Specific Metabolic Pathways Research Articles

Long-term proliferation of immature hypoxia-dependent JMML cells supported by a 3D invitro system.

Juvenile myelomonocytic leukemia (JMML) is a rare clonal stem cell disorder that occurs in early childhood and is characterized by the hyperactivation of the RAS pathway in 95% of the patients. JMML is characterized by a hyperproliferation of granulocytes and monocytes, and little is known about the heterogeneous nature of leukemia-initiating cells, as well as of the cellular hierarchy of the JMML bone marrow. In this study, we report the generation and characterization of a novel patient-derived three-dimensional (3D) invitro JMML model, called patient-derived JMML Atypical Organoid (pd-JAO), sustaining the long-term proliferation of JMML cells with stem cell features and patient-specific hallmarks. JMML cells brewed in a 3D model under different microenvironmental conditions acquired proliferative and survival advantages when placed under low oxygen tension. Transcriptomic and microscopic analyses revealed the activation of specific metabolic energy pathways and the inactivation of processes leading to cell death. Furthermore, we demonstrated the pd-JAO-derived cells' migratory, propagation, and self-renewal capacities. Our study contributes to the development of a robust JMML 3D invitro model for studying and defining the impact of microenvironmental stimuli on JMML disease and the molecular mechanisms that regulate JMML initiating and propagating cells. Pd-JAO may become a promising model for compound tests focusing on new therapeutic interventions aimed at eradicating JMML progenitors and controlling JMML disease.

Characterization of rumen microbiome and metabolome from oro-esophageal tubing and rumen cannula in Holstein dairy cows

Less invasive rumen sampling methods, such as oro-esophageal tubing, became widely popular for exploring the rumen microbiome and metabolome. However, it remains unclear if such methods represent well the rumen contents from the rumen cannula technique. Herein, we characterized the microbiome and metabolome in the rumen content collected by an oro-esophageal tube and by rumen cannula in ten multiparous lactating Holstein cows. The 16S rRNA gene was amplified and sequenced using the Illumina MiSeq platform. Untargeted metabolome was characterized using gas chromatography of a time-of-flight mass spectrometer. Bacteroidetes, Firmicutes, and Proteobacteria were the top three most abundant phyla representing ~ 90% of all samples. Although the pH of oro-esophageal samples was greater than rumen cannula, we found no difference in alpha and beta-diversity among their microbiomes. The overall metabolome of oro-esophageal samples was slightly different from rumen cannula samples yet more closely related to the rumen cannula content as a whole, including its fluid and particulate fractions. Enrichment pathway analysis revealed a few differences between sampling methods, such as when evaluating unsaturated fatty acid pathways in the rumen. The results of the current study suggest that oro-esophageal sampling can be a proxy to screen the 16S rRNA rumen microbiome compared to the rumen cannula technique. The variation introduced by the 16S rRNA methodology may be mitigated by oro-esophageal sampling and the possibility of increasing experimental units for a more consistent representation of the overall microbial population. Studies should consider an under or over-representation of metabolites and specific metabolic pathways depending on the sampling method.

Bioinformatics analysis of potential key ferroptosis-related genes involved in tubulointerstitial injury in patients with diabetic nephropathy

Diabetic nephropathy (DN) is the primary complication of diabetes mellitus. Ferroptosis is a form of cell death that plays an important role in DN tubulointerstitial injury, but the specific molecular mechanism remains unclear. Here, we downloaded the DN tubulointerstitial datasets GSE104954 and GSE30529 from the Gene Expression Omnibus database. We examined the differentially expressed genes (DEGs) between DN patients and healthy controls, and 36 ferroptosis-related DEGs were selected. Pathway-enrichment analyses showed that many of these genes are involved in metabolic pathways, phosphoinositide 3-kinase/Akt signaling, and hypoxia-inducible factor-1 signaling. Ten of the 36 ferroptosis-related DEGs (CD44, PTEN, CDKN1A, DPP4, DUSP1, CYBB, DDIT3, ALOX5, VEGFA, and NCF2) were identified as key genes. Expression patterns for six of these (CD44, PTEN, DDIT3, ALOX5, VEGFA, and NCF2) were validated in the GSE30529 dataset. Nephroseq data indicated that the mRNA expression levels of CD44, PTEN, ALOX5, and NCF2 were negatively correlated with the glomerular filtration rate (GFR), while VEGFA and DDIT3 mRNA expression levels were positively correlated with GFR. Immune infiltration analysis demonstrated altered immunity in DN patients. Real-time quantitative PCR (qPCR) analysis showed that ALOX5, PTEN, and NCF2 mRNA levels were significantly upregulated in high-glucose-treated human proximal tubular (HK-2) cells, while DDIT3 and VEGFA mRNA levels were significantly downregulated. Immunohistochemistry analysis of human renal biopsies showed positive staining for ALOX5 and NCF2 protein in DN samples but not the controls. These key genes may be involved in the molecular mechanisms underlying ferroptosis in patients with DN, potentially through specific metabolic pathways and immune/inflammatory mechanisms.

Glioblastomas: Hijacking Metabolism to Build a Flexible Shield for Therapy Resistance.

Significance: Glioblastomas (GBMs) are among the most lethal tumors despite the almost exclusive localization to the brain. This is largely due to therapeutic resistance. Radiation and chemotherapy significantly increase the survival for GBM patients, however, GBMs always recur, and the median overall survival is just over a year. Proposed reasons for such intractable resistance to therapy are numerous and include tumor metabolism, in particular, the ability of tumor cells to reconfigure metabolic fluxes on demand (metabolic plasticity). Understanding how the hard-wired, oncogene-driven metabolic tendencies of GBMs intersect with flexible, context-induced metabolic rewiring promises to reveal novel approaches for combating therapy resistance. Recent Advances: Personalized genome-scale metabolic flux models have recently provided evidence that metabolic flexibility promotes radiation resistance in cancer and identified tumor redox metabolism as a major predictor for resistance to radiation therapy (RT). It was demonstrated that radioresistant tumors, including GBM, reroute metabolic fluxes to boost the levels of reducing factors of the cell, thus enhancing clearance of reactive oxygen species that are generated during RT and promoting survival. Critical Issues: The current body of knowledge from published studies strongly supports the notion that robust metabolic plasticity can act as a (flexible) shield against the cytotoxic effects of standard GBM therapies, thus driving therapy resistance. The limited understanding of the critical drivers of such metabolic plasticity hampers the rational design of effective combination therapies. Future Directions: Identifying and targeting regulators of metabolic plasticity, rather than specific metabolic pathways, in combination with standard-of-care treatments have the potential to improve therapeutic outcomes in GBM. Antioxid. Redox Signal. 39, 957-979.

Untargeted metabolomics of saliva in caries-active and caries-free children in the mixed dentition.

To compare the differences in salivary metabolites between caries-active and caries-free children in the mixed dentition, and explore their correlation with caries status. The study involved 20 children (aged 8-9 years) in the mixed dentition, including 10 caries-active (aged 8.6 ± 0.49years) and 10 caries-free children(aged 8.5 ± 0.5years), with a male/female ratio of 1:1. The saliva samples were collected from all children. Metabolite extraction, LC-MS/MS-based untargeted metabolomics, qualitative and semi-quantitative analysis and bioinformatics analysis were performed to identify differential metabolites between the two sample groups. The differential metabolites identified were further analyzed in an attempt to find their correlations with caries status. In the positive ion mode, a total of 1606 molecular features were detected in the samples of the two groups, 189 of which were differential metabolites when comparing the caries-active group with the caries-free group, including 104 up-regulated and 85 down-regulated metabolites. In the negative ion mode, a total of 532 molecular features were detected in the samples of two groups, 70 of which were differential metabolites when comparing the caries-active group with the caries-free group, including 37 up-regulated and 33 down-regulated metabolites. In the positive ion mode, two of the top 5 up-regulated differential metabolites were found in and annotated to specific metabolic pathways, whereas in the negative ion mode, only one of the top 5 up-regulated differential metabolites was found in and annotated to specific metabolic pathways. In both the positive and negative ion modes, the top 5 down-regulated differential metabolites were both annotated to the metabolic pathways. KEGG pathway enrichment analysis of differential metabolites showed that histamine and arachidonic acid identified in the positive ion mode, as well as succinate and L-histidine identified in the negative ion mode were enriched in the top 3 significantly altered pathways. The enriched differential metabolites including histamine, L-histidine and succinate were correlated with the presence of dental caries, but their role in the caries process needs to be further investigated.

Selected Articles from This Issue

Highlights| April 01 2023 Selected Articles from This Issue Author & Article Information Online ISSN: 1557-3125 Print ISSN: 1541-7786 ©2023 American Association for Cancer Research2023American Association for Cancer Research Mol Cancer Res (2023) 21 (4): 291. https://doi.org/10.1158/1541-7786.MCR-21-4-HI Related Content A commentary has been published: Multi-substrate Metabolic Tracing Reveals Marked Heterogeneity and Dependency on Fatty Acid Metabolism in Human Prostate Cancer A commentary has been published: Targeting ULK1 Decreases IFNγ-Mediated Resistance to Immune Checkpoint Inhibitors A commentary has been published: Evolutionary Characteristics and Immunologic Divergence of Lung and Brain Metastasis Lesions in NSCLC View more A commentary has been published: Scaffolding Protein Connector Enhancer of Kinase Suppressor of Ras 1 (CNKSR1) Regulates MAPK Inhibition Responsiveness in Pancreas Cancer via Crosstalk with AKT Signaling View less Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Get Permissions Cite Icon Cite Search Site Article Versions Icon Versions Version of Record April 1 2023 Citation Selected Articles from This Issue. Mol Cancer Res 1 April 2023; 21 (4): 291. https://doi.org/10.1158/1541-7786.MCR-21-4-HI Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest Search Advanced Search While metabolic reprogramming is an established hallmark of cancer, specific metabolic pathways that are altered in human prostate tumors — as well as the degree of heterogeneity to which they are altered among tumors — remain largely unsolved. In their study, Fidelito and colleagues performed radiometric and stable isotope tracing using serially transplantable patient-derived xenografts (PDXs) to define the metabolic landscape of human prostate tumors. The authors found that the PDXs oxidize diverse substrates including glucose, glutamine, lactate, and fatty acids, and to a greater degree than do benign prostate tissues. Isotope tracing revealed that prostate tumor cells tend to use glucose for acetyl-CoA production, and process glutamine via the tricarboxylic acid cycle. Notably, substrate utilization exhibited marked heterogeneity among samples, and, correspondingly, responses to pharmacologic inhibitors targeting diverse metabolic pathways varied among samples. However, adenocarcinoma, neuroendocrine, primary, and metastatic PDX-derived organoids all displayed dependencies on fatty acid uptake and... You do not currently have access to this content.

Evaluation of Hypoxia in Hepatocellular Carcinoma Using Quantitative MRI: Significances, Challenges, and Advances.

This review aimed to perform a scoping review of promising MRI methods in assessing tumor hypoxia in hepatocellular carcinoma (HCC). The hypoxic microenvironment and upregulated hypoxic metabolism in HCC are determining factors of poor prognosis, increased metastatic potential, and resistance to chemotherapy and radiotherapy. Assessing hypoxia in HCC is essential for personalized therapy and predicting prognoses. Oxygen electrodes, protein markers, optical imaging, and positron emission tomography can evaluate tumor hypoxia. These methods lack clinical applicability because of invasiveness, tissue depth, and radiation exposure. MRI methods, including blood oxygenation level-dependent, dynamic contrast-enhanced MRI, diffusion-weighted imaging, MRI spectroscopy, chemical exchange saturation transfer MRI, and multinuclear MRI, are promising noninvasive methods that evaluate the hypoxic microenvironment by observing biochemical processes in vivo, which may inform on therapeutic options. This review summarizes the recent challenges and advances in MRI techniques for assessing hypoxia in HCC and highlights the potential of MRI methods for examining the hypoxic microenvironment via specific metabolic substrates and pathways. Although the utilization of MRI methods for evaluating hypoxia in patients with HCC is increasing, rigorous validation is needed in order to translate these MRI methods into clinical use. Due to the limited sensitivity and specificity of current quantitative MRI methods, their acquisition and analysis protocols require further improvement. EVIDENCE LEVEL: 3. TECHNICAL EFFICACY: Stage 4.

Metabolomic Studies in Inborn Errors of Metabolism: Last Years and Future Perspectives.

The inborn errors of metabolism (IEMs or Inherited Metabolic Disorders) are a heterogeneous group of diseases caused by a deficit of some specific metabolic pathways. IEMs may present with multiple overlapping symptoms, sometimes difficult delayed diagnosis and postponed therapies. Additionally, many IEMs are not covered in newborn screening and the diagnostic profiling in the metabolic laboratory is indispensable to reach a correct diagnosis. In recent years, Metabolomics helped to obtain a better understanding of pathogenesis and pathophysiology of IEMs, by validating diagnostic biomarkers, discovering new specific metabolic patterns and new IEMs itself. The expansion of Metabolomics in clinical biochemistry and laboratory medicine has brought these approaches in clinical practice as part of newborn screenings, as an exam for differential diagnosis between IEMs, and evaluation of metabolites in follow up as markers of severity or therapies efficacy. Lastly, several research groups are trying to profile metabolomics data in platforms to have a holistic vision of the metabolic, proteomic and genomic pathways of every single patient. In 2018 this team has made a review of literature to understand the value of Metabolomics in IEMs. Our review offers an update on use and perspectives of metabolomics in IEMs, with an overview of the studies available from 2018 to 2022.

Integrative Analysis of the Ethanol Tolerance of Saccharomyces cerevisiae

Ethanol (EtOH) alters many cellular processes in yeast. An integrated view of different EtOH-tolerant phenotypes and their long noncoding RNAs (lncRNAs) is not yet available. Here, large-scale data integration showed the core EtOH-responsive pathways, lncRNAs, and triggers of higher (HT) and lower (LT) EtOH-tolerant phenotypes. LncRNAs act in a strain-specific manner in the EtOH stress response. Network and omics analyses revealed that cells prepare for stress relief by favoring activation of life-essential systems. Therefore, longevity, peroxisomal, energy, lipid, and RNA/protein metabolisms are the core processes that drive EtOH tolerance. By integrating omics, network analysis, and several other experiments, we showed how the HT and LT phenotypes may arise: (1) the divergence occurs after cell signaling reaches the longevity and peroxisomal pathways, with CTA1 and ROS playing key roles; (2) signals reaching essential ribosomal and RNA pathways via SUI2 enhance the divergence; (3) specific lipid metabolism pathways also act on phenotype-specific profiles; (4) HTs take greater advantage of degradation and membraneless structures to cope with EtOH stress; and (5) our EtOH stress-buffering model suggests that diauxic shift drives EtOH buffering through an energy burst, mainly in HTs. Finally, critical genes, pathways, and the first models including lncRNAs to describe nuances of EtOH tolerance are reported here.

Integrated Metabolic and Inflammatory Signatures Associated with Severity of, Fatality of, and Recovery from COVID-19.

Severe manifestations of coronavirus disease 2019 (COVID-19) and mortality have been associated with physiological alterations that provide insights into the pathogenesis of the disease. Moreover, factors that drive recovery from COVID-19 can be explored to identify correlates of protection. The cellular metabolism represents a potential target to improve survival upon severe disease, but the associations between the metabolism and the inflammatory response during COVID-19 are not well defined. We analyzed blood laboratorial parameters, cytokines, and metabolomes of 150 individuals with mild to severe disease, of which 33 progressed to a fatal outcome. A subset of 20 individuals was followed up after hospital discharge and recovery from acute disease. We used hierarchical community networks to integrate metabolomics profiles with cytokines and markers of inflammation, coagulation, and tissue damage. Infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) promotes significant alterations in the plasma metabolome, whose activity varies according to disease severity and correlates with oxygen saturation. Differential metabolism underlying death was marked by amino acids and related metabolites, such as glutamate, glutamyl-glutamate, and oxoproline, and lipids, including progesterone, phosphocholine, and lysophosphatidylcholines (lysoPCs). Individuals who recovered from severe disease displayed persistent alterations enriched for metabolism of purines and phosphatidylinositol phosphate and glycolysis. Recovery of mild disease was associated with vitamin E metabolism. Data integration shows that the metabolic response is a hub connecting other biological features during disease and recovery. Infection by SARS-CoV-2 induces concerted activity of metabolic and inflammatory responses that depend on disease severity and collectively predict clinical outcomes of COVID-19. IMPORTANCE COVID-19 is characterized by diverse clinical outcomes that include asymptomatic to mild manifestations or severe disease and death. Infection by SARS-CoV-2 activates inflammatory and metabolic responses that drive protection or pathology. How inflammation and metabolism communicate during COVID-19 is not well defined. We used high-resolution mass spectrometry to investigate small biochemical compounds (<1,500 Da) in plasma of individuals with COVID-19 and controls. Age, sex, and comorbidities have a profound effect on the plasma metabolites of individuals with COVID-19, but we identified significant activity of pathways and metabolites related to amino acids, lipids, nucleotides, and vitamins determined by disease severity, survival outcome, and recovery. Furthermore, we identified metabolites associated with acute-phase proteins and coagulation factors, which collectively identify individuals with severe disease or individuals who died of severe COVID-19. Our study suggests that manipulating specific metabolic pathways can be explored to prevent hyperinflammation, organ dysfunction, and death.

In Vitro Analysis of Bacterial Microcompartments and Shell Protein Superstructures by Confocal Microscopy.

The shell proteins that comprise bacterial microcompartments (BMCs) can self-assemble into an array of superstructures such as nanotubes, flat sheets, and icosahedra. The physical characterization of BMCs and these superstructures typically relies on electron microscopy, which decouples samples from their solution context. We hypothesize that an investigation of fluorescently tagged BMCs and shell protein superstructures in vitro using high-resolution confocal microscopy will lead to new insights into the solution behavior of these entities. We find that confocal imaging is able to capture nanotubes and sheets previously reported by transmission electron microscopy (TEM). Using a combination of fluorescent tags, we present qualitative evidence that these structures intermix with one another in a hetero- and homotypic fashion. Complete BMCs are also able to accomplish intermixing as evidenced by colocalization data. Finally, a simple colocalization experiment suggests that fluorescently modified encapsulation peptides (EPs) may prefer certain shell protein binding partners. Together, these data demonstrate that high-resolution confocal microscopy is a powerful tool for investigating microcompartment-related structures in vitro, particularly for colocalization analyses. These results also support the notion that BMCs may intermix protein components, presumably from the outer shell. IMPORTANCE Microcompartments are large, organelle-like structures that help bacteria catabolize targeted metabolites while also protecting the cytosol against highly reactive metabolic intermediates. Their protein shell self-assembles into a polyhedral structure of approximately 100 to 200 nm in diameter. Inside the shell are thousands of copies of cargo enzymes, which are responsible for a specific metabolic pathway. While different approaches have revealed high-resolution structures of individual microcompartment proteins, it is less clear how these factors self-assemble to form the full native structure. In this study, we show that laser scanning confocal microscopy can be used to study microcompartment proteins. We find that this approach allows researchers to investigate the interactions and potential exchange of shell protein subunits in solution. From this, we conclude that confocal microscopy offers advantages for studying the in vitro structures of other microcompartments as well as carboxysomes and other bacterial organelles.

GutSMASH predicts specialized primary metabolic pathways from the human gut microbiota.

The gut microbiota produce hundreds of small molecules, many of which modulate host physiology. Although efforts have been made to identify biosynthetic genes for secondary metabolites, the chemical output of the gut microbiome consists predominantly of primary metabolites. Here we introduce the gutSMASH algorithm for identification of primary metabolic gene clusters, and we used it to systematically profile gut microbiome metabolism, identifying 19,890 gene clusters in 4,240 high-quality microbial genomes. We found marked differences in pathway distribution among phyla, reflecting distinct strategies for energy capture. These data explain taxonomic differences in short-chain fatty acid production and suggest a characteristic metabolic niche for each taxon. Analysis of 1,135 individuals from a Dutch population-based cohort shows that the level of microbiome-derived metabolites in plasma and feces is almost completely uncorrelated with the metagenomic abundance of corresponding metabolic genes, indicating a crucial role for pathway-specific gene regulation and metabolite flux. This work is a starting point for understanding differences in how bacterial taxa contribute to the chemistry of the microbiome.

First metabolic profiling of 4-n-nonylphenol in human liver microsomes by integrated approaches to testing and assessment: Metabolites, pathways, and biological effects

4-n-nonylphenol (4-n-NP), a typical endocrine disrupting chemical, has been so far frequently detected in various environmental mediums and editable food. However, the specific metabolic pathways in human and potential adverse effects of metabolites have not been elucidated yet. Here, metabolic profiling of 4-n-NP in human liver microsome (HLM) was comprehensively characterized by integrated approaches of testing and assessment. A total of 21 metabolites were identified using nontarget analysis with high-resolution mass spectrum, including three groups of unique phase I metabolites first determined in HLM. Seven various metabolic pathways of 4-n-NP were identified by both in silico and in vitro, and CYP1A2, 2C19, and 2D6 were the mainly participating enzymes. Two secondary metabolites with carbonyl groups on side chains (M4, M7) presented most abundant in HLM, which were also predicted to have high binding affinities towards HPG-axis-related receptors (AR, ER, and PR). ESRs (estrogen receptors) were shared core protein targets for all metabolites revealed by protein-protein interaction networks. Biological functions enrichment analysis indicated that 4-n-NP metabolites might primarily involve in ESR-mediated signaling, GPCR ligand binding, Class A/1 (Rhodopsin-like receptors) and metabolism-related pathways. These findings of 4-n-NP metabolites, pathways, and biological effects provide insightful information for its environmental exposure and risk assessment.

Gut Microbiota and Drug-Related Liver Injury: Challenges and Perspectives

Drug-related liver injury (DILI) is increasing in the incidence of liver injury due to nonviral liver disease and has become a health problem that should not be underestimated. As a hot research topic in recent years, gut microbiota have been studied in various tumors, cardiovascular metabolic diseases, and human immunity. However, there is still a lack of research related to gut microbiota and DILI. It is known that they can influence each other through the regulation of the “gut-liver axis,” and the relationship between them and the possible mechanisms of action are still at the research stage. Human leukocyte antigen (HLA) gene polymorphisms are closely related to the development of DILI, and the gene can also affect changes in the composition of gut microbes. In this paper, we review the possible relationships and mechanisms between DILI and gut microbiota in order to provide new research directions for the prevention and treatment of DILI in the future. In the future, untargeted therapies using antibiotics, probiotics, or FMT will be replaced by personalised and precision medicine approaches, such as bioengineered bacterial strains or drugs that modulate specific bacterial enzymes and metabolic pathways.

Cellular Uptake, Metabolism and Sensing of Long-Chain Fatty Acids.

Fatty acids (FAs) are critical nutrients that regulate an organism's health and development in mammal. Long-chain fatty acids (LCFAs) can be divided into saturated and unsaturated fatty acids, depending on whether the carbon chain contains at least 1 double bond. The fatty acids that are required for humans and animals are obtained primarily from dietary sources, and LCFAs are absorbed from outside of cells in mammals. LCFAs enter cells through several mechanisms, including passive diffusion and protein-mediated translocation across the plasma membrane, the latter in which FA translocase (FAT/CD36), plasma membrane FA-binding protein (FABPpm), FA transport protein (FATP), and caveolin-1 are believed to have important functions. The LCFAs that are taken up by cells bind to FA-binding proteins (FABPs) and are transported to the specific organelles, where they are activated into acyl-CoA to target specific metabolic pathways. LCFA-CoAs can be esterified to phospholipids, triacylglycerol, cholesteryl ester, and other specialized lipids. Non-esterified free fatty acids are preferentially stored as triacylglycerol molecules. The main pathway by which fatty acids are catabolized is β-oxidation, which occurs in mitochondria and peroxisomes. stearoyl-CoA desaturase (SCD)-dependent and Fatty acid desaturases (FADS)-dependent fatty acid desaturation pathways coexist in cells and provide metabolic plasticity. The process of fatty acid elongation occurs by cycling through condensation, reduction, dehydration, and reduction. Extracellular LCFA can be mediated by membrane protein G protein-coupled receptor 40 (GPR40) or G protein-coupled receptor 120 (GPR120) to activate mammalian target of rapamycin complex 1 (mTORC1) signaling, and intracellular LCFA's sensor remains to be determined. The crystal structures of a phosphatidic acid phosphatase and a membrane-bound fatty acid elongase-condensing enzyme and other LCFA-related proteins provide important insights into the mechanism of utilization, increasing our understanding of the cellular uptake, metabolism and sensing of LCFAs.

Starvation alters gut microbiome and mitigates off-flavors in largemouth bass (Micropterus salmoides).

The present study aimed to investigate the response of intestinal microbiota during 3weeks' starvation of largemouth bass (Micropterus salmoides), an economically important freshwater fish, using 16S rRNA gene amplicon sequencing and PICRUSt2 predictive functional profiling. Overall, the microbiota was mainly represented by Mycoplasma, Pseudomonas, Acinetobacter, and Microbacterium in the initial group. This pattern contrasted with that of Cetobacterium and Aeromonas, which were major representative genera in the starved group. Significant differences in the richness and composition of intestinal microbial community induced by starvation were observed. Notably, earthy-musty off-flavor compounds (geosmin and 2-methylisoborneol) were significantly decreased during starvation, which were significantly correlated with the abundance of certain actinobacterial taxa, namely, Microbacterium and Nocardioides. Additionally, the functional pathways involved in synthesis of off-flavor compounds, protein digestion, fatty acid degradation, and biosynthesis of cofactors greatly decreased with starvation, indicating that microbiota modulated the specific metabolic pathway to adapt to food deprivation. These results emphasize that starvation can modulate diversity, community structure, and functions of the intestinal microbiota and mitigate the off-flavors, which has important implications for strategies to eliminate off-flavor odorants through the application of probiotics to manipulate the gut microbiome and ultimately enhance flesh quality of freshwater fish.

Comparative bioinformatics analysis of the biosynthetic pathways and key candidate genes of three species, Vitis vinifera, Fragaria vesca and Olea europaea, furnish enzyme sets for the production of pharmaceutically valuable terpenes in heterologous hosts

Plants represent a rich repository of taxonomically restricted, yet chemically diverse, secondary metabolites that are synthesised via specific metabolic pathways. Enzyme specificity and biosynthetic gene clustering are the bottleneck of secondary metabolite evolution. As economically important food crops, grape, strawberry, and olive produce many pharmaceutically important molecules; however, their specific biosynthetic pathways remain inaccessible. Our genomic-based analysis of these three species reveal the biosynthetic diversity of their specialised secondary metabolites. We found over 20 BGCs predicted, most of which were characterised in two species, grape and strawberry. Gene annotation of the biosynthetic candidate genes predicted the production of many medically and industrially important compounds including cycloartenol, nerolidol, farnesene and valencene. Although most of the predicted clusters are concentrated in specific genomic positions, some have shown gene duplications in their clusters, which is suggestive of pseudogenes or misassembled genomes. Our genome mining and putative functional analysis of the biosynthetic genes annotated in the three species indicated the evolutionary processes that have shaped their current genetic structure and the structural diversity of their chemical compositions. Revealing the biogenetic background of these natural molecules is a step forward towards the expansion of their chemical diversification via engineering their biosynthetic genes heterologously, as well as the identification of their role in the interaction between those plants and their biotic and abiotic conditions.

Designing a novel tomato ideotype for future cultivation in space manned missions

Introduction: Methods for production of fresh, health food are needed in view of long-term, deep-space manned missions. To this end, crops tailored for better performance under non-terrestrial conditions may be obtained by the exploitation of biochemical patterns related to specialized metabolites known to confer protection against environmental challenges and to be beneficial to human health.Methods: In this work, for the first time, MicroTom plants have been engineered specifically for agrospace applications to express PhAN4, a MYB-like transcription factor able to regulate the biosynthesis of anthocyanins that influence tomato genes possibly involved in agrospace-relevant functions. Results:PhAN4 engineering underpinned the genetic background of the dwarf tomato MicroTom while maintaining yield and photosynthetic capacity. PhAN4 expression resulted in the accumulation of anthocyanins and polyphenols, a differential carotenoid profile, increased antioxidant scavenging capacities of fruits compared to the original genotype. Improved ability to counteract ROS generation and to preserve plant protein folding after ex-vivo gamma irradiation was observed.Discussion: These results highlights that the manipulation of specific metabolic pathways is a promising approach to design novel candidate varieties for agrospace applications.

Unraveling Key Functional Bacteria across Land-Use Types on the Tibetan Plateau

Soil bacteria are vital to the modulation of soil carbon and nutrient cycling. However, the response of key microbiota and the metabolic potential of soil bacteria to tolerate disturbance have yet to be fully investigated across land-use types, especially in alpine ecosystems. Here, the potential of soil bacteria to conduct change to affect biogeochemical processes was evaluated across 4 paired natural land-use types (i.e., forest converted to shrubland or grassland, shrubland to grassland, and grassland degradation) on the Tibetan Plateau. Based on the FAPROTAX database, we found 574, 106, and 22 bacterial genera that were possibly related to the carbon, nitrogen, and sulfur cycles, respectively. Among the core and/or key genera involved in carbon and/or nitrogen cycles,BradyrhizobiumandSolirubrobacterwere common before and after disturbance, whereasBryobacter,Mycobacterium, andArthrobacterwere sensitive to disturbance. Disturbance had diverse effects on soil bacterial percentages in specific metabolic pathways. In particular, soil bacteria may lead to the decreases in carbon and nitrogen fixation, nitrite oxidation, and sulfate reduction under grassland degradation. Annual precipitation and plant Shannon index were important factors driving bacterial functional groups. These findings shed light on the substantial impacts of disturbance on bacterial metabolism, and suggest that some important bacterial taxa must be taken into consideration in policymaking and management strategies for the enhancement and maintenance of ecosystem functions.

Updates and Original Case Studies Focused on the NMR-Linked Metabolomics Analysis of Human Oral Fluids Part III: Implementations for the Diagnosis of Non-Cancerous Disorders, Both Oral and Systemic.

This communication represents Part III of our series of reports based on the applications of human saliva as a useful and conveniently collectable medium for the discovery, identification and monitoring of biomarkers, which are of some merit for the diagnosis of human diseases. Such biomarkers, or others reflecting the dysfunction of specific disease-associated metabolic pathways, may also be employed for the prognostic pathological tracking of these diseases. Part I of this series set the experimental and logistical groundwork for this report, and the preceding paper, Part II, featured the applications of newly developed metabolomics technologies to the diagnosis and severity grading of human cancer conditions, both oral and systemic. Clearly, there are many benefits, both scientific and economic, associated with the donation of human saliva samples (usually as whole mouth saliva) from humans consenting to and participating in investigations focused on the discovery of biomolecular markers of diseases. These include usually non-invasive collection protocols, relatively low cost when compared against blood sample collection, and no requirement for clinical supervision during collection episodes. This paper is centred on the employment and value of 'state-of-the-art' metabolomics technologies to the diagnosis and prognosis of a wide range of non-cancerous human diseases. Firstly, these include common oral diseases such as periodontal diseases (from type 1 (gingivitis) to type 4 (advanced periodontitis)), and dental caries. Secondly, a wide range of extra-oral (systemic) conditions are covered, most notably diabetes types 1 and 2, cardiovascular and neurological diseases, and Sjögren's syndrome, along with a series of viral infections, e.g., pharyngitis, influenza, HIV and COVID-19. Since the authors' major research interests lie in the area of the principles and applications of NMR-linked metabolomics techniques, many, but not all, of the studies reviewed were conducted using these technologies, with special attention being given to recommended protocols for their operation and management, for example, satisfactory experimental model designs; sample collection and laboratory processing techniques; the selection of sample-specific NMR pulse sequences for saliva analysis; and strategies available for the confirmation of resonance assignments for both endogenous and exogenous molecules in this biofluid. This article also features an original case study, which is focussed on the use of NMR-based salivary metabolomics techniques to provide some key biomarkers for the diagnosis of pharyngitis, and an example of how to 'police' such studies and to recognise participants who perceive that they actually have this disorder but do not from their metabolic profiles and multivariate analysis pattern-based clusterings. The biochemical and clinical significance of these multidimensional metabolomics investigations are discussed in detail.