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Journal of Microbiological Methods Jun 2024The mucin-degrading gut commensal Akkermansia muciniphila (A. muciniphila) negatively correlates with various diseases, including metabolic disorders, neurodegenerative...
The mucin-degrading gut commensal Akkermansia muciniphila (A. muciniphila) negatively correlates with various diseases, including metabolic disorders, neurodegenerative disorders, and cancers, through interacting with host receptors by diverse molecules. Still, their exact metabolic capability within the nutrient-rich environment (such as in the human gut) is not fully characterized. Therefore, in the present study, we investigated the comprehensive metabolome and lipidome of A. muciniphila after supplementation of four major gut microbial nutrients: mucin, inorganic salts, bile salts, and short-chain fatty acids (SCFAs). Our results showed that mucin is the predominant driver of the different lipidomic and metabolomic profiles of A. muciniphila, and it promotes the overall growth of this bacteria. While the addition of inorganic salts, bile salts, and SCFAs was found to inhibit the growth of A. muciniphila. Interestingly, inorganic salts affected the purine metabolism in A. muciniphila cultures, while adding bile salts significantly increased the production of other bile acids and N-acyl amides. Lastly, SCFAs were identified to alter the A. muciniphila energy utilization of triglycerides, fatty acyls, and phosphatidylethanolamines. To our knowledge, this is the first study to examine the comprehensive lipidome and metabolome of A. muciniphila, which highlights the importance of nutritional impacts on the lipidome and metabolome of A. muciniphila and hence providing foundational knowledge to unveil the potential effects of A. muciniphila on host health.
PubMed: 38889842
DOI: 10.1016/j.mimet.2024.106975 -
RSC Advances Jun 2024This study presents the synthesis and characterization of phenazinium dyes with absorption ranging from red to far-red, as well as emission extending into the far-red to...
This study presents the synthesis and characterization of phenazinium dyes with absorption ranging from red to far-red, as well as emission extending into the far-red to near-infrared (NIR) region. The procedure involves the post-functionalization of a triamino-phenazinium that was recently reported as a theranostic agent. The introduction of electron-withdrawing moieties is accomplished through acylation or aromatic nucleophilic substitution. For one of the obtained products, a further substitution step could be achieved with primary amines to tune the electron density of the phenazinium core. The isolated dyes exhibit promising features that hold potential for future applications as biological markers or therapeutic agents.
PubMed: 38887642
DOI: 10.1039/d4ra03245d -
Beilstein Journal of Organic Chemistry 2024Tandem Diels-Alder reactions are often used for the straightforward formation of complex natural compounds and the fused polycyclic systems contained in their...
Tandem Diels-Alder reactions are often used for the straightforward formation of complex natural compounds and the fused polycyclic systems contained in their precursors. In the second step of this reaction, regio- and stereochemically controlled intramolecular cyclization leads to the formation of versatile nitrogen-containing tricyclic systems. However, these useful organic transformations are usually carried out in highly toxic organic solvents such as benzene, toluene, chloroform, etc. Despite recent efforts by 'green chemists', synthetic chemists still use these traditional toxic organic solvents in many of their reactions, even though safer alternatives are available. However, in addition to the harmful effects of these petrochemical solvents on the environment, the prediction that their resources will run out in the near future has led 'green chemists' to explore solvents that can be derived from renewable resources and used effectively in various organic transformations. In this context, we have shown for the first time that the 100% atom-economical tandem Diels-Alder reaction between aminofuranes and maleic anhydride can be carried out successfully in vegetable oils and waxes. The reaction was successfully carried out in sunflower seed oil, olive oil, oleic acid and lauryl myristate under mild reaction conditions. A series of epoxyisoindole-7-carboxylic acid and bisepoxyisoindole-7-carboxylic acids were obtained in good yields after a practical isolation procedure. The results obtained in this study demonstrate the potential of vegetable oils and their renewable materials to provide a reaction medium that is more sustainable than conventional organic solvents in cascade Diels-Alder reactions and can be used repeatedly without significant degradation. These materials also allow the reaction to be completed in less time, with less energy consumption and higher yields.
PubMed: 38887569
DOI: 10.3762/bjoc.20.114 -
Plant-environment Interactions... Jun 2024To better understand the salt tolerance of the wild rice, , root tissue-specific untargeted comparative metabolomic profiling was performed against the salt-sensitive ....
To better understand the salt tolerance of the wild rice, , root tissue-specific untargeted comparative metabolomic profiling was performed against the salt-sensitive . Under control, exhibited abundant levels of most metabolites, while salt caused their downregulation in contrast to metabolites in . Under control conditions, itaconate, vanillic acid, threonic acid, eicosanoids, and a group of xanthin compounds were comparatively abundant in . Similarly, eight amino acids showed constitutive abundance in . In contrast, under control, glycerolipid abundances were lower in and salt stress further reduced their abundance. Most phospholipids also showed a distribution similar to the glycerolipids. Fatty acyls were however significantly induced in but organic acids were prominently induced in . Changes in metabolite levels suggest that there was upregulation of the arachidonic acid metabolism in . In addition, the phenylpropanoid biosynthesis as well as cutin, suberin, and wax biosynthesis were also more enriched in , likely contributing to its anatomical traits responsible for salt tolerance. The comparative variation in the number of metabolites like gelsemine, allantoin, benzyl alcohol, specific phospholipids, and glycerolipids may play a role in maintaining the superior growth of in salt. Collectively, our results offer a comprehensive analysis of the metabolite profile in the roots of salt-tolerant and salt-sensitive , which confirm potential targets for metabolic engineering to improve salt tolerance and resilience in commercial rice genotypes.
PubMed: 38882243
DOI: 10.1002/pei3.10155 -
Food Science & Nutrition Jun 2024The aims of this research were to investigate the usability of black grape pomace in the production of shalgam juice, which is a traditional fermented Turkish beverage,...
Evaluation of black grape pomace, a fruit juice by-product, in shalgam juice production: Effect on phenolic compounds, anthocyanins, resveratrol, tannin, and in vitro antioxidant activity.
The aims of this research were to investigate the usability of black grape pomace in the production of shalgam juice, which is a traditional fermented Turkish beverage, to transform the pomace into the high value-added product and to enrich the shalgam juice with phenolic compounds. Black grape pomace and black carrot were used as the sources of polyphenols and five different formulations were obtained according to the amounts of black carrot and black grape pomace. During the fermentation, the samples were taken at different periods and analyzed for anthocyanins, phenolic compounds, antioxidant activity, and tannin content. Gentisic, caffeic, ferulic, coumaric, and chlorogenic acids, catechin, glucosides of kaemferol and isorhamnetin, resveratrol, rutin, cyanidin-3-xylosylglucosylgalactoside, cyanidin-3-xylosylgalactoside, cyanidin-3-xylosylglucosylgalactoside acylated with sinapic acid, ferulic acid, or coumaric acid, and glucosides of cyanidin, petunidin, and malvidin were identified in the shalgam juices that contained both black grape pomace and black carrot in their formulation. Some of these polyphenols were not detected detect in the shalgam juices that were produced from only the black carrot or black grape pomace. During the fermentation, a decrease in the amount of anthocyanins originated from black carrots and an increase in the amount of anthocyanins orginated from black grape pomace were determined. Black grape pomace addition to the formulation before the fermentation caused an increase in the amount of tannin in the shalgam juice samples. Consequently, it is thought that black grape pomace can be fruitfully evaluated in shalgam juice production and can be enhanced by polyphenolic profile of shalgam juice.
PubMed: 38873455
DOI: 10.1002/fsn3.4104 -
Biomedicine & Pharmacotherapy =... Jul 2024The intricate crosstalk between long noncoding RNAs (lncRNAs) and epigenetic modifications such as chromatin/histone methylation and acetylation offer new perspectives... (Review)
Review
The intricate crosstalk between long noncoding RNAs (lncRNAs) and epigenetic modifications such as chromatin/histone methylation and acetylation offer new perspectives on the pathogenesis and treatment of kidney diseases. lncRNAs, a class of transcripts longer than 200 nucleotides with no protein-coding potential, are now recognized as key regulatory molecules influencing gene expression through diverse mechanisms. They modulate the epigenetic modifications by recruiting or blocking enzymes responsible for adding or removing methyl or acetyl groups, such as DNA, N6-methyladenosine (m6A) and histone methylation and acetylation, subsequently altering chromatin structure and accessibility. In kidney diseases such as acute kidney injury (AKI), chronic kidney disease (CKD), diabetic nephropathy (DN), glomerulonephritis (GN), and renal cell carcinoma (RCC), aberrant patterns of DNA/RNA/histone methylation and acetylation have been associated with disease onset and progression, revealing a complex interplay with lncRNA dynamics. Recent studies have highlighted how lncRNAs can impact renal pathology by affecting the expression and function of key genes involved in cell cycle control, fibrosis, and inflammatory responses. This review will separately address the roles of lncRNAs and epigenetic modifications in renal diseases, with a particular emphasis on elucidating the bidirectional regulatory effects and underlying mechanisms of lncRNAs in conjunction with DNA/RNA/histone methylation and acetylation, in addition to the potential exacerbating or renoprotective effects in renal pathologies. Understanding the reciprocal relationships between lncRNAs and epigenetic modifications will not only shed light on the molecular underpinnings of renal pathologies but also present new avenues for therapeutic interventions and biomarker development, advancing precision medicine in nephrology.
Topics: RNA, Long Noncoding; Humans; Epigenesis, Genetic; Histones; Acetylation; DNA Methylation; Kidney Diseases; Chromatin; Animals
PubMed: 38870627
DOI: 10.1016/j.biopha.2024.116922 -
Nanoscale Advances Jun 2024In this research, a heterogeneous acid catalyst was synthesized by room temperature encapsulation of phosphomolybdic acid (PMA) in the pores of the MIL-53 (Fe) metal...
In this research, a heterogeneous acid catalyst was synthesized by room temperature encapsulation of phosphomolybdic acid (PMA) in the pores of the MIL-53 (Fe) metal organic framework (MOF) under ultrasonic conditions. Then the catalytic activity of PMA@MIL-53 (Fe) was investigated in Friedel-Crafts -acylation of -fluorophenol, and this procedure was optimized using response surface methodology based on central composite design (RSM-CCD). The impact of critical reaction parameters including reaction duration, catalyst dosage, and PMA amount in the catalyst was optimized, leading to the formation of the target product in excellent yield at a short reaction time.
PubMed: 38868818
DOI: 10.1039/d3na01126g -
Molecular & Cellular Proteomics : MCP Jun 2024Histone post-translational modifications (PTMs) have crucial roles in a multitude of cellular processes, and their aberrant levels have been linked with numerous...
Histone post-translational modifications (PTMs) have crucial roles in a multitude of cellular processes, and their aberrant levels have been linked with numerous diseases, including cancer. Although histone PTM investigations have focused so far on methylations and acetylations, alternative long-chain acylations emerged as new dimension, as they are linked to cellular metabolic states and affect gene expression through mechanisms distinct from those regulated by acetylation. Mass spectrometry (MS) is the most powerful, comprehensive and unbiased method to study histone PTMs. However, typical MS-based protocols for histone PTM analysis do not allow identification of naturally occurring propionylation and butyrylation. Here, we present improved state-of-the-art sample preparation and analysis protocols to quantitate these classes of modifications. After testing different derivatization methods coupled to protease digestion, we profiled common histone PTMs and histone acylations in seven mouse tissues and human normal and tumor breast clinical samples, obtaining a map of propionylations and butyrylations found in different tissue contexts. A quantitative histone PTM analysis also revealed a contribution of histone acylations in discriminating different tissues, also upon perturbation with antibiotics, and breast cancer samples from the normal counterpart. Our results show that profiling only classical modifications is limiting and highlight the importance of using sample preparation methods that allows the analysis of the widest possible spectrum of histone modifications, paving the way for deeper insights into their functional significance in cellular processes and disease states.
PubMed: 38866077
DOI: 10.1016/j.mcpro.2024.100799 -
Journal of Chemical Information and... Jun 2024Epigenetic modifications of histone N-terminal tails play a critical role in regulating the chromatin structure and biological processes such as transcription and DNA...
Epigenetic modifications of histone N-terminal tails play a critical role in regulating the chromatin structure and biological processes such as transcription and DNA repair. One of the key post-translational modifications (PTMs) is the acetylation of lysine residues on histone tails. Epigenetic modifications are ubiquitous in the development of diseases, such as cancer and neurological disorders. Histone H2B tails are critical regulators of nucleosome dynamics, biological processes, and certain diseases. Here, we report all-atomistic molecular dynamics (MD) simulations of the nucleosome to demonstrate that acetylation of the histone tails changes their conformational space and interaction with DNA. We perform simulations of H2B tails, critical regulators of gene regulation, in both the lysine-acetylated (ACK) and unacetylated wild type (WT) states. To explore the effects of salt concentration, we use two different NaCl concentrations to perform simulations at microsecond time scales. Salt can modulate the effects of electrostatic interactions between the DNA phosphate backbone and histone tails. Upon acetylation, H2B tails shift their secondary structure helical propensity. The number of contacts between the DNA and the H2B tail decreases. We characterize the conformational dynamics of the H2B tails by principal component analysis (PCA). The ACK tails become more compact at increased salt concentrations, but conformations from the WT tails display the most contacts with DNA at both salt concentrations. Mainly, H2B acetylation may increase the DNA accessibility for regulatory proteins to bind, which can aid in gene regulation and NCP stability.
Topics: Molecular Dynamics Simulation; Histones; Nucleosomes; DNA; Acetylation; Protein Conformation; Principal Component Analysis
PubMed: 38865599
DOI: 10.1021/acs.jcim.4c00059 -
Acetylation of histones and non-histone proteins is not a mere consequence of ongoing transcription.Nature Communications Jun 2024In all eukaryotes, acetylation of histone lysine residues correlates with transcription activation. Whether histone acetylation is a cause or consequence of...
In all eukaryotes, acetylation of histone lysine residues correlates with transcription activation. Whether histone acetylation is a cause or consequence of transcription is debated. One model suggests that transcription promotes the recruitment and/or activation of acetyltransferases, and histone acetylation occurs as a consequence of ongoing transcription. However, the extent to which transcription shapes the global protein acetylation landscapes is not known. Here, we show that global protein acetylation remains virtually unaltered after acute transcription inhibition. Transcription inhibition ablates the co-transcriptionally occurring ubiquitylation of H2BK120 but does not reduce histone acetylation. The combined inhibition of transcription and CBP/p300 further demonstrates that acetyltransferases remain active and continue to acetylate histones independently of transcription. Together, these results show that histone acetylation is not a mere consequence of transcription; acetyltransferase recruitment and activation are uncoupled from the act of transcription, and histone and non-histone protein acetylation are sustained in the absence of ongoing transcription.
Topics: Acetylation; Histones; Transcription, Genetic; Humans; Ubiquitination; p300-CBP Transcription Factors; Protein Processing, Post-Translational; Histone Acetyltransferases; Lysine
PubMed: 38862536
DOI: 10.1038/s41467-024-49370-2