Archives of Biochemistry and Biophysics

Aiming to develop a high-throughput fluorimetric assay for the activity CYP1A2, we introduced 6-Methoxy-2-naphthoic acid (MONA) as a new fluorogenic substrate for this important metabolizer of antidepressants and psychotropic drugs in human liver. We demonstrated that oxidative demethylation of MONA by liver microsomes results in a red shift and a substantial increase in fluorescence. This effect, which is exceptionally well pronounced at alkaline pH, allowed us to develop a sensitive and robust high-throughput assay of MONA metabolism. Probing the activity of 15 individual recombinant human P450 enzymes, we found that only two P450 species exhibited activity in MONA demethylation: CYP1A2 (kcat=11.9{+/-}2.2 min-1, KM=578{+/-}106 {micro}M) and CYP2A6 (kcat=0.48{+/-}0.07 min-1, KM=54{+/-}15 {micro}M). Since the KM values of the two enzymes are well resolved and the turnover rate observed with CYP2A6 is much lower than that of CYP1A2, this new fluorogenic substrate is useful as a specific probe for CYP1A2 activity in HLM. Importantly, MONA is not metabolized by CYP1A1 and CYP2C19, which distinguishes it from all known CYP1A2 fluorogenic substrates. We then used MONA to investigate the effects of chronic alcohol exposure on CYP1A2 activity using a series of 23 proteomically characterized individual HLM preparations from donors with various levels of alcohol consumption. The substrate saturation profiles (SSP) acquired with these preparations were subjected to global kinetic analysis by approximating them with combinations of two Michaelis-Menten equations with globally optimized KM values of 11 and 553 {micro}M. The amplitudes (Vmax values) of both components showed a pronounced increase with increasing alcohol exposure of the liver donors. The Vmax of the minor high-affinity component was best correlated with the abundance of alcohol-inducible CYP2E1 enzyme. The correlation was further improved by combining it with the abundances of CYP2A6 and CPR. This finding suggests that this minor component reflects the activity of CYP2A6 in the complex with alcohol-inducible CYP2E1 protein. In contrast, the Vmax of the predominant CYP1A2-catalyzed low-affinity component revealed a pronounced correlation with the abundances of CYP1A2 and NADPH cytochrome P450 reductase (CPR). These results suggest a considerable increase in the rate of metabolism of drug substrates of CYP1A2 by chronic alcohol exposure that takes place despite an alcohol-induced decrease in CYP1A2 expression.

Aiming to examine the effect of chronic alcohol exposure on the activity of CYP3A enzymes in human liver, we studied the metabolism of two CYP3A-specific substrates, 7-benzyloxyquinoline (7-BQ) and ivermectin, in 23 preparations of human liver microsomes (HLM) obtained from donors with documented alcohol exposure, grading from non-drinkers to heavy alcoholics. All HLM samples were characterized for the composition of the cytochrome P450 pool and the abundances of other drug-metabolizing and endoplasmic reticulum-stress-related enzymes by global proteomics. Our studies revealed a striking increase in the activities of CYP3A enzymes caused by chronic alcohol exposure. This effect is not associated with changes in CYP3A enzyme levels, which do not correlate with alcohol exposure. Instead, the rates of 7-BQ and ivermectin metabolism correlate with the content of alcohol-inducible CYP2E1. However, this enzyme does not metabolize ivermectin, and its activity with 7-BQ is negligible. These results suggest that the observed acceleration of the elimination of drugs metabolized by CYP3A enzymes by alcohol exposure is due to functional effects of the interaction between CYP3A and CYP2E1. To elucidate the potential mechanism of this effect, we studied the formation of CYP2E1-CYP3A4 complexes in CYP3A4-containing Supersomes with co-incorporated CYP2E1 using tag-transfer chemical crosslinking mass spectrometry (CX-MS). These experiments confirmed physical interactions between the proteins and allowed the identification of CYP3A4 residues at the sites of contact. This information was used to build structural models of the CYP2E1-CYP3A4 complex and to propose possible mechanisms for the observed effects.

The importance of human aldehyde oxidase (hAOX1) has increased over the last decades due to its involvement in drug metabolism. Inhibition studies concerning hAOX1 are extensive and a common reducing agent, dithiothreitol (DTT), was recently found to inactivate the enzyme. However, in previous crystallographic studies of hAOX1, DTT was found to be essential for crystallization. To surpass this concern another reducing agent used in crystallization trials. Using tris(2-carboxyethyl)phosphine (TCEP), a sulphur-free reducing agent, it was possible to obtain well-ordered crystals from hAOX1 wild type and variant, hAOX1_6A, which diffracted beyond 2.3 [A]. Instead of the typical star-shaped crystals of hAOX1, at pH 4.7, plates are obtained in the orthorhombic space group (P22121) with two molecules in the asymmetric unit. Activity assays with the enzyme incubated with both reducing agents show that contrary to DTT, TCEP does not lead to irreversible inactivation of the enzyme. The replacement of DTT with TCEP in crystallization of hAOX1 provides a strategy to circumvent enzyme inactivation during crystallographic studies, allowing future applications of new assays, such as time-resolved crystallography.

Autophagy is a critical neuroprotective mechanism, the impairment of which can lead to severe neurodegenerative diseases. Spinocerebellar ataxia type 1 (SCA1) is a monogenic neurodegenerative disorder, characterised by the presence of protein aggregates and consequent loss of cellular functions. The expression of mutant Ataxin1 (ATXN1) in glial cells has been demonstrated to induce inflammatory responses and loss of supportive functions, thereby exacerbating neuronal degeneration in SCA1. Autophagic dysfunction has been shown to affect both neurons and glial cells, resulting in widespread pathological consequences. In this work, we aimed to evaluate the efficacy of two small-molecule autophagy activators, AUTEN-67 and AUTEN-99, in models of glia-specific SCA1 in Drosophila. Our results demonstrate that AUTEN-99 has a stronger autophagy enhancing effect, with significantly improved response times and survival rates, compared to untreated ATXN1 mutants. Glia-specific assays in mouse primary hippocampal cultures also confirmed that AUTEN-99 is a more effective activator. Ultimately, co-treatment of neuronal and glial cultures did not reveal any synergistic benefits from combining the two AUTEN compounds compared to single-agent treatment. Our findings contribute to a better understanding of the utility of AUTENs and may help to understand the critical role of autophagy in neurodegenerative diseases.

IntroductionPrevious studies have shown that Aquamin(R), a multi-mineral extract from red marine algae, enhances barrier integrity proteins in the human colon. These findings prompted further investigation into Aquamin(R)s effects on gastrointestinal barrier function and permeability. MethodsSubjects with mild or in remission ulcerative colitis (UC) and healthy controls were enrolled in an open-label trial and received Aquamin(R) capsules (800 mg calcium/day) for 90 days. Intestinal permeability was evaluated before and after the 90-day intervention by urinary mannitol excretion after ingestion of a 5 g mannitol solution, with collections across several time intervals (pre-drink, 0-2 h, 2-8 h, and 8-24 h). The primary outcome was the change in mannitol excretion. Serum samples were also collected to assess liver and renal function. ResultsIn this pilot study (NCT04855799), which included UC patients and healthy controls (n = 8 per group), baseline urine mannitol levels in the 0-2 h sample were 54% higher in UC patients compared to healthy subjects (p = 0.006). Following 90 days of Aquamin(R) supplementation, urinary mannitol levels in UC patients decreased by 28%, 26%, and 41% at the 0-2 h, 2-8 h, and 8-24 h timepoints, respectively; the reduction at the 0-2 h interval reached statistical significance (p = 0.015). Overall, Aquamin(R) supplementation reduced total post-intervention mannitol excretion by 29% (p = 0.024). Aquamin(R) was well tolerated, with no serious adverse events reported. The serum metabolic panel revealed a modest but statistically significant reduction in alkaline phosphatase levels after 90 days of intervention. ConclusionThese results provide preliminary evidence that Aquamin(R) supplementation beneficially modulates gut barrier function and supports epithelial integrity in UC patients. These findings support further investigation of Aquamin(R) as a safe and promising adjunct to current UC management strategies, with potential utility as a barrier therapy in UC. SummaryAquamin(R) supplementation for 90 days reduced intestinal permeability in ulcerative colitis patients, as measured by urinary mannitol excretion. The intervention was well tolerated, suggesting Aquamin(R) may be a safe, promising adjunct for enhancing gut barrier function in UC management.

AimsThe development of a method for isolating mitochondria from a specific cell type within a given tissue, while preserving their structural and functional integrity to the greatest possible extent, remains an ongoing challenge. The aim of this study was to establish a protocol for the isolation of mitochondria from rodent cardiomyocytes, characterized by minimal contamination with other cell types and a high yield of mitochondrial fractions originating from distinct subcellular regions of cardiomyocytes. Methods and resultsIn the present study, cardiomyocytes from guinea pig and rat hearts were isolated using a standard enzymatic digestion protocol in a Langendorff heart perfusion system. Traditionally, the isolation of organelles, including mitochondria, from whole cardiac tissue as well as from cardiomyocytes has relied primarily on mechanical tissue homogenization These conventional approaches involve the localized application of high pressure to cells, which may potentially damage delicate organelles, particularly mitochondria. Moreover, such homogenization preferentially releases mitochondria located in the subsarcolemmal region of cardiomyocytes rather than representing the entire mitochondrial population. In our study, we employed an alternative approach based on the gentle mechanical disruption of cardiomyocytes by passing the cell suspension through selected cell strainers using a cell scraper. This strategy facilitated mild disruption of cellular structures, significantly increasing the yield of mitochondria released from interfibrillar regions while preserving mitochondrial functionality. Moreover, this method decrease probability of sample contamination with mitochondria from other cells, based on cell size differences. The effectiveness of this method was confirmed by transmission electron microscopy, and high-resolution respirometry, which revealed no evidence of outer mitochondrial membrane damage, as indicated by the lack of response to the addition of exogenous cytochrome c to the incubation chamber. Moreover, mitochondrial oxygen consumption increased by 7.39 {+/-} 1.25-fold following the addition of 100 {micro}M ADP, reflecting efficient ADP-stimulated respiration. Furthermore, fluorescence measurements were performed. to assess changes in the mitochondrial inner membrane potential ({Delta}{Psi}). The isolated mitochondria were also suitable for electrophysiological studies using the single-channel patch-clamp technique. Additionally, mitochondria isolated using the protocol developed in our laboratory exhibited a high capacity for transplantation into H9c2 cells. ConclusionIn summary, our mitochondrial isolation method is rapid, efficient, and yields functionally competent mitochondria. These preparations are suitable for a wide range of downstream applications, including patch-clamp electrophysiology, analyses of oxygen consumption under various pharmacological conditions, as well as mitochondrial transplantation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=162 HEIGHT=200 SRC="FIGDIR/small/716092v1_ufig1.gif" ALT="Figure 1"> View larger version (85K): org.highwire.dtl.DTLVardef@613495org.highwire.dtl.DTLVardef@1c34338org.highwire.dtl.DTLVardef@722900org.highwire.dtl.DTLVardef@e1f7a6_HPS_FORMAT_FIGEXP M_FIG C_FIG

Mitochondria are essential for metabolic homeostasis and neuronal function, extending beyond ATP production to roles in cell signaling, inflammation, and stress responses. Mitochondrial dysfunction, marked by abnormal morphology, ATP deficiency, and oxidative stress, is a key feature of aging-related diseases and neurodegenerative disorders like Parkinsons. Given the importance of mitochondrial homeostasis to brain function, this study aimed to determine the possible vitamin D (VD3) effects on mitochondrial susceptibility to Ca2+-induced mitochondrial permeability transition pore (mPTP), bioenergetics in brain mitochondria, and redox balance. We demonstrated that VD3 protects isolated brain mitochondria. Male rats were divided into control and VD3-treated groups. Brain mitochondria were isolated for assessments of Ca2+-induced mitochondrial swelling secondary to MPTP opening, oxygen consumption (states 3 - ADP-stimulated and state 4 - in the presence of oligomycin), and the respiratory control ratio (RCR). Oxidative stress parameters (nitrite and lipid peroxidation), superoxide dismutase (SOD) activity, and reduced glutathione (GSH) levels were also evaluated. The results revealed that VD3 treatment blocked Ca2+-induced mitochondrial swelling secondary to MPTP opening. Additionally, VD3 improved mitochondrial RCR compared to controls, in the presence of complex I (malate/glutamate) and complex II (succinate) substrates, reduced mitochondrial succinate-driven H2O2 release, and enhanced SOD activity and GSH levels. These changes occurred in parallel with decreased nitrite and TBARS formation. These results suggest that vitamin D{square} confers mitochondrial neuroprotection, emphasizing its prospective role in maintaining neuronal homeostasis and mitigating neurodegenerative processes.

Amyloid beta (A{beta}), one of the hallmark proteins of Alzheimers Disease (AD), aggregates into plaques that are strongly linked to cognitive decline and neuronal death. Reducing its aggregation propensity may provide a strategy to slow the progression of AD. While chirality modulation has emerged as an innovative approach to disrupt this process, research has primarily focused on alterations at the C position, often overlooking the impact of the second chiral center, such as the C{beta} atom of Threonine. Furthermore, the underlying mechanisms governing these chiral effects remain elusive. Given the intrinsically disordered nature of the A{beta} peptide, we employed temperature-replica exchange molecular dynamics (T-REMD) simulations to explore its rugged conformational landscape. We considered sequence mutations (A2T, A2V), N-terminal chirality inversion of the first six residues (A2V1-6D and WT1-6D), and alteration of the second chiral center (C{beta}) of Threonine (A2TC{beta}). By analyzing the effect size and population change induced by these mutations and chiral modulation, we concluded that the modulation at the N-termini is not confined locally but also exerts specific effects on the central hydrophobic core (CHC) region. Inspection of their free energy landscape and representative structures reveals that the protective or pathogenic effects of these variants correlate with their similarity to the wild type (WT) ensemble. Beyond these static thermodynamics analyses, a direct connection to phase transitions was made by estimating heat capacity as a function of temperature. Both analyses predict that A2TC{beta} may exert a pathogenic effect, in contrast to the protective nature of A2T. These findings offer a deeper understanding of the effects of site-specific mutations and chirality and shed light on the development of advanced therapeutic strategies for AD.

Synaptic vesicle glycoproteins 2 (SV2) are integral membrane proteins essential for neurotransmitter release and are implicated in neurological disorders including epilepsy and Parkinsons disease. In the attempt to develop a ligand selective for SV2C, and in collaboration with UCB, UCB-F was identified as a potential candidate. However, the affinity of UCB-F to SV2C was found to be temperature dependent, decreasing by about 10-fold from +4 to 37 degrees. UCB1A was subsequently identified as SV2C ligand displaying in vitro a 100-fold selectivity for SV2C compared with SV2A. In this study we investigated whether the binding of UCB-1A to SV2A and SV2C was affected by the temperature. A combination of experimental binding assay data and molecular dynamics (MD) simulations were used. The binding studies revealed that UCB1A affinity for SV2A decreased significantly at 37 {degrees}C compared with 4 {degrees}C, whereas binding to SV2C remained largely unchanged. MD simulations reproduced these observations, namely that ligand RMSD values at 310 K showed that UCB1A binding fluctuated markedly in the SV2A complex, with many trajectories exceeding the 3.0 [A] stability cutoff, whereas UCB1A remained relatively well-anchored in SV2C under the same conditions. Structural analysis showed that, while UCB1A adopts a conserved binding pose across all isoforms stabilized by {pi}- {pi} stacking and a hydrogen bond with Asp, SV2C possesses a unique stabilizing feature. In SV2C, Tyr298 is less exposed to the solvent and engages in a persistent hydrogen bond with Asparagine, a structural feature that reinforces pocket stability and limits temperature-induced destabilization. This interaction is absent in SV2A, consistent with its greater temperature sensitivity. Together, these findings provide a mechanistic explanation for the experimentally observed temperature independence of UCB1A binding to SV2C. More broadly, the results highlight the importance of incorporating physiologically relevant temperatures into SV2 ligand evaluation and demonstrate how combining experiments with simulations can uncover isoform-specific mechanisms of ligand recognition and stability.

High-sensitivity flow cytometry (FC) allows multiparametric analysis of nanoparticles (NPs) and extracellular vesicles (EVs). With new instruments available, studies that evaluate their performance using the same materials in a controlled environment are required. Here, we performed a comparative study to investigate the capabilities of three flow cytometers, namely the NanoFCM (NF), BD Influx (IF) and CytoFLEX LX (CF). Firstly, we analyzed a mixed population of silica NPs (SiNPs, 68, 91, 114 and 155 nm) by using light-scatter based detection thresholds (SSC, FSC, VSSC) across a concentration range from 106 to 109 particles/mL. Next, we analyzed fluorescent recombinant EVs (rEVs) by comparing light-scatter based thresholding (488 nm SSC available for all platforms), the combination of SSC thresholding with a fluorescent gate, and fluorescent thresholding for their qualitative and quantitative analysis. We here provide the strengths and limitations for each platform regarding the analysis of differently sized NPs at different sample concentrations.

C-X-C motif chemokine ligand 17 (CXCL17) has recently been identified as an agonist of the poorly characterized G protein-coupled receptor 25 (GPR25). Although GPR25 orthologs are widely distributed across vertebrates, non-mammalian CXCL17 orthologs have only been identified in some fish species in our recent studies. In this study, we systematically searched public databases for amphibian CXCL17 orthologs based on conserved C-terminal motif, gene synteny, and genomic architecture. Using this approach, we identified up to eighteen CXCL17 orthologs from diverse amphibian species. These amphibian CXCL17s exhibit no significant overall sequence similarity to known mammalian or fish CXCL17s, thus they were previously classified as uncharacterized proteins or even unannotated. Compared with known mammalian or fish CXCL17s, most amphibian CXCL17s display distinctive features, including four cysteine residues in their mature peptide and an additional residue following the conserved C-terminal Xaa-Pro-Yaa motif. A representative ortholog from the tropical clawed frog (Xenopus tropicalis) was recombinantly expressed and functionally characterized using cell-based assays, inducing ligand-receptor binding, {beta}-arrestin recruitment, and chemotactic cell migration. The recombinant amphibian CXCL17 directly bound to and efficiently activated its cognate GPR25 receptor and induced chemotactic migration of the transfected human embryonic kidney (HEK) 293T cells, but deletion of four C-terminal residues largely abolished its activity, indicating that all CXCL17 orthologs employ a conserved mechanism for receptor binding and activation. These findings establish the presence of a functional CXCL17-GPR25 signaling system in amphibians and provide new insights into the phylogenetic distribution and sequence diversity of CXCL17 orthologs across vertebrate lineages.

Rotavirus is a major cause of severe diarrheal disease in children under the age of five, with reduced vaccine effectiveness in low-resource settings causing substantial morbidity and mortality. In the absence of approved antiviral therapeutics, treatment is largely supportive, urging the need for targeted and precision-based interventions. VP4 protein plays an essential role in viral attachment, entry, and infectivity, making it a suitable target for targeted therapy. In this context, RNA interference is a specific method for inhibiting viral gene expression with its efficacy depending on sequence conservation, target accessibility, and compatibility with the RISC-loading machinery. In the present study, an integrative in silico approach was employed to design and evaluate siRNAs targeting conserved regions of the VP4 gene across six geographically diverse countries. Candidate siRNAs were screened using established design rules and regression-based scoring with off-target filtering. Three optimized siRNAs were further assessed through structural modeling, molecular docking, and molecular dynamics simulations to examine interactions with human Dicer, TRBP, and Argonaute-2. Comparative dynamic analyses identified one siRNA with enhanced structural compatibility, reduced conformational fluctuations, and stable interactions with RISC-loading proteins. These findings provide a rational computational basis for VP4-targeted siRNA development, facilitating experimental validation.

The enzyme nitric oxide synthase (NOS) breaks down the semi-essential amino acid L-arginine (L-Arg) in the cell to produce citrulline and nitric oxide (NO). NO is a crucial signalling molecule in cells that controls the metabolism of fats and carbohydrates. The aim of this study was to investigate two important genes in the L-Arg-NOS-NO signalling pathway, AMPK and ACC-1, as markers of the molecular mechanisms that are triggered when liver cells sense elevated L-Arg. Mouse liver epithelial insulin-sensitive BNL CL2 cells were used as a model system and cultured with 0, 400 or 800 {micro}M L-Arg. Cell growth parameters were analysed alongside qRT-PCR based analysis of target transcripts involved in lipid and glucose metabolic pathways. In a further experiment, NOS inhibitor; L-NAME (40 mM) and external NO donor; SNAP (100 {micro}M) were added and the effect on target gene expression analysed. L-Arg addition impacted culture viability and cell growth. AMP-activated protein kinase (AMPK) was regulated in response to L-Arg addition with increasing extracellular concentrations elevating AMPK mRNA and protein expressions. L-NAME decreased target gene expression in an L-Arg addition dependent manner. SNAP (100 {micro}M) addition increased target gene expression after 6 and 24 h. NO, produced as a result of L-Arg addition and the factors L-NAME and SNAP, that regulate NO bioavailability, impacted BNL CL2 cell NO/AMPK/ACC-1 signalling pathways via regulating mRNA expression and subsequently protein expression.

Sanguinarine (SNG) is a natural component belonging to the benzophenanthridine alkaloids. In recent years, due to its remarkable biological activities, it has gained wide interest in the pharmaceutical industry. Various studies have reported its potential as a therapeutic agent in treating chronic human diseases such as cancer. SNG is widely reported to cause programmed cell death in various cancer cell lines. The mechanism by which SNG triggers apoptosis remains poorly elucidated, especially in vivo. Previous studies reported that sanguinarine induces apoptosis by increasing reactive oxygen species (ROS). In this study, we aimed to characterize the effects of SNG using an in vivo Caenorhabditis elegans (C. elegans) model. Treating C. elegans with various SNG concentrations resulted in apoptotic cell death in the proliferative germline. Interestingly, SNG-induced apoptosis depends on the core apoptotic machinery initiated by the DNA-damage-induced activity of the p53/CEP-1 protein. We have also demonstrated that the increase in germ cell apoptosis is caused by elevated levels of reactive oxygen species (ROS) following SNG treatment. Notably, the apoptotic phenotype induced by SNG was resolved upon treatment with the ROS scavenger. Altogether, our study demonstrates that SNG increases ROS, leading to activation of DNA damage-induced apoptosis in the proliferative germline of C. elegans.

The replacement of a single codon in the human prion gene, causing the substitution of glycine with valine at position 127 (G127V) of the prion protein (PrP), prevents development of prion disease. We set out to explore if prion disease survival extension manifests in mice if the V127 mutant is delivered through a recombinant adeno-associated virus (rAAV) packaged as a self-complementary DNA. The notorious delivery limitations of rAAVs were overcome using a cross-correction approach that relied on the expression of the mutation in the context of glycosylphosphatidylinositoI-anchorless ({Delta}GPI) PrP. In this proof-of-concept study, we inoculated Rocky Mountain Laboratory (RML) prions into knock-in mice, in which the endogenous murine prion protein gene (Prnp) was replaced with the bank vole prion protein gene (BvPrnp). Prion-inoculated mice that were retro-orbitally transduced with a protective rAAV vector encoding BvPrnpV127{Delta}GPI survived [~]50 days longer than control mice that were unprotected. A deep proteomic analysis revealed that BvPrnpV127{Delta}GPI was protective by slowing perturbations to the proteome observed in late-stage RML prion disease. In addition to capturing details of synaptic decay and depletion of proteins in proximity to PrP, the proteomic dataset revealed the identity of proteins of potential diagnostic value that may be central to the brains attempt to fight prion disease by contributing to astrocytosis or microgliosis, by coping with calcium influx, or by enhancing the endoplasmic reticulum processing of essential proteins. Taken together, our results demonstrate that a gene therapy based on a GPI-anchorless PrP containing the G127V mutation can delay the onset of prion disease in mice, providing a framework for development of a corresponding therapy in humans. AUTHOR SUMMARYA rare change in the human prion protein, involving a single building block, has been linked to strong protection against prion diseases--fatal neurodegenerative disorders. This study tested whether that protective effect could be reproduced using gene therapy in mice. To this end, we exposed the animals to infectious prions and then delivered the protective version of the protein into mice using a viral carrier. Treated mice survived about seven weeks longer than untreated animals, showing that the approach can meaningfully slow disease progression. To understand why, we examined changes in brain proteins during disease and found that treatment helped preserve the normal protein levels of cellular proteins, particularly those involved in communication between nerve cells. The analysis also identified proteins altered in the disease that are linked to the brains defense responses, including inflammation, stress handling, and protein processing, some of which may serve as future disease markers. Importantly, the limited protection observed was not due to poor delivery of the therapy but likely reflects biological limits of the model used. Overall, the findings support the idea that gene therapies based on naturally protective human variants could help slow prion diseases and improve understanding of how the brain responds to them.

Oxidative stress results from excessive accumulation of reactive oxygen species (ROS) and plays a central role in numerous physiological and pathological processes. Accurate quantification of antioxidant enzyme activities is therefore essential in redox biology research. However, data analysis for commonly used assays, such as superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx), is frequently performed using spreadsheets or manual calculations, which are time-consuming and prone to error. Here, we present Redoxyme, a free, open-source, Python-based graphical user interface designed to standardize and automate the calculation of antioxidant enzyme activities. The software integrates protein normalization, enzyme-specific calculation routines, data visualization, and Excel export within an intuitive interface that does not require programming expertise. Redoxyme was validated using experimental data obtained from animal tissues (rats and mice), demonstrating excellent agreement with manual calculations and established analytical methods. Redoxyme provides a practical solution for improving reproducibility and efficiency in antioxidant enzyme activity analysis. The software is currently distributed as a standalone executable for Windows (locally installed), and an interactive web-based calculator implemented in Streamlit, enabling direct use without local installation. The source code and version-controlled development history are openly accessible via GitHub, promoting transparency, reproducibility, community-driven improvements, and can, in principle, be adapted for other operating systems. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=63 SRC="FIGDIR/small/703993v2_ufig1.gif" ALT="Figure 1"> View larger version (10K): org.highwire.dtl.DTLVardef@120cc68org.highwire.dtl.DTLVardef@4be246org.highwire.dtl.DTLVardef@1f47134org.highwire.dtl.DTLVardef@1341100_HPS_FORMAT_FIGEXP M_FIG C_FIG

Zinc is an essential transition metal that participates in many biological processes. In C. elegans, excess zinc is stored in lysosomes in intestinal cells; this process involves increasing the expression of the zinc transporter CDF-2 and remodeling of lysosomes characterized by an increase in the volume of the expansion compartment. To determine if this is a more general property, we investigated other metals. Here we report that lysosomes are remodeled in response to excess copper, manganese, and cadmium, with each metal causing an increase in the volume of the expansion compartment. Mutants with a reduced number of lysosomes were hypersensitive to growth retardation caused by excess copper and manganese, suggesting metal toxicity is prevented by metal sequestration in lysosomes. Using a novel method to analyze isolated lysosomes by X-ray Fluorescence Microscopy we demonstrated that zinc, copper and manganese are detectable in the lumen of lysosomes. To further analyze copper, we examined localization of CUA-1.1, a copper transporter that moves copper into the lumen of lysosomes. Like the zinc transporter CDF-2, CUA-1.1 localizes to both the acidified and expansion compartments in excess copper. These results indicate that the same intestinal lysosomes store zinc, copper and manganese. Lysosome remodeling characterized by an increase in volume of the expansion compartment is not specific to zinc but is a more general phenomenon during metal storage in lysosomes.

Synthetic 6-Br-Q0C10 has been shown to exhibit a partial electron transfer activity of native coenzyme Q in the isolated mitochondria. It reduces energy coupling efficiency by approximately 30%, suggesting that it may be useful in modulating cell growth in tissue culture. Whether or not it behaves in the same way in the whole cells, or animal, however, has not yet been fully examined. Recently we have investigated the effect of 6-Br-Q0C10 across multiple cell lines using three detection methods. Treatment with 6-Br-Q0C10 reduces cell proliferation in all cell lines tested, with different effectiveness. Obesity-related cell lines were the most susceptible, and a pronounced inhibitory effect was also observed in cancer cell lines. These results strengthen the idea of using 6-Br-Q0C10 to manage obesity or to retard the growth of rate cancer cells and thus prolonging life.

BackgroundTau, encoded by the microtubule-associated protein tau gene (MAPT), is traditionally associated with neuronal function in maintaining cytoskeletal stability and regulating intracellular transport. Its dysregulation is implicated in a range of neurodegenerative disorders. Beyond its well-established high levels of expression in neurons of the central and peripheral nervous systems, increasing evidence indicates that Tau is also expressed in non-neuronal cells/tissues such as muscle, kidney, testis, and pancreas, albeit at much lower levels than in neurons. However, the assessment of low levels of non-neuronal Tau requires that the specificities of the anti-Tau antibodies used are fully validated. MethodsThree previously validated anti-Tau antibodies (Tau-12, Tau-1, RD3) were used to test Tau expression levels in 33 mouse and 66 human tissues using Food and Drug Administration-quality tissue microarrays in immunocytochemistry and western blot analyses. ResultsThe presence of Tau was confirmed in salivary gland, kidney, skeletal muscle, heart, pancreas and oesophagus in both human and mouse tissues. ConclusionsDysregulation of Tau protein expression and alterations in its post-translational modification is a causative factor in neurodegenerative disease. We have demonstrated a wider Tau expression in other tissues and cells, outside the brain, which may be dysregulated in other diseases.

Aims/hypothesisAutophagy plays a critical role in the survival and microbial clearance function of tissues that encounter the environment, such as airway epithelial cells (AECs). Contrary to the known roles of azithromycin (AZM) in promoting microbial clearance, our evidence shows that AZM is a potent inhibitor of autophagy - an effect consistent with bacterial residency. Here we investigate the structure-activity relationship of AZM vs other macrolides and AZM-3-N-oxide (AZM-[O]), to mitigate the off-target arrest of autophagy. MethodAZM-[O] was synthesised in-house via selective oxidation of the desosamine amine of AZM. Human peripheral blood mononuclear cells (PBMC) were used to assess autophagy ex vivo in an organotypic manner via transmission electron microscopy and Western blot analysis. For in vitro studies, the 16HBE14o-AEC line and Western blot was used to assess macrolide vs autophagy structure-activity relationships, and autophagic flux by quantifying the protein abundance of LC3B-II vs Sequestosome-1. Subsequent assessments of antimicrobial activity were conducted using the micro-broth dilution method. Immunomodulatory outcomes were assessed by quantifying the secretion of IL-6 in a lipopolysaccharide PMA-stimulated THP-1 macrophage model. ResultsAZM significantly inhibited autophagic flux in both the ex vivo PBMC and in vitro 16HBE14o-AEC models, evidenced by the accumulation of autophagosome-related vacuoles and LC3B-II and Sequestosome-1 protein, compared to its precursors and other macrolides including roxithromycin and clarithromycin. Notably, oxidation of AZM to produce AZM-[O] significantly alleviated this inhibitory effect on autophagy, but without completely preserving its antimicrobial and immunomodulatory functions. Conclusion/DirectionsWe show for the first time that AZM inhibits PBMC autophagy in human blood ex vivo and there is a high probability this phenomenon occurs in the clinical setting. Importantly, chemical modification of AZM to generate AZM-[O] substantially alleviated this effect, consistent with altered ionisation properties. We are now assessing clinically derived blood samples in participants treated with AZM, defining the AZM-mammalian protein interactome and developing further AZM derivatives that preserve immunomodulatory activity while minimising disruption of autophagy.