In vivo evaluation of biomaterials largely relies on histology to assess biocompatibility and foreign body responses. While effective for capturing end-stage outcomes, these methods offer limited insight into the cellular mechanisms driving tissue remodeling, hindering efforts to rationally design better biomaterials. Transcriptomics has revolutionized our understanding of gene activity driving cellular function, yet remains underutilized in biomaterial evaluation. Recent advances in high-resolution spatial transcriptomics now enable precise mapping of gene expression within tissue, offering detailed insight into cellular states and spatial organization. To align biomaterial research with advances in spatial biology, we develop a bioinformatics workflow for the Xenium platform to analyze in vivo responses to implanted materials. Applying this workflow to evaluate electrospun polycaprolactone (PCL) scaffolds implanted subcutaneously in mice, we identify spatially distinct macrophage and fibroblast subpopulations with unique gene expression profiles. Spatial analyses show shared phenotypic features between co-localized macrophages and fibroblasts, oriented from the scaffold body to its surface. Gene ontology linked these spatial transitions to functional roles, with immune cell recruitment occurring within the scaffold and fibrosis at the surface. These transitions were not detectable by histology, highlighting spatial transcriptomics as a powerful approach for uncovering cellular dynamics and enabling better biologically-informed design of biomaterials.

Bone regeneration is initiated after a bone injury, such as a bone fracture or tooth extraction. It is a highly complex biological process involving multiple cell types, signaling molecules, and molecular pathways. The hypoxic microenvironment in the early stage of bone regeneration poses challenges to cell status and the final outcome of bone regeneration. During this phase, two key regulators-HIF-1α (the critical mediator of hypoxia response) and BMAL1 (the central component of the circadian rhythm)-orchestrate the activities of bone-regenerating cells, ensuring proper cellular function and orderly progression of bone repair. Existing studies have shown that there is a close crosstalk between HIF-1α and BMAL1, including regulation of gene expression, protein interaction, and regulation of downstream pathways. In this review, we discuss the respective regulatory roles of HIF-1α and BMAL1 in bone regeneration and further summarize their interactions within cells. Additionally, we extend the discussion to their interactions in other bone-related diseases, and summarize the existing research directions and deficiencies, providing new insights for in-depth studies of the hypoxia response and circadian rhythm systems.

Chromatin loops play a crucial role in gene regulation and cellular function, providing key insights into understanding the 3D structure of the genome and its impact on cellular homeostasis. Nanopore sequencing technology, with its advantages in simultaneously detecting sequences and methylation patterns, brings new opportunities for studying 3D genome structures. We introduce NanoLoop, the first algorithmic framework attempting to predict genome-wide chromatin interactions using Nanopore data. In experiments across four human lymphoblastoid cell lines, NanoLoop demonstrated excellent predictive performance and cross-cell line generalization capabilities. We also discovered four distinct methylation patterns at loop anchors that influence histone modification levels and determine various loop types. NanoLoop further predicted previously uncharacterized long-range chromatin loops, highlighting the potential link between DNA methylation and 3D genome organization and providing new insights into the complex regulatory relationships between epigenetic modifications and 3D genome organization.

Introduction The fat tail in sheep is a distinctive adaptive trait, yet the cellular mechanisms controlling its development remain poorly understood. Although PDGFD is a high-priority candidate gene from selective sweep analyses, its precise cellular function and underlying molecular mechanisms are uncharacterized. Methods We first defined E70–E80 as the critical fetal period for the initial formation of rump or tail adipose tissue in sheep. To delineate the functional role of PDGFD , we performed knockdown experiments in ovine adipose-derived stem cells (ADSCs) and conducted transcriptomic profiling. Results PDGFD knockdown significantly inhibited ADSCs proliferation and concurrently upregulated key adipogenic markers ( PPARγ , FABP4 ). Transcriptomics revealed that this phenotype was mediated primarily through the profound downregulation of the chemokine CXCL8 . Pathway analysis demonstrated that the PDGFD-CXCL8 axis co-regulates adipose plasticity by modulating both the PI3K-Akt and MAPK signaling pathways. Conclusion We conclude that PDGFD is a master regulator of adipose tissue plasticity, driving progenitor expansion via a CXCL8-dependent mechanism. This PDGFD-CXCL8 regulatory axis orchestrates the cellular groundwork essential for the extensive fat deposition that defines the ovine fat-tail phenotype.

Quantum Neural Networks (QNNs) are emerging as promising tools for complex biological data analysis due to their ability to exploit quantum mechanics for enhanced computational power. In Section 2 of this review, we provide readers with a comprehensive overview of proteins, DNA sequencing, and recent updates on classical approaches to PTM prediction, protein function analysis, and DNA analysis. Furthermore, we present recent findings that underscore the limitations of traditional methods and justify the need for quantum approaches. This section also highlights the unique advantages and potential benefits that quantum-based methods offer over classical techniques, paving the way for more powerful and accurate solutions in biological data analysis. These tasks are critical for understanding protein regulation, cellular processes, and genetic information. In Section 3, we provide a comprehensive review of various Quantum Neural Network (QNN) architectures that have been proposed to date, categorized based on current theoretical and practical developments. The models discussed include Quantum M-P (McCulloch-Pitts) Neural Networks, Quantum Competitive Neural Networks, Quantum-Inspired Neural Networks, Quantum Dot Neural Networks, Quantum Cellular Neural Networks, and Quantum Associative Neural Networks. Each of these models offers unique computational mechanisms rooted in quantum principles such as superposition, entanglement, and interference, enabling them to capture complex patterns in high-dimensional biological data. We further highlight their potential and emerging applications in bioinformatics, particularly in the prediction of protein post-translational modifications (PTMs). Given the critical role of PTMs in regulating protein activity and cellular functions, leveraging QNNs provides a promising avenue for improving prediction accuracy and interpretability in large-scale proteomic datasets. In Section 4, we present the latest advancements in the application of quantum machine learning in genomics, quantum computing for protein structure and function prediction, as well as quantum machine learning in drug discovery and molecular modeling. Section 5 discusses the current limitations of quantum hardware and the challenges in training quantum models. In Section 6, we propose potential improvements for quantum machine learning models in bioinformatics, including hybrid quantum-classical architectures and more efficient quantum circuit designs. Finally, Section 7 concludes the review by summarizing the key insights and outlining specific future research directions, particularly focusing on extending our recent findings into the broader field of quantum machine learning. Together with a system of illustrative figures presented in Sections 2, 3, and 4, as well as concrete examples of algorithms discussed in Section 4, this review provides a solid foundation for future applications of quantum machine learning in bioinformatics and highlights the transformative potential of quantum models in revolutionizing biological data analysis.

RNA modifications represent a dynamic layer of gene expression regulation, RNA stability, and translation with profound implications for cellular function and disease. However, the critical regulation and functions of RNA-modifying proteins (RMPs) remain poorly understood. Here, we present a large-scale characterization of RMPs through 378 multiomics datasets encompassing genomics, bulk and single-cell transcriptomics, epitranscriptomics, proteomics, and posttranslational modifications (PTMs) across 63 human tissues. Our analysis of experimental perturbations of RMPs revealed dynamic differential modification peaks and expressed genes. We applied nonnegative matrix factorization to annotate RMP-mediated cell types in single-cell transcriptomes. Functional annotations in acute myeloid leukemia (AML) revealed RMPs such as ALKBH5 as critical mediators of m6A dynamics, influencing pathways involved in translation initiation, immune regulation, and tumorigenesis. We revealed cell type-specific modification patterns, including those in ALKBH5-enriched AML stem cells with special ligand‒receptor interactions and genetic variations modulated by m6A. We integrated proteogenomic data to uncover PTM-associated regulatory, mutation, and protein‒protein interaction networks linked to RMPs. We developed RMzyme, a platform that consolidates our findings and provides insights into RMPs and their downstream effects. This resource is expected to facilitate biomedical research into the molecular mechanisms of human diseases through the lens of RNA modifications and multiomics data integration.

ABSTRACT Metabolism is a critical process for biology and is of great interest to those researching geobiological processes and the origins of life. A metabolism comprises a network of chemical reactions for molecular synthesis, energy conversion pathways, and cellular function. Understanding the mechanisms underlying metabolic processes provides insight into the evolution of electrochemical processes in complex systems and informs the possible pathways by which abiotic chemistry transitioned to biochemistry. Modern enzymes utilize cofactors to mediate chemical reactions and overcome energetic limitations. While enzymes are specific, large, and complex biological proteins, cofactors are simpler ions and molecules incorporated within the larger protein complex. Cofactors play a fundamental role in supplementing an enzyme's catalytic role and may represent a convergence between abiotic and biotic chemistry, allowing studies of cofactors to reveal potential prebiotic processes. Here, we review some of the organic / nucleotide cofactors participating in the electron transport chain (ETC): their structures, capacity for energy conversion, and their putative role in the origins of life. We choose to focus on four specific organic cofactors that have evolved to be key in extant mitochondrial ETCs—adenosine triphosphate (ATP), nicotinamide adenine dinucleotide (NADH), flavins (FAD, FMN), and quinones (ubiquinone)—to conceptually bridge the gap between the earliest inorganic cofactors and the protein complexes of modern biochemistry. We then make recommendations for future research topics and avenues.

Ectoine is a small, amino acid-derived osmolyte produced by extremophilic bacteria that acts as a compatible solute, protecting cellular macromolecules and structures from extreme environmental stress without disrupting essential cellular functions. The aim of this study was to evaluate the biocompatibility of ectoine with bull sperm and to assess the potential of ectoine to enhance the resilience of sperm under varying stress conditions. Thawed bovine sperm in the presence (0.5, 5 and 50 mM) or absence (control; 0 mM) of ectoine were subjected to a biocompatibility test (37 °C for 6 h; n = 8 bulls), heat stress (39 or 42 °C for 6 h; n = 8 bulls), osmotic stress (150 or 400 mOsm for 15 min; n = 12 bulls) whereby motility and kinematic parameters, as well as viability, acrosome integrity and membrane fluidity by flow cytometry were assessed. Sperm motility in cervicovaginal mucus (37 °C for 3 h; n = 6 bulls) was also assessed. All results are reported as mean ± s.e.m. Ectoine displayed a non-toxic effect across all motility and functional parameters (viability, acrosome integrity and membrane fluidity). Nonetheless, a reduction in kinematic parameters including straight line velocity (VSL), average path velocity (VAP) and straightness (STR) was observed at 50 mM ectoine. Under heat stress at 39 and 42 °C, ectoine concentrations of 0.5 and 5 mM maintained motility and viability, comparable to controls across all time points. In hypoosmotic conditions (150 mOsm), individual bulls displayed different degrees of osmotic resistance. In those bulls with poor osmotic resistance (n = 4), ectoine (0.5 and 5 mM) maintained sperm viability similar to the 0 mM control. However, the viability of sperm incubated with 50 mM solute was 2-fold higher relative to the control (P < 0.001). In hyperosmotic conditions, addition of ectoine to sperm prior to exposure did not affect the total motility or viability compared to the no ectoine treatment (P > 0.05). When sperm were incubated in cervicovaginal mucus, there was an effect of ectoine treatment. Sperm treated with 50 mM ectoine exhibited higher motility throughout incubation compared to the control (0 mM) (P < 0.05). In conclusion, these findings establish ectoine as a promising candidate for improving sperm resilience and warrants further studies to assess additional protective effects of ectoine.

Calcium-mediated mitigation of aged nanoplastic-induced stress in microalgae: Insights into photosynthesis, energy metabolism, and antioxidant defense from physiological and multi-omics analyses.

Transcription is essential for cellular function, but it can also lead to genetic instability, particularly through the formation of secondary structures such as R-loops, which consist of an RNA-DNA hybrid and a displaced DNA strand. Unscheduled R-loop accumulation is a major source of DNA damage and has been associated with several human diseases, including cancer. While multiple factors involved in RNA biogenesis, export, and chromatin remodeling play a role in preventing R-loop accumulation, the function of essential proteins in R-loop metabolism remains unexplored. Here, we performed a genetic screening in Saccharomyces cerevisiae using over 1200 temperature-sensitive mutants to identify novel proteins involved in the prevention of R-loop-associated genomic instability. Our results reveal that the SWI/SNF-like protein Mot1 plays a key role in preventing R-loop accumulation and R-loop-associated genome instability. Its role is particularly important during S phase, where Mot1 dysfunction leads to R-loop dependent replication impairment, presumably due to transcription-replication conflicts (TRCs). Epistatic relationships between mutations in MOT1 and the S-phase specific DNA-RNA helicase SEN1 further support the role of Mot1 in TRCs. The study highlights the importance of transcriptional regulators in maintaining genome stability by mitigating TRCs and regulating R-loop homeostasis.

Inositol 1,4,5-trisphosphate receptors (IP3Rs) are tetrameric calcium (Ca2+) release channels localized in the endoplasmic reticulum (ER), where they regulate cellular function by mediating local and global Ca2+ fluxes toward the cytosol, cell membrane, and organelles including mitochondria. Disruptions in these Ca2+ signals, whether excessive or diminished, due to alterations in IP3R function have been implicated in a wide range of diseases and pathophysiological conditions. Consequently, the Ca2+-flux properties, protein abundance, and localization of IP3Rs must be tightly regulated. Various mechanisms, including interactions with accessory proteins, ensure proper IP3R function across diverse physiological contexts. In this review, we highlight the role of posttranslational modifications (PTMs) in modulating IP3R activity, including phosphorylation/dephosphorylation, redox modifications, glycosylation, palmitoylation, ubiquitination, proteolysis, and transglutaminase-mediated cross-linking. We discuss not only the functional consequences of these PTMs but also provide structural insights when specific modified IP3R residues have been identified. Furthermore, whenever possible, we emphasize IP3R isoform-specific effects of PTMs, offering a nuanced perspective on their regulatory significance.

Background: Chronic noncommunicable diseases account for nearly 80% of global deaths and are strongly associated with insulin resistance (IR). One of the most significant clinical findings of the past two decades is that the molecular mechanisms underlying immune and metabolic systems have been evolutionarily conserved across species. Methods: This study included 34 volunteers (19 men and 15 women). Demographic data were collected using validated questionnaires. Anthropometric measurements (weight, height, waist-to-hip ratio, and body composition assessed by tetrapolar bioimpedance) were obtained directly. Laboratory analyses included fasting glucose and insulin, glycated hemoglobin, HDL cholesterol, total cholesterol, triglycerides, organic aciduria, and additional biochemical markers assessed using standard methods. Group comparisons were performed using parametric or nonparametric statistical tests according to data distribution, as specified in the figure legends. Results: The primary analyses focused on identifying early metabolomic alterations associated with insulin resistance in individuals whose conventional biochemical parameters were within laboratory reference ranges. Individuals with a TG/HDL ratio &gt; 2 and increased urinary kynurenate excretion exhibited a 3.6-fold higher relative risk of insulin resistance, while elevated insulin levels combined with urinary α-ketoisovalerate were associated with a 2.7-fold increased risk. Significant differences in plasma insulin, HbA1c, and HOMA-IR were observed between healthy and diseased individuals (p &lt; 0.05), indicating early metabolic dysfunction preceding clinical disease onset. Conclusions: Metabolomic biomarkers serve as reliable indicators of subclinical metabolic disturbances, revealing significant risks in major metabolic pathways even in individuals with conventional exams within normal limits. Early detection through these metabolomic markers may enable personalized interventions aimed at preserving cellular function and systemic metabolic balance.

Precise regulation of chromatin structure is essential for ensuring genome stability and cellular function. In Saccharomyces cerevisiae, the YEATS (Yaf9-ENL-AF9-Taf14-Sas5) domain protein Yaf9 is a shared component of the NuA4 acetyltransferase and the SWR1 chromatin remodelling complexes. We investigated the function of Yaf9 and discovered that it becomes essential for survival when histone H4 acetylation is impaired. The loss of Yaf9 in a strain with impaired H4 acetylation led to cell cycle arrest in the G2/M phase and activation of the homologous recombination pathway. This synthetic lethality was not recapitulated by inactivating the Yaf9 YEATS domain, suggesting that it is independent of Yaf9's ability to recognise acyl-modified lysine residues. We also found that Yaf9 was required in both NuA4 and SWR1 complexes to ensure cell viability in the absence of H4 acetylation. Together, these findings reveal a compensatory relationship between Yaf9 and histone H4 acetylation, suggesting that Yaf9 acts as a functional link between chromatin remodelling and histone modification pathways to maintain genome integrity under conditions of chromatin stress.

Pseudomonas aeruginosa is an opportunistic pathogen responsible for severe infections in immunocompromised individuals, including burn patients and those with cystic fibrosis. β-Ketoacyl-ACP synthases play essential roles in bacterial fatty acid metabolism, influencing both cellular function and pathogenicity. Two types of long-chain β-ketoacyl-ACP synthases have been identified: FabB and FabF. This study aims to elucidate the roles of the fabF1 and fabF2 genes in fatty acid biosynthesis and virulence of P. aeruginosa PAO1. Complementation assays in Escherichia coli revealed that fabF2 could functionally replace E. coli FabB, whereas FabF1 exhibited FabF-like activity. In P. aeruginosa PAO1, deletion of fabF1 significantly reduced cis-vaccenic acid levels while increasing palmitoleic acid, whereas deletion of fabF2 had no measurable effect. The double mutant exhibited a pronounced reduction in cis-vaccenic acid levels. Virulence assays demonstrated that the ΔfabF1 strain exhibited a 63% decrease in rhamnolipid production, while the ΔfabF2 strain showed a 45% reduction. The double mutant retained only 28% of wild-type rhamnolipid levels. Furthermore, pyoverdine secretion was markedly reduced in the double mutant, and pyocyanin production was impaired. Motility assays indicated diminished swimming, twitching, and swarming abilities in the mutants. Additionally, proper expression levels of fabF2 were required to genetically complement fabF2 deletion in the mutant strain, as both overexpression and insufficient expression failed to restore the mutant phenotype effectively. These findings highlight the critical roles of fabF1 and fabF2 in fatty acid biosynthesis, virulence factor production, and motility in P. aeruginosa. This study provides new insights into the functional divergence of FabF homologs and identifies potential targets for antimicrobial development.

Ovarian aging, recognized as one of the initial signs of systemic aging, is marked by a progressive reduction in both the number and quality of oocytes, which has a profound effect on female fertility. In spite of the advancements in assisted reproductive technologies, these methods fail to tackle the fundamental molecular mechanisms that drive ovarian senescence. Recent surveys have underscored the significant role of epitranscriptomic regulation, especially the N6-methyladenosine (m6A) modification, in regulating RNA stability, translation, and cellular functionality. Fat mass and obesity-associated (FTO), a m6A demethylase, has been identified as a crucial regulator of granulosa cell homeostasis, influencing pathways related to oxidative stress, mitochondrial integrity, apoptosis, and cellular senescence. A decrease in FTO expression in aging ovaries is associated with increased m6A levels, destabilization of heterochromatin, dysregulation of transposable elements, and the upregulation of senescence-associated genes such as FOS. Moreover, regulation of genes such as MFN2, MMP2, and P53 by FTO has been shown to sustain mitochondrial function, uphold ERK signaling, and prevent apoptosis in granulosa cells. In summary, these discoveries position FTO as a pivotal element in the molecular framework governing ovarian aging, presenting promising opportunities for therapeutic strategies aimed at preserving female reproductive capacity.

Background and Objectives: Glioblastoma (GBM) is the most aggressive form of primary brain tumor, characterised by high recurrence rates and poor patient prognosis. This study aimed to identify gene-expression signatures and molecular networks associated with primary and recurrent GBM to better understand the biological mechanisms underlying tumor progression. Materials and Methods: Gene expression analysis of TCGA data was conducted to identify differentially expressed genes across tumor, recurrent, and normal brain tissues. Analysis of overlapping differentially expressed gene sets revealed both common and specific gene-expression profiles across the groups, highlighting genes potentially involved in GBM recurrence. Gene network and canonical pathway analyses were performed using Ingenuity Pathway Analysis (IPA) to identify key pathways and cellular functions altered in GBM. Results: Our data identified distinct molecular signatures in tumor, recurrent, and normal brain samples, highlighting dysregulated genes associated with cellular growth, proliferation, and movement. Transcriptomic stratification revealed progressive tumor- and recurrence-adapted states, with composite Tumor Scores (TS) and Recurrence Scores (RS) classifying samples into four classes: normal-like, proliferative, transitional, and recurrence-adapted tumor states. Conclusions: These findings provide insights into the signaling networks and biological mechanisms underlying GBM recurrence and may guide the identification of potential therapeutic targets to improve the management of this malignancy.

Recent advances in phosphatases as new biomarker in personalized medicine.

Brain activity is costly, and aerobic metabolism supplies ∼90% of the ATP for cellular and synaptic function. Accordingly, oxygen consumption varies to match activity demands of neural circuits, and mitochondrial defects that reduce aerobic metabolism cause various neurological disorders. Brain activity in frogs has energy demands typical of an average vertebrate, but surprisingly, improves function upon stopping oxidative metabolism from a few minutes to hours following hibernation. While this represents a large capacity to shift to glycolysis as a lone ATP source in an adult brain circuit, we hypothesized activity’s reliance on oxygen may be globally reduced. We tested this by simultaneously assessing tissue oxygen consumption and neural activity from a brainstem motor network. We show that hibernation triggers a reduction in the oxygen consumed by neural activity and activity-independent mitochondrial respiration. In accordance with lower aerobic requirements, network output remained stable over a wide range of tissue oxygen levels, from baseline to anoxia, whereas controls were disrupted by moderate hypoxia. Despite operating with reduced aerobic metabolism, network activity was similar to controls, and activity increases did not accelerate oxygen consumption until seizure-like bursts ensued. Therefore, circuits in the vertebrate brain have the surprising capacity to uphold normal network functions with reduced aerobic metabolism. These findings introduce low-cost states can lie dormant within otherwise energetically expensive circuits and raise the question why costly designs are the default when they, in some cases, may be unnecessary and predispose organisms to metabolic pathologies.

Polyamine homeostasis is essential for normal cellular function and is maintained through coordinated regulation of polyamine biosynthesis, catabolism, and transport. This balance is frequently disrupted in breast cancer, a biologically heterogeneous disease comprising distinct molecular subtypes. However, whether polyamine metabolism and transport are differentially regulated across breast cancer subtypes remains poorly defined. Here, we systematically interrogate polyamine homeostasis across representative breast cancer subtypes by integrating cell line profiling combined with analysis of publicly available patient datasets. We found subtype-associated differences across the polyamine pathway and identify polyamine transport as a key contributor to inter- and intra-subtype heterogeneity. Notably, ATP13A3 emerges as a previously unrecognized adverse prognostic marker, particularly in basal-like breast cancer, where its expression associates with proliferative and oncogenic signaling programs. In contrast, ATP13A2 shows an opposing association with patient survival, suggesting divergent functional roles for these closely related transporters. Together, our findings demonstrate that polyamine regulation in breast cancer is highly subtype dependent and highlight the importance of molecular stratification when considering polyamine-directed therapeutic strategies in breast cancer.

Lignocellulosic jute-based nanofiber composite as biomimetic tissue scaffold.