The biological roots of mental illness: their ramifications through cerebral metabolism, synaptic activity, genetics, and the environment.
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Adult↗
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Results for “Root metabolism”
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Soil and plant factors influencing the accumulation of heavy metals by plants.
The use of plants to monitor heavy metal pollution in the terrestrial environment must be based on a cognizance of the complicated, integrated effects of pollutant source and soil-plant variables. To be detectable in plants, pollutant sources must significantly increase the plant available metal concentration in soil. The major factor governing metal availability to plants in soils is the solubility of the metal associated with the solid phase, since in order for root uptake to occur, a soluble species must exist adjacent to the root membrane for some finite period. The rate of release and form of this soluble species will have a strong influence on the rate and extent of uptake and, perhaps, mobility and toxicity in the plant and consuming animals. The factors influencing solubility and form of available metal species in soil vary widely geographically and include the concentration and chemical form of the element entering soil, soil properties (endogenous metal concentration, mineralogy, particle size distribution), and soil processes (e.g., mineral weathering, microbial activity), as these influence the kinetics of sorption reactions, metal concentration in solution and the form of soluble and insoluble chemical species. The plant root represents the first barrier to the selective accumulation of ions present in soil solution. Uptake and kinetic data for nutrient ions and chemically related nonnutrient analogs suggest that metabolic processes associated with root absorption of nutrients regulate both the affinity and rate of absorption of specific nonnutrient ions. Detailed kinetic studies of Ni, Cd, and Tl uptake by intact plants demonstrate multiphasic root absorption processes over a broad concentration range, and the use of transport mechanisms in place for the nutrient ions Cu, Zn, and K. Advantages and limitations of higher plants as indicators of increased levels of metal pollution are discussed in terms of these soil and plant phenomena.
Absorption↗
Metabolically stable non-histone chromosomal proteins in growing maize roots.
DNA and non-histone chromosomal proteins (NHCP) of meristematic cells of maize primary roots were double labelled in vivo with [3H]- or [14C] thymidine and [14C]- or [3H]-tryptophan respectively. The ratio of labelled tryptophan to labelled DNA was followed during the transition of the meristematic cells of the root tip into the distal zones of finally differentiated cells. It was found that only 20% of the newly synthesized NHCP in the proliferating cells were turned over, while the rest were preserved and found as metabolically stable proteins in the zone of final differentiation. This result is consistent with the hypothesis that some NHCP remain permanently associated with chromatin of non-dividing differentiated cells in order to maintain the genomic characteristics of a given cellular type.
Cell Division↗
A global survey of taxa-metabolic associations across mouse microbiome communities.
Host-microbiota mutualism is rooted in the exchange of dietary and metabolic molecules. Microbial diversity broadens the metabolite pool, with each taxon contributing distinct compounds in varying proportions. In the human microbiome, high variability in consortial composition is largely compensated by similar metabolic functions across different taxa. However, the extent of compensation in lower diversity mouse models, and whether vivaria are metabolically equivalent, is unknown. We provide a searchable resource of microbiome composition variability across 51 murine vivaria and 12 wild mouse colonies worldwide, with vivarium-specific variants mapped according to predicted 3D structures for each microbial species. Our matched metabolomics data show that realized metabolic potential has relatively low variability, providing functional evidence for metabolic compensation. Additionally, variability is related to taxonomic composition rather than vivarium, revealing taxa-metabolite associations that are potentially relevant to phenotypic differences between vivaria. Collectively, this resource offers tools to strengthen microbiome studies and collaborative science.
Animals↗
Integrated Metabolomic and Transcriptomic Analysis Reveals Tissue-Specific Secondary Metabolic Differentiation and Indole Alkaloid Accumulation in Evodia rutaecarpa.
Evodia rutaecarpa is a valuable medicinal plant, yet its non-medicinal tissues remain largely underexplored. Here, we integrated ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)-based widely targeted metabolomics and RNA sequencing (RNA-seq) transcriptomics to systematically profile the metabolic and transcriptional landscapes of roots, stems, leaves, and flowers of Evodia rutaecarpa (Juss.) Benth. Our aim was to characterize tissue-specific metabolic differentiation and its underlying transcriptional regulatory mechanisms. Metabolomic analysis, employing principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) with robust model parameters (R2Y > 0.9, Q2 > 0.5), identified 3090 differential metabolite features (variable importance in projection, VIP > 1.0; p < 0.05) across the four tissues, which exhibited distinct tissue-specific clustering patterns. Integrated Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and weighted gene co-expression network analysis (WGCNA) revealed that roots specifically accumulated quinolone alkaloids and flavonoid glycosides, accompanied by the coordinated upregulation of genes involved in flavonoid and phenylpropanoid biosynthetic pathways. In contrast, stems, leaves, and flowers were enriched in indole alkaloids (evodiamine and rutaecarpine) and volatile oil precursors, with concurrent upregulation of genes involved in tryptophan metabolism and indole alkaloid biosynthesis (e.g., tryptophan decarboxylase, TDC; s N-methyltransferase, NMT). Notably, leaves and flowers displayed particularly high accumulation levels of these bioactive alkaloids, suggesting their potential as alternative sources for industrial and pharmaceutical applications. WGCNA further identified multiple transcription factors and structural gene modules tightly correlated with evodiamine accumulation, offering promising candidate regulators for future biosynthetic pathway engineering. Collectively, this multi-omics integration study systematically elucidates the tissue-partitioned secondary metabolism of Evodia rutaecarpa (Juss.) Benth. and provides a solid scientific foundation for full-plant resource utilization, targeted development of non-medicinal tissues, and future metabolic engineering of indole alkaloid production.
Evodia rutaecarpa↗
Root growth promotion by Penicillium melinii : mechanistic insights and agricultural applications.
This study characterizes Penicillium melinii , an endophytic fungus isolated from Arabidopsis thaliana roots, as a plant growth-promoting fungus with potential use as a model to study root development and as a biostimulant for sustainable agriculture. Although endophytes are known to promote plant growth, the underlying molecular mechanisms often remain poorly understood. Here, we aimed to elucidate how P. melinii enhances root system development and to assess its applicability across different crops. Phenotypic assays were conducted in Arabidopsis, quinoa and tomato under in vitro , greenhouse and field conditions. Root architecture and biomass were quantified using image-based phenotyping. Transcriptomic and phytohormone profiling assessed plant responses, and fungal genome sequencing coupled with secretome analysis was used to identify candidate effectors and metabolic traits. P. melinii consistently promoted root growth and increased plant biomass across species and environments, both in vitro and in the greenhouse. In tomato field trials, this translated into a significant increase in yield. The fungus colonized root surfaces without vascular penetration and triggered a mild transcriptomic response: early activation of stress-response genes followed by their attenuation and sustained upregulation of auxin-related pathways. Notably, the interaction modulates the SLR-ARF-LBD pathway and the number of pre-branch sites probably through increased auxin signalling in the oscillation zone. Additional hormonal changes were limited and mainly associated with the attenuation of the plant response to microorganisms. P. melinii enhances lateral root formation through a subtle molecular and metabolic dialogue with the host plant, underscoring its relevance as a model for studying root developmental plasticity. Its strong and reproducible growth-promoting effect, demonstrated with different fungal strains and under controlled and field conditions, supports its potential as a biostimulant for sustainable crop production.
Journal Article↗
Metabolic factors and the utilization of phosphorus by plants.
The overall process of entry and transport of phosphate by plants has been separated into its component parts. Rapid esterification is involved but a small proportion of the total transport may occur by a non-metabolic route. Mannose alters the metabolism of phosphate in roots of cereals and thereby reduces the transport to the shoot by as much as 99% whereas dicotyledonous species are much less sensitive. The sequestration of phosphate as mannose 6-phosphate is reversible in some species depending on the extent of its conversion into fructose 6-phosphate and it is possible that in vivo controls of this type operate in whole plants. The factors involved in the control of distribution of inorganic phosphate between cellular organelles and throughout the plant are discussed. Enzymic hydrolysis of organic forms by roots and associated microorganisms may also be important in soils where available orthophosphate is limiting. Other inorganic nutrients, particularly boron, play an important role during the transport of phosphate across membranes. Major differences have been found in the capacities of different species to transport absorbed phosphate to the shoot. Peas and field beans absorb efficiently in the early weeks of growth but the rate of transport is about one thirtieth that of oats, barley, mung bean or sunflower. The relevance of the experimental findings to the wider problem of efficiency of fertilizer use and the possible selection of genotypes with high capacities for absorption and transport are discussed.
Absorption↗
Effect of spraying developed shoot system with insecticide "endrin" on rhizosphere mycoflora of both okra and lupins.
Spraying shoot system of okra and lupins plants with insecticide endrin caused changes in plant metabolism. These changes reflected themselves on root exudates. Accordingly, the balance between the higher plant and the fungal population in the root zone was disturbed.
Carbohydrate Metabolism↗
Metabolism of 2,4-dichlorophenoxyacetic acid. 10. Identication of metabolites in rice root callus tissue cultures.
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2,4-Dichlorophenoxyacetic Acid↗
A chromosome-level genome assembly of Lycoris radiata reveals the evolutionary origin of Amaryllidaceae alkaloids and elucidates the complete galanthamine biosynthetic pathway.
Amaryllidaceae alkaloids (AmAs) comprise a structurally diverse group of specialized metabolites produced almost exclusively by species of the Amaryllidoideae subfamily and are of substantial pharmacological importance. However, the limited availability of high-quality genomes from Amaryllidoideae plants has constrained systematic investigations of the genes and evolutionary processes underlying AmA biosynthesis. Here, we present a chromosome-level genome assembly of Lycoris radiata, which enabled the discovery of key downstream enzymes in the galanthamine biosynthetic pathway and uncovered reversible reactions between two critical metabolite pairs. These findings provide new mechanistic insight into pathway architecture and enable reconstruction of the galanthamine biosynthetic pathway in Yarrowia lipolytica. Comparative genomic analyses indicate that several core genes for AmA biosynthesis originated in ancestral angiosperms, whereas the complete pathway was likely assembled in the Amaryllidoideae subfamily through gene duplication and neofunctionalization. Furthermore, integrated metabolomic and transcriptomic analyses suggest that roots contribute actively to AmA metabolism in Lycoris. Together, these findings provide a genomic and biochemical framework for understanding the evolution and engineering of AmA biosynthesis.
Lycoris↗
[Nutrition and disease].
An essentially new concept of the effect of nutrition on the development and evolution of diseases has been advanced. At its root there lies the theory of metabolic current as a main path for maintaining the homeokinesis. In the aspect of this concept the pathogenesis of malnutrition diseases is considered as affections due to imbalanced alimentation at the cellular level. Changes in the biochemical status of the organism occurring under stressor effects and the part played by the nutrition factor in adaptive reactions of the organism in response to the stressor effects are analyzed. Investigations concerning the role of nutrition in the genesis of adiposity and atherosclerosis are summarized. The paper offers a summary of the material contained in numerous research works of the author and his collaborators, as well as information published in the world literature that leave no doubt as to the effectiveness of enzymological approaches and, in particular, the validity of the metabolis current concept, all this being essential for understanding the significance of alimentary factors in preventing and treatment of many diseases.
Alcohol Oxidoreductases↗
Accelerated mineralization of two organophosphate insecticides in the rhizosphere.
Numerous xenobiotic compounds, including the organophosphate insecticides O, O-diethyl-O-(2-isopropyl-6-methyl-4-pyrimidinyl) phosphorothioate (diazinon) and O, O-diethyl-O-p-nitrophenyl phosphorothioate (parathion), appear to be degraded in the soil environment by an initial cometabolic attack. Comparing the mineralization rates of radiolabeled diazinon and parathion in root-free and in rhizosphere soil, we tested our hypothesis that, because of the presence of root exudates, the rhizosphere is an especially favorable environment for such co-metabolic transformations. The insecticides were added individually at 5 mug/g to sealed flasks containing either soil permeated by the root system of a bush bean plant or identical soil without roots. Periodically, the flask atmospheres were flushed through traps and the evolved (14)CO(2) was quantitated. Bush bean plant roots without associated rhizosphere microorganisms failed to produce a significant amount of (14)CO(2). During 1 month of incubation, rhizosphere flasks mineralized 12.9 and 17.9% of the added diazinon and parathion radiocarbon, respectively, compared to 5.0 and 7.8% by the soil without roots. The mineralization of parathion but not of diazinon was stimulated in a similar manner when soil without roots was repeatedly irrigated with a root exudate produced in aseptic solution culture. Viable counts of microorganisms on soil extract agar were not significantly altered by root permeation or by root exudate treatment of the soil, leaving population selection and/or enhanced cometabolic activity as the most plausible interpretations for the observed stimulatory effects. Rhizosphere interactions may substantially shorten the predicted half-lives of some xenobiotic compounds in soil.
Bacteria↗
GH secretion in open-angle glaucoma.
Open-angle glaucoma is frequently observed in patients with acromegaly suggesting that the somatotropic hormone might facilitate a condition of glaucoma. The open-angle glaucoma patients studied, displayed higher plasma human growth hormone (HGH) levels than control subjects 60 min (30.3 +/- 1.7 against 16.8 +/- 2.7 ng/ml; p less than 0.001) and 90 min (19.0 +/- 1.9 against 9.3 +/- 1.2 ng/ml; p less than 0.001) after intravenous administration of arginine (25 g in 30 min). The authors support the hypothesis that the increased plasma HGH level may interfere with the regulation of ocular pressure by modifying the flow of aqueous humor from the eyeball via changes in the sclero-corneal trabecular meshwork; these changes are also found in diabetic subjects. The interplay between HGH and changes of carbohydrate metabolism (frequently occurring in glaucomatous patients) may be at the root of the variations of intraocular pressure in open-angle glaucoma.
Arginine↗
Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth.
The genus Streptomyces has consistently been found enriched in drought-stressed plant root microbiomes, yet the ecological basis and functional variation underlying this enrichment at the strain and isolate level remain unclear. Using two 16S rRNA sequencing methods with different levels of taxonomic resolution, we confirmed drought-associated enrichment (DE) of Streptomyces in field-grown sorghum roots and identified five closely related but distinct amplicon sequence variants (ASVs) belonging to the genus with variable drought enrichment patterns. From a culture collection of sorghum root endophytes, we selected 12 Streptomyces isolates representing these ASVs for phenotypic and genomic characterization. Whole-genome sequencing revealed substantial variation in gene content, even among closely related isolates, and exometabolomic profiling showed distinct metabolic responses to media supplemented with drought- versus well-watered root tissue. Traits linked to drought survival, including osmotic stress tolerance, siderophore production, and carbon utilization, varied widely among isolates and were not phylogenetically conserved. Using a broader panel of 48 Streptomyces, we demonstrate that DE scores, determined through mono-association experiments in gnotobiotic sorghum systems, showed high variability and lacked correlation with plant growth promotion. Pangenome-wide association identified orthogroups involved in osmolyte transport (e.g., proP) and membrane biosynthesis (e.g., fabG) as positively associated with DE, though most associations lacked phylogenetic signal. Collectively, these results demonstrate that Streptomyces DE is not a conserved genus-level trait but is instead strain-specific and functionally heterogeneous. Furthermore, DE in the root microbiome was shown not to predict beneficial effects on plant growth. This work underscores the need to resolve functional traits at the strain level and highlights the complexity of microbe-host-environment interactions under abiotic stress.
Streptomyces↗
The effect of a non-metabolizable analog on mandelate catabolism in Pseudomonas putida.
DL-2,3,4,5,6-pentafluoromandelic acid (PFM) specifically inhibits the growth of Pseudomonas putida (ATCC 12633) on medium containing mandelate as sole carbon and energy source by competitive inhibition of mandelate dehydrogenase. PFM is not metabolized and is neither an inducer of the mandelate catabolic enzymes nor an antagonist of induction. Mutants resistant to the inhibitory effects of PFM (PFMr) were isolated; most prove to be superinducible, i.e. synthesize corrdinately the mandelate-specific catabolic enzymes at elevated levels following induction. In at least one case the PFMr mutation maps very near the structural genes that encode the enzymes functional in the first two steps of mandelate catabolism. It is reasoned that the PFMr mutation is of the promotor type. Resistance to substrate analogs such as PFM offers a general method for isolation of regulatory mutants in catabolic metabolism.
Biological Transport↗
[Morphological and biochemical investigations of hairs in inborn errors of amino acid metabolism (author's transl)].
The influence of inborn errors of metabolism on the amino acid content, the structure and growth of human hair has been studied in patients suffering from Phenylketonuria, Cystinosis, Homocystinuria and Tyrosinosis. Examiniation of hairs under the scanning electron microscope reveals defects and abnormalities such as a plicated pattern of the cuticula in patients with Phenylketonuria and Cystinosis. The amino acid content of the hydrolized hair keratin of all patients was within normal range and did not reveal significant changes of phenylalanine, cystine, homocystine, methionine or tyrosine. Disturbance in hair growth was determined by evaluation of standardized hair root samples. The results indicate an increase in hair root atrophy with increasing severity of the disorder of amino acid metabolism.
Amino Acid Metabolism, Inborn Errors↗
Quantitative trait locus qLDC5 regulates primary root branching in an auxin-dependent manner.
L-type lateral root (LLR) density determines root system architecture, affecting nutrient acquisition in rice (Oryza sativa L.), particularly under low-phosphorus conditions. Previous studies identified genotypic differences in LLR density and a quantitative trait locus (QTL) enhancing LLR density on crown roots (qLDC5). We showed that LLR densities on crown and primary roots were closely correlated and confirmed higher LLR density on primary roots in qLDC5 donor DJ123 compared with the African variety NERICA4 using X-ray micro-computed tomography. We confirmed the qLDC5 effect in a field experiment for LLR density on primary roots. LLR densities on primary and crown roots, therefore, appear under similar genetic control. Developmental analyses revealed that DJ123 and NDJ188-a derivative line harboring qLDC5-initiate more lateral root primordia than NERICA4, with a higher proportion progressing to elongation, but that exogenous auxin application reversed this ranking. Within qLDC5, auxin biosynthesis gene OsYUCCA2 and auxin response factor OsARF15 were up-regulated in DJ123. Transcriptome analysis revealed an indirect auxin-mediated regulatory network underlying LLR variation. Differentially expressed genes in DJ123 and NDJ188 were enriched for ent-kaurene and gibberellin metabolism, including the robust induction of OsGA2ox5. These findings suggest qLDC5 increases lateral root density by coordinating gibberellin, auxin, and terpene pathways.
Oryza↗
Recent advances in calcium metabolism. II. Disorders of calcium homeostasis.
Abnormalities of calcium and mineral metabolism are described in relation to the differential diagnosis, clinical characteristics, diagnostic procedures, and treatment of infants and children with hypocalcemia, hypercalcemia, rickets, chronic renal insufficiency, and other disorders of calcium metabolism. Understanding of the basic pathogenesis of each abnormality of calcium homeostasis is essential for the rational management of affected patients.
Adolescent↗