Mol Cell Proteomics. 2025 Mar 7:100934. doi: 10.1016/j.mcpro.2025.100934. Online ahead of print.

ABSTRACT

Limited proteolysis combined with mass spectrometry (LiP-MS) facilitates probing structural changes on a proteome-wide scale. This method leverages differences in the proteinase K accessibility of native protein structures to concurrently assess structural alterations for thousands of proteins in situ. Distinguishing different contributions to the LiP-MS signal, such as changes in protein abundance or chemical modifications, from structural protein alterations remains challenging. Here, we present the first comprehensive computational pipeline to infer structural alterations for LiP-MS data using a two-step approach. (1) We remove unwanted variations from the LiP signal that are not caused by protein structural effects and (2) infer the effects of variables of interest on the remaining signal. Using LiP-MS data from three species we demonstrate that this approach outperforms previously employed approaches. Our framework provides a uniquely powerful approach for deconvolving LiP-MS signals and separating protein structural changes from changes in protein abundance, post-translational modifications and alternative splicing. Our approach may also be applied to analyze other types of peptide-centric structural proteomics data, such as FPOP or molecular painting data.

PMID:40058498 | DOI:10.1016/j.mcpro.2025.100934

Cell Rep. 2025 Mar 7;44(3):115392. doi: 10.1016/j.celrep.2025.115392. Online ahead of print.

ABSTRACT

Streptomyces albidoflavus is a widely used strain for natural product discovery and production through heterologous biosynthetic gene clusters (BGCs). However, the transcriptional regulatory network (TRN) and its impact on secondary metabolism remain poorly understood. Here, we characterize the TRN using independent component analysis on 218 RNA sequencing (RNA-seq) transcriptomes across 88 unique growth conditions. We identify 78 independently modulated sets of genes (iModulons) that quantitatively describe the TRN across diverse conditions. Our analyses reveal (1) TRN adaptation to different growth conditions, (2) conserved and unique characteristics of the TRN across diverse lineages, (3) transcriptional activation of several endogenous BGCs, including surugamide, minimycin, and paulomycin, and (4) inferred functions of 40% of uncharacterized genes in the S. albidoflavus genome. These findings provide a comprehensive and quantitative understanding of the S. albidoflavus TRN, offering a knowledge base for further exploration and experimental validation.

PMID:40057950 | DOI:10.1016/j.celrep.2025.115392

Best Pract Res Clin Endocrinol Metab. 2025 Mar 3:101985. doi: 10.1016/j.beem.2025.101985. Online ahead of print.

ABSTRACT

Primary hyperparathyroidism is a common endocrine disorder characterized by inappropriate elevation of parathyroid hormone and hypercalcemia. While predominantly an asymptomatic disease in Western populations, symptomatic presentations are more prevalent in Eastern countries. The molecular pathogenesis of sporadic PHPT primarily involves genetic and epigenetic alterations leading to abnormal parathyroid cell proliferation and altered calcium sensing mechanism. To date, MEN1 and cyclin D1 are the only established drivers of sporadic PHPT. Somatic MEN1 gene mutations occur in 30-40 % of sporadic parathyroid adenomas (PA), with a recent study on symptomatic cases reporting germline variants.Cyclin D1 overexpression in sporadic PA has been observed in 20-40 % of cases in Western populations and 80 % of cases in Eastern populations, with an inverse association with cyclin-dependent kinase inhibitors CDKN2A and CDKN2B expression. The calcium-sensing receptor expression was significantly lower in symptomatic compared to asymptomatic PHPT, strongly supported by epigenetic deregulation (promoter hypermethylation and histone methylation). Recent studies have highlighted the potential involvement of EZH2, a histone methyltransferase, in parathyroid tumorigenesis. Additionally, parathyroid-specific transcription factors like GCM2, PAX1, and GATA3 are emerging as putative tumor suppressors, especially from the symptomatic PHPT. Next-generation sequencing has identified novel potential drivers such as PIK3CA, MTOR, and NF1 in sporadic PC, alongside CDC73. The molecular landscape of sporadic PHPT appears to differ between Eastern and Western populations. This heterogeneity underscores the need for further large-scale studies, particularly in symptomatic cases from developing nations, to comprehensively elucidate the molecular drivers of parathyroid tumorigenesis.

PMID:40057423 | DOI:10.1016/j.beem.2025.101985

Biochim Biophys Acta Mol Basis Dis. 2025 Mar 6:167781. doi: 10.1016/j.bbadis.2025.167781. Online ahead of print.

ABSTRACT

Non-coding RNAs (ncRNAs) are frequently dysregulated in various cancers and have been implicated in the etiology and progression of cancer. Ovarian cancer, the most fatal gynecological cancer, has a poor prognosis and a high patient fatality rate due to metastases. In this study, we classified patients with ovarian cancer into three groups based on their ncRNA expression levels. Notably, an ncRNA transcribed by RNA polymerase III, RNA component of mitochondrial RNA processing endoribonuclease (RMRP), is highly expressed in a group with a poor prognosis. Functional assays using SKOV3 and HeyA8 human ovarian cancer cell lines revealed that while RMRP modulation had no significant effect on cell viability, it markedly enhanced cell invasion. Knockdown and ectopic expression experiments demonstrated that RMRP promotes the secretion of matrix metalloproteinase (MMP)-2 and -9, thereby facilitating ovarian cancer cell invasiveness. Transcriptomic analysis further revealed a positive correlation between RMRP expression and genes involved in cellular localization, including RAB31, a member of the Ras-related protein family. Notably, RAB31 knockdown abrogated the pro-invasive effects of RMRP, identifying it as a key downstream effector in SKOV3 and HeyA8 cells. In addition, MechRNA analysis identified RAB31 as a putative RMRP-interacting transcript. These findings establish RMRP as a critical regulator of RAB31-dependent MMP secretion and ovarian cancer cell invasion. Moreover, our results suggest that RMRP could serve as a promising prognostic biomarker for ovarian cancer.

PMID:40057205 | DOI:10.1016/j.bbadis.2025.167781

Environ Toxicol Pharmacol. 2025 Mar 6:104672. doi: 10.1016/j.etap.2025.104672. Online ahead of print.

ABSTRACT

5-hydroxy-N,N-dimethyltryptamine (5-OH-DMT), known as bufotenine, is proven to have psychoactive effects in high concentrations. Duttyphrynus melanostictus, which produces bufotenine, has migrated to the city of Toamasina in Madagascar, thus, the determination bufotenine's levels in the species' samples is necessary. This study aimed to quantify bufotenine in eggs, tadpoles and toad's skin samples of the Duttyphrynus melanostictus as well as in its predator Hoplobatrachus tigerinus and Haemopis sanguisiga. Two extraction protocols were applied depending on the sample type both based on liquid liquid extraction. Spiked calibration samples were prepared at six concentration levels (10-1000ng/mL), and performance parameters were evaluated: linearity, accuracy (bias%), precision (CV%) and limit of detection. The proposed protocol is simple and quick, and the UHPLC-MS/MS system used exhibited adequate sensitivity. The target analyte was detected in all samples except for the eggs of Duttyphrynus melanostictus, with concentrations increasing in line with the animal's development.

PMID:40057147 | DOI:10.1016/j.etap.2025.104672

Biomed Pharmacother. 2025 Mar 7;185:117944. doi: 10.1016/j.biopha.2025.117944. Online ahead of print.

ABSTRACT

PURPOSE: To analyze the response of different retinal ganglion cell (RGC) populations to NMDA-induced retinal excitotoxicity and the effect of an intraperitoneal treatment with 7,8-Dihydroxyflavone (DHF), a potent selective TrkB agonist.

METHODS: Adult albino rats were treated the day prior to NMDA injection and the three following days with intraperitoneal vehicle (1 %DMSO in 0.09 %NaCl) or DHF (5 mg/kg in vehicle) injections. DHF-afforded protection was studied in the population of Brn3a+RGCs, OPN+RGCs (α-RGCs), OPN+ Tbr2+RGCs (αONs-RGCs), OPN+ Tbr2-Brn3a-RGCs (αONt-RGCs) and OPN+Brn3a+RGCs (αOFF-RGCs) at 3,7,14, or 21 days. The functional response was analyzed longitudinally with full-field electroretinograms. The mechanisms underlying DHF-afforded neuroprotection were assessed by western blot (WB) analysis of the levels of phosphorylated and total TrkB, phosphatidylinositol 3 kinase (PIK3/AKT) and mitogen-activated protein kinase (MAPK).

RESULTS: NMDA intravitreal injection resulted in a significant diminution of the mean amplitudes of the pSTR and b-waves, as well as in severe depletion of all RGCs studied except αONt-RGCs. DHF treatment resulted in rescued mean amplitudes of the pSTR and b-waves up to 21 days after NMDA. WB analysis revealed an increase in p-TrkB which correlates to the increase of TRKB protein and an increase in normalized pAKT/AKT. pMAPK/MAPK was upregulated earlier and significantly higher in DHF-treated retinas. DHF afforded survival of up to 49 % of the Brn3a+RGCs versus 25 % of the vehicle group at 21 days after NMDA, and improved survival of the α-RGC and αONs-RGCs but did not rescue the αOFF-RGCs.

CONCLUSION: Different RGC types exhibit variable susceptibilities to NMDA injury, and DHF-mediated activation of TrkB affords neuroprotection.

PMID:40056826 | DOI:10.1016/j.biopha.2025.117944

Talanta. 2025 Mar 4;291:127891. doi: 10.1016/j.talanta.2025.127891. Online ahead of print.

ABSTRACT

Diabetic liver injury (DLI) is a significant complication of diabetes mellitus, leading to severe liver dysfunction and non-alcoholic fatty liver disease (NAFLD). Understanding the metabolic alterations and reprogramming in DLI is critical for identifying therapeutic targets. Despite the prevalence of DLI, its underlying metabolic mechanisms remain poorly understood, and effective treatments are lacking. In this study, we employed a multimodal mass spectrometry imaging approach, combining air-flow-assisted desorption electrospray ionization (AFADESI-MSI) with matrix-assisted laser desorption ionization (MALDI-MSI) to achieve a comprehensive spatial analysis of metabolic changes in DLI model rats, focusing on the potential therapeutic effects of ferulic acid, a compound known for its antioxidant and anti-inflammatory properties. This approach allowed for the wide-coverage and high-resolution visualization of over 200 metabolites in the liver tissues of DLI model rats. The study involved comparing metabolic profiles between control, DLI, and ferulic acid-treated groups, with ferulic acid administered at a dosage of 50 mg/kg daily for 20 weeks. The analysis revealed significant metabolic reprogramming in DLI, characterized by alterations in glucose, lipid, bile acid, and nucleotide metabolism. Specifically, we identified over 100 metabolites with heterogeneous distributions across liver sections, highlighting region-specific metabolic impairments. Ferulic acid treatment notably reversed many of these metabolic disturbances, particularly in glucose and lipid metabolism, suggesting its potential to restore metabolic homeostasis in DLI. This study provides critical insights into the metabolic underpinnings of DLI and demonstrates the therapeutic potential of ferulic acid in modulating these pathways. The findings underscore the utility of AFADESI- and MALDI-MSI in studying liver diseases and suggest that the metabolites identified could serve as novel biomarkers for DLI diagnosis and treatment.

PMID:40056655 | DOI:10.1016/j.talanta.2025.127891

J Neuroinflammation. 2025 Mar 8;22(1):71. doi: 10.1186/s12974-025-03388-5.

ABSTRACT

BACKGROUND: Olfactory dysfunction is an underestimated symptom in multiple sclerosis (MS). Here, we examined the pathogenic mechanisms underlying inflammation-induced dysfunction of the olfactory bulb using the animal model of MS, experimental autoimmune encephalomyelitis (EAE).

RESULTS: Reduced olfactory function in EAE was associated with the degeneration of short-axon neurons, immature neurons, and both mitral and tufted cells, along with their synaptic interactions and axonal repertoire. To dissect the mechanisms underlying the susceptibility of mitral cells, the main projection neurons of the olfactory bulb, we profiled their responses to neuroinflammation by single-nucleus RNA sequencing followed by functional validation. Neuroinflammation resulted in the induction of potassium channel transcripts in mitral cells, which was reflected in increased halothane-induced outward currents of these cells, likely contributing to the impaired olfaction in EAE animals.

CONCLUSION: This study reveals the crucial role of mitral cells and their potassium channel activity in the olfactory bulb during EAE, thereby enhancing our understanding of neuroinflammation-induced neurodegeneration in MS.

PMID:40057769 | DOI:10.1186/s12974-025-03388-5

Evodevo. 2025 Mar 8;16(1):2. doi: 10.1186/s13227-025-00238-6.

ABSTRACT

BACKGROUND: Relatively little is known about the diversity of embryonic development across lineages of spiders, even though the study of embryonic development is a primary step in evo-devo studies and essential for understanding phenotypic evolution. Practically nothing is known about embryogenesis in cave-dwelling spiders, animals which play an important role in cave ecosystems and may have remarkable adaptations to aphotic habitats such as loss of eyes.

RESULTS: Here, we describe embryogenesis and study the expression patterns of several genes of the Retinal Determination Network (RDN) in the troglophile (species that have pre-adaptations to life in caves, and can complete their life cycle in caves, as well as in epigean habitats) eye-bearing funnel-web spider species Tegenaria pagana C. L. Koch, 1840, using fluorescent staining and confocal microscopy. We discuss the characteristic features of T. pagana embryogenesis and key RDN genes. Although in many respects the embryonic development of different species of entelegyne spiders is similar, we found differences in the rate of development, and the details of the opisthosoma, respiratory system, and brain morphogenesis in comparison with established spider model species. Our data supports the hypothesis of a conserved role of sine oculis gene in the eye formation of arachnids.

CONCLUSIONS: Given the recent discovery of congeneric cave species with different degrees of eye reduction throughout Israel, these data sets provide a foundational point of comparison for studying eye reduction and eye loss events in the spider genus Tegenaria.

PMID:40057742 | DOI:10.1186/s13227-025-00238-6

Sci Rep. 2025 Mar 8;15(1):8103. doi: 10.1038/s41598-025-92756-5.

ABSTRACT

Tinospora cordifolia has been used for thousands of years to treat various health conditions, including neurodegenerative diseases. The study aimed to elucidate the mechanism of action and protein targets of T. cordifolia in the context of Alzheimer's disease through untargeted metabolomics and network pharmacology. LC-MS/MS analysis resulted in 1186 metabolites, including known bioactive compounds such as liquiritin, Plastoquinone 3, and Shoyuflavone A, to name a few. The network pharmacology analysis highlighted the metabolite-protein interaction with the enrichment of 591 human proteins, including neurotransmitter receptors and other regulatory proteins. Pathway analysis highlighted the enrichment of cAMP, mTOR, MAPK, and PI3K-Akt signaling pathways along with cholinergic, dopaminergic, serotonergic, glutamatergic synapse, and apoptosis. The docking results suggest that T. cordifolia metabolites could interact with key Alzheimer's disease targets BACE1 and MAO-B, suggesting its role in neuroprotection. These findings provide insights into the biochemical pathways underlying T. cordifolia's therapeutic effects and provides a foundation for future exploration of T. cordifolia in the context of translational research.

PMID:40057579 | DOI:10.1038/s41598-025-92756-5

J Mol Biol. 2025 Mar 7:169046. doi: 10.1016/j.jmb.2025.169046. Online ahead of print.

ABSTRACT

The vast array of cellular ribonucleic acid (RNA) modifications hold a crucial role in regulating RNA stability, folding, localization, and the accuracy of translation. Numerous diseases have been associated with mutations found in genes of RNA-modifying enzymes that can lead to truncated or misfolded proteins incapable of modifying their RNA substrates, causing downstream defects. In contrast, dysregulated levels of RNA-modifying enzymes and the resulting changes in RNA modifications on their substrates are increasingly linked to the activation of oncogenic pathways. This phenomenon has been especially studied through the lens of methyltransferases such as METTL1 and METTL3. The field has developed several small molecule inhibitors of RNA-modifying enzymes to mitigate their related diseases, including targeting the upregulation of METTL3 in cancer. However, increasing evidence suggests that RNA-modifying enzymes play essential roles in numerous cellular processes, including the immune response, neural health, and regeneration, among others. This could lead to off-target effects when treating proteins with small molecules, particularly when these enzymes are upregulated. We propose that developing treatments to specifically target the RNA substrates mis-regulated due to abnormal levels of RNA-modifying enzymes responsible for malignant hallmarks may offer an alternative strategy for treating diseases. We review current RNA-targeted therapies and the diseases they target, including advancements in oligonucleotide modalities and small molecules. We also identify gaps in knowledge that need to be addressed to enhance drug development in the epitranscriptome field to use these therapies to target mis-regulated RNA stemming from altered RNA-modifying enzyme levels.

PMID:40057447 | DOI:10.1016/j.jmb.2025.169046

Int J Biol Macromol. 2025 Mar 6:141823. doi: 10.1016/j.ijbiomac.2025.141823. Online ahead of print.

ABSTRACT

Fungi are widespread organisms with complex multienzyme systems crucial for diverse biochemical processes. This study systematically reviewed research on multienzyme complexes, focusing on their isolation and identification, while examining their potential classification as metabolons. Using a theoretical framework based on PRISMA guidelines, the review analysed literature from 2013 to 2023 across databases such as Medline, Web of Science, and ScienceDirect, employing targeted descriptors to identify relevant studies. The articles were selected by two independent reviewers among those published in English in the last 10 years. From 2313 papers identified through bibliographic searches, 13 were selected for qualitative analysis. Purification methods for fungal multienzyme complexes vary, each offering unique advantages and requiring tailored approaches for specific enzyme systems. The isolation and characterisation of multienzyme complexes face significant challenges. Their classification as metabolons depends on three criteria: substrate channelling, functional coupling, and dynamic assembly. Although research highlights the significance of substrate channelling and the function of stabilising proteins in improving metabolic efficiency, evidence for dynamic assembly is limited. Future research should emphasise new stabilising measures, real-time monitoring of intricate dynamics, and a more profound investigation of molecular causes.

PMID:40057082 | DOI:10.1016/j.ijbiomac.2025.141823

Cell Rep Med. 2025 Mar 6:101996. doi: 10.1016/j.xcrm.2025.101996. Online ahead of print.

ABSTRACT

Liver-expressed antimicrobial peptide 2 (LEAP2) is an endogenous antagonist and inverse agonist of the ghrelin receptor, countering ghrelin's effects on cell signaling and feeding. However, despite an emerging interest in LEAP2's physiology and pharmacology, its endocrine regulation remains unclear. Here, we report that plasma LEAP2 levels decrease significantly upon glucagon infusions during somatostatin clamps in humans. This effect is preserved in patients with obesity and type 2 diabetes while diminished following a hypercaloric diet and a sedentary lifestyle for 2 weeks. Additionally, insulin receptor antagonism offsets the upregulation of LEAP2 during the postprandial state in mice. Finally, insulin and glucagon receptor-expressing hepatocytes are the primary source of hepatic LEAP2 expression, coinciding with a putative enhancer-like signature bound by insulin- and glucagon-regulated transcription factors at the LEAP2 locus. Collectively, our findings implicate insulin and glucagon in regulating LEAP2 and warrant further investigations into the exact mechanisms orchestrating this endocrine axis.

PMID:40056903 | DOI:10.1016/j.xcrm.2025.101996

Water Res. 2025 Mar 2;279:123368. doi: 10.1016/j.watres.2025.123368. Online ahead of print.

ABSTRACT

The interface between groundwater and surface water is a critical zone influencing ecohydrological and biogeochemical cycles within surface water ecosystems. It is characterized by complex redox gradients, with groundwater-mediated inflow of reduced substances affecting the oxygen budget of stream water. In this study, we have experimentally simulated the inflow of Fe(II)-rich groundwater into the open stream water of a flume system to quantify its effect on dissolved oxygen concentration in both the stream water and the hyporheic zone. The experimental setup consisted of 12 flumes, half used for input of groundwater augmented with Fe(II), while the other half served as a control. We studied the effects of coarse (6% fine sediment content) sediment vs. fine (28 % fine sediment content) sediment as well as and moderate (3 L s-1) vs. low (0.5 L s-1) flow rate in a fully-crossed, 3-way-replicated design. Weekly sampling campaigns were performed to analyze Fe(II), Fe(III), DOC, and dissolved oxygen (DO) concentrations in the pore water (hyporheic zone) and in the open water over five consecutive weeks. Our results indicate that Fe(II) inflow substantially decreased DO concentrations in both the pore and open waters. Oxygen uptake rates increased from 7.4 up to 8.6 g O2 m-2 d-1 at a moderate flow rate and from 1.7 to 1.9 g O2 m-2 d-1 at a low flow rate. This corresponds to a contribution of the Fe(II) input to the overall oxygen uptake rate in the flumes of 21 and 17%, respectively. Treatment with FeCl2 also led to a substantial increase in DOC from ∼ 55 mg L-1 in the control flumes to > 60 mg L-1 suggesting a linkage between Fe(II) mobilization and the occurrence of DOC. In conclusion, this study highlights the need to consider the effects of hyporheic and riparian redox processes and subsequent inflow of Fe(II) into streams on the oxygen budget and the health of stream ecosystems.

PMID:40056473 | DOI:10.1016/j.watres.2025.123368

J Agric Food Chem. 2025 Mar 7. doi: 10.1021/acs.jafc.4c09501. Online ahead of print.

ABSTRACT

Betalains, a group of pigments widely distributed in various plants, are extensively applied in the food, beverage, and medicinal industries. The biosynthesis of betalains involves the enzymatic action of 4,5-DOPA-dioxygenase, which catalyzes the key ring-opening reaction of DOPA to produce betalamic acid, a crucial intermediate in the pathway. The crystal structure of a 4,5-DOPA-dioxygenase from Beta vulgaris (BvDOD) was determined in this study. The structural analysis revealed that BvDOD exhibited a structural fold similar to that of other members of the extradiol dioxygenase family. Moreover, the Fe-ligand residues His15, His53, and His229 indicated the enzyme's reliance on nonheme iron for catalyzing the ring-opening reaction. Molecular docking and mutational analysis identified two conserved residues, His119 and His175, in the active site essential for the catalytic reaction. In addition, Thr17, Asp254, and Tyr260 contributed to properly positioning the substrate in the active site. This study has provided structural insights into substrate recognition and catalytic mechanisms of BvDOD, which can be applied to develop enzymes for improved betalain production.

PMID:40055856 | DOI:10.1021/acs.jafc.4c09501

J Phys Chem B. 2025 Mar 7. doi: 10.1021/acs.jpcb.4c07794. Online ahead of print.

ABSTRACT

Small molecule kinase inhibitors are critical in the modern treatment of cancers, evidenced by the existence of over 80 FDA-approved small-molecule kinase inhibitors. Unfortunately, intrinsic or acquired resistance, often causing therapy discontinuation, is frequently caused by mutations in the kinase therapeutic target. The advent of clinical tumor sequencing has opened additional opportunities for precision oncology to improve patient outcomes by pairing optimal therapies with tumor mutation profiles. However, modern precision oncology efforts are hindered by lack of sufficient biochemical or clinical evidence to classify each mutation as resistant or sensitive to existing inhibitors. Structure-based methods show promising accuracy in retrospective benchmarks at predicting whether a kinase mutation will perturb inhibitor binding, but comparisons are made by pooling disparate experimental measurements across different conditions. We present the first prospective benchmark of structure-based approaches on a blinded dataset of in-cell kinase inhibitor affinities to Abl kinase mutants using a NanoBRET reporter assay. We compare NanoBRET results to structure-based methods and their ability to estimate the impact of mutations on inhibitor binding (measured as ΔΔG). Comparing physics-based simulations, Rosetta, and previous machine learning models, we find that structure-based methods accurately classify kinase mutations as inhibitor-resistant or inhibitor-sensitizing, and each approach has a similar degree of accuracy. We show that physics-based simulations are best suited to estimate ΔΔG of mutations that are distal to the kinase active site. To probe modes of failure, we retrospectively investigate two clinically significant mutations poorly predicted by our methods, T315A and L298F, and find that starting configurations and protonation states significantly alter the accuracy of our predictions. Our experimental and computational measurements provide a benchmark for estimating the impact of mutations on inhibitor binding affinity for future methods and structure-based models. These structure-based methods have potential utility in identifying optimal therapies for tumor-specific mutations, predicting resistance mutations in the absence of clinical data, and identifying potential sensitizing mutations to established inhibitors.

PMID:40053698 | DOI:10.1021/acs.jpcb.4c07794

STAR Protoc. 2025 Mar 5;6(1):103671. doi: 10.1016/j.xpro.2025.103671. Online ahead of print.

ABSTRACT

Reverse vaccine technology, supported by advancements in immunoinformatics, facilitates the development of multi-epitope vaccines for rapidly evolving pathogens, thereby strengthening the immune defense. Here, we present a protocol for a peptide-based multi-epitope vaccine targeting monkeypox virus (MPXV) using an open-source approach. We describe steps for evaluating physicochemical properties and allergenicity. We then detail procedures for validating pattern recognition receptor (PRR)-binding affinity and stable major histocompatibility complex (MHC) I/II presentation. Molecular dynamics (MD) simulations confirm immune receptor interactions, enhancing vaccine stability. For complete details on the use and execution of this protocol, please refer to Kaur et al.1.

PMID:40053448 | DOI:10.1016/j.xpro.2025.103671

Elife. 2025 Mar 7;13:RP99545. doi: 10.7554/eLife.99545.

ABSTRACT

The principle of efficient coding posits that sensory cortical networks are designed to encode maximal sensory information with minimal metabolic cost. Despite the major influence of efficient coding in neuroscience, it has remained unclear whether fundamental empirical properties of neural network activity can be explained solely based on this normative principle. Here, we derive the structural, coding, and biophysical properties of excitatory-inhibitory recurrent networks of spiking neurons that emerge directly from imposing that the network minimizes an instantaneous loss function and a time-averaged performance measure enacting efficient coding. We assumed that the network encodes a number of independent stimulus features varying with a time scale equal to the membrane time constant of excitatory and inhibitory neurons. The optimal network has biologically plausible biophysical features, including realistic integrate-and-fire spiking dynamics, spike-triggered adaptation, and a non-specific excitatory external input. The excitatory-inhibitory recurrent connectivity between neurons with similar stimulus tuning implements feature-specific competition, similar to that recently found in visual cortex. Networks with unstructured connectivity cannot reach comparable levels of coding efficiency. The optimal ratio of excitatory vs inhibitory neurons and the ratio of mean inhibitory-to-inhibitory vs excitatory-to-inhibitory connectivity are comparable to those of cortical sensory networks. The efficient network solution exhibits an instantaneous balance between excitation and inhibition. The network can perform efficient coding even when external stimuli vary over multiple time scales. Together, these results suggest that key properties of biological neural networks may be accounted for by efficient coding.

PMID:40053385 | DOI:10.7554/eLife.99545

FASEB J. 2025 Mar 15;39(5):e70411. doi: 10.1096/fj.202402726R.

ABSTRACT

Viral infections can cause cellular dysregulation of metabolic reactions. Viruses alter host metabolism to meet their replication needs. The impact of viruses on specific metabolic pathways is not well understood, even in well-studied viruses, such as human adenovirus. Adenoviral infection is known to influence cellular glycolysis and respiration; however, global effects on overall cellular metabolism in response to infection are unclear. Furthermore, few studies have employed an untargeted approach, combining emphasis on viral dosage and infection. To address this, we employed untargeted metabolomics to quantify the dynamic metabolic shifts in fibroblasts infected with human adenovirus serotype 5 (HAdV-5) at three dosages (0.5, 1.0, and 2.0 multiplicity of infection [MOI]) and across 4 time points (6-, 12-, 24-, and 36-h post-infection [HPI]). The greatest differences in individual metabolites were observed at 6- and 12-h post-infection, correlating with the early phase of the HAdV-5 infection cycle. In addition to its effects on glycolysis and respiration, adenoviral infection downregulates cysteine and unsaturated fatty acid metabolism while upregulating aspects of purine metabolism. These results reveal specific metabolic pathways dysregulated by adenoviral infection and the associated dynamic shifts in metabolism, suggesting that viral infections alter energetics via profound changes in lipid, nucleic acid, and protein metabolism. The results revealed previously unconsidered metabolic pathways disrupted by HAdV-5 that can alter cellular metabolism, thereby prompting further investigation into HAdV mechanisms and antiviral targeting.

PMID:40052831 | DOI:10.1096/fj.202402726R

Brief Bioinform. 2025 Mar 4;26(2):bbaf082. doi: 10.1093/bib/bbaf082.

ABSTRACT

Cancer cells acquire necessary functional capabilities for malignancy through the influence of the nervous system. We evaluate the extent of neural infiltration within the tumor microenvironment (TME) across multiple cancer types, highlighting its role as a cancer hallmark. We identify cancer-related neural genes using 40 bulk RNA-seq datasets across 10 cancer types, developing a predictive score for cancer-related neural infiltration (C-Neural score). Cancer samples with elevated C-Neural scores exhibit perineural invasion, recurrence, metastasis, higher stage or grade, or poor prognosis. Epithelial cells show the highest C-Neural scores among all cell types in 55 single-cell RNA sequencing datasets. The epithelial cells with high C-Neural scores (epi-highCNs) characterized by increased copy number variation, reduced cell differentiation, higher epithelial-mesenchymal transition scores, and elevated metabolic level. Epi-highCNs frequently communicate with Schwann cells by FN1 signaling pathway. The co-culture experiment indicates that Schwann cells may facilitate cancer progression through upregulation of VDAC1. Moreover, C-Neural scores positively correlate with the infiltration of antitumor immune cells, indicating potential response for immunotherapy. Melanoma patients with high C-Neural scores may benefit from trametinib. These analyses illuminate the extent of neural influence within TME, suggesting potential role as a cancer hallmark and offering implications for effective therapeutic strategies against cancer.

PMID:40052442 | DOI:10.1093/bib/bbaf082