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BMC Genomic Data May 2024Primulina juliae has recently emerged as a novel functional vegetable, boasting a significant biomass and high calcium content. Various breeding strategies have been...
BACKGROUND
Primulina juliae has recently emerged as a novel functional vegetable, boasting a significant biomass and high calcium content. Various breeding strategies have been employed to the domestication of P. juliae. However, the absence of genome and transcriptome information has hindered the research of mechanisms governing the taste and nutrients in this plant. In this study, we conducted a comprehensive analysis, combining the full-length transcriptomics and metabolomics, to unveil the molecular mechanisms responsible for the development of nutrients and taste components in P. juliae.
RESULTS
We obtain a high-quality reference transcriptome of P. juliae by combing the PacBio Iso-seq and Illumina sequencing technologies. A total of 58,536 cluster consensus sequences were obtained, including 28,168 complete protein coding transcripts and 8,021 Long Non-coding RNAs. Significant differences were observed in the composition and content of compounds related to nutrients and taste, particularly flavonoids, during the leaf development. Our results showed a decrease in the content of most flavonoids as leaves develop. Malate and succinate accumulated with leaf development, while some sugar metabolites were decreased. Furthermore, we identified the different accumulation of amino acids and fatty acids, which are associated with taste traits. Moreover, our transcriptomic analysis provided a molecular basis for understanding the metabolic variations during leaf development. We identified 4,689 differentially expressed genes in the two developmental stages, and through a comprehensive transcriptome and metabolome analysis, we discovered the key structure genes and transcription factors involved in the pathways.
CONCLUSIONS
This study provides a high-quality reference transcriptome and reveals molecular mechanisms associated with the development of nutrients and taste components in P. juliae. These findings will enhance our understanding of the breeding and utilization of P. juliae as a vegetable.
Topics: Transcriptome; Taste; Metabolomics; Plant Leaves; Gene Expression Regulation, Plant; Gene Expression Profiling; Nutrients; Flavonoids; Amino Acids; RNA, Long Noncoding; Metabolome; Malates
PubMed: 38783179
DOI: 10.1186/s12863-024-01231-z -
Bioresources and Bioprocessing May 2024Dodecanedioic acid (DDA), a typical medium-chain dicarboxylic fatty acid with widespread applications, has a great synthetic value and a huge industrial market demand....
BACKGROUND
Dodecanedioic acid (DDA), a typical medium-chain dicarboxylic fatty acid with widespread applications, has a great synthetic value and a huge industrial market demand. Currently, a sustainable, eco-friendly and efficient process is desired for dodecanedioic acid production.
RESULTS
Herein, a multi-enzymatic cascade was designed and constructed for the production of DDA from linoleic acid based on the lipoxygenase pathway in plants. The cascade is composed of lipoxygenase, hydroperoxide lyase, aldehyde dehydrogenase, and unidentified double-bond reductase in E. coli for the main cascade reactions, as well as NADH oxidase for cofactor recycling. The four component enzymes involved in the cascade were co-expressed in E. coli, together with the endogenous double-bond reductase of E. coli. After optimizing the reaction conditions of the rate-limiting step, 43.8 g L d of DDA was obtained by a whole-cell one-pot process starting from renewable linoleic acid.
CONCLUSIONS
Through engineering of the reaction system and co-expressing the component enzymes, a sustainable and eco-friendly DDA biosynthesis route was set up in E. coli, which afforded the highest space time yield for DDA production among the current artificial multi-enzymatic routes derived from the LOX-pathway, and the productivity achieved here ranks the second highest among the current research progress in DDA biosynthesis.
PubMed: 38780695
DOI: 10.1186/s40643-024-00770-8 -
Chemical Research in Toxicology Jun 2024Electronic (e-) cigarette formulations containing nicotine salts from a range of organic acid conjugates and pH values have dominated the commercial market. The acids in...
Electronic (e-) cigarette formulations containing nicotine salts from a range of organic acid conjugates and pH values have dominated the commercial market. The acids in the nicotine salt formulations may alter the redox environment in e-cigarettes, impacting free radical formation in e-cigarette aerosol. Here, the generation of aerosol mass and free radicals from a fourth-generation e-cigarette device was evaluated at 2 wt % nicotine salts (pH 7, 30:70 mixture propylene glycol to vegetable glycerin) across eight organic acids used in e-liquids: benzoic acid (BA), salicylic acid (SLA), lactic acid (LA), levulinic acid (LVA), succinic acid (SA), malic acid (MA), tartaric acid (TA), and citric acid (CA). Furthermore, 2 wt % BA nicotine salts were studied at the following nicotine to acid ratios: 1:2 (pH 4), 1:1 (pH 7), and 2:1 (pH 8), in comparison with freebase nicotine (pH 10). Radical yields were quantified by spin-trapping and electron paramagnetic resonance (EPR) spectroscopy. The EPR spectra of free radicals in the nicotine salt aerosol matched those generated from the Fenton reaction, which are primarily hydroxyl (OH) radicals and other reactive oxygen species (ROS). Although the aerosol mass formation was not significantly different for most of the tested nicotine salts and acid concentrations, notable ROS yields were observed only from BA, CA, and TA under the study conditions. The e-liquids with SLA, LA, LVA, SA, and MA produced less ROS than the 2 wt % freebase nicotine e-liquid, suggesting that organic acids may play dual roles in the production and scavenging of ROS. For BA nicotine salts, it was found that the ROS yield increased with a higher acid concentration (or a lower nicotine to acid ratio). The observation that BA nicotine salts produce the highest ROS yield in aerosol generated from a fourth-generation vape device, which increases with acid concentration, has important implications for ROS-mediated health outcomes that may be relevant to consumers, manufacturers, and regulatory agencies.
Topics: Electronic Nicotine Delivery Systems; Nicotine; Free Radicals; Vaping; Salts; Solutions; Benzoic Acid; Levulinic Acids; Malates
PubMed: 38778043
DOI: 10.1021/acs.chemrestox.4c00065 -
International Journal of Medical... 2024Clinical studies have shown that endodontically-treated nonvital teeth exhibit less root resorption during orthodontic tooth movement. The purpose of this study was to...
Clinical studies have shown that endodontically-treated nonvital teeth exhibit less root resorption during orthodontic tooth movement. The purpose of this study was to explore whether hypoxic dental pulp stem cells (DPSCs) can promote osteoclastogenesis in orthodontically induced inflammatory root resorption (OIIRR). Succinate in the supernatant of DPSCs under normal and hypoxic conditions was measured by a succinic acid assay kit. The culture supernatant of hypoxia-treated DPSCs was used as conditioned medium (Hypo-CM). Bone marrow-derived macrophages (BMDMs) from succinate receptor 1 (SUCNR1)-knockout or wild-type mice were cultured with conditioned medium (CM), exogenous succinate or a specific inhibitor of SUCNR1 (4c). Tartrate-resistant acid phosphatase (TRAP) staining, Transwell assays, qPCR, Western blotting, and resorption assays were used to evaluate osteoclastogenesis-related changes. The concentration of succinate reached a maximal concentration at 6 h in the supernatant of hypoxia-treated DPSCs. Hypo-CM-treated macrophages were polarized to M1 proinflammatory macrophages. Hypo-CM treatment significantly increased the formation and differentiation of osteoclasts and increased the expression of osteoclastogenesis-related genes, and this effect was inhibited by the specific succinate inhibitor 4c. Succinate promoted chemotaxis and polarization of M1-type macrophages with increased expression of osteoclast generation-related genes. SUCNR1 knockout decreased macrophage migration, M1 macrophage polarization, differentiation and maturation of osteoclasts, as shown by TRAP and NFATc1 expression and cementum resorption. Hypoxic DPSC-derived succinate may promote osteoclast differentiation and root resorption. The regulation of the succinate-SUCNR1 axis may contribute to the reduction in the OIIRR.
Topics: Animals; Mice; Dental Pulp; Osteoclasts; Root Resorption; Humans; Succinic Acid; Osteogenesis; Mice, Knockout; Stem Cells; Cell Differentiation; Macrophages; Cell Hypoxia; Receptors, G-Protein-Coupled; Culture Media, Conditioned; Cells, Cultured
PubMed: 38774749
DOI: 10.7150/ijms.94972 -
BMJ Open May 2024Intracranial aneurysm (IA) is a common cerebrovascular disease. Considering the risks and benefits of surgery, a significant proportion of patients with unruptured IA...
INTRODUCTION
Intracranial aneurysm (IA) is a common cerebrovascular disease. Considering the risks and benefits of surgery, a significant proportion of patients with unruptured IA (UIA) choose conservative observation. Previous studies suggest that inflammation of aneurysm wall is a high-risk factor of rupture. Dimethyl fumarate (DMF) acts as an anti-inflammatory agent by activating nuclear factor erythroid 2-related factor 2 (Nrf2) and other pathways. Animal experiments found DMF reduces the formation and rupture of IAs. In this study, DMF will be evaluated for its ability to reduce inflammation of the aneurysm wall in high-resolution vessel wall imaging.
METHODS AND ANALYSIS
This is a multi-centre, randomised, controlled, double-blind clinical trial. Three hospitals will enrol a total of 60 patients who have UIA with enhanced wall. Participants will be assigned randomly in a 1:1 proportion, taking either 240 mg DMF or placebo orally every day for 6 months. As the main result, aneurysm wall enhancement will be measured by the signal intensity after 6 months of DMF treatment. Secondary endpoints include morphological changes of aneurysms and factors associated with inflammation. This study will provide prospective data on the reduction of UIA wall inflammation by DMF.
ETHICS AND DISSEMINATION
This study has been approved by Medical Ethics Committee of the Beijing Tiantan Hospital, Capital Medical University (approval no: KY2022-064-02). We plan to disseminate our research findings through peer-reviewed journal publication and relevant academic conferences.
TRIAL REGISTRATION NUMBER
NCT05959759.
Topics: Humans; Dimethyl Fumarate; Intracranial Aneurysm; Double-Blind Method; Randomized Controlled Trials as Topic; Adult; Male; Middle Aged; Female; Anti-Inflammatory Agents
PubMed: 38772883
DOI: 10.1136/bmjopen-2023-080333 -
Journal of the American Chemical Society Jun 2024Sulfur trioxide (SO) is an important oxide of sulfur and a key intermediate in the formation of sulfuric acid (HSO, SA) in the Earth's atmosphere. This conversion to SA...
Sulfur trioxide (SO) is an important oxide of sulfur and a key intermediate in the formation of sulfuric acid (HSO, SA) in the Earth's atmosphere. This conversion to SA occurs rapidly due to the reaction of SO with a water dimer. However, gas-phase SO has been measured directly at concentrations that are comparable to that of SA under polluted mega-city conditions, indicating gaps in our current understanding of the sources and fates of SO. Its reaction with atmospheric acids could be one such fate that can have significant implications for atmospheric chemistry. In the present investigation, laboratory experiments were conducted in a flow reactor to generate a range of previously uncharacterized condensable sulfur-containing reaction products by reacting SO with a set of atmospherically relevant inorganic and organic acids at room temperature and atmospheric pressure. Specifically, key inorganic acids known to be responsible for most ambient new particle formation events, iodic acid (HIO, IA) and SA, are observed to react promptly with SO to form iodic sulfuric anhydride (IOSOH, ISA) and disulfuric acid (HSO, DSA). Carboxylic sulfuric anhydrides (CSAs) were observed to form by the reaction of SO with C and C monocarboxylic (acetic and propanoic acid) and dicarboxylic (oxalic and malonic acid)-carboxylic acids. The formed products were detected by a nitrate-ion-based chemical ionization atmospheric pressure interface time-of-flight mass spectrometer (NO-CI-APi-TOF; NO-CIMS). Quantum chemical methods were used to compute the relevant SO reaction rate coefficients, probe the reaction mechanisms, and model the ionization chemistry inherent in the detection of the products by NO-CIMS. Additionally, we use NO-CIMS ambient data to report that significant concentrations of SO and its acid anhydride reaction products are present under polluted, marine and polar, and volcanic plume conditions. Considering that these regions are rich in the acid precursors studied here, the reported reactions need to be accounted for in the modeling of atmospheric new particle formation.
PubMed: 38771742
DOI: 10.1021/jacs.4c04531 -
STAR Protocols Jun 2024Lysine malonylation is a protein posttranslational modification. We present a protocol to generate stable gene-knockdown K562 cell lines through lentiviral infection of...
Lysine malonylation is a protein posttranslational modification. We present a protocol to generate stable gene-knockdown K562 cell lines through lentiviral infection of a CRISPR interference (CRISPRi) system followed by lysine malonylation measurement using mass spectrometry (MS). We detail guide RNA (gRNA) vector cloning, lentiviral infection, cell line purification, protein digestion, malonyl-lysine enrichment, desalting, and MS acquisition and analysis. For complete details on the use and execution of this protocol, please refer to Zhang et al. and Bons et al..
Topics: Humans; K562 Cells; Lysine; Mass Spectrometry; Lysine Acetyltransferases; CRISPR-Cas Systems; Protein Processing, Post-Translational; Malonates; RNA, Guide, CRISPR-Cas Systems
PubMed: 38771695
DOI: 10.1016/j.xpro.2024.103074 -
Clinical and Translational Medicine May 2024A series of studies have demonstrated the emerging involvement of transfer RNA (tRNA) processing during the progression of tumours. Nevertheless, the roles and...
BACKGROUND
A series of studies have demonstrated the emerging involvement of transfer RNA (tRNA) processing during the progression of tumours. Nevertheless, the roles and regulating mechanisms of tRNA processing genes in neuroblastoma (NB), the prevalent malignant tumour outside the brain in children, are yet unknown.
METHODS
Analysis of multi-omics results was conducted to identify crucial regulators of downstream tRNA processing genes. Co-immunoprecipitation and mass spectrometry methods were utilised to measure interaction between proteins. The impact of transcriptional regulators on expression of downstream genes was measured by dual-luciferase reporter, chromatin immunoprecipitation, western blotting and real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR) methods. Studies have been conducted to reveal impact and mechanisms of transcriptional regulators on biological processes of NB. Survival differences were analysed using the log-rank test.
RESULTS
c-Myc was identified as a transcription factor driving tRNA processing gene expression and subsequent malate-aspartate shuttle (MAS) in NB cells. Mechanistically, c-Myc directly promoted the expression of glutamyl-prolyl-tRNA synthetase (EPRS) and leucyl-tRNA synthetase (LARS), resulting in translational up-regulation of glutamic-oxaloacetic transaminase 1 (GOT1) as well as malate dehydrogenase 1 (MDH1) via inhibiting general control nonrepressed 2 or activating mechanistic target of rapamycin signalling. Meanwhile, lamin A (LMNA) inhibited c-Myc transactivation via physical interaction, leading to suppression of MAS, aerobic glycolysis, tumourigenesis and aggressiveness. Pre-clinically, lobeline was discovered as a LMNA-binding compound to facilitate its interaction with c-Myc, which inhibited aminoacyl-tRNA synthetase expression, MAS and tumour progression of NB, as well as growth of organoid derived from c-Myc knock-in mice. Low levels of LMNA or elevated expression of c-Myc, EPRS, LARS, GOT1 or MDH1 were linked to a worse outcome and a shorter survival time of clinical NB patients.
CONCLUSIONS
These results suggest that targeting c-Myc transactivation by LMNA inhibits tRNA processing essential for MAS and tumour progression.
Topics: Humans; Mice; Proto-Oncogene Proteins c-myc; Animals; Aspartic Acid; Malates; RNA, Transfer; Neuroblastoma; Disease Progression; Transcriptional Activation; Cell Line, Tumor; Disease Models, Animal
PubMed: 38769668
DOI: 10.1002/ctm2.1680 -
Nature Communications May 2024Elevated intracellular sodium Na adversely affects mitochondrial metabolism and is a common feature of heart failure. The reversibility of acute Na induced metabolic...
Elevated intracellular sodium Na adversely affects mitochondrial metabolism and is a common feature of heart failure. The reversibility of acute Na induced metabolic changes is evaluated in Langendorff perfused rat hearts using the Na/K ATPase inhibitor ouabain and the myosin-uncoupler para-aminoblebbistatin to maintain constant energetic demand. Elevated Na decreases Gibb's free energy of ATP hydrolysis, increases the TCA cycle intermediates succinate and fumarate, decreases ETC activity at Complexes I, II and III, and causes a redox shift of CoQ to CoQH, which are all reversed on lowering Na to baseline levels. Pseudo hypoxia and stabilization of HIF-1α is observed despite normal tissue oxygenation. Inhibition of mitochondrial Na/Ca-exchange with CGP-37517 or treatment with the mitochondrial ROS scavenger MitoQ prevents the metabolic alterations during Na elevation. Elevated Na plays a reversible role in the metabolic and functional changes and is a novel therapeutic target to correct metabolic dysfunction in heart failure.
Topics: Animals; Rats; Mitochondria, Heart; Sodium; Male; Myocardium; Hypoxia-Inducible Factor 1, alpha Subunit; Heart Failure; Adenosine Triphosphate; Citric Acid Cycle; Rats, Sprague-Dawley; Organophosphorus Compounds; Sodium-Calcium Exchanger; Ubiquinone; Sodium-Potassium-Exchanging ATPase; Oxidation-Reduction; Succinic Acid
PubMed: 38769288
DOI: 10.1038/s41467-024-48474-z -
Journal of the American Chemical Society Jun 2024Manipulation of cell-cell interactions via cell surface modification is crucial in tissue engineering and cell-based therapy. To be able to monitor intercellular...
Manipulation of cell-cell interactions via cell surface modification is crucial in tissue engineering and cell-based therapy. To be able to monitor intercellular interactions, it can also provide useful information for understanding how the cells interact and communicate. We report herein a facile bioorthogonal strategy to promote and monitor cell-cell interactions. It involves the use of a maleimide-appended tetrazine-caged boron dipyrromethene (BODIPY)-based fluorescent probe and a maleimide-substituted bicyclo[6.1.0]non-4-yne (BCN) to modify the membrane of macrophage (RAW 264.7) and cancer (HT29, HeLa, and A431) cells, respectively, via maleimide-thiol conjugation. After modification, the two kinds of cells interact strongly through inverse electron-demand Diels-Alder reaction of the surface tetrazine and BCN moieties. The coupling also disrupts the tetrazine quenching unit, restoring the fluorescence emission of the BODIPY core on the cell-cell interface, and promotes phagocytosis. Hence, this approach can promote and facilitate the detection of intercellular interactions, rendering it potentially useful for macrophage-based immunotherapy.
Topics: Humans; Boron Compounds; Mice; Animals; Fluorescent Dyes; Cell Communication; RAW 264.7 Cells; Maleimides; HeLa Cells
PubMed: 38767615
DOI: 10.1021/jacs.4c04317