Search Results (224)

Polycomb Group (PcG) proteins, particularly E(z) (Enhancer of Zeste) genes, play essential roles in transcriptional repression and developmental regulation. To investigate their evolutionary history, we conducted a comprehensive comparative genomic analysis of E(z) homologs across green plants. Phylogenetic analysis revealed that E(z) genes are highly conserved, predominantly occurring as single copies in green algae and early land plants. In seed plants, however, E(z) homologs diverged into two major clades, CLF and SWN, likely originating from an ancient duplication predating seed plant diversification. Conserved domain and motif analyses showed that while all E(z) proteins contain the hallmark SET domain, certain lineages also harbor CXC and SANT domains. Moreover, lineage-specific motif divergence was observed, suggesting functional diversification. In angiosperms, further duplications shaped the SWN lineage: in Brassicaceae, SWN genes split into SWN and MEA subclades, whereas in Fabaceae, SWN genes diverged into SWN1 and SWN2. Structural comparisons revealed that both Brassicaceae MEA and Fabaceae SWN2 proteins independently lost approximately 200 amino acids in the central region, indicating convergent structural modifications. Molecular evolutionary analysis showed that Fabaceae SWN1 genes are under purifying selection, consistent with retention of ancestral functions, whereas SWN2 genes experienced strong positive selection, implying functional innovation. Expression profiling of soybean E(z) genes further supported this scenario: SWN1 is broadly expressed across tissues, while SWN2 expression is restricted to the heart-shaped embryo. This pattern mirrors Arabidopsis MEA, suggesting that Fabaceae SWN2 may have evolved imprinted gene functions critical for seed development. Together, our results highlight the evolutionary conservation of E(z) genes in plants and reveal how gene duplication and lineage-specific divergence have driven functional specialization, particularly in Fabaceae SWN2. Full article

Background/Objectives: Oocyte maturation is a process involving both nuclear and cytoplasmic development regulated by epigenetic changes in gene expression. Cyclin-B3 (CCNB3) and cyclin-A2 (CCNA2) genes are thought to be involved in oocyte maturation; however, the expression profiles and key function in Metaphase-I (MI) and Metaphase-II (MII) phases have yet to be fully elucidated. Small non-coding RNA sequences are involved in epigenetic regulation of specific transcriptional targets, whereas microRNAs (miRNAs) participate in the post-transcriptional and translational repression of target genes. This study examined the expression levels of CCNB3, CCNA2, and their associated miRNAs (miR-17, miR-106b, miR-190a, miR-1275) in cumulus oophorous complex (COC) cells derived from MI and MII oocytes of NOR and DOR IVF cases, with particular emphasis on elucidating their functions during the transition from MI to MII stage. Methods: Follicular fluid containing cumulus–oocyte complex (COC) cells obtained from oocytes of 120 cases in each group NOR MI (n = 30), NOR MII (n = 30), DOR MI (n = 30), and DOR MII (n = 30) who were admitted to the Istanbul Bahçeci Health Group Assisted Reproductive Treatment Center. Following total RNA isolation from COC cells, the gene and protein expression levels of CCNB3 and CCNA2, along with the expression of miR-17, miR-106b, miR-190a, and miR-1275, were assessed using (qPCR-based assay) and immunohistochemistry (IHC). To investigate the functional roles of COC cell populations, morphological analysis was performed using H&E staining. Additionally, metadata of the cases, including age, number of oocytes, fertilization, and embryonic development rates, were evaluated. Results: The expressions of miR-17 and miR-1275 were significantly elevated in both NOR MI and DOR MI groups compared to their respective NOR MII and DOR MII groups (p < 0.05). Additionally, miR-106b levels were higher in the NOR MII group relative to NOR MI (p < 0.05), while an increase was also observed in DOR MI compared to DOR MII (p < 0.05). No difference was observed in miR-190a expression between the NOR and DOR (p > 0.05). Based on the results of H and E staining, the NOR MI, NOR MII, DOR MI, and DOR MII groups exhibited distinct variations in cellular morphology, nuclear characteristics, cytoplasmic volume, and cell density. Conclusions: CCNB3 is predicted to be a potential candidate for determining MI between the NOR and DOR cases. On the other hand, only for the NOR MII cases could CCNA2 provide evidence of oocyte maturation. Moreover, we determined the relationship between related genes and miRNAs which target CCNA2 and CCNB3. Genetic and protein expression analysis across diverse molecular pathways and miRNAs yielded comprehensive preliminary data regarding the developmental stages of oocytes at the MI and MII phases, and their fertilization potential following maturation shows potential and warrants prospective validation with clinical performance evaluation. Full article

Human remains detection (HRD) dogs are vital tools in forensic science and disaster response, but their training is limited by the restricted availability of human material. Synthetic odorants such as Sigma Pseudo™ formulations provide safer, standardized alternatives, yet current products reproduce only a fraction of the volatile organic compound (VOC) profile of decomposition. In particular, sulfur-containing volatiles, which are highly odor-active and consistently present in human remains, are often missing, reducing biological fidelity. Here, we integrate analytical chemistry with canine olfactory genetics and molecular biology to explain these limitations. Dogs possess one of the largest olfactory receptor (OR) repertoires among mammals, with high allelic diversity and specialized trace amine-associated receptors (TAARs) tuned to cadaveric amines. Together with olfactory binding proteins (OBPs) and ciliary signal transduction cascades, these molecular mechanisms highlight why incomplete VOC mixtures may fail to activate the full receptor network required for reliable odor imprinting. We propose the “sulfur gap hypothesis” and suggest hybrid training strategies combining improved synthetics with ethically sourced biological samples to enhance HRD dog performance. Full article

This study reports the development of a fiber-optic localized surface plasmon resonance (FO-LSPR) sensor incorporating a three-dimensional micropillar array functionalized with gold nanoparticles. The micropillar structures were fabricated on the fiber facet using a single-mask imprint lithography process, followed by nanoparticle immobilization to create a composite plasmonic surface. Compared with flat polymer-coated fibers, the micropillar array markedly increased the effective sensing surface and enhanced light trapping by providing anti-reflective conditions at the interface. Consequently, the sensor demonstrated superior performance in refractive index sensing, yielding a sensitivity of 4.54 with an R² of 0.984, in contrast to 3.13 and 0.979 obtained for the flat counterpart. To validate its biosensing applicability, Interleukin-8 (IL-8), a cancer-associated cytokine, was selected as a model analyte. Direct immunoassays revealed quantitative detection across a broad dynamic range (0.1–1000 pg/mL) with a limit of detection of 0.013 pg/mL, while specificity was confirmed against non-target proteins. The proposed FO-LSPR platform thus offers a cost-effective and reproducible route to overcome the surface-area limitations of conventional designs, providing enhanced sensitivity and stability. These results highlight the potential of the micropillar-based FO-LSPR sensor for practical deployment in point-of-care diagnostics and real-time biomolecular monitoring. Full article

Alzheimer’s disease (AD) requires early and accurate identification of affected brain regions, which can be achieved through the detection of specific biomarkers to enable timely intervention. Carbon nanomaterials (CNMs), including graphene derivatives, carbon nanotubes, graphitic carbon nitride, carbon black, fullerenes, and carbon dots, offer high conductivity, large electroactive surface area, and versatile surface chemistry that enhance biosensor performance. While such properties benefit a wide range of transduction principles (e.g., electrochemical, optical, and plasmonic), this review focuses on their role in electrochemical biosensors. This review summarizes CNM-based electrochemical platforms reported from 2020 to mid-2025, employing aptamers, antibodies, and molecularly imprinted polymers for AD biomarker detection. Covered topics include fabrication strategies, transduction formats, analytical performance in complex matrices, and validation. Reported devices achieve limits of detection from the femtomolar to picogram per milliliter range, with linear ranges typically spanning 2–3 orders of magnitude (e.g., from femtomolar to picomolar, or from picogram to nanogram per milliliter levels). They exhibit high selectivity against common interferents such as BSA, glucose, uric acid, ascorbic acid, dopamine, and non-target peptides, along with growing capabilities for multiplexing and portable operation. Remaining challenges include complex fabrication, limited long-term stability and reproducibility data, scarce clinical cohort testing, and sustainability issues. Opportunities for scalable production and integration into point-of-care workflows are outlined. Full article

Molecularly imprinted polymer (MIP) biosensors offer an attractive strategy for selective biomolecule detection, yet imprinting proteins with structural fidelity remains a major challenge. In this work, we present a rationally designed electrochemical biosensor for matrix metal-loproteinase-8 (MMP-8), a key salivary biomarker of periodontal disease. By integrating graphene oxide (GO) with electropolymerized poly(eriochrome black T, EBT) films on screen-printed carbon electrodes, the partially reduced GO interface enhanced electrical conductivity and facilitated the formation of well-defined poly(EBT) films with re-designed polymerization route, while template extraction generated artificial antibody-like sites capable of specific protein binding. The MIP-based electrodes were comprehensively validated through morphological, spectroscopic, and electrochemical analyses, demonstrating stable and selective recognition of MMP-8 against structurally similar interferents. Complementary density functional theory (DFT) modeling revealed energetically favorable interactions between the EBT monomer and catalytic residues of MMP-8, providing molecular-level insights into imprinting specificity. These experimental and computational findings highlight the importance of rational monomer selection and nanomaterial-assisted polymerization in achieving selective protein imprinting. This work presents a systematic approach that integrates electrochemical engineering, nanomaterial interfaces, and computational validation to address long-standing challenges in protein-based MIP biosensors. By bridging molecular design with practical sensing performance, this study advances the translational potential of MIP-based electrochemical biosensors for point-of-care applications. Full article

The methylation of CpG sites with 5mC mark is a dynamic epigenetic modification. However, the relationship between the methylation and the surrounding genomic sequence context remains poorly explored. Investigation of the allele methylation provides an opportunity to decipher the interplay between differences in the primary DNA sequence and epigenetic variation. Here, we performed high-coverage long-read whole-genome direct DNA sequencing of one individual using Oxford Nanopore technology. We also used Illumina whole-genome sequencing of the parental genomes in order to identify allele-specific methylation sites with a trio-binning approach. We have compared the results of the haplotype-specific methylation detection and revealed that trio binning outperformed other approaches that do not take into account parental information. Also, we analysed the cis-regulatory effects of the genomic variations for influence on CpG methylation. To this end, we have used available Deep Learning models trained on the primary DNA sequence to score the cis-regulatory potential of the genomic loci. We evaluated the functional role of the allele-specific epigenetic changes with respect to gene expression using long-read Nanopore RNA sequencing. Our analysis revealed that the frequency of SNVs near allele-specific methylation positions is approximately four times higher compared to the biallelic methylation positions. In addition, we identified that allele-specific methylation sites are more conserved and enriched at the chromatin states corresponding to bivalent promoters and enhancers. Together, these findings suggest that significant impact on methylation can be encoded in the DNA sequence context. In order to elucidate the effect of the SNVs around sites of allele-specific methylation, we applied the Deep Learning model for detection of the cis-regulatory modules and estimated the impact that a genomic variant brings with respect to changes to the regulatory activity of a DNA loci. We revealed higher cis-regulatory impact variants near differentially methylated sites that we further coupled with transcriptomic long-read sequencing results. Our investigation also highlights technical aspects of allele methylation analysis and the impact of sequencing coverage on the accuracy of genomic phasing. In particular, increasing coverage above 30X does not lead to a significant improvement in allele-specific methylation discovery, and only the addition of trio binning information significantly improves phasing. We investigated genomic variation in a single human individual and coupled computational discovery of cis-regulatory modules with allele-specific methylation (ASM) profiling. In this proof-of-concept analysis, we observed that SNPs located near methylated CpG sites on the same haplotype were enriched for sequence features suggestive of high-impact regulatory potential. This finding—derived from one deeply sequenced genome—illustrates how phased genetic and epigenetic data analyses can jointly put forward a hypotheses about the involvement of regulatory protein machinery in shaping allele-specific epigenetic states. Our investigation provides a methodological framework and candidate loci for future studies of genomic imprinting and cis-mediated epigenetic regulation in humans. Full article

Long noncoding RNAs (lncRNAs) have emerged as key regulators of gene expression during seed development and physiology. This review examines the diverse roles of lncRNAs in key stages of seed development, including embryogenesis, maturation, dormancy, germination, and aging. It integrates the current understanding of the biogenesis and classification of lncRNAs, emphasizing their functional mechanisms in seeds, particularly those acting in cis and trans. These mechanisms include the scaffolding of polycomb and SWI/SNF chromatin remodeling complexes, the guidance of RNA-directed DNA methylation, the ability to function as molecular decoys, and the modulation of small RNA pathways via competitive endogenous RNA activity. This review highlights the regulatory influence of lncRNAs on abscisic acid (ABA) and gibberellin (GA) signaling pathways, as well as light-responsive circuits that control dormancy and embryonic root formation. Endosperm imprinting processes that link parental origin to seed size and storage are also discussed. Emerging evidence for epitranscriptomic modifications, such as m6A methylation, and the formation of LncRNA–RNA-binding protein condensates that maintain resting states and coordinate reserve biosynthesis are also reviewed. Advances in methodologies, including single-cell and spatial transcriptomics, nascent transcription, direct RNA sequencing, and RNA–chromatin interaction mapping, are expanding the comprehensive lncRNA landscape during seed development and germination. These advances facilitate functional annotation. Finally, possible translational research applications are explored, with a focus on developing lncRNA-based biomarkers for seed vigor and longevity. Full article

Background/Objectives: This study investigated variations in DNA methylation patterns associated with chronic pain and propensity for recurrent pressure injuries (PrI) in persons with spinal cord injury (SCI). Methods: Whole blood was collected from 81 individuals with SCI. DNA methylation was quantified using Illumina genome-wide arrays (EPIC and EPICv2). Comprehensive clinical profiles collected included secondary health complications, in particular current PrI and chronic pain. Relationships between recurrent PrI and chronic pain and whether the co-occurrence of both traits was mediated by changes in DNA methylation were investigated using R packages limma, DMRcate and mCSEA. Results: Three differentially methylated positions (DMPs) (cg09867095, cg26559694, cg24890286) and one region in the micro-imprinted locus for BLCAP/NNAT are associated with chronic pain in persons with SCI. The study cohort was stratified by PrI status to identify any sites associated with chronic pain and while the same three sites and region were replicated in the group with no recurrent PrI, two novel, hypermethylated (cg21756558, cg26217441) sites and one region in the protein-coding gene FDFT1 were identified in the group with recurrent PrI. Gene enrichment and genes associated with specific promoters using MetaScape identified several shared disorders and ontology terms between independent phenotypes of pain and recurrent PrI and interactive sub-groups. Conclusions: DMR analysis using mCSEA identified several shared genes, promoter-associated regions and CGI associated with overall pain and PrI history, as well as sub-groups based on recurrent PrI history. These findings suggest that a much larger gene regulatory network is associated with each phenotype. These findings require further validation. Full article

Background/Objectives: The 3-dimensional (3D) architecture of the genome in the nucleus of a living cell plays an unexpected yet fundamental regulatory role in cell biology. As an imprint of the cellular genetic, epigenetic and metabolic status, it discriminates pathological conditions through conditional changes to long-range 3D interactions (up to 300 kb) and thus could act as a powerful molecular biomarker linked closely to clinical outcomes. Methods: Here an assessment is made of the latest paradigm shift in molecular biology from a supply chain where information flows from DNA to RNA to protein, to the concept of heritable 3D folding of the genome reflecting the epigenetic and metabolic state of the cell, and which serves as a molecular biomarker for complex clinical outcome. Results: While biomarkers based on individual components of the supply chain fail to accurately reflect clinical outcomes, 3D genomics offers highly informative insights, exemplified for immuno-oncology and prostate cancer diagnosis by clinical tests of superior performance, already in practice in the US and UK. Conclusions: A more complete understanding of human biology will require models that account for the flow of information to and from the 3D genomic architecture in living cells, together with its regulation and logic. Integrating these principles into biomarker discovery and therapeutic design, along with other frontline approaches in precision medicine, including multi-omics and other system-level tools, will be essential for advancing precision medicine beyond its current limitations. Full article

Background: Uniparental disomy (UPD) refers to the condition in which both chromosomes (or part of chromosome) of a pair are inherited from the same parent. There are two types of UPD: uniparental isodisomy (both chromosomes inherited from one parent are identical copies) and uniparental heterodisomy (two different chromosomes are inherited from one parent). UPD presents two primary developmental risks: recessive trait inheritance or an imprinting disorder. These risks may coexist, leading to an ultra-rare comorbidity. Managing the comorbidities associated with rare diseases presents unique clinical challenges. Results: The existence of such phenomena is evidenced by our case report of a boy who was ultimately diagnosed with two rare diseases: Prader–Willi syndrome (PWS), due to the maternal uniparental disomy of chromosome 15 (UPD), and autosomal recessive Lodder–Merla type 1 syndrome, linked to a novel pathogenic variant in the G protein subunit β 5 (GNB5) gene, as detailed in this paper. Conclusions: An unusual or severe phenotype in a patient diagnosed with PWS should invariably prompt the consideration of a comorbid genetic disease attributable to genes located in the PWS critical region of chromosome 15q, or elsewhere on chromosome 15. In cases of epileptic encephalopathy with cardiac arrhythmia, prompt consultation with a cardiologist and comprehensive genetic testing are essential to reduce the risks associated with untreated arrhythmia and ensure the provision of appropriate and safe anti-epileptic therapy. The presented case provides further support for the hypothesis that uniparental disomy may serve as an underlying cause of Lodder–Merla syndrome. This underscores the significance of comprehensive genetic testing, encompassing parental testing and familial cascade testing (in selected cases where there is consanguinity, or the likelihood of close common ancestral background between partners) to establish the recurrence risk. Full article

Surface-imprinted polymers (SIPs) represent an exciting and cost-effective alternative to antibodies for electrochemical impedance spectroscopy (EIS)-based biosensing. They can be produced using simple printing techniques and have shown high efficacy in detecting large biomolecules and microorganisms. Stamp imprinting, a novel SIP method, creates the target analyte’s imprint using a soft lithography mask of the analyte matrix, thereby reducing material complexities and eliminating the need for cross-linking, which makes the process more scalable than the conventional SIPs. In this work, we demonstrate a stamp-imprinted EIS biosensor using a biocompatible polymer, polycaprolactone (PCL), for quantifying amyloid beta-42 (Aβ-42), a small peptide involved in the pathophysiology of Alzheimer’s disease. The evaluated SIP-EIS biosensors showed a detection limit close to 10 fg/mL, and a detection range covering the physiologically relevant concentration range of the analyte in blood serum (from 10 fg/mL to 10 μg/mL). The device sensitivity, which is found to be comparable to antibody-based EIS devices, demonstrates the potential of SIP-EIS biosensors as an exciting alternative to conventional antibody-based diagnostic approaches. We also evaluate the viability of analyzing these proteins in complex media, notably in the presence of serum albumin proteins, which cause biofouling and non-specific interactions. The combination of high sensitivity, selectivity, and ease of fabrication makes SIP-EIS biosensors particularly suited for portable and point-of-care applications. Full article

The ubiquitin-protein ligase E3A (UBE3A, aka E6-AP), an E3 ligase belonging to the HECT family, plays crucial roles in the stability of various proteins through the proteasomal degradation system. Abnormal UBE3A activity is essential for the initiation and progression of several cancers. A gain of function and an overdosage of maternal UBE3A is associated with an increased risk of autism spectrum disorders. Conversely, a loss of function due to mutations, deletions, paternal duplications, or imprinting defects in neurons leads to Angelman syndrome. Emerging evidence suggests that abnormal UBE3A activity may also contribute to the development of various brain disorders, including schizophrenia, Huntington’s disease, Parkinson’s disease, and Alzheimer’s disease, making UBE3A a protein of significant interest. However, research on UBE3A’s functions in the brain has primarily focused on neurons due to the imprinting of UBE3A in mature neuronal cells, while being obscured in glia. This review outlines the expression of UBE3A in neurons and glial cells based on published studies, highlights newly identified patterns of UBE3A, such as its secretion, and emphasizes the involvement of UBE3A in neurodegenerative diseases. Furthermore, we summarize glial UBE3A and propose a model of bi-directional interactions between the neurons and glia mediated by UBE3A that underlies brain functions. Insights gained from this research could provide new avenues for therapeutic interventions targeting various brain disorders. Full article

Anadromous migration toward riverine tributaries is often challenged by altered environmental cues, food scarcity, and energy demands, sometimes at the expense of life itself. Tenualosa ilisha (Clupeiformes: Dorosomatidae), the national fish of Bangladesh, an anadromous shad, offers a model for understanding the molecular mechanisms of migration. To this end, we present a chromosome-level genome of T. ilisha and compare its transcriptomic imprints from muscle and liver across environments to trace the physiological shifts driving the migration. We observed rapid expansion of gene families to facilitate efficient signaling and osmotic balance, as well as a substantial selection pressure in metabolism regulatory genes, potentially relevant to a highly anadromous fish. We detected 1298 and 252 differentially expressed transcripts between sea and freshwater in the liver and muscle of T. ilisha, respectively, reflecting habitat and organ-specific adaptations. Co-expression analysis led us to hypothesize that the strength required for breeding migration toward upstream rivers is fueled by muscle protein catabolism forming ubiquitin-proteasomal complexes. In the liver, we observed a group of genes promoting fatty acid (FA) synthesis significantly in the riverine habitat. Regulation of FADS2 and ELOVL2 in the river reasoned the natural abundance of LC-PUFAs with better energy utilization in T. ilisha. Moreover, active gluconeogenesis and reduced insulin signaling in the liver are possibly linked to glucose homeostasis, potentially induced by prolonged starvation during migration. These genomic resources will accelerate the future evolutionary and functional genomics studies of T. ilisha. Full article

Depression and anxiety are two common mental health issues that require serious attention, as they have significant impacts on human well-being, with both being emotionally and physically reflected in the increasing number of suicide cases globally. The World Health Organization (WHO) estimated that about 322 million people around the world experienced mental illnesses in 2017, and this number continues to increase. Cortisol is a major stress-controlled hormone that is regulated by the hypothalamic–pituitary–adrenal (HPA) axis. The HPA axis has three main components, including the hypothalamus, pituitary gland, and adrenal gland, where cortisol, the primary stress hormone, is released. It plays crucial roles in responding to stress, energy balance, and the immune system. The cortisol level in the bloodstream usually increases when stress develops. Molecularly imprinted polymers (MIPs) have been highlighted in terms of creating artificial bioreceptors by mimicking the shape of detected biomolecules, making natural bioreceptor molecules no longer required. MIPs can overcome the limitations of chemicals and physical properties reducing over time and the short-time shelf life of natural bioreceptors. MIPs’ benefits are reflected in their ease of use, high sensitivity, high specificity, reusability, durability, and the lack of requirement for complicated sample preparation before use. Moreover, MIPs incur low costs in manufacturing, giving them a favorable budget for the market with simple utilization. MIPs can be formulated by only three key steps, including formation, the polymerization of functional monomers, and the creation of three-dimensional cavities mimicking the shape and size of targeting molecules. MIPs have a high potential as biosensors, especially working as bioanalytics for protein, anti-body, antigen, or bacteria detection. Herein, this research proposes an MIP-based cortisol biosensor in which cortisol is imprinted on methyl methacrylate (MMA) and methacrylic acid (MAA) produced by UV polymerization. This MIP-based biosensor may be an alternative method with which to detect and monitor the levels of hormones in biological samples such as serum, saliva, or urine due to its rapid detection ability, which would be of benefit for diagnosing depression and anxiety and prescribing treatment. In this study, quantitative detection was performed using an electrochemical technique to measure the changes in electrical signals in different concentrations of a cortisol solution ranging from 0.1 to 1000 pg/mL. The MIP-based biosensor, as derived by calculation, achieved its best detection limit of 1.035 pg/mL with a gold electrode. Tests were also performed on molecules with a similar molecular structure, including Medroxyprogesterone acetate and drospirenone, to ensure the sensitivity and accuracy of the sensors, demonstrating a low sensitivity and low linear response. Full article