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Nature Communications Jun 2024METTL3 is the catalytic subunit of the methyltransferase complex, which mediates mA modification to regulate gene expression. In addition, METTL3 regulates transcription...
METTL3 is the catalytic subunit of the methyltransferase complex, which mediates mA modification to regulate gene expression. In addition, METTL3 regulates transcription in an enzymatic activity-independent manner by driving changes in high-order chromatin structure. However, how these functions of the methyltransferase complex are coordinated remains unknown. Here we show that the methyltransferase complex coordinates its enzymatic activity-dependent and independent functions to regulate cellular senescence, a state of stable cell growth arrest. Specifically, METTL3-mediated chromatin loops induce Hexokinase 2 expression through the three-dimensional chromatin organization during senescence. Elevated Hexokinase 2 expression subsequently promotes liquid-liquid phase separation, manifesting as stress granule phase separation, by driving metabolic reprogramming. This correlates with an impairment of translation of cell-cycle related mRNAs harboring polymethylated mA sites. In summary, our results report a coordination of mA-dependent and -independent function of the methyltransferase complex in regulating senescence through phase separation driven by metabolic reprogramming.
Topics: Methyltransferases; Chromatin; Cellular Senescence; Humans; Stress Granules; Hexokinase; RNA, Messenger; Adenosine; HEK293 Cells; Metabolic Reprogramming; Phase Separation
PubMed: 38926365
DOI: 10.1038/s41467-024-49745-5 -
Science Advances Jun 2024Thoeris defense systems protect bacteria from infection by phages via abortive infection. In these systems, ThsB proteins serve as sensors of infection and generate...
Thoeris defense systems protect bacteria from infection by phages via abortive infection. In these systems, ThsB proteins serve as sensors of infection and generate signaling nucleotides that activate ThsA effectors. Silent information regulator and SMF/DprA-LOG (SIR2-SLOG) containing ThsA effectors are activated by cyclic ADP-ribose (ADPR) isomers 2'cADPR and 3'cADPR, triggering abortive infection via nicotinamide adenine dinucleotide (NAD) depletion. Here, we characterize Thoeris systems with transmembrane and macro domain (TM-macro)-containing ThsA effectors. We demonstrate that ThsA macro domains bind ADPR and imidazole adenine dinucleotide (IAD), but not 2'cADPR or 3'cADPR. Combining crystallography, in silico predictions, and site-directed mutagenesis, we show that ThsA macro domains form nucleotide-induced higher-order oligomers, enabling TM domain clustering. We demonstrate that ThsB can produce both ADPR and IAD, and we identify a ThsA TM-macro-specific ThsB subfamily with an active site resembling deoxy-nucleotide and deoxy-nucleoside processing enzymes. Collectively, our study demonstrates that Thoeris systems with SIR2-SLOG and TM-macro ThsA effectors trigger abortive infection via distinct mechanisms.
Topics: Protein Domains; Bacteriophages; Bacterial Proteins; Models, Molecular; NAD; Protein Binding
PubMed: 38924412
DOI: 10.1126/sciadv.adn3310 -
PloS One 2024Cholangiocarcinoma (CCA) is an aggressive cancer originating from bile duct epithelium, particularly prevalent in Asian countries with liver fluke infections. Current...
Cholangiocarcinoma (CCA) is an aggressive cancer originating from bile duct epithelium, particularly prevalent in Asian countries with liver fluke infections. Current chemotherapy for CCA often fails due to drug resistance, necessitating novel anticancer agents. This study investigates the potential of 5'-deoxy-5'-methylthioadenosine (MTA), a naturally occurring nucleoside, against CCA. While MTA has shown promise against various cancers, its effects on CCA remain unexplored. We evaluated MTA's anticancer activity in CCA cell lines and drug-resistant sub-lines, assessing cell viability, migration, invasion, and apoptosis. The potential anticancer mechanisms of MTA were explored through proteomic analysis using LC-MS/MS and bioinformatic analysis. The results show a dose-dependent reduction in CCA cell viability, with enhanced effects on cancer cells compared to normal cells. Moreover, MTA inhibits growth, induces apoptosis, and suppresses cell migration and invasion. Additionally, MTA enhanced the anticancer effects of gemcitabine on drug-resistant CCA cells. Proteomics revealed the down-regulation of multiple proteins by MTA, affecting various molecular functions, biological processes, and cellular components. Network analysis highlighted MTA's role in inhibiting proteins related to mitochondrial function and energy derivation, crucial for cell growth and survival. Additionally, MTA suppressed proteins involved in cell morphology and cytoskeleton organization, important for cancer cell motility and metastasis. Six candidate genes, including ZNF860, KLC1, GRAMD1C, MAMSTR, TANC1, and TTC13, were selected from the top 10 most down-regulated proteins identified in the proteomics results and were subsequently verified through RT-qPCR. Further, KLC1 protein suppression by MTA treatment was confirmed through Western blotting. Additionally, based on TCGA data, KLC1 mRNA was found to be upregulated in the tissue of CCA patients compared to that of normal adjacent tissues. In summary, MTA shows promising anticancer potential against CCA by inhibiting growth, inducing apoptosis, and suppressing migration and invasion, while enhancing gemcitabine's effects. Proteomic analysis elucidates possible molecular mechanisms underlying MTA's anticancer activity, laying the groundwork for future research and development of MTA as a treatment for advanced CCA.
Topics: Cholangiocarcinoma; Humans; Proteomics; Cell Line, Tumor; Deoxyadenosines; Bile Duct Neoplasms; Apoptosis; Cell Movement; Thionucleosides; Antineoplastic Agents; Gemcitabine; Deoxycytidine; Cell Survival; Cell Proliferation; Drug Resistance, Neoplasm
PubMed: 38923999
DOI: 10.1371/journal.pone.0306060 -
Microbial Biotechnology Jun 2024Pyruvate dehydrogenase (PDH) catalyses the irreversible decarboxylation of pyruvate to acetyl-CoA, which feeds the tricarboxylic acid cycle. We investigated how the loss...
Inactivation of Pseudomonas putida KT2440 pyruvate dehydrogenase relieves catabolite repression and improves the usefulness of this strain for degrading aromatic compounds.
Pyruvate dehydrogenase (PDH) catalyses the irreversible decarboxylation of pyruvate to acetyl-CoA, which feeds the tricarboxylic acid cycle. We investigated how the loss of PDH affects metabolism in Pseudomonas putida. PDH inactivation resulted in a strain unable to utilize compounds whose assimilation converges at pyruvate, including sugars and several amino acids, whereas compounds that generate acetyl-CoA supported growth. PDH inactivation also resulted in the loss of carbon catabolite repression (CCR), which inhibits the assimilation of non-preferred compounds in the presence of other preferred compounds. Pseudomonas putida can degrade many aromatic compounds, most of which produce acetyl-CoA, making it useful for biotransformation and bioremediation. However, the genes involved in these metabolic pathways are often inhibited by CCR when glucose or amino acids are also present. Our results demonstrate that the PDH-null strain can efficiently degrade aromatic compounds even in the presence of other preferred substrates, which the wild-type strain does inefficiently, or not at all. As the loss of PDH limits the assimilation of many sugars and amino acids and relieves the CCR, the PDH-null strain could be useful in biotransformation or bioremediation processes that require growth with mixtures of preferred substrates and aromatic compounds.
Topics: Pseudomonas putida; Catabolite Repression; Pyruvate Dehydrogenase Complex; Hydrocarbons, Aromatic; Biodegradation, Environmental; Acetyl Coenzyme A; Pyruvic Acid; Gene Deletion; Metabolic Networks and Pathways
PubMed: 38923400
DOI: 10.1111/1751-7915.14514 -
Brazilian Journal of Biology = Revista... 2024Despite being valuable for producing a natural sweetener Curculin, Curculigo latifolia has a low growth and difficult to domestificate. So, to solve this problem,...
Despite being valuable for producing a natural sweetener Curculin, Curculigo latifolia has a low growth and difficult to domestificate. So, to solve this problem, propagation on in vitro culture will be an alternative method to propagated this spesies under different cytokinins and light condition. Cytokinins and light has major role in organogenesis, growth and gene expression of many species. Thus, in this study, we aimed to improve the Curculigo latifolia growth on in vitro condition and expression of curculin gene by combining cytokinins addition and different light exposure. Four weeks seedlings were sub-cultured into medium (MS free hormone) containing 3 mg/L benzyladenine (BA) and various concentrations of meta-Topolin (mT) including 0.1 mg/L, 0.5 mg/L, and 5 mg/L. The cultures then incubated under different light types (red, blue, white LED lights and white fluorescence light) with 16-h light/ 18-h dark photoperiod for 14 weeks at 25 ± 2°C. Several parameters, including plant height, leaf number, chlorophyll contents, stomatal structure, and density and curculin expression, were observed every week. Unexpectedly, our results showed that C. latifolia growth displayed significant improvement when it was treated under white LED light without any additional cytokinins. In sum, white LED light further improves plantlets phenotype, such as plant height, leaf number, chlorophyll production, and stomatal number and structure, whereas, red LED light lead to a decreased phenotypes but increase the curculin gene expression.
Topics: Cytokinins; Light; Curculigo; Plant Growth Regulators; Gene Expression Regulation, Plant
PubMed: 38922193
DOI: 10.1590/1519-6984.280778 -
Dentistry Journal May 2024Dental caries is a dynamic, multifactorial disease that destroys teeth and can affect anyone's quality of life because it can cause tooth loss and make chewing...
BACKGROUND
Dental caries is a dynamic, multifactorial disease that destroys teeth and can affect anyone's quality of life because it can cause tooth loss and make chewing difficult. Dental caries involves various factors, such as and host factors. Currently, adjuvant therapies, such as curcumin, have emerged, but how they work has not been adequately described. Therefore, this work aims to identify the molecular mechanism of curcumin in caries and .
METHODS
We obtained differentially expressed genes from a GEO dataset, and curcumin targets were obtained from other databases. The common targets were analyzed according to gene ontology enrichment, key genes were obtained, and binding to curcumin was verified by molecular docking.
RESULTS
Our analysis showed that curcumin presents 134 therapeutic targets in caries. According to the gene ontology analysis, these targets are mainly involved in apoptosis and inflammation. There are seven key proteins involved in the action of curcumin on caries: MAPK1, BCL2, KRAS, CXCL8, TGFB1, MMP9, and IL1B, all of which spontaneously bind curcumin. In addition, curcumin affects metabolic pathways related to lipid, purine, and pyrimidine metabolism in .
CONCLUSIONS
Curcumin affects both host carious processes and .
PubMed: 38920854
DOI: 10.3390/dj12060153 -
Biosensors May 2024In this study, we report a multiplexed platform for the simultaneous determination of five marine toxins. The proposed biosensor is based on a disposable electrical...
In this study, we report a multiplexed platform for the simultaneous determination of five marine toxins. The proposed biosensor is based on a disposable electrical printed (DEP) microarray composed of eight individually addressable carbon electrodes. The electrodeposition of gold nanoparticles on the carbon surface offers high conductivity and enlarges the electroactive area. The immobilization of thiolated aptamers on the AuNP-decorated carbon electrodes provides a stable, well-orientated and organized binary self-assembled monolayer for sensitive and accurate detection. A simple electrochemical multiplexed aptasensor based on AuNPs was designed to synchronously detect multiple cyanotoxins, namely, microcystin-LR (MC-LR), Cylindrospermopsin (CYL), anatoxin-α, saxitoxin and okadaic acid (OA). The choice of the five toxins was based on their widespread presence and toxicity to aquatic ecosystems and humans. Taking advantage of the conformational change of the aptamers upon target binding, cyanotoxin detection was achieved by monitoring the resulting electron transfer increase by square-wave voltammetry. Under the optimal conditions, the linear range of the proposed aptasensor was estimated to be from 0.018 nM to 200 nM for all the toxins, except for MC-LR where detection was possible within the range of 0.073 to 150 nM. Excellent sensitivity was achieved with the limits of detection of 0.0033, 0.0045, 0.0034, 0.0053 and 0.0048 nM for MC-LR, CYL, anatoxin-α, saxitoxin and OA, respectively. Selectivity studies were performed to show the absence of cross-reactivity between the five analytes. Finally, the application of the multiplexed aptasensor to tap water samples revealed very good agreement with the calibration curves obtained in buffer. This simple and accurate multiplexed platform could open the window for the simultaneous detection of multiple pollutants in different matrices.
Topics: Marine Toxins; Biosensing Techniques; Microcystins; Gold; Aptamers, Nucleotide; Electrochemical Techniques; Saxitoxin; Metal Nanoparticles; Cyanobacteria Toxins; Bacterial Toxins; Uracil; Tropanes; Alkaloids; Okadaic Acid; Electrodes; Limit of Detection
PubMed: 38920572
DOI: 10.3390/bios14060268 -
HemaSphere Jun 2024Mitapivat is an investigational, oral, small-molecule allosteric activator of pyruvate kinase (PK). PK is a regulatory glycolytic enzyme that is key in providing the red...
Mitapivat is an investigational, oral, small-molecule allosteric activator of pyruvate kinase (PK). PK is a regulatory glycolytic enzyme that is key in providing the red blood cell (RBC) with sufficient amounts of adenosine triphosphate (ATP). In sickle cell disease (SCD), decreased 2,3-DPG levels increase the oxygen affinity of hemoglobin, thereby preventing deoxygenation and polymerization of sickle hemoglobin. The PK activator mitapivat has been shown to decrease levels of 2,3-DPG and increase levels of ATP in RBCs in patients with SCD. In this phase 2, investigator-initiated, open-label study (https://www.clinicaltrialsregister.eu/ NL8517; EudraCT 2019-003438-18), untargeted metabolomics was used to explore the overall metabolic effects of 8-week treatment with mitapivat in the dose-finding period. In total, 1773 unique metabolites were identified in dried blood spots of whole blood from ten patients with SCD and 42 healthy controls (HCs). The metabolic phenotype of patients with SCD revealed alterations in 139/1773 (7.8%) metabolites at baseline when compared to HCs (false discovery rate-adjusted < 0.05), including increases of (derivatives of) polyamines, purines, and acyl carnitines. Eight-week treatment with mitapivat in nine patients with SCD altered 85/1773 (4.8%) of the total metabolites and 18/139 (12.9%) of the previously identified altered metabolites in SCD (unadjusted < 0.05). Effects were observed on a broad spectrum of metabolites and were not limited to glycolytic intermediates. Our results show the relevance of metabolic profiling in SCD, not only to unravel potential pathophysiological pathways and biomarkers in multisystem diseases but also to determine the effect of treatment.
PubMed: 38919958
DOI: 10.1002/hem3.109 -
The Iowa Orthopaedic Journal 2024Septic arthritis is an orthopedic emergency. Diagnosis is difficult in patients with concomitant crystalline arthropathy (gout or pseudogout). The symptomatology of...
BACKGROUND
Septic arthritis is an orthopedic emergency. Diagnosis is difficult in patients with concomitant crystalline arthropathy (gout or pseudogout). The symptomatology of crystal arthritis mimics septic arthritis, clouding clinical diagnosis. Arthrocentesis and synovial fluid analysis are the standard diagnostic tests for both pathologies. Crystals on microscopy are diagnostic of crystal arthritis, however their presence does not rule out septic arthritis. Septic arthritis is diagnosed by positive microbiology culture. Though septic arthritis is associated with elevated synovial total nucleated count (TNC), TNC elevations can also occur with gout. The literature suggests that a TNC count of > 50,000 cells in a crystal-positive joint should raise suspicion for concurrent septic arthritis, however data is limited. Further diagnostic indicators are needed to help clinicians promptly identify crystal positive septic arthritis as the treatments and prognoses are different.
METHODS
Patients were retrospectively identified who had arthrocentesis of a native joint positive for monosodium urate (MSU) and/or (CPPD) crystals. Laboratory data was collected including synovial fluid cultures, total nucleated cell count (TNC), percent polymorphic neutrophils (%PMN), and crystal analysis; and serum CRP, ESR, and white blood cell count (WBC). Statistical analysis performed using Spearman correlation, Univariate-Fischer's exact and Wilcoxon tests, and multivariate analysis.
RESULTS
442 joints identified with positive CPPD and/or MSU crystals, 31% female, 69% male. Of 442 aspirates, 58 had positive cultures. Patients were more likely to have positive cultures if synovial TNC > 50,000 (odds ratio 7.7), CRP > 10 mg/dL (OR 3.2), PMN > 90% (OR 2.17), and if the patient was female (OR 1.9), all were statistically significant with p < 0.05. There were 55 patients who underwent irrigation and debridement based on clinical suspicion or a positive gram stain, 37 of these ultimately had a positive culture (67%), the remaining 18 had negative cultures.
CONCLUSION
Results are consistent with the literature, a TNC > 50,000 warrants a high suspicion for concurrent septic arthritis and should prompt providers to critically evaluate other patient laboratory data. Results further suggests that a patient with positive crystals, synovial TNC > 50,000 cells, PMN > 90%, and serum CRP > 10mg/dL is at high risk for having a concurrent septic arthritis and may warrant urgent irrigation and debridement and antibiotic therapy. This data serves as a supporting to develop an infection risk calculator for crystal positive septic arthritis. .
Topics: Humans; Arthritis, Infectious; Female; Male; Retrospective Studies; Synovial Fluid; Aged; Middle Aged; Crystal Arthropathies; Arthrocentesis; Uric Acid; Adult; Aged, 80 and over
PubMed: 38919362
DOI: No ID Found -
BMC Public Health Jun 2024Pre-exposure prophylaxis (PrEP) with oral emtricitabine/tenofovir disoproxil (FTC/TDF) proved highly efficient in preventing HIV. Since 09/2019, FTC/TDF-PrEP is covered...
BACKGROUND
Pre-exposure prophylaxis (PrEP) with oral emtricitabine/tenofovir disoproxil (FTC/TDF) proved highly efficient in preventing HIV. Since 09/2019, FTC/TDF-PrEP is covered by health insurances in Germany, if prescribed by licensed specialists. However, methods to longitudinally monitor progress in PrEP implementation in Germany are lacking.
METHODS
Utilizing anonymous FTC/TDF prescription data from 2017-2021, we developed a mathematical model to disentangle HIV-treatment from PrEP prescriptions, as well as to translate PrEP prescriptions into number of PrEP users. We used the model to estimate past- and future PrEP uptake dynamics, to predict coverage of PrEP needs and to quantify the impact of COVID-19 on PrEP uptake on a national and regional level.
RESULTS
We identified significant (p<0.01) decelerating effects of the first- and second COVID-19-lockdown on PrEP uptake in 04/2020 and 12/2020. We estimated 26,159 (CI: 25,751-26,571) PrEP users by 12/2021, corresponding to 33% PrEP coverage of people in need. We projected 64,794 (CI: 62,956-66,557) PrEP users by 12/2030, corresponding to 81% PrEP coverage. We identified profound regional differences, with high PrEP coverage and uptake in metropoles and low coverage in more rural regions.
CONCLUSIONS
Our approach presents a comprehensive solution to monitor and forecast PrEP implementation from anonymous data and highlighted that the COVID-19 pandemic significantly decelerated PrEP uptake in Germany. Moreover, slow PrEP uptake in rural areas indicate that structural barriers in PrEP care, education or information exist that may hamper the goal of ending the AIDS epidemic by 2030.
Topics: Humans; Pre-Exposure Prophylaxis; Germany; HIV Infections; COVID-19; Anti-HIV Agents; Male; Emtricitabine, Tenofovir Disoproxil Fumarate Drug Combination; Female; Models, Theoretical; Adult
PubMed: 38918748
DOI: 10.1186/s12889-024-19198-y