-
Scientific Data Jun 2024The concentration of chlorophyll a in phytoplankton and periphyton represents the amount of algal biomass. We compiled an 18-year record (2005-2022) of pigment data from...
The concentration of chlorophyll a in phytoplankton and periphyton represents the amount of algal biomass. We compiled an 18-year record (2005-2022) of pigment data from water bodies across the United States (US) to support efforts to develop process-based, machine learning, and remote sensing models for prediction of harmful algal blooms (HABs). To our knowledge, this dataset of nearly 84,000 sites and over 1,374,000 pigment measurements is the largest compilation of harmonized discrete, laboratory-extracted chlorophyll data for the US. These data were compiled from the Water Quality Portal (WQP) and previously unpublished U.S. Geological Survey's National Water Quality Laboratory (NWQL) data. Data were harmonized for reporting units, pigment type, duplicate values, collection depth, site name, negative values, and some extreme values. Across the country, data show great variation by state in sampling frequency, distribution, and methods. Uses for such data include the calibration of models, calibration of field sensors, examination of relationship to nutrients and other drivers, evaluation of temporal trends, and other applications addressing local to national scale concerns.
Topics: United States; Lakes; Chlorophyll A; Phytoplankton; Rivers; Environmental Monitoring; Harmful Algal Bloom; Chlorophyll
PubMed: 38866750
DOI: 10.1038/s41597-024-03453-3 -
Science Advances Jun 2024Certain cyanobacteria alter their photosynthetic light absorption between green and red, a phenomenon called complementary chromatic acclimation. The acclimation is...
Certain cyanobacteria alter their photosynthetic light absorption between green and red, a phenomenon called complementary chromatic acclimation. The acclimation is regulated by a cyanobacteriochrome-class photosensor that reversibly photoconverts between green-absorbing (Pg) and red-absorbing (Pr) states. Here, we elucidated the structural basis of the green/red photocycle. In the Pg state, the bilin chromophore adopted the extended C15-, structure within a hydrophobic pocket. Upon photoconversion to the Pr state, the bilin is isomerized to the cyclic C15-, structure, forming a water channel in the pocket. The solvation/desolvation of the bilin causes changes in the protonation state and the stability of π-conjugation at the B ring, leading to a large absorption shift. These results advance our understanding of the enormous spectral diversity of the phytochrome superfamily.
Topics: Light; Cyanobacteria; Acclimatization; Photosynthesis; Phytochrome; Models, Molecular; Bile Pigments; Bacterial Proteins; Red Light
PubMed: 38865454
DOI: 10.1126/sciadv.adn8386 -
Science Advances Jun 2024Semi-artificial Z-scheme systems offer promising potential toward efficient solar-to-chemical conversion, yet sustainable and stable designs are currently lacking. Here,...
Semi-artificial Z-scheme systems offer promising potential toward efficient solar-to-chemical conversion, yet sustainable and stable designs are currently lacking. Here, we developed a sustainable hybrid Z-scheme system capable for visible light-driven overall water splitting by integrating the durability of inorganic photocatalysts with the interfacial adhesion and regenerative property of bacterial biofilms. The Z-scheme configuration is fabricated by drop casting a mixture of photocatalysts onto a glass plate, followed by the growth of biofilms for conformal conductive paste through oxidative polymerization of pyrrole molecules. Notably, the system exhibited scalability indicated by consistent catalytic efficiency across various sheet areas, resistance observed by remarkable maintaining of photocatalytic efficiency across a range of background pressures, and high stability as evidenced by minimal decay of photocatalytic efficiency after 100-hour reaction. Our work thus provides a promising avenue toward sustainable and high-efficiency artificial photosynthesis, contributing to the broader goal of sustainable energy solutions.
PubMed: 38865453
DOI: 10.1126/sciadv.adn6211 -
Microbiology Spectrum Jul 2024Clorobiocin is a well-known, highly effective inhibitor of DNA gyrase belonging to the aminocoumarin antibiotics. To identify potentially novel derivatives of this...
UNLABELLED
Clorobiocin is a well-known, highly effective inhibitor of DNA gyrase belonging to the aminocoumarin antibiotics. To identify potentially novel derivatives of this natural product, we conducted an untargeted investigation of clorobiocin biosynthesis in the known producer DS 12.976 using LC-MS, molecular networking, and analysis of fragmentation spectra. Previously undescribed clorobiocin derivatives uncovered in this study include bromobiocin, a variant halogenated with bromine instead of chlorine, hydroxylated clorobiocin, carrying an additional hydroxyl group on its 5-methyl-pyrrole 2-carboxyl moiety, and two other derivatives with modifications on their 3-dimethylallyl 4-hydroxybenzoate moieties. Furthermore, we identified several compounds not previously considered clorobiocin pathway products, which provide new insights into the clorobiocin biosynthetic pathway. By supplementing the medium with different concentrations of potassium bromide, we confirmed that the clorobiocin halogenase can utilize bromine instead of chlorine. The reaction, however, is impeded such that non-halogenated clorobiocin derivatives accumulate. Preliminary assays indicate that the antibacterial activity of bromobioin against and efflux-impaired matches that of clorobiocin. Our findings emphasize that yet unexplored compounds can be discovered from established strains and biosynthetic gene clusters by means of metabolomics analysis and highlight the utility of LC-MS-based methods to contribute to unraveling natural product biosynthetic pathways.
IMPORTANCE
The aminocoumarin clorobiocin is a well-known gyrase inhibitor produced by the gram-positive bacterium DS 12.976. To gain a deeper understanding of the biosynthetic pathway of this complex composite of three chemically distinct entities and the product spectrum, we chose a metabolite-centric approach. Employing high-resolution LC-MS analysis, we investigated the pathway products in extracted culture supernatants of the natural producer. Novel pathway products were identified that expand our understanding of three aspects of the biosynthetic pathway, namely the modification of the noviose, transfer and methylation of the pyrrole 2-carboxyl moiety, and halogenation. For the first time, brominated products were detected. Their levels and the levels of non-halogenated products increased in medium supplemented with KBr. Based on the presented data, we propose that the enzyme promiscuity contributes to a broad product spectrum.
Topics: Metabolomics; Streptomyces; Anti-Bacterial Agents; Novobiocin; Biosynthetic Pathways; Chromatography, Liquid
PubMed: 38864648
DOI: 10.1128/spectrum.00423-24 -
Beijing Da Xue Xue Bao. Yi Xue Ban =... Jun 2024To investigate the effect of tofacitinib, a pan-Janus kinase (JAK) inhibitor, on transforming growth factor-beta 1 (TGF-β1)-induced fibroblast to myofibroblast...
OBJECTIVE
To investigate the effect of tofacitinib, a pan-Janus kinase (JAK) inhibitor, on transforming growth factor-beta 1 (TGF-β1)-induced fibroblast to myofibroblast transition (FMT) and to explore its mechanism. To provide a theoretical basis for the clinical treatment of connective tissue disease-related interstitial lung disease (CTD-ILD).
METHODS
(1) Human fetal lung fibroblast 1 (HFL-1) were cultured , and 6 groups were established: DMSO blank control group, TGF-β1 induction group, and TGF-β1 with different concentrations of tofacitinib (0.5, 1.0, 2.0, 5.0 μmol/L) drug intervention experimental groups. CCK-8 was used to measure the cell viability, and wound-healing assay was performed to measure cell migration ability. After 48 h of combined treatment, quantitative real-time PCR (RT-PCR) and Western blotting were used to detect the gene and protein expression levels of α-smooth muscle actin (α-SMA), fibronectin (FN), and collagen type Ⅰ (COL1). (2) RT-PCR and enzyme-linked immunosorbnent assay (ELISA) were used to detect the interleukin-6 (IL-6) gene and protein expression changes, respectively. (3) DMSO carrier controls, 1.0 μmol/L and 5.0 μmol/L tofacitinib were added to the cell culture media of different groups for pre-incubation for 30 min, and then TGF-β1 was added to treat for 1 h, 6 h and 24 h. The phosphorylation levels of Smad2/3 and signal transducer and activator of transcription 3 (STAT3) protein were detected by Western blotting.
RESULTS
(1) Tofacitinib inhibited the viability and migration ability of HFL-1 cells after TGF-β1 induction. (2) The expression of , and genes of HFL-1 in the TGF-β1-induced groups was significantly up-regulated compared with the blank control group ( < 0.05). Compared with the TGF-β1 induction group, expression in the 5.0 μmol/L tofacitinib intervention group was significantly inhi-bited ( < 0.05). Compared with the TGF-β1-induced group, gene was significantly inhibited in each intervention group at a concentration of 0.5-5.0 μmol/L ( < 0.05). Compared with the TGF-β1-induced group, the gene expression in each intervention group did not change significantly. (3) Western blotting results showed that the protein levels of α-SMA and FN1 in the TGF-β1-induced group were significantly higher than those in the control group ( < 0.05), and there was no significant difference in the expression of COL1A1. Compared with the TGF-β1-induced group, the α-SMA protein level in the intervention groups with different concentrations decreased. And the differences between the TGF-β1-induced group and 2.0 μmol/L or 5.0 μmol/L intervention groups were statistically significant ( < 0.05). Compared with the TGF-β1-induced group, the FN1 protein levels in the intervention groups with different concentrations showed a downward trend, but the difference was not statistically significant. There was no difference in COL1A1 protein expression between the intervention groups compared with the TGF-β1-induced group. (4) After TGF-β1 acted on HFL-1 cells for 48 h, the gene expression of the was up-regulated and IL-6 in culture supernatant was increased, the intervention with tofacitinib partly inhibited the TGF-β1-induced gene expression and IL-6 in culture supernatant. TGF-β1 induced the increase of Smad2/3 protein phosphorylation in HFL-1 cells for 1 h and 6 h, STAT3 protein phosphorylation increased at 1 h, 6 h and 24 h, the pre-intervention with tofacitinib inhibited the TGF-β1-induced Smad2/3 phosphorylation at 6 h and inhibited TGF-β1-induced STAT3 phosphorylation at 1 h, 6 h and 24 h.
CONCLUSION
Tofacitinib can inhibit the transformation of HFL-1 cells into myofibroblasts induced by TGF-β1, and the mechanism may be through inhibiting the classic Smad2/3 pathway as well as the phosphorylation of STAT3 induced by TGF-β1, thereby protecting the disease progression of pulmonary fibrosis.
Topics: Humans; Pyrimidines; Piperidines; STAT3 Transcription Factor; Fibroblasts; Transforming Growth Factor beta1; Myofibroblasts; Lung; Signal Transduction; Fibronectins; Cell Movement; Pyrroles; Actins; Collagen Type I; Janus Kinases; Cell Survival; Smad2 Protein; Lung Diseases, Interstitial; Interleukin-6; Smad3 Protein; Cells, Cultured
PubMed: 38864137
DOI: 10.19723/j.issn.1671-167X.2024.03.018 -
Frontiers in Immunology 2024This study aimed to develop a prognostic nomogram for predicting the recurrence-free survival (RFS) of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC)...
Machine learning-based model for predicting tumor recurrence after interventional therapy in HBV-related hepatocellular carcinoma patients with low preoperative platelet-albumin-bilirubin score.
INTRODUCTION
This study aimed to develop a prognostic nomogram for predicting the recurrence-free survival (RFS) of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) patients with low preoperative platelet-albumin-bilirubin (PALBI) scores after transarterial chemoembolization (TACE) combined with local ablation treatment.
METHODS
We gathered clinical data from 632 HBV-related HCC patients who received the combination treatment at Beijing You'an Hospital, affiliated with Capital Medical University, from January 2014 to January 2020. The patients were divided into two groups based on their PALBI scores: low PALBI group (n=247) and high PALBI group (n=385). The low PALBI group was then divided into two cohorts: training cohort (n=172) and validation cohort (n=75). We utilized eXtreme Gradient Boosting (XGBoost), random survival forest (RSF), and multivariate Cox analysis to pinpoint the risk factors for RFS. Then, we developed a nomogram based on the screened factors and assessed its risk stratification capabilities and predictive performance.
RESULTS
The study finally identified age, aspartate aminotransferase (AST), and prothrombin time activity (PTA) as key predictors. The three variables were included to develop the nomogram for predicting the 1-, 3-, and 5-year RFS of HCC patients. We confirmed the nomogram's ability to effectively discern high and low risk patients, as evidenced by Kaplan-Meier curves. We further corroborated the excellent discrimination, consistency, and clinical utility of the nomogram through assessments using the C-index, area under the curve (AUC), calibration curve, and decision curve analysis (DCA).
CONCLUSION
Our study successfully constructed a robust nomogram, effectively predicting 1-, 3-, and 5-year RFS for HBV-related HCC patients with low preoperative PALBI scores after TACE combined with local ablation therapy.
Topics: Humans; Carcinoma, Hepatocellular; Liver Neoplasms; Male; Female; Middle Aged; Machine Learning; Bilirubin; Neoplasm Recurrence, Local; Nomograms; Hepatitis B virus; Chemoembolization, Therapeutic; Prognosis; Blood Platelets; Hepatitis B; Adult; Serum Albumin; Retrospective Studies; Platelet Count
PubMed: 38863693
DOI: 10.3389/fimmu.2024.1409443 -
Cirugia Y Cirujanos 2024Estimating which patients might require surgical intervention is crucial. Patients with complete bowel obstructions exhibit disrupted enterohepatic cycles of bile and...
OBJECTIVE
Estimating which patients might require surgical intervention is crucial. Patients with complete bowel obstructions exhibit disrupted enterohepatic cycles of bile and bacteremia due to bacterial translocation. The goal of this study was to develop a prediction index using laboratory inflammatory data to identify patients who may need surgery.
MATERIALS AND METHODS
The patients were divided into two groups based on their management strategy: Non-operative management (Group 1) and surgical management (Group 2).
RESULTS
The indirect bilirubin, direct bilirubin, and total bilirubin were significantly higher in Group 2 than in Group 1 (p = 0.001, p < 0.001, and p < 0.001, respectively). The neutrophil-to-lymphocyte ratio (NLR), platelet-to-NLR (PNLR), and direct bilirubin-to-lymphocyte ratio (DBR) were significantly higher in Group 2 compared to Group 1 (p = 0.041, p = 0.020, and p < 0.001, respectively). In group 2, 78% have viable bowels. Resection was performed in 40% of cases, with 12% mortality and a 10-day average hospital stay. DLR performs the best overall accuracy (72%), demonstrating a well-balanced sensitivity (62%) and specificity (81%).
CONCLUSIONS
This study suggested that DBR is a more accurate predictive index for surgical intervention in pediatric adhesive small bowel obstruction patients compared to NLR and PNLR, providing valuable guidance for treatment strategies.
Topics: Humans; Intestinal Obstruction; Bilirubin; Male; Female; Tissue Adhesions; Intestine, Small; Infant; Lymphocyte Count; Neutrophils; Lymphocytes; Child, Preschool; Retrospective Studies; Sensitivity and Specificity; Child; Length of Stay; Predictive Value of Tests
PubMed: 38862103
DOI: 10.24875/CIRU.23000524 -
Planta Jun 2024In this review, we summarize how chlorophyll metabolism in angiosperm is affected by the environmental factors: light, temperature, metal ions, water, oxygen, and... (Review)
Review
In this review, we summarize how chlorophyll metabolism in angiosperm is affected by the environmental factors: light, temperature, metal ions, water, oxygen, and altitude. The significance of chlorophyll (Chl) in plant leaf morphogenesis and photosynthesis cannot be overstated. Over time, researchers have made significant advancements in comprehending the biosynthetic pathway of Chl in angiosperms, along with the pivotal enzymes and genes involved in this process, particularly those related to heme synthesis and light-responsive mechanisms. Various environmental factors influence the stability of Chl content in angiosperms by modulating Chl metabolic pathways. Understanding the interplay between plants Chl metabolism and environmental factors has been a prominent research topic. This review mainly focuses on angiosperms, provides an overview of the regulatory mechanisms governing Chl metabolism, and the impact of environmental factors such as light, temperature, metal ions (iron and magnesium), water, oxygen, and altitude on Chl metabolism. Understanding these effects is crucial for comprehending and preserving the homeostasis of Chl metabolism.
Topics: Chlorophyll; Magnoliopsida; Light; Temperature; Water; Oxygen; Photosynthesis; Plant Leaves; Environment; Altitude
PubMed: 38861219
DOI: 10.1007/s00425-024-04437-8 -
Optics Express Apr 2024Chlorophyll a (Chl-a) in lakes serves as an effective marker for assessing algal biomass and the nutritional level of lakes, and its observation is feasible through...
Chlorophyll a (Chl-a) in lakes serves as an effective marker for assessing algal biomass and the nutritional level of lakes, and its observation is feasible through remote sensing methods. HJ-1 (Huanjing-1) satellite, deployed in 2008, incorporates a CCD capable of a 30 m resolution and has a revisit interval of 2 days, rendering it a superb choice or supplemental sensor for monitoring trophic state of lakes. For effective long-term and regional-scale mapping, both the imagery and the evaluation of machine learning algorithms are essential. The several typical machine learning algorithms, i.e., Support Vector Regression (SVR), Gradient Boosting Decision Trees (GBDT), XGBoost (XGB), Random Forest (RF), K-Nearest Neighbor (KNN), Kernel Ridge Regression (KRR), and Multi-Layer Perception Network (MLP), were developed using our in-situ measured Chl-a. A cross-validation grid to identify the most effective hyperparameter combinations for each algorithm was used, as well as the selected optimal superparameter combinations. In Chl-a mapping of three typical lakes, the R2 of GBDT, XGB, RF, and KRR all reached 0.90, while XGB algorithm also exhibited stable performance with the smallest error (RMSE = 3.11 μg/L). Adjustments were made to align the Chl-a spatial-temporal patterns with past data, utilizing HJ1-A/B CCD images mapping through XGB algorithm, which demonstrates its stability. Our results highlight the considerable effectiveness and utility of HJ-1 A/B CCD imagery for evaluation and monitoring trophic state of lakes in a cold arid region, providing the application cases contribute to the ongoing efforts to monitor water qualities.
Topics: Lakes; Machine Learning; Chlorophyll A; Environmental Monitoring; Algorithms; Chlorophyll; Satellite Imagery; Remote Sensing Technology
PubMed: 38859266
DOI: 10.1364/OE.520667 -
PLoS Biology Jun 2024As Toxoplasma gondii disseminates through its host, the parasite must sense and adapt to its environment and scavenge nutrients. Oxygen (O2) is one such environmental...
As Toxoplasma gondii disseminates through its host, the parasite must sense and adapt to its environment and scavenge nutrients. Oxygen (O2) is one such environmental factor and cytoplasmic prolyl 4-hydroxylases (PHDs) are evolutionarily conserved O2 cellular sensing proteins that regulate responses to changes in O2 availability. Toxoplasma expresses 2 PHDs. One of them, TgPHYa hydroxylates SKP1, a subunit of the SCF-E3 ubiquitin ligase complex. In vitro, TgPHYa is important for growth at low O2 levels. However, studies have yet to examine the role that TgPHYa or any other pathogen-encoded PHD plays in virulence and disease. Using a type II ME49 Toxoplasma TgPHYa knockout, we report that TgPHYa is important for Toxoplasma virulence and brain cyst formation in mice. We further find that while TgPHYa mutant parasites can establish an infection in the gut, they are unable to efficiently disseminate to peripheral tissues because the mutant parasites are unable to survive within recruited immune cells. Since this phenotype was abrogated in IFNγ knockout mice, we studied how TgPHYa mediates survival in IFNγ-treated cells. We find that TgPHYa is not required for release of parasite-encoded effectors into host cells that neutralize anti-parasitic processes induced by IFNγ. In contrast, we find that TgPHYa is required for the parasite to scavenge tryptophan, which is an amino acid whose levels are decreased after IFNγ up-regulates the tryptophan-catabolizing enzyme, indoleamine dioxygenase (IDO). We further find, relative to wild-type mice, that IDO knockout mice display increased morbidity when infected with TgPHYa knockout parasites. Together, these data identify the first parasite mechanism for evading IFNγ-induced nutritional immunity and highlight a novel role that oxygen-sensing proteins play in pathogen growth and virulence.
Topics: Animals; Toxoplasma; Interferon-gamma; Mice; Protozoan Proteins; Oxygen; Mice, Inbred C57BL; Virulence; Indoleamine-Pyrrole 2,3,-Dioxygenase; Female; Brain; Toxoplasmosis, Animal; Toxoplasmosis
PubMed: 38857298
DOI: 10.1371/journal.pbio.3002690