The rapid escalation of global plastic consumption, coupled with the environmental impacts of petrochemical polymers, has sparked a surge of interest in bioplastics, particularly those derived from microbial and enzymatic processes. This review provides a comprehensive overview of the metabolic pathways, structural properties and emerging technological innovations shaping the next generation of bioplastics, with a particular focus on polyhydroxyalkanoates (PHA). The following sections outline the conceptual distinctions between bio-based and biodegradable plastics, the key bacterial pathways responsible for the biosynthesis of PHA, PLA precursors, bacterial cellulose, microbial polyamides and other bio-derived polymers. The physicochemical and morphological features of PHA-based materials are analysed as well. These features include monomer composition, crystallinity, copolymer architecture and molecular weight. The relationship between these features and the mechanical and thermal performance of the materials is then investigated. A dedicated section is allocated to recent advances in in vitro enzymatic PHA synthesis, covering PHA synthase (PhaC) classes, engineered variants, cell-free metabolic engineering platforms, enzyme immobilisation and surface-display strategies that enable fully programmable and modular polymerisation. Finally, we discuss future perspectives, with particular emphasis on sustainable feedstocks, process intensification through synthetic biology, techno-economic challenges and the regulatory landscape required for large-scale adoption. The present review integrates biochemical, structural and bioprocessing insights to map current progress and identify strategic directions for enabling enzymatic bioplastics as scalable, customisable and environmentally sound alternatives within a circular bioeconomy framework. Impact statement This review highlights recent advances in microbial and enzymatic routes for producing polyhydroxyalkanoate-based bioplastics, with emphasis on engineered enzymes and cell-free systems. By integrating biochemical and bioprocess insights, it outlines strategies to enable scalable and sustainable biopolymer production within a circular bioeconomy.
Plastic pollution from fossil fuel-derived materials has become a pressing environmental and public health issue, driving urgent demand for sustainable alternatives. Conventional plastics can take centuries to degrade and, instead of breaking down completely, fragment into micro- and nanoplastics that are now found in oceans, rivers, soil and atmosphere. These particles have been detected in drinking water, food and animal tissues, raising serious concerns about their impact on human health and ecosystems. Millions of tons of plastic enter the oceans each year, forming massive debris patches that accumulate along coastlines. Many organisms mistakenly ingest or become entangled in plastic, causing injury, starvation and often death. Birds, turtles, fish and marine mammals are among the most affected. On land, plastic waste clogs waterways, pollutes landscapes and overwhelms waste management systems, especially in regions lacking adequate recycling infrastructure. The development of bioplastics-materials derived from renewable sources and designed to biodegrade naturally-represents a promising path forward. Bioplastics aim to reduce dependence on fossil resources, minimize environmental persistence and offer tailored properties for specific applications. Transitioning to bio-based alternatives is not only a scientific and technological challenge but also a crucial step towards safeguarding environmental health and ensuring a more sustainable future. In this context, this 'In the Limelight' issue of FEBS Open Bio presents five review articles focusing on the production, characterization and biodegradation of novel bioplastics from diverse renewable sources. Together, the results may contribute to reduced plastic pollution, offering a more sustainable and conscious approach to material design.
Innovative pedagogies and support systems are critical for engaging diverse students in biochemistry and molecular biology education. This qualitative study explored biomedical science students' experiences of teaching, learning and support at a UK post-92 university through surveys and focus groups (n = 15). Reflexive thematic analysis revealed three themes. Students' motivations were shaped by scientific curiosity and career aspirations in bioscience. Barriers to progression included financial strain, pandemic-related disruption to laboratory access and cultural exclusion. Support and belonging were mediated through peer networks, while institutional support was inconsistently accessed and curriculum gaps limited experiential skill development in practical laboratory work. The findings underscore the need for pedagogies that blend active, experiential learning with codesigned curricula and integrated support. Such innovations are crucial for creating inclusive bioscience learning environments, improving retention and addressing structural inequalities in science education. These insights provide actionable guidance for biochemistry and molecular biology educators seeking to enhance student engagement and success.
UiO-66-type zirconium metal-organic frameworks (MOFs) have emerged as robust and highly tunable nanoplatforms for biomedical applications owing to their permanent porosity, exceptional chemical stability, and versatile functionalization pathways. Here, we summarize recent advances in engineering UiO-66-based nanoparticles for drug delivery, multimodal bioimaging, photodiagnostics, and photodynamic therapy (PDT). Precise control over composition, surface chemistry, and postsynthetic modifications allow for high drug loading, stimuli-responsive release, and improved colloidal stability in biological environments. Strategies for active targeting using antibodies, peptides, aptamers, and small-molecule ligands significantly enhance tumor specificity. Furthermore, UiO-66 is increasingly used as a carrier for photosensitizers, contrast agents, and imaging probes, supporting multimodal fluorescence, CT, MRI, and photoacoustic imaging. The framework's ability to coordinate photosensitizers and modulate oxygen availability provides powerful opportunities for PDT, especially in hypoxic tumors. However, key challenges remain, including long-term biocompatibility, clearance, and scalable synthesis. Future prospects include programmable degradation, advanced surface architectures, biomimetic coatings, and multimodal phototheranostic platforms.
The SNARE proteins syntaxin-1, synaptobrevin, and SNAP-25 mediate neurotransmitter release by forming SNARE complexes that fuse synaptic vesicles with the plasma membrane. SNARE complex assembly is orchestrated by Munc18-1 and Munc13-1 through a highly regulated pathway that starts with syntaxin-1 folded into a closed conformation and bound to Munc18-1. It is well-established that Munc13-1 opens syntaxin-1, likely acting catalytically, and that this step is crucial for neurotransmitter release. However, the underlying molecular mechanism remains unknown because it is difficult to obtain structural information on Munc13-1-syntaxin-1 interactions experimentally. Initial attempts with AlphaFold using the syntaxin-1 cytoplasmic region yielded structures of Munc13-1-syntaxin-1 complexes but syntaxin-1 remained closed. Interestingly, when using a shorter syntaxin-1 fragment designed to destabilize the closed conformation, AlphaFold generated a model of Munc13-1 bound to an open syntaxin-1 conformation that explains abundant experimental data and suggests an attractive hypothesis of how Munc13-1 opens syntaxin-1. These results indicate that a judicious selection of protein fragments can help AlphaFold to predict structures of kinetic intermediates in complex biomolecular processes.
In preparation for a university-wide Curriculum Transformation project across the University of Bath, a survey of student opinions of the skills training they received, required and developed during their bioscience studies was undertaken. Separate focus group discussions with first and final-year students defined the parameters of initial and follow-up questionnaires used to determine perceived confidence in 16 different transferrable skills. With responses to the first questionnaire from 204 students (23% of the cohort) the sample size was sufficient to perform statistical analysis on the results. The responses to both questionnaires showed, that by the end of their course the students valued having improved their academic/transferrable skills more than their practical laboratory skills. The survey data and focus group discussions revealed that teamwork, study, time management and organisational skills were perceived to be well developed before arrival at university. While some skills were recognised as having improved through formal teaching (Academic and scientific writing, research, laboratory, analytical and presentation skills), other more transferrable skills were thought to have improved as they are inherent to successful independent living at university and on placement. Actionable suggestions were made for enhancements to formal teaching of important transferrable skills that are not addressed in the current provision such as leadership (through role rotation in group work), resilience and problem-solving (e.g. in practical classes requiring adjustment to succeed). This work suggests that many important transferrable skills are acquired inherently, allowing formal skills training to focus on communication, laboratory, research, leadership, resilience and problem-solving.
FcγRI is a high-affinity receptor for IgG, associated with autoimmune disease pathology and determines clinical responses to antibody-based immunotherapies. FcγRI has a complex evolutionary history that is not fully understood, and to address this we explored signatures of positive selection in the receptor's functional gene, FCGR1A, using codon-based selection tests on aligned 1-1 orthologous sequences from placental mammals (n = 32). Signatures of positive selection have occurred at several locations within the gene, with two sites (H148 (M2a ω 0.997 & M8 ω = 0.993)) and (W149 (M2a ω = 0.999 & M8 ω = 1.000)) exhibiting highest posterior probabilities, suggesting strong evidence of positive selection; these positions are known to form one of the FcγRI-IgG binding interfaces. We employed ancestral reconstruction to statistically infer prior codon sequences at these sites and identified ancestral H148P and W149R codons at different nodes in the phylogeny. Employing molecular dynamics simulations, we determined how evolutionary changes at these sites may have influenced the binding of FcγRI-IgG of modern-day Homo sapiens. Measuring RMSD, free energy, radius of gyration, hydrogen bond formation, and analyzing free energy landscapes, we demonstrate that structural instability between mutant structures vs the WT counterpart; however, overall binding potential increases at position 148, yet decreases at 149 in potential. H148P protonation at physiological pH remains similar, yet during acidotic calculations, protonation is likely reduced, with predicted reduction in affinity for IgG. While ancestral W149R substitutions demonstrate an implication for electron conjugation. Examining key sites at this binding FcγRI-IgG interface, our data demonstrate that these two codons have evolved in humans to be relatively insensitive to shifts in pH promoting a more stable interaction with the Fc portion of IgG during diseases that promote acidosis.
Clinical risk stratification for postoperative recurrence in patients with pathological stage II (pStage II) colorectal cancer (CRC) is essential for guiding the use of postoperative adjuvant chemotherapy (ACT). In this study, we identified novel prognostic gene expression biomarkers in patients with pStage II CRC and developed a new risk stratification framework for ACT decision-making. First, genome-wide biomarker discovery was conducted to identify prognostic gene expression biomarkers associated with recurrence risk in pStage II CRC. This analysis identified 10 differentially expressed genes as potential biomarkers for recurrence. The efficacy of these biomarkers was then tested using 188 clinical surgical specimens obtained from patients with pStage II CRC. A predictive panel was developed using qRT-PCR and used to assess 93 clinical specimens with an area under the curve (AUC) of 0.82, and its performance was further validated in an independent cohort (n = 95). By incorporating key clinicopathological features, a Gene expression-based Prediction of Recurrence in pStage II CRC (GPRSC) signature was developed, which robustly predicted postoperative recurrence (AUC: 0.80). Finally, combining the GPRSC signature, microsatellite instability status, and conventional criteria, we developed a novel risk stratification system for postoperative ACT decision-making in pStage II CRC. Overall, we identified novel gene expression biomarkers and developed a prognostic signature that informs clinical decision-making regarding postoperative ACT in patients with pStage II CRC.
J. Chen, C. Chen, Y. Lin, Y. Su, X. Yu, Y. Jiang, Z. Chen, SY. Ke, SZ. Lin, L. Chen, Z. Zhang, and T. Zhang, "Downregulation of SUMO2 inhibits hepatocellular carcinoma cell proliferation, migration and invasion," FEBS Open Bio 11, no. 6 (2021): 1771-1784. https://doi.org/10.1002/2211-5463.13173. The above article, published online on 14 May 2021 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editor-in-Chief, Miguel De la Rosa; the Federation of European Biochemical Societies; and John Wiley & Sons Ltd. A third party reported that images in the Bel-7404 cell migration assay in Figure 5A contained overlapping duplicated sections and that the SMMC-7721 cell invasion assay in Figure 5C also contained overlapping duplicated sections. Further investigation by the editors and the publisher found additional overlapping duplicated sections in the SMMC-7721 cell migration assay images in Figure 5A and potential duplication of a portion of the GAPDH band between the Bel-7404 image in Figure 4B and Bel-7404 image in Figure 5F. The authors responded to an inquiry by the publisher. However, the editors found that the explanation and raw data provided by the authors did not adequately address the concerns. The evidence of image overlap and duplication in several figures has compromised the editor's confidence in the conclusions presented in the manuscript. As a result, the Editor-in-Chief, FEBS Press, and John Wiley and Sons Ltd. have determined that a retraction is necessary. The authors were informed about the retraction.
High-fat diet (HFD) exposure is a recognized risk factor for tendinopathy and impaired tendon healing in adults, yet its effects on baseline tendon properties following early-life exposure remain poorly understood. In this study, we investigated the structural, biomechanical, and transcriptomic characteristics of Achilles tendons in 12-week-old rat offspring born to dams fed an HFD or a normal diet during gestation. Compared with controls, HFD-exposed tendons exhibited a significant reduction in anteroposterior diameter on sagittal ultrasound imaging. However, histological assessment revealed comparable cellular density and collagen fiber organization between groups. Biomechanically, HFD exposure was associated with a significant increase in tendon stiffness, while the maximum tensile load was not significantly altered. Transcriptomic profiling identified 980 differentially expressed genes, including a marked downregulation of key tenogenic markers such as Scx and Eya2, along with an enrichment of pathways related to extracellular matrix remodeling and inflammation. Gene set enrichment further revealed an upregulation of inflammatory response, adipogenesis, and osteoblast differentiation signatures. Together, these findings demonstrate that early-life HFD exposure induces biomechanical and molecular alterations in intact Achilles tendons, suggesting compromised tendon quality that may increase susceptibility to mechanical overload and injury later in life.
Cellular senescence, a state of stable cell-cycle arrest accompanied by profound metabolic and secretory changes, has emerged as a central hallmark of aging and a key contributor to age-associated diseases. Despite the great progress in understanding the characteristics, the underlying molecular mechanisms, and the role of senescent cells in several pathologies, many crucial issues remain unresolved. In this 'In the Limelight' special issue of FEBS Open Bio, three review articles deal with the accurate detection of senescent cells in vivo, changes in intercompartmental communication in senescent cells, and the role of lipid metabolism in neuronal senescence.
The effects of time-restricted feeding (TRF) on immune responses during bacterial infection are not well-studied. Here, we subjected mice (6-8 weeks, male) to 8 h of TRF for 30 days and then infected them with a low dose of Mycobacterium tuberculosis (Mtb) H37Rv. During the first 15 days, TRF improved glucose tolerance with marginal weight loss. However, global serum and liver metabolomics alongside liver proteomics indicated that TRF perturbed fatty acid biosynthesis and degradation, steroid hormone biosynthesis, and tyrosine metabolism. Together, these results indicate that TRF potentially affected the distribution and functionality of host immune cells. TRF mice had similar mycobacterial burdens in lungs and spleen at 21 days postinfection but had significantly lower CD3+ T cells in bone marrow and CD4+ T cells in both bone marrow and lungs. Ultimately, we show that TRF induced changes in amino acid and lipid metabolism persist during Mtb infection.
Directed evolution has become a central methodology for engineering proteins with improved or entirely new functions, enabling applications across biotechnology, medicine, and synthetic chemistry. By iteratively coupling genetic diversification with screening or selection, directed evolution allows functional optimization even when detailed structural or mechanistic knowledge is unavailable. While display-based selection platforms have enabled the efficient evolution of binders from extremely large libraries, enzyme evolution relies primarily on quantitative screening strategies that preserve genotype-phenotype linkage, often through compartmentalization. This review focuses primarily on enzyme directed evolution, using binder evolution as a comparative reference point to highlight key methodological differences and parallel advances. Major technological advances-including in vitro emulsions, droplet microfluidics, ultrahigh-throughput sorting, genetically encoded biosensors, and alternative detection modalities-have dramatically expanded screening capacity and analytical resolution. We also discuss why stability remains a central constraint on evolvability, why assay design continues to limit translational relevance, and how failures such as surrogate-substrate bias, droplet leakage, tracking errors, and overfitted machine-learning models can misdirect campaigns. By integrating classical strategies with emerging continuous and data-driven approaches, enzyme directed evolution is moving toward more predictive, automated, and industrially translatable workflows.
Postdoctoral supervision and research leadership are crucial yet underexamined dimensions of academic work. In this perspectives piece, we reflect on mentorship across Singapore and France and situate it within output-driven research ecosystems that risk reducing groups to production units. Using a narrative and workshop-based approach, including a mentorship workshop at the FEBS-IUBMB ENABLE 2024 conference in Singapore, we explore how mentees define good mentorship. Participants consistently prioritised everyday human interactions over traditional metrics, highlighting empathy, trust, humility, availability, and clear communication. Integrating these insights with educational literature, we illustrate that humane, ethically grounded mentorship is essential for research integrity, well-being and sustainable scientific capacity.
In vitro liver models combined with metabolomics approaches offer promising alternatives to animal testing in toxicology. In this study, we investigated concentration-dependent effects of hydrogen peroxide (H2O2) on the intra- and extracellular metabolome of HepG2 cells using 1H Nuclear Magnetic Resonance (NMR) spectroscopy. After cells were exposed to low, medium or high concentrations of H2O2, metabolomic analysis revealed a progressive increase in metabolic perturbation with rising toxin concentration. Significant alterations were detected in a limited subset of metabolites after low H2O2 exposure, and substantially broader disruptions occurred after medium or high H2O2 exposure, with most measured metabolites affected at the highest exposure level. To enhance metabolic competence, cells were pretreated with rifampicin to induce cytochrome P450 (CYP450) activity, which is typically low in HepG2 cells. Comparative analysis of rifampicin-pretreated and untreated cells exposed to high H2O2 concentrations demonstrated disruption of multiple biochemical pathways, including energy metabolism, lipid metabolism and amino acid metabolism. Notably, rifampicin pretreatment attenuated the magnitude of metabolic perturbations, as reflected by reduced intracellular alterations and minimal changes in extracellular metabolite profiles. Furthermore, rifampicin-treated cells exhibited metabolite signatures more consistent with human liver physiology in vivo, including increased glutathione and 2-hydroxybutyrate levels. Collectively, these findings demonstrate that pretreatment with rifampicin prior to toxin exposure enhances the physiological relevance of HepG2-based hepatotoxicity models and improves their potential to predict human liver responses. Moreover, the results highlight the sensitivity of NMR-based metabolomics to detect toxin induced metabolic changes across a range of exposure concentrations.
Chemokines and their cognate receptors are central orchestrators of the immune response to Mycobacterium tuberculosis (Mtb) infection. While their overall significance in tuberculosis (TB) is well-established, this review synthesizes recent advances to clarify the distinct roles of CC and CXC chemokines in differentiating active disease, latent infection, and the often overlooked subclinical TB state. We evaluate the potential of specific chemokine signatures as emerging diagnostic biomarkers compared to conventional standards and assess their promise as novel therapeutic targets in personalized clinical settings. Furthermore, we examine paradoxical findings in the field, including how certain chemokines (such as CCL5, CXCL12, and CXCL16) can simultaneously support host defense and facilitate pathogen evasion. By integrating these complex narratives, we offer a renewed perspective on chemokine dynamics in TB immunity, bridge important gaps between bench research and clinical application, and establish a strong foundation for developing precision diagnostics and host-directed therapies.
Nicotinamidases (PncA) catalyze the hydrolysis of nicotinamide to nicotinic acid, a key step in NAD+ salvage pathways. In the Lyme disease spirochete Borrelia burgdorferi, the plasmid-encoded gene bbe22 encodes a PncA enzyme that is essential for survival in both mammalian and tick hosts. Previous genetic and biochemical studies demonstrated that translation of B. burgdorferi PncA initiates from a rare non-canonical AUU start codon, resulting in a protein that is 24 residues longer than the sequence currently annotated in major databases. Despite these findings, public resources such as UniProt and KEGG still list a truncated protein beginning at residue 36, which lacks part of the N-terminal region required for enzymatic activity. Here we report the crystal structure of full-length B. burgdorferi PncA determined at 3.2 Å resolution. The structure reveals the canonical fold of bacterial nicotinamidases and clear electron density for a ligand in the active site consistent with nicotinic acid, the product of the enzymatic reaction. Structural comparison with homologous PncA enzymes demonstrates conservation of the catalytic architecture, including residues involved in substrate binding and catalysis. Importantly, the experimentally determined structure confirms that the longer N-terminal sequence described previously is required for formation of the correct fold and active-site geometry, whereas the truncated annotation is structurally inconsistent with the observed fold and with AlphaFold predictions. Our results provide the first structural characterization of B. burgdorferi PncA and resolve the long-standing annotation discrepancy for bbe22, validating the correct protein sequence and providing the structural basis for nicotinamidase activity in this essential metabolic enzyme.
Immune-related/mediated disorders (IDs) comprise a very diverse group of diseases affecting millions worldwide. The complexity and heterogeneity of IDs, coupled with individual variability in immune system responses, create multiple challenges for developing targeted therapies. These challenges often result in prolonged diagnostic timelines, higher treatment costs, and frequent failures in clinical trials. Recent advances in artificial intelligence (AI) and digital twin (DT) technology offer promising solutions to support and accelerate drug discovery and development for these conditions, with anticipated substantial improvement in success rates. As virtual replicas of biological systems, DTs can be constructed using multimodal data sources, including multi-omics, molecular profiling, imaging and clinical records. These in silico tools can accelerate precision medicine by identifying relevant drug targets, designing personalised treatments and predicting individual immune responses to drug candidates. Here, we review the current landscape of DTs supporting drug development for IDs. We describe the concepts behind mixed reality approaches combining AI-based models, traditional mathematical and computational models based on low-throughput experiments and empirical studies. We highlight concrete examples of precision medicine strategies for IDs informed by computational modelling. We also address the benefits, limitations, and ethical considerations of these approaches, and outline future directions for research and clinical translation. Impact statement This manuscript addresses the use of digital twins (DT) to accelerate drug discovery and development for Immune-mediated Disorders. It provides a comprehensive overview of the field and helps clarify complex concepts. Furthermore, it provides concrete examples of DT applications on immune-mediated disorders, and discusses perspectives, and current challenges.
Optical pooled CRISPR screens have become an attractive tool for the rapid identification of genes involved in biological processes. In such screens, mixed populations of cells, each with a single gene knocked out, are screened by microscopy for phenotypes of interest. Identified hit cells can then be tagged by photoactivation of a co-expressed marker, such as PA-mCherry, and subsequently isolated by FACS to identify the responsible guide RNA by next-generation sequencing. Photoactivation is typically performed by selective irradiation of cells with UV light, using either a digital mirror device (DMD), an external fixed UV laser, or, conveniently, by using the 405 nm laser line present in most confocal scanning microscopes. In this study, the latter approach is optimized for PA-mCherry, a bright red phototag used by us and others in optical pooled screens. We find that although normal scanning with intense 405 nm light can rapidly activate PA-mCherry, it also leads to rapid photobleaching. Instead, much higher cellular brightness is achieved by limiting intensity and pixel dwell time during scanning, as well as by slightly defocusing the laser. These results should help optimize cell tagging for genotype-phenotype mapping in optical pooled screens, as well as for other applications.
Cellular senescence represents a response to sublethal damage, characterized by persistent growth arrest and a robust pro-inflammatory trait, the senescence-associated secretory phenotype (SASP). Senescent cells accumulate in the body with age, promoting tissue dysfunction and age-related disease. In addition to profound reprogramming of gene expression patterns, senescent cells undergo broad remodeling of cellular compartments, including the plasma membrane, nucleus, endoplasmic reticulum (ER), Golgi apparatus, endolysosomal system, mitochondria, biomolecular condensates, and cytoskeleton. These changes alter the intracellular communication networks required for homeostasis. Here, we review how senescence alters (i) vesicular trafficking along secretory, endocytic, and autophagic routes, (ii) interorganelle contact sites such as those among mitochondria, ER, and lysosomes to modulate lipid and calcium exchange, and (iii) diffusion and transport of regulatory signals across the cytosol and membranes. We discuss how the impaired crosstalk among compartments increases ROS, exacerbates proteostatic stress, impairs clearance of damaged components, and activates p53/p21, p16/Rb, cGAS-STING, NF-κB, and mTOR pathways, enhancing apoptosis resistance and the SASP. Finally, we highlight emerging technologies to study the senescent organelle 'interactome' and identify therapeutic vulnerabilities in age-associated declines and diseases linked to senescence. Impact statement We synthesize evidence that cellular senescence arises not only from gene expression changes but also from disrupted interorganelle communication. We discuss defects in vesicle trafficking and organelle contact sites that redefine senescence as failure of the organellar interactome, highlighting future mechanistic work and therapeutic opportunities in age-related disease.