Frontiers in bioscience (Landmark edition)最新文献

Measurement of the adenosine triphosphate (ATP) concentration among different cells, tissues and organs and even across the phylogenetic tree ordinarily yields exceedingly high concentrations at the millimolar (mM) level. This represents a conundrum in that ATP-driven cellular functions only require micromolar (μM) values. Considering that nature is ordinarily conservative in the generation of high-energy phosphatic metabolites such as ATP, a potential major role for ATP has been completely overlooked and may be of paramount importance because ATP is a hydrotrope. In all phylogenetic domains, reports have established that the excessively high mM concentration of ATP is present in studies of eukaryotic cellular and tissue homogenates, living tissues, and a living organ as well as archaeotic and prokaryotic organisms. These ATP concentrations are also present in contemporary relatives of microorganisms having progenitors existing in the Precambrian Era. This feature is fundamental to cell biology across taxonomic domains. These features are interpreted as serving a foundational molecular function for maintaining organismal homeostasis. We hypothesize that ATP prevents pathological protein aggregation and maintains protein solubility through its hydrotropic feature in cells, tissues, and organs.

Background: Macrophage polarization is involved in the development of ulcerative colitis (UC). This study investigated the mechanism by which high mobility group box-1 protein (HMGB1) regulates macrophage polarization through metabolic reprogramming, thereby contributing to the pathogenesis of UC.

Methods: Dextran sulfate sodium (DSS) was used to induce colitis in mice. RAW264.7 cells were polarized to M1 or M2 macrophages in vitro by stimulating with lipopolysaccharide (LPS)/interferon-γ (IFN-γ) or Interleukin-4 (IL-4), respectively. Macrophage infiltration and distribution within colon tissue were assessed by immunohistochemistry and flow cytometry. Glycolysis, fatty acid oxidation (FAO), and inflammatory factors were evaluated using relevant reagent kits. Chromatin Immunoprecipitation (ChIP) and luciferase reporter experiments were performed to study the regulation of Carnitine palmitoyltransferase 1A (Cpt1a) promoter transcriptional activity by HMGB1.

Results: The mouse UC model showed upregulated HMGB1 and increased macrophage infiltration. Overexpression of HMGB1 promoted M1 macrophage polarization, increased glycolysis, and reduced FAO, whereas knockdown of HMGB1 promoted M2 macrophage polarization, reduced glycolysis, and increased FAO. HMGB1 negatively regulated Cpt1a expression by inhibiting transcription of the Cpt1a promoter. Knockdown of Cpt1a reversed the effects of small interfering RNA targeting HMGB1 (si-HMGB1) on macrophage metabolism and polarization. Administration of adeno-associated virus (AAV)-shHMGB1 in vivo caused a reduction in UC symptoms and inflammation.

Conclusions: HMGB1 modulates macrophage metabolism in UC by inhibiting Cpt1a expression, leading to increased M1 polarization. This provides a theoretical basis for the clinical application of HMGB1 inhibitors in the treatment of UC.

Background: Coenzyme Q₁₀ (CoQ₁₀), also known as ubiquinone-10, is an important molecule of the mitochondrial respiratory chain that acts as an electron carrier between complexes I, II, and III and additionally functions as an antioxidant. Due to its bioenergetic properties, CoQ₁₀ is of high interest for therapeutic and cosmetic use. This study aims to characterize the metabolic impact of CoQ₁₀ on primary human dermal fibroblasts (HDF) using fluorescence lifetime imaging microscopy (FLIM) and electron microscopy.

Methods: FLIM of nicotinamide adenine dinucleotide (NADH) is a robust method to characterize cellular energy metabolism that also provides spatial information. Electron microscopy offers a way to characterize the ultrastructure of mitochondria and reveal features not visible in FLIM.

Results: We reported a shift towards longer lifetimes of NADH in primary fibroblasts from ten different donors upon treatment with CoQ₁₀, which indicates the stimulation of oxidative phosphorylation. This is confirmed by phasor-based metabolic pattern segmentation, which showed localization of longer NADH lifetimes in CoQ₁₀-treated cells, indicating activated mitochondria in the cytoplasm. In addition, a complementary investigation of the mitochondrial ultrastructure using transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) tomography showed a reduction in stress granules in CoQ₁₀-treated cells.

Conclusions: Together, FLIM and electron microscopy (EM) imaging strongly imply that CoQ₁₀ stimulates cellular energy metabolism.

Background: Zophobas atratus larval meal (ZLM) is a high-quality feed supplement with potential activities that can improve fish growth performance and promote meat quality. However, there have been limited recent studies investigating the metabolic effects of ZLM. Therefore, this study aims to uncover the metabolomic mechanism through which ZLM improves tilapia meat flavor using metabolomic strategies.

Method: In this study, soybean meal in the basal diets was replaced with 15%, 30%, or 60% ZLM, where anti-nutrient factors were destroyed by high temperature treatment. After being fed these ZLM supplements for 30 days, dorsal muscles were collected from tilapia for meat sensory evaluation tests. Liver samples were also collected for metabolomic analysis using the gas chromatography-mass spectrometry (GC-MS) platform and combined with biochemical assays to verify metabolism-related enzyme activities and reveal crucial metabolic pathways and critical biomarkers associated with ZLM's ability to improve meat flavor.

Results: In tilapia livers, ZLM enhanced the activity of enzymes involved in energy metabolism including succinate dehydrogenase (SDH), pyruvate dehydrogenase (PDH), α-ketoglutarate dehydrogenase (α-KGDH), NADP-malate dehydrogenase (NAD-MDH) and mitochondrial isocitrate dehydrogenase (ICDHm). This resulted in increased levels of reduced nicotinamide adenine dinucleotide (NADH), acetyl CoA and ATP which led to accumulation of flavor fatty acids such as arachidonic acid, linoleic acid (9,12-Octadecadienoic acid), linolenic acid (9,12,15-Octadecatrienoic acid) and oleic acid (9-Octadecenoic acid). Additionally, there was an increase in flavor nucleotides like guanosine adenosine-5'-monophosphate and uridine-5'-monophosphate while off-flavor metabolites like inosine and hypoxanthine decreased. Furthermore, beneficial metabolomic responses led to a decrease in off-flavor metabolites such as 2-methylisoborneol trimethylamine and geosmin while increasing umami metabolites like 2-methyl-3-furanthiol and nonanal.

Conclusions: This metabolomic study demonstrates that inclusion of ZLM diets enhances the flavor profile of tilapia dorsal muscle. The accumulation of flavor compounds, coupled with a reduction in earthy taste and off-flavor metabolites, contributes to an improved meat flavor and freshness. Additionally, there is an increase in the levels of flavor-related amino acids and nucleotides. These previously unidentified metabolic effects highlight the potential significance of ZLM as a dietary supplement for enhancing the biosynthesis of flavor metabolites in tilapia.

Background: Age-related macular degeneration (AMD) is the most common cause of vision loss in people above the age of 50, affecting approximately 10% of the population worldwide and the incidence is rising. Hyperreflective foci (HRF) are a major predictor of AMD progression. The purpose of this study was to use the sodium iodate mouse model to study HRF formation in retinal degeneration.

Methods: Sodium iodate (NaIO₃) treated rodents were studied to characterize HRF. 3-month-old male wild-type (WT) C57Bl/6J mice were injected with phosphate-buffered saline (PBS) or varying doses of NaIO₃ (15-60 mg/kg). Optical Coherence Tomography (OCT) images were collected at baseline and several days post-NaIO₃ injection. Retinal thicknesses were measured using Bioptigen software. Seven days post-injection, eyes were prepared for either transmission electron microscopy (TEM), Hematoxylin & Eosin (H&E), or immunofluorescence.

Results: OCT imaging of the mice given higher doses of NaIO₃ revealed HRF formation in the neural retina (n = 4). The amount of HRF correlated with the degree of retinal tissue loss. H&E and TEM imaging of the retinas seven days post-NaIO₃ injection revealed several pigmented bodies in multiple layers of the retina (n = 3-5). Immunofluorescence revealed that some pigmented bodies were positive for macrophage markers and an epithelial-to-mesenchymal transition marker, while all were retinal pigment epithelium (RPE) 65-negative (n = 4).

Conclusions: The data suggest that NaIO₃ induces the formation of HRF in the outer retina and their abundance correlates with retinal tissue loss. The experiments in this study highlight NaIO₃ as a clinically relevant model of intermediate AMD that can be used to study HRF formation and to discover new treatment targets.

Background: There is an assumption about the presence of a specific nucleotides sequence in DNA molecule, which contributes to the genesis of open states (OS). In addition, it would be logical to assume that OS zones should form in DNA regions with a large proportion of Adenine-Thymine (AT) pairs, since they contain fewer hydrogen bonds than Guanine- Cytosine (GC) base pairs. However, studies have shown that in areas rich in AT pairs, the probability of open states will not always be higher.

Methods: In this work, for two genes containing different numbers of regions with a large AT pairs proportion, we calculated the ratio of AT and GC pairs in the OS zones. For calculations, we used a coarse-grained angular mechanical DNA model.

Results: It has been established that small OS zones can appear on any part of the DNA molecule. They mainly consist of AT pairs, but as the size of OS zones increases, the content of AT pairs in them decreases.

Conclusions: The occurrence of long-length OS zones is "tied" to regions of the DNA molecule with a large proportion of AT pairs; if there are several such areas, then, depending on the magnitude of the torque, OS zones can arise in different areas of the gene. Thus, the genesis probability of large OS zones in a DNA segment depends not only on the "strength" of the nucleotide sequence of this area, but also on the factors determining the dynamics of DNA.

Regulatory T-cells (Tregs) play a crucial role in maintaining immune homeostasis, ensuring a balanced immune response. Tregs primarily operate in an antigen-specific fashion, facilitated by their distinct distribution within discrete niches. Tregs have been studied extensively, from their point of origin in the thymus origin to their fate in the periphery or organs. Signals received from antigen-presenting cells (APCs) stimulate Tregs to dampen inflammation. Almost all tumors are characterized by a pathological abundance of immune suppression in their microenvironment. Conversely, the lack thereof proves detrimental to immunological disorders. Achieving a balanced expression of Tregs in relation to other immune compartments is important in establishing an effective and adaptable immune tolerance towards cancer cells and autoantigens. In the context of cancer, it is essential to decrease the frequency of Tregs to overcome tumor suppression. A lower survival rate is associated with the presence of excessive exhausted effector immune cells and an increased frequency of regulatory cells. However, when it comes to treating graft rejection and autoimmune diseases, the focus lies on immune tolerance and the transfer of Tregs. Here, we explore the complex mechanisms that Tregs use in human disease to balance effector immune cells.

This paper is dedicated to the memory of Oleg B. Ptitsyn (1929-1999) and presents an answer to his question: "What is the role of conserved non-functional residues in protein folding?". This answer follows from the experimental works of three labs. The role of non-functional but conserved residues of apomyoglobin (apoMb) in the formation of the native protein fold in the molten globule state has been experimentally revealed. This research proves that the non-functional but conserved residues of apoMb are necessary for the formation and maintenance of the correct topological arrangement of the main elements in the apoMb secondary structure already in the early folding intermediate.

Background: In the twentieth century, the textbook idea of packaging genomic material in the cell nucleus and metaphase chromosomes was the presence of a hierarchy of structural levels of chromatin organization: nucleosomes - nucleosomal fibrils -30 nm fibrils - chromomeres - chromonemata - mitotic chromosomes. Chromomeres were observed in partially decondensed chromosomes and interphase chromatin as ~100 nm globular structures. They were thought to consist of loops of chromatin fibres attached at their bases to a central protein core. However, Hi-C and other related methods led to a new concept of chromatin organization in the nuclei of higher eukaryotes, according to which nucleosomal fibrils themselves determine the spatial configuration of chromatin in the form of topologically associating domains (TADs), which are formed by a loop extrusion process and are regions whose DNA sequences preferentially contact each other. Somatic macronuclei of ciliates are transcriptionally active, highly polyploid nuclei. A feature of macronuclei is that their genome is represented by a large number of "gene-sized" (~1-25 kb) or of "subchromosomal" (~50-1700 kb) size minichromosomes. The inactive macronuclear chromatin of "subchromosomal" ciliates usually looks like bodies 100-200 nm in size. The aim of this work was to find out which of the models (chromomeres or TADs) is more consistent with the confocal and electron microscopic data on structural organization of chromatin bodies.

Methods: Macronuclear chromatin of four "subchromosomal" ciliate species (Bursaria truncatella, Paramecium multimicronucleatum, Didinium nasutum, Climacostomum virens) was examined using electron microscopy and confocal microscopy during regular growth, starvation and encystment.

Results: Chromatin bodies ~70-200 nm in size observed in the interphase macronuclei consisted of tightly packed nucleosomes. Some of them were interconnected by one or more chromatin fibrils. Under hypotonic conditions in vitro, chromatin bodies decompacted, forming rosette-shaped structures of chromatin fibrils around an electron-dense centre. When the activity of the macronucleus decreased during starvation or encystment, chromatin bodies assembled into chromonema-like fibrils 100-300 nm thick. This data allows us to consider chromatin bodies as analogues of chromomeres. On the other hand, most likely, the formation of DNA loops in chromatin bodies occurs by the loop extrusion as in TADs.

Conclusions: The data obtained is well explained by the model, according to which the chromatin bodies of ciliate macronuclei combine features inherent in both chromomeres and TADs; that is, they can be considered as chromomeres with loops packed in the same way as the loops in TADs.

Systemic lupus erythematosus (SLE) is a multi-factorial autoimmune-mediated disease with hyper-stimulation of immune cells especially the T lymphocytes. By this method, it might facilitate the systematic damages in multiple tissues and organs. Otherwise, SLE is also correlated with diverse cardio-metabolic comorbidities, including dyslipidemia, insulin resistance, and hypertension. It is worth-noting that the risk of cardio-metabolic disorders is significantly higher compared with the healthy patients which was reported as approximately one-third of SLE patients were proved as obesity. Notably, current focus is shifting to implementing cardio-metabolic protective strategies as well as elucidating underlying mechanisms of lupus-mediated obese status. On the other hand, adipocyte, as the most abundant endocrine cell in fat tissue, are dysfunctional in obese individuals with aberrant secretion of adipokines. It is proposing that the adipokine might link the pathology of cardio-metabolic disorders and SLE, whereas the related mechanism is complicated. In the current review, the functions of adipokine and the potential mechanisms by which the adipokine link cardio-metabolic disorders and SLE was well listed. Furthermore, the recommendations, which identify the adipokine as the potential therapeutic targets for the treatment of cardio-metabolic disorders and SLE, were also summarized.