study maps the main factors influencing this condition, addressing gaps in the current research landscape. Methods: Following Arksey and O'Malley's scoping review framework, databases such as PubMed, Web of Science (WOS), Embase, Cochrane Library, CINAHL plus with full text, China National Knowledge Infrastructure (CNIK), Weipu Chinese Journal Service Platform (VIP), Wanfang Data Knowledge Service Platform, and China Biomedical Literature Database (CBM) were searched on February 1, 2023. Studies in Chinese and English involving pregnant and postpartum women, focusing on delayed onset of lactogenesis, were included without restrictions on publication date or geography. Results: Forty-six studies published between 2002 and 2022 met the inclusion criteria, revealing variable incidences of delayed lactogenesis among different groups. Thirty-four influencing factors were identified and organized into five themes: maternal-infant characteristics, perinatal mental state, physical activity participation during pregnancy, breastfeeding behaviors, and medical staff interventions. Within eighteen major factors highlighted, factors such as age, pre-pregnancy BMI, gestational weight gain, average LATCH score within 24 hours postpartum, labor analgesia, sleep, frequency of postpartum breastfeeding, and timing of initial breast suckling/pumping showed inconsistent or conflicting conclusions. Conclusion: High and variable incidences of delayed lactogenesis underline its multifactorial nature. Effective interventions require strong advocacy from healthcare professionals and adherence by pregnant women. Further research using standardized methods is essential to clarify inconsistent or conflicting findings on the influencing factors.

9.
Sci Adv ; 10(22): eadn7553, 2024 May 31.
Article in English | MEDLINE | ID: mdl-38809970

ABSTRACT

Long-range ordered phases in most high-entropy and medium-entropy alloys (HEAs/MEAs) exhibit poor ductility, stemming from their brittle nature of complex crystal structure with specific bonding state. Here, we propose a design strategy to severalfold strengthen a single-phase face-centered cubic (fcc) Ni2CoFeV MEA by introducing trigonal κ and cubic L12 intermetallic phases via hierarchical ordering. The tri-phase MEA has an ultrahigh tensile strength exceeding 1.6 GPa and an outstanding ductility of 30% at room temperature, which surpasses the strength-ductility synergy of most reported HEAs/MEAs. The simultaneous activation of unusual dislocation multiple slip and stacking faults (SFs) in the κ phase, along with nano-SF networks, Lomer-Cottrell locks, and high-density dislocations in the coupled L12 and fcc phases, contributes to enhanced strain hardening and excellent ductility. This work offers a promising prototype to design super-strong and ductile structural materials by harnessing the hierarchical ordered phases.

10.
Lab Invest ; 104(6): 102059, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38615731

ABSTRACT

High-grade serous ovarian cancer (HGSOC) remains the most lethal female cancer by far. Herein, clinical HGSOC samples had higher N6-methyladenosine (m6A) modification than normal ovarian tissue, and its dysregulation had been reported to drive aberrant transcription and translation programs. However, Kringle-containing transmembrane protein 2 (KREMEN2) and its m6A modification have not been fully elucidated in HGSOC. In this study, the data from the high-throughput messenger RNA (mRNA) sequencing of clinical samples were processed using the weighted correlation network analysis and functional enrichment analysis. Results revealed that KREMEN2 was a driver gene in the tumorigenesis of HGSOC and a potential target of m6A demethylase fat-mass and obesity-associated protein (FTO). KREMEN2 and FTO levels were upregulated and downregulated, respectively, and correlation analysis showed a significant negative correlation in HGSOC samples. Importantly, upregulated KREMEN2 was remarkably associated with lymph node metastasis, distant metastasis, peritoneal metastasis, and high International Federation of Gynecology and Obstetrics stage (Ⅲ/Ⅳ), independent of the age of patients. KREMEN2 promoted the growth of HGSOC in vitro and in vivo, which was dependent on FTO. The methylated RNA immunoprecipitation qPCR and RNA immunoprecipitation assays were performed to verify the m6A level and sites of KREMEN2. FTO overexpression significantly decreased m6A modification in the 3' and 5' untranslated regions of KREMEN2 mRNA and downregulated its expression. In addition, we found that FTO-mediated m6A modification of KREMEN2 mRNA was recognized and stabilized by the m6A reader IGF2BP1 rather than by IGF2BP2 or IGF2BP3. This study highlights the m6A modification of KREMEN2 and extends the importance of RNA epigenetics in HGSOC.


Subject(s)
Adenosine , Alpha-Ketoglutarate-Dependent Dioxygenase FTO , Ovarian Neoplasms , Receptors, Cell Surface , Animals , Female , Humans , Mice , Middle Aged , Adenosine/analogs & derivatives , Alpha-Ketoglutarate-Dependent Dioxygenase FTO/genetics , Carcinogenesis/genetics , Cell Line, Tumor , Cystadenocarcinoma, Serous/genetics , Cystadenocarcinoma, Serous/secondary , Disease Progression , Gene Expression Regulation, Neoplastic , Membrane Proteins/metabolism , Membrane Proteins/genetics , Mice, Nude , Ovarian Neoplasms/genetics , Ovarian Neoplasms/pathology , Receptors, Cell Surface/genetics
11.
Healthcare (Basel) ; 12(7)2024 Mar 22.
Article in English | MEDLINE | ID: mdl-38610125

ABSTRACT

Non-pharmaceutical midwifery techniques, including perineal warm compresses, to improve maternal outcomes remain controversial. The aims of this study are to assess the effects of perineal warm compresses on reducing perineal trauma and postpartum perineal pain relief. This systematic review included randomized controlled trials (RCTs). We searched seven bibliographic databases, three RCT register websites, and two dissertation databases for publications from inception to 15 March 2023. Chinese and English publications were included. Two independent reviewers conducted the risk of bias assessment, data extraction, and the evaluation of the certainty of the evidence utilizing the Cochrane risk of bias 2.0 assessment criteria, the Review Manager 5.4, and the online GRADEpro tool, respectively. Seven RCTs involving 1362 primiparous women were included. The combined results demonstrated a statistically significant reduction in the second-, third- and/or fourth- degree perineal lacerations, the incidence of episiotomy, and the relief of the short-term perineal pain postpartum (within two days). There was a potential favorable effect on improving the integrity of the perineum. However, the results did not show a statistically significant supportive effect on reducing first-degree perineal lacerations and the rate of perineal lacerations requiring sutures. In summary, perineal warm compresses effectively reduced the second-, third-/or fourth-degree perineal trauma and decreased the short-term perineal pain after birth.

12.
Acta Pharmacol Sin ; 2024 Apr 19.
Article in English | MEDLINE | ID: mdl-38641746

ABSTRACT

Acute kidney injury (AKI) is defined as sudden loss of renal function characterized by increased serum creatinine levels and reduced urinary output with a duration of 7 days. Ferroptosis, an iron-dependent regulated necrotic pathway, has been implicated in the progression of AKI, while ferrostatin-1 (Fer-1), a selective inhibitor of ferroptosis, inhibited renal damage, oxidative stress and tubular cell death in AKI mouse models. However, the clinical translation of Fer-1 is limited due to its lack of efficacy and metabolic instability. In this study we designed and synthesized four Fer-1 analogs (Cpd-A1, Cpd-B1, Cpd-B2, Cpd-B3) with superior plasma stability, and evaluated their therapeutic potential in the treatment of AKI. Compared with Fer-1, all the four analogs displayed a higher distribution in mouse renal tissue in a pharmacokinetic assay and a more effective ferroptosis inhibition in erastin-treated mouse tubular epithelial cells (mTECs) with Cpd-A1 (N-methyl-substituted-tetrazole-Fer-1 analog) being the most efficacious one. In hypoxia/reoxygenation (H/R)- or LPS-treated mTECs, treatment with Cpd-A1 (0.25 µM) effectively attenuated cell damage, reduced inflammatory responses, and inhibited ferroptosis. In ischemia/reperfusion (I/R)- or cecal ligation and puncture (CLP)-induced AKI mouse models, pre-injection of Cpd-A1 (1.25, 2.5, 5 mg·kg-1·d-1, i.p.) dose-dependently improved kidney function, mitigated renal tubular injury, and abrogated inflammation. We conclude that Cpd-A1 may serve as a promising therapeutic agent for the treatment of AKI.

13.
Food Chem ; 448: 139136, 2024 Aug 01.
Article in English | MEDLINE | ID: mdl-38581964

ABSTRACT

Instant dark tea (IDT), prepared by liquid-state fermentation using Aspergillus niger, is known for its high theabrownins content and lipid-lowering effect. To explore the impact of fungal fermentation on IDT compositions and its pancreatic lipase inhibitory ability (PLIA), untargeted and targeted metabolomic analysis were applied to track the changes of metabolites over a 9-day fermentation period, and correlation analysis was then conducted between metabolites and PLIA of IDT. There were 54 differential metabolites exhibited significant changes from day 3 to day 5 of fermentation. The concentrations of theabrownins and caffeine increased during fermentation, while phenols and free amino acids decreased. The PLIA of IDT samples significantly increased from day 5 to day 9 of fermentation. Theabrownins not only positively correlated with the PLIA but also exhibited a high inhibition rate. These findings provide a theoretical basis to optimize the production of IDT as functional food ingredient.

14.
Huan Jing Ke Xue ; 45(5): 3047-3058, 2024 May 08.
Article in Chinese | MEDLINE | ID: mdl-38629565

ABSTRACT

In order to comprehensively evaluate the effects of vermicomposting on compost quality and the conversion of heavy metals under different control conditions, 109 studies were reviewed. The effects of earthworm species, pre-compost time, ventilation methods, initial C/N, initial pH, and initial moisture of the raw materials on compost quality and the heavy metal toxicity were quantitatively discussed during the vermicomposting process through Meta-analysis. The results showed that the six subgroups of factors all showed obvious influences on the compost quality and heavy metal toxicity. After vermicomposting, the contents of NO3--N (116.2%), TN (29.1%), TP (31.2%), and TK (15.0%) were significantly increased, whereas NH4+-N (-14.8%) and C/N (-36.3%) were significantly decreased. Meanwhile, the total amount of Cu and Cr of the final compost and their bioavailability were significantly reduced. Considering the influences of grouping factors on compost quality and heavy metals, it is recommended to adjust the initial moisture of pile materials to 70%-80%, C/N to 30-85, and pH to 6-7 and to conduct pre-composting for 0-15 d; additionally, vermicomposting should be naturally placed when the composting is aimed at promoting the compost quality. If the main purpose is to weaken the perniciousness of heavy metals in the raw material, it is recommended to adjust the initial moisture of the material to 50%-60%, C/N to less than 30, and pH to 7-8; to conduct no pre-compost; regularly turn the piles; and use the earthworm Eudrilus eugeniae for vermicomposting.


Subject(s)
Composting , Metals, Heavy , Oligochaeta , Animals , Soil/chemistry , Sewage/chemistry , Metals, Heavy/analysis
15.
J Health Popul Nutr ; 43(1): 55, 2024 Apr 23.
Article in English | MEDLINE | ID: mdl-38654371

ABSTRACT

PURPOSE: This study aimed to analyse the correlation between blood glucose control and the severity of COVID-19 infection in patients with diabetes. METHODS: Clinical and imaging data of a total of 146 patients with diabetes combined with COVID-19 who visited our hospital between December 2022 and January 2023 were retrospectively collected. The patients were divided into the 'good blood glucose control' group and the 'poor blood glucose control' group based on an assessment of their blood glucose control. The clinical data, computed tomography (CT) appearance and score and the severity of COVID-19 infection of the two groups were compared, with the severity of COVID-19 infection being the dependent variable to analyse other influencing factors. RESULTS: The group with poor blood glucose control showed a higher lobar involvement degree and total CT severity score (CTSS) than the group with good blood glucose control (13.30 ± 5.25 vs. 10.38 ± 4.84, p < 0.05). The two groups exhibited no statistically significant differences in blood lymphocyte, leukocyte, C-reaction protein, pleural effusion, consolidation, ground glass opacity or crazy-paving signs. Logistic regression analysis showed that the total CTSS significantly influences the clinical severity of patients (odds ratio 1.585, p < 0.05), whereas fasting plasma glucose and blood glucose control are not independent factors influencing clinical severity (both p > 0.05). The area under the curve (AUC) of CTSS prediction of critical COVID-19 was 0.895 with sensitivity of 79.3% and specificity of 88.1% when the threshold value is 12. CONCLUSION: Blood glucose control is significantly correlated with the CTSS; the higher the blood glucose is, the more severe the lung manifestation. The CTSS can also be used to evaluate and predict the clinical severity of COVID-19.


Subject(s)
Blood Glucose , COVID-19 , Severity of Illness Index , Tomography, X-Ray Computed , Humans , COVID-19/complications , COVID-19/blood , Male , Female , Middle Aged , Retrospective Studies , Blood Glucose/analysis , Aged , Diabetes Mellitus/blood , SARS-CoV-2 , Adult
16.
Heliyon ; 10(8): e29382, 2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38660246

ABSTRACT

CRISPR-based screens have discovered novel functional genes involving in diverse tumor biology and elucidated the mechanisms of the cancer pathological states. Recently, with its randomness and unbiasedness, CRISPR screens have been used to discover effector genes with previously unknown roles for AML. Those novel targets are related to AML survival resembled cellular pathways mediating epigenetics, synthetic lethality, transcriptional regulation, mitochondrial and energy metabolism. Other genes that are crucial for pharmaceutical targeting and drug resistance have also been identified. With the rapid development of novel strategies, such as barcodes and multiplexed mosaic CRISPR perturbation, more potential therapeutic targets and mechanism in AML will be discovered. In this review, we present an overview of recent progresses in the development of CRISPR-based screens for the mechanism and target identification in AML and discuss the challenges and possible solutions in this rapidly growing field.

17.
Methods ; 226: 151-160, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38670416

ABSTRACT

Chromatin loop is of crucial importance for the regulation of gene transcription. Cohesin is a type of chromatin-associated protein that mediates the interaction of chromatin through the loop extrusion. Cohesin-mediated chromatin interactions have strong cell-type specificity, posing a challenge for predicting chromatin loops. Existing computational methods perform poorly in predicting cell-type-specific chromatin loops. To address this issue, we propose a random forest model to predict cell-type-specific cohesin-mediated chromatin loops based on chromatin states identified by ChromHMM and the occupancy of related factors. Our results show that chromatin state is responsible for cell-type-specificity of loops. Using only chromatin states as features, the model achieved high accuracy in predicting cell-type-specific loops between two cell types and can be applied to different cell types. Furthermore, when chromatin states are combined with the occurrence frequency of CTCF, RAD21, YY1, and H3K27ac ChIP-seq peaks, more accurate prediction can be achieved. Our feature extraction method provides novel insights into predicting cell-type-specific chromatin loops and reveals the relationship between chromatin state and chromatin loop formation.


Subject(s)
CCCTC-Binding Factor , Cell Cycle Proteins , Chromatin , Chromosomal Proteins, Non-Histone , Cohesins , Chromosomal Proteins, Non-Histone/metabolism , Chromosomal Proteins, Non-Histone/genetics , Cell Cycle Proteins/metabolism , Cell Cycle Proteins/genetics , Chromatin/metabolism , Chromatin/genetics , Humans , CCCTC-Binding Factor/metabolism , CCCTC-Binding Factor/genetics , YY1 Transcription Factor/metabolism , YY1 Transcription Factor/genetics , Nuclear Proteins/metabolism , Nuclear Proteins/genetics , Computational Biology/methods , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Histones/metabolism , Histones/genetics , Phosphoproteins/metabolism , Phosphoproteins/genetics , Chromatin Immunoprecipitation Sequencing/methods
18.
Biotechnol J ; 19(4): e2300710, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38581096

ABSTRACT

Reconstruction and optimization of biosynthetic pathways can help to overproduce target chemicals in microbial cell factories based on genetic engineering. However, the perturbation of biosynthetic pathways on cellular metabolism is not well investigated and profiling the engineered microbes remains challenging. The rapid development of omics tools has the potential to characterize the engineered microbial cell factory. Here, we performed label-free quantitative proteomic analysis and metabolomic analysis of engineered sabinene overproducing Saccharomyces cerevisiae strains. Combined metabolic analysis andproteomic analysis of targeted mevalonate (MVA) pathway showed that co-ordination of cytosolic and mitochondrial pathways had balanced metabolism, and genome integration of biosynthetic genes had higher sabinene production with less MVA enzymes. Furthermore, comparative proteomic analysis showed that compartmentalized mitochondria pathway had perturbation on central cellular metabolism. This study provided an omics analysis example for characterizing engineered cell factory, which can guide future regulation of the cellular metabolism and maintaining optimal protein expression levels for the synthesis of target products.


Subject(s)
Bicyclic Monoterpenes , Metabolic Engineering , Saccharomyces cerevisiae , Saccharomyces cerevisiae/metabolism , Proteomics , Mitochondria/genetics , Mitochondria/metabolism
19.
Article in English | MEDLINE | ID: mdl-38592427

ABSTRACT

The current CAR-T cell therapy products have been hampered in their druggability due to the personalized preparation required, unclear pharmacokinetic characteristics, and unpredictable adverse reactions. Enabling standardized manufacturing and having clear efficacy and pharmacokinetic characteristics are prerequisites for ensuring the effective practicality of CAR-T cell therapy drugs. This review provides a broad overview of the different approaches for controlling behaviors of CAR-T cells in vivo. The utilization of genetically modified vectors enables in vivo production of CAR-T cells, thereby abbreviating or skipping the lengthy in vitro expansion process. By equipping CAR-T cells with intricately designed control elements, using molecule switches or small-molecule inhibitors, the control of CAR-T cell activity can be achieved. Moreover, the on-off control of CAR-T cell activity would yield potential gains in phenotypic remodeling. These methods provide beneficial references for the future development of safe, controllable, convenient, and suitable for standardized production of CAR-T cell therapy products.

20.
Biochim Biophys Acta Mol Basis Dis ; 1870(5): 167159, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38583815

ABSTRACT

Chimeric antigen receptor T (CAR-T) cell therapy is regarded as a potent immunotherapy and has made significant success in hematologic malignancies by eliciting antigen-specific immune responses. However, response rates of CAR-T cell therapy against solid tumors with immunosuppressive microenvironments remain limited. Co-engineering strategies are advancing methods to overcome immunosuppressive barriers and enhance antitumor responses. Here, we engineered an IL-2 mutein co-engineered CAR-T for the improvement of CAR-T cells against solid tumors and the efficient inhibition of solid tumors. We equipped the CAR-T cells with co-expressing both tumor antigen-targeted CAR and a mutated human interleukin-2 (IL-2m), conferring enhanced CAR-T cells fitness in vitro, reshaped immune-excluded TME, enhanced CAR-T infiltration in solid tumors, and improved tumor control without significant systemic toxicity. Overall, this subject demonstrates the universal CAR-T cells armed strategy for the development and optimization of CAR-T cells against solid tumors.


Subject(s)
Immunotherapy, Adoptive , Interleukin-2 , Neoplasms , Receptors, Chimeric Antigen , T-Lymphocytes , Humans , Interleukin-2/genetics , Interleukin-2/immunology , Receptors, Chimeric Antigen/immunology , Receptors, Chimeric Antigen/genetics , Immunotherapy, Adoptive/methods , Animals , Neoplasms/therapy , Neoplasms/immunology , Neoplasms/genetics , Mice , T-Lymphocytes/immunology , T-Lymphocytes/metabolism , Tumor Microenvironment/immunology , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/immunology , Antigens, Neoplasm/immunology , Antigens, Neoplasm/genetics , Cell Line, Tumor , Xenograft Model Antitumor Assays
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