Redox Regulation of Immunometabolism in Microglia Underpinning Diabetic Retinopathy.

Diabetic retinopathy (DR) is the leading cause of visual impairment and blindness among the working-age population. Microglia, resident immune cells in the retina, are recognized as crucial drivers in the DR process. Microglia activation is a tightly regulated immunometabolic process. In the early stages of DR, the M1 phenotype commonly shifts from oxidative phosphorylation to aerobic glycolysis for energy production. Emerging evidence suggests that microglia in DR not only engage specific metabolic pathways but also rearrange their oxidation-reduction (redox) system. This redox adaptation supports metabolic reprogramming and offers potential therapeutic strategies using antioxidants. Here, we provide an overview of recent insights into the involvement of reactive oxygen species and the distinct roles played by key cellular antioxidant pathways, including the NADPH oxidase 2 system, which promotes glycolysis via enhanced glucose transporter 4 translocation to the cell membrane through the AKT/mTOR pathway, as well as the involvement of the thioredoxin and nuclear factor E2-related factor 2 antioxidant systems, which maintain microglia in an anti-inflammatory state. Therefore, we highlight the potential for targeting the modulation of microglial redox metabolism to offer new concepts for DR treatment.

Ethanolamine as a biomarker and biomarker-based therapy for diabetic retinopathy in glucose-well-controlled diabetic patients.

Diabetic retinopathy (DR) is the leading cause of blindness among the working-age population. Although controlling blood glucose levels effectively reduces the incidence and development of DR to less than 50%, there are currently no diagnostic biomarkers or effective treatments for DR development in glucose-well-controlled diabetic patients (GW-DR). In this study, we established a prospective GW-DR cohort by strictly adhering to glycemic control guidelines and maintaining regular retinal examinations over a median 2-year follow-up period. The discovery cohort encompassed 71 individuals selected from a pool of 292 recruited diabetic patients at baseline, all of whom consistently maintained hemoglobin A1c (HbA1c) levels below 7% without experiencing hypoglycemia. Within this cohort of 71 individuals, 21 subsequently experienced new-onset GW-DR, resulting in an incidence rate of 29.6%. In the validation cohort, we also observed a significant GW-DR incidence rate of 17.9%. Employing targeted metabolomics, we investigated the metabolic characteristics of serum in GW-DR, revealing a significant association between lower levels of ethanolamine and GW-DR risk. This association was corroborated in the validation cohort, exhibiting superior diagnostic performance in distinguishing GW-DR from diabetes compared to the conventional risk factor HbA1c, with AUCs of 0.954 versus 0.506 and 0.906 versus 0.521 in the discovery and validation cohorts, respectively. Furthermore, in a streptozotocin (STZ)-induced diabetic rat model, ethanolamine attenuated diabetic retinal inflammation, accompanied by suppression of microglial diacylglycerol (DAG)-dependent protein kinase C (PKC) pathway activation. In conclusion, we propose that ethanolamine is a potential biomarker and represents a viable biomarker-based therapeutic option for GW-DR.

Branched-Chain Amino Acids Metabolism and Their Roles in Retinopathy: From Relevance to Mechanism.

Retinopathy is one of the leading causes of irreversible blindness and vision loss worldwide. Imbalanced nutrients play important roles in the pathogenesis and pathophysiology of retinal diseases. Branched-Chain Amino Acids (BCAAs), as essential amino acids, perform a variety of biological functions, including protein synthesis, glucose metabolism, lipid metabolism, inflammation, and oxidative stress in metabolic tissues of diabetes and aging-related diseases. Recently, it has been shown that BCAAs are highly related to neuroprotection, oxidative stress, inflammatory and glutamate toxicity in the retina of retinopathy. Therefore, this review summarizes the alterations of BCAA levels in retinopathy, especially diabetic retinopathy and aging-related macular disease, and the genetics, functions, and mechanisms of BCAAs in the retina as well as other metabolic tissues for reference. All of these efforts aim to provide fundamental knowledge of BCAAs for further discoveries and research on retina health based on the sensing and signaling of essential amino acids.

Amino Acids Metabolism in Retinopathy: From Clinical and Basic Research Perspective.

Retinopathy, including age-related macular degeneration (AMD), diabetic retinopathy (DR), and retinopathy of prematurity (ROP), are the leading cause of blindness among seniors, working-age populations, and children. However, the pathophysiology of retinopathy remains unclear. Accumulating studies demonstrate that amino acid metabolism is associated with retinopathy. This study discusses the characterization of amino acids in DR, AMD, and ROP by metabolomics from clinical and basic research perspectives. The features of amino acids in retinopathy were summarized using a comparative approach based on existing high-throughput metabolomics studies from PubMed. Besides taking up a large proportion, amino acids appear in both human and animal, intraocular and peripheral samples. Among them, some metabolites differ significantly in all three types of retinopathy, including glutamine, glutamate, alanine, and others. Studies on the mechanisms behind retinal cell death caused by glutamate accumulation are on the verge of making some progress. To develop potential therapeutics, it is imperative to understand amino acid-induced retinal functional alterations and the underlying mechanisms. This review delineates the significance of amino acid metabolism in retinopathy and provides possible direction to discover therapeutic targets for retinopathy.

Characterizing natural variability of lignin abundance and composition in fine roots across temperate trees: a comparison of analytical methods.

Lignin is an important root chemical component that is widely used in biogeochemical models to predict root decomposition. Across ecological studies, lignin abundance has been characterized using both proximate and lignin-specific methods, without much understanding of their comparability. This uncertainty in estimating lignin limits our ability to comprehend the mechanisms regulating root decomposition and to integrate lignin data for large-scale syntheses. We compared five methods of estimating lignin abundance and composition in fine roots across 34 phylogenetically diverse tree species. We also assessed the feasibility of high-throughput techniques for fast-screening of root lignin. Although acid-insoluble fraction (AIF) has been used to infer root lignin and decomposition, AIF-defined lignin content was disconnected from the lignin abundance estimated by techniques that specifically measure lignin-derived monomers. While lignin-specific techniques indicated lignin contents of 2-10% (w/w) in roots, AIF-defined lignin contents were c. 5-10-fold higher, and their interspecific variation was found to be largely unrelated to that determined using lignin-specific techniques. High-throughput pyrolysis-gas chromatography-mass spectrometry, when combined with quantitative modeling, accurately predicted lignin abundance and composition, highlighting its feasibility for quicker assessment of lignin in roots. We demonstrate that AIF should be interpreted separately from lignin in fine roots as its abundance is unrelated to that of lignin polymers. This study provides the basis for informed decision-making with respect to lignin methodology in ecology.

Coordination between compound-specific chemistry and morphology in plant roots aligns with ancestral mycorrhizal association in woody angiosperms.

Recent studies on fine root functional traits proposed a root economics hypothesis where adaptations associated with mycorrhizal dependency strongly influence the organization of root traits, forming a dominant axis of trait covariation unique to roots. This conclusion, however, is based on tradeoffs of a few widely studied root traits. It is unknown how other functional traits fit into this mycorrhizal-collaboration gradient. Here, we provide a significant extension to the field of root ecology by examining how fine root secondary compounds coordinate with other root traits. We analyzed a dataset integrating compound-specific chemistry, morphology and anatomy of fine roots and leaves from 34 temperate tree species spanning major angiosperm lineages. Our data uncovered previously undocumented coordination where root chemistry, morphology and anatomy covary with each other. This coordination, aligned with mycorrhizal colonization, reflects tradeoffs between chemical protection and mycorrhizal dependency, and provides mechanistic support for the mycorrhizal-collaboration gradient. We also found remarkable phylogenetic structuring in root chemistry. These patterns were not mirrored by leaves. Furthermore, chemical protection was largely decoupled from the leaf economics spectrum. Our results unveil broad organization of root chemistry, demonstrate unique belowground adaptions, and suggest that root strategies and phylogeny could impact biogeochemical cycles through their links with root chemistry.

Multicellular gene network analysis identifies a macrophage-related gene signature predictive of therapeutic response and prognosis of gliomas.

BACKGROUND: The tumor-associated microenvironment plays important roles in tumor progression and drug resistance. However, systematic investigations of macrophage-tumor cell interactions to identify novel macrophage-related gene signatures in gliomas for predicting patient prognoses and responses to targeted therapies are lacking. METHODS: We developed a multicellular gene network approach to investigating the prognostic role of macrophage-tumor cell interactions in tumor progression and drug resistance in gliomas. Multicellular gene networks connecting macrophages and tumor cells were constructed from re-grouped drug-sensitive and drug-resistant samples of RNA-seq data in mice gliomas treated with BLZ945 (a CSF1R inhibitor). Subsequently, a differential network-based COX regression model was built to identify the risk signature using a cohort of 310 glioma samples from the Chinese Glioma Genome Atlas database. A large independent validation set of 690 glioma samples from The Cancer Genome Atlas database was used to test the prognostic significance and accuracy of the gene signature in predicting prognosis and targeted therapeutic response of glioma patients. RESULTS: A macrophage-related gene signature was developed consisting of twelve genes (ANPEP, DPP4, PRRG1, GPNMB, TMEM26, PXDN, CDH6, SCN3A, SEMA6B, CCDC37, FANCA, NETO2), which was tested in the independent validation set to examine its prognostic significance and accuracy. The generation of 1000 random gene signatures by a bootstrapping scheme justified the non-random nature of the macrophage-related gene signature. Moreover, the discovered gene signature was verified to be predictive of the sensitivity or resistance of glioma patients to molecularly targeted therapeutics and outperformed other existing gene signatures. Additionally, the macrophage-related gene signature was an independent and the strongest prognostic factor when adjusted for clinicopathologic risk factors and other existing gene signatures. CONCLUSION: The multicellular gene network approach developed herein indicates profound roles of the macrophage-mediated tumor microenvironment in the progression and drug resistance of gliomas. The identified macrophage-related gene signature has good prognostic value for predicting resistance to targeted therapeutics and survival of glioma patients, implying that combining current targeted therapies with new macrophage-targeted therapy may be beneficial for the long-term treatment outcomes of glioma patients.

Long-Term Simulated Atmospheric Nitrogen Deposition Alters Leaf and Fine Root Decomposition.

Atmospheric nitrogen deposition increases forest carbon sequestration across broad parts of the Northern Hemisphere. Slower organic matter decomposition and greater soil carbon accumulation could contribute to this increase in carbon sequestration. We investigated the effects of chronic simulated nitrogen deposition on leaf litter and fine root decomposition at four sugar maple (Acer saccharum)- dominated northern hardwood forests. At these sites, we previously observed that nitrogen additions increased soil organic carbon and altered litter chemistry. We conducted a 3-year decomposition study with litter bags. Litter production of leaves and fine roots were combined with decomposition dynamics to estimate how fine roots and leaf litter contribute to soil organic carbon. We found that nitrogen additions marginally stimulated early-stage decomposition of leaf litter, an effect associated with previously documented changes in litter chemistry. In contrast, nitrogen additions inhibited the later stages of fine root decomposition, which is consistent with observed decreases in lignin-degrading enzyme activities with nitrogen additions at these sites. At the ecosystem scale, slower fine root decomposition led to additional root mass retention (g m-2), and this greater retention of root residues was estimated to explain 5-51% of previously documented carbon accumulation in the surface soil due to nitrogen additions. Our results demonstrated that simulated nitrogen deposition created contrasting effects on the decomposition of leaf litter and fine roots. Although previous nitrogen deposition studies have focused on leaf litter, this work suggests that slower fine root decomposition is a major driver of soil organic carbon accumulation under elevated nitrogen deposition.

Higher-order error bound for the difference of two functions.

Error bounds play an important role in the research of mathematical programming. Using some techniques of nonsmooth analysis, we establish some results on the existence of higher-order error bounds for difference functions with set constraints.

Chronic nitrogen deposition influences the chemical dynamics of leaf litter and fine roots during decomposition.

Atmospheric nitrogen deposition induces a forest carbon sink across broad parts of the Northern Hemisphere; this carbon sink may partly result from slower litter decomposition. Although microbial responses to experimental nitrogen deposition have been well-studied, evidence linking these microbial responses to changes in the degradation of specific compounds in decaying litter is sparse. We used wet chemistry and Fourier transform infrared spectroscopy (FTIR) methods to study effects of chronic simulated nitrogen deposition on leaf litter and fine root chemistry during a three-year decomposition experiment at four northern hardwood forests in the north-central USA. Leaf litter and fine roots were highly different in initial chemistry, such as concentrations of acid-insoluble fraction (AIF, or Klason lignin) and condensed tannins (CTs). These initial differences persisted over the course of decomposition. Gravimetrically-defined AIF and lignin/carbohydrate reference IR peak ratios both provide evidence that lignin in fine roots was selectively preserved under simulated nitrogen deposition. Lignin/carbohydrate peak ratios were strongly correlated with AIF, suggesting that AIF is a good predictor of lignin. Because AIF is abundant in fine roots, slower AIF degradation was the major driver of the slower fine root decomposition under nitrogen enrichment, explaining 73.5% of the additional root mass retention. Nitrogen enrichment also slowed the loss of CTs and proteins in fine roots. Nitrogen additions initially slowed the loss of AIF, CTs, and proteins in leaf litter, which was comparatively low in AIF, but these effects disappeared at the later stage and did not affect leaf litter mass loss during the experiment. Our results suggest that decomposition of chemical classes subject to oxidative degradation, such as lignin and CTs, is generally inhibited by nitrogen enrichment; but whether this inhibition eventually slows litter mass loss and leads to organic matter accumulation depends on the initial quantities of these classes in litter.

Fine roots are the dominant source of recalcitrant plant litter in sugar maple-dominated northern hardwood forests.

Most studies of forest litter dynamics examine the biochemical characteristics and decomposition of leaf litter, but fine roots are also a large source of litter in forests. We quantified the concentrations of eight biochemical fractions and nitrogen (N) in leaf litter and fine roots at four sugar maple (Acer saccharum)-dominated hardwood forests in the north-central United States. We combined these results with litter production data to estimate ecosystem biochemical fluxes to soil. We also compared how leaf litter and fine root biochemistry responded to long-term simulated N deposition. Compared with leaf litter, fine roots contained 2.9-fold higher acid-insoluble fraction (AIF) and 2.3-fold more condensed tannins; both are relatively difficult to decompose. Comparatively, leaf litter had greater quantities of more labile components: nonstructural carbohydrates, cellulose and soluble phenolics. At an ecosystem scale, fine roots contributed over two-thirds of the fluxes of AIF and condensed tannins to soil. Fine root biochemistry was also less responsive than leaf litter to long-term simulated N deposition. Fine roots were the dominant source of difficult-to-decompose plant carbon fractions entering the soil at our four study sites. Based on our synthesis of the literature, this pattern appears to be widespread in boreal and temperate forests.

Transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus L.).

Cucumber (Cucumis sativus L.) fruit is a type of fleshy fruit that is harvested immaturely. Early fruit development directly determines the final fruit length and diameter, and consequently the fruit yield and quality. Different cucumber varieties display huge variations of fruit length, but how fruit length is determined at the molecular level remains poorly understood. To understand the genes and gene networks that regulate fruit length in cucumber, high throughout RNA-Seq data were used to compare the transcriptomes of early fruit from two near isogenic lines with different fruit lengths. 3955 genes were found to be differentially expressed, among which 2368 genes were significantly up-regulated and 1587 down-regulated in the line with long fruit. Microtubule and cell cycle related genes were dramatically activated in the long fruit, and transcription factors were implicated in the fruit length regulation in cucumber. Thus, our results built a foundation for dissecting the molecular mechanism of fruit length control in cucumber, a key agricultural trait of significant economic importance.

Ephemeral root modules in Fraxinus mandshurica.

Historically, ephemeral roots have been equated with 'fine roots' (i.e. all roots of less than an arbitrary diameter, such as 2 mm), but evidence shows that 'fine roots' in woody species are complex branching systems with both rapid-cycling and slow-cycling components. A precise definition of ephemeral roots is therefore needed. Using a branch-order classification, a rhizotron method and sequential sampling of a root cohort, we tested the hypothesis that ephemeral root modules exist within the branching Fraxinus mandshurica (Manchurian ash) root system as distal nonwoody lateral branches, which show anatomical, nutritional and physiological patterns distinct from their woody mother roots. Our results showed that in F. mandshurica, distal nonwoody root branch orders die rapidly as intact lateral branches (or modules). These nonwoody branch orders exhibited highly synchronous changes in tissue nitrogen concentrations and respiration, dominated root turnover, nutrient flux and root respiration, and never underwent secondary development. The ephemeral root modules proposed here may provide a functional basis for differentiating and sampling short-lived absorptive roots in woody plants, and represent a conceptual leap over the traditional coarse-fine root dichotomies based on arbitrary size classes.

Anatomical traits associated with absorption and mycorrhizal colonization are linked to root branch order in twenty-three Chinese temperate tree species.

* Different portions of tree root systems play distinct functional roles, yet precisely how to distinguish roots of different functions within the branching fine-root system is unclear. * Here, anatomy and mycorrhizal colonization was examined by branch order in 23 Chinese temperate tree species of both angiosperms and gymnosperms forming ectomycorrhizal and arbuscular-mycorrhizal associations. * Different branch orders showed marked differences in anatomy. First-order roots exhibited primary development with an intact cortex, a high mycorrhizal colonization rate and a low stele proportion, thus serving absorptive functions. Second and third orders had both primary and secondary development. Fourth and higher orders showed mostly secondary development with no cortex or mycorrhizal colonization, and thus have limited role in absorption. Based on anatomical traits, it was estimated that c. 75% of the fine-root length was absorptive, and 68% was mycorrhizal, averaged across species. * These results showed that: order predicted differences in root anatomy in a relatively consistent manner across species; anatomical traits associated with absorption and mycorrhizal colonization occurred mainly in the first three orders; the single diameter class approach may have overestimated absorptive root length by 25% in temperate forests.