gene editing

Polyhydroxybutyrate (PHB) production from halophiles: a comprehensive review

The growing environmental impact of petroleum-based plastics has intensified the search for sustainable and biodegradable alternatives. Polyhydroxybutyrate (PHB), a microbial polyester from the polyhydroxyalkanoate (PHA) family, has emerged as a promising biopolymer due to its biodegradability, biocompatibility, and thermoplastic qualities that rival those of conventional polymers. Halophilic bacteria have attracted considerable attention among PHB-producing microorganisms because they thrive in hypersaline environments, enabling non-sterile cultivation, reducing contamination risks, and facilitating cost-effective downstream recovery by osmotic cell lysis. This review provides a comprehensive overview of recent improvements in PHB production by halophilic bacteria, covering physiological adaptations, metabolic pathways, substrate usage, fermentation techniques, and bioreactor optimisation. Particular emphasis is placed on the use of agro-industrial residues and waste-derived feedstocks as sustainable carbon sources to reduce production costs and increase circular bioeconomy results. Recent advances in downstream processing, such as green extraction technologies, metabolic engineering, CRISPR-based gene editing, and synthetic biology approaches to increasing PHB productivity, are critically reviewed. Additionally, developments in polymer modification, life cycle assessment, industrial scalability, regulatory frameworks, and potential applications in packaging, agriculture, and biomedical engineering are discussed. Despite significant progress, issues such as process economics, saline wastewater control, polymer brittleness, and large-scale commercialisation remain. Integrating halophilic biotechnology with waste valorisation, green recovery technologies, sophisticated metabolic engineering, and circular biorefinery concepts offers a promising strategy for developing economically and environmentally sustainable PHB production systems.

CRISPR-Based Therapeutic Approaches in Lung Cancer

This research paper explores the potential of CRISPR-based therapeutic approaches in the diagnosis, treatment, and management of lung cancer. It examines how CRISPR-Cas genome-editing technologies can be used to identify and modify cancer-associated genes, investigate molecular mechanisms of tumor development, and develop targeted therapeutic strategies. The study highlights the potential applications of CRISPR in precision oncology, including gene correction, cancer-cell targeting, drug resistance research, and personalized treatment. It also discusses current challenges and limitations, including off-target effects, delivery systems, tumor heterogeneity, safety concerns, and ethical considerations, while emphasizing the future potential of CRISPR technology in improving lung cancer therapy.

Molecular Scissors With a Search Bar: A Critical Survey Review of CRISPR and the Editing of the Genome

This article presents a narrative review of CRISPR and the Editing of the Genome in the context of Biology. The literature on this topic has expanded substantially over recent decades, yet it remains fragmented across subfields, methods, and national research traditions. Drawing on an interpretive synthesis of representative contributions, the review reconstructs the historical development of the area, examines the conceptual foundations and definitional disputes that organize its debates, and maps the contemporary landscape of research, including the methodological shift toward data-intensive approaches and the institutional pressures that shape publication practice. Particular attention is given to the role of CRISPR and gene editing as organizing themes, and to the conditions under which findings from different research traditions can be brought into productive comparison. The review identifies three synthetic conclusions: the literature is cumulatively strong but organizationally weak; methodological pluralism is better understood as a resource than as a defect; and the growing practical salience of the topic raises the stakes of its unresolved conceptual questions. An agenda for future work is proposed, emphasizing integrative research designs, transparent synthesis practices, and the protection of definitional and infrastructural work on which cumulative progress depends. The article is intended as both a reference map for newcomers and a provocation for specialists in Biology.

Kcnv2 E151X Mouse Captures Hallmarks of KCNV2 ‐Associated Retinal Dystrophy

ABSTRACT Background KCNV2‐associated retinopathy is a rare inherited retinal dystrophy caused by variants in the KCNV2 gene, leading to disrupted photoreceptor behaviour and progressive deterioration of vision. Patients have characteristic electroretinography abnormalities, including reduced cone response, delayed and reduced rod response to low light flashes and paradoxically large rod‐driven response to bright flashes of light. To model this condition, we have generated a Kcnv2 E151X mouse line and assessed its structural and functional retinal features. Methods We have employed CRISPR/Cas 9 gene editing technology to generate a mouse line with an early stop mutation in position E151—orthologous to the commonly encountered E143X mutation in humans—and performed a combination of immunohistochemistry and Western blot to confirm the absence of the full‐length KCNV2—encoded protein, Kv8.2. Next, to assess how closely it models the human disease, we have characterised the KCNV2 mutant mouse line at histological and functional levels, via immunohistochemistry and electroretinography experiments, respectively. Results Kcnv2 mutant mice showed markedly reduced photopic responses and reproduced the supernormal rod phenotype described in affected individuals. In the morphological context, mutant retinas demonstrated strong glial fibrillary acidic protein upregulation together with reduced cone arrestin positive cell counts and photoreceptor layers, indicating photoreceptor loss. Conclusions The Kcnv2 mutant mouse line replicates key functional and structural hallmarks of KCNV2‐associated retinopathy. This model provides a relevant platform for mechanistic studies and preclinical evaluation of gene‐based or pharmacological therapies targeting cone and rod photoreceptor dysfunction.

Chromosome editing Escherichia coli for efficient production of colanic acid

Genetic Basis and Molecular Breeding Strategies for Processing Quality in Chestnut (Castanea spp.)

Processing quality in chestnut (Castanea spp.) is a complex trait jointly determined by fruit development, postharvest metabolic changes, and responses to processing. However, its genetic basis and regulatory networks remain poorly understood. This review provides an integrated framework linking product-specific processing requirements with their biochemical basis, candidate genes, and molecular breeding strategies. Starch composition and fine structure primarily determine cooked texture, storage hardening, and digestibility; starch degradation and sugar metabolism affect sweetness and thermally induced flavor formation; and phenolic substrates, together with oxidative enzymes, determine browning potential and color stability. We review the biochemical basis underlying these traits and summarize candidate genes and regulatory pathways involved in starch synthesis and structural modification, starch-to-sugar conversion, enzymatic browning, flavor formation, and the accumulation of nutritional and bioactive compounds. Nevertheless, stable quantitative trait loci, favorable haplotypes, and causal genes associated with chestnut processing quality remain insufficiently validated. Future research should develop product-oriented, standardized phenotyping systems and integrate multi-environment genetic analyses, multi-omics network dissection, marker-assisted selection, genomic selection, and gene editing to elucidate the genetic mechanisms underlying chestnut processing quality and enable the precision breeding of processing-specific cultivars.

Xenotransplantation

OBJECTIVE: To review the current state of liver xenotransplantation and evaluate emerging strategies using genetically modified porcine organs for the management of acute liver failure. BACKGROUND: The shortage of donor organs continues to limit transplantation, with substantial waitlist mortality, especially in acute liver failure. Progress in the last decades has been driven by advances in gene editing and immunomodulation, allowing for clinical solid-organ xenotransplantation trials since 2021, with early kidney and heart experiences demonstrating feasibility. Liver xenotransplantation might be more challenging because of the liver's metabolic, synthetic, and hemodynamic roles. METHODS: This review summarizes the development of liver xenotransplantation and focuses on modern approaches using genetically modified pigs. We discuss 2 main liver-directed strategies: extracorporeal liver support using ex vivo perfusion of whole porcine livers and the transplantation of genetically engineered porcine liver for patients with acute liver failure. Practical aspects of organ preservation, transportation, and application of long-term machine perfusion are also discussed. RESULTS: Recent first clinical applications of genetically modified porcine liver as auxiliary transplants or associated with extracorporeal circulation systems demonstrated preserved function for several days to weeks without evidence of acute rejection, both in deceased and living recipients. These trials suggest technical feasibility and short-term physiological efficacy, while exposing unresolved challenges related to coagulopathy and immunologic injury. CONCLUSIONS: Liver xenotransplantation using genetically modified porcine organs has progressed from experimental concept to early clinical application. Current evidence supports its potential role as a bridging strategy for acute liver failure, although further refinement is needed for broader clinical adoption.

Divalent cation depletion enhances intrinsic neuronal excitability through CaSR-dependent modulation of threshold ion channels

Abstract External calcium ([Ca2+]e) and magnesium ([Mg2+]e) concentrations fluctuate across physiological and pathological brain states. For example, [Ca2+]e decreases during intense neuronal activity and epilepsy, whereas it rises during sleep. Similarly, [Mg2+]e varies with the sleep/wake cycle and is reduced in epilepsy. Lowering either [Ca2+]e or [Mg2+]e increases intrinsic excitability and hyperpolarizes the action potential (AP) threshold, yet the underlying mechanisms remain unclear. Here, we confirm that reducing [Ca2+]e or [Mg2+]e enhances intrinsic excitability and hyperpolarizes the AP threshold of CA1 pyramidal neurons. Physiological reductions in [Mg2+]e (0.8 → 0.4 mM) have minimal effect, whereas decreases from supraphysiological levels (2.0 → 0.4 mM) robustly increase excitability. Using pharmacology and CRISPR/Cas9 gene editing, we identify the calcium-sensing receptor (CaSR) as a mediator of these effects. The calcilytic NPS-2143 mimics and largely occludes both the intrinsic excitability increase and the AP-threshold hyperpolarization, while genetic reduction of CaSR produces similar outcomes. We further show that AP-threshold hyperpolarization induced by low divalent cations involves both Kv1 and Nav1.2 channels. Together, these findings reveal that CaSR participate in the enhancement of intrinsic neuronal excitability induced by external divalent cation levels.

Target, silence, replace: a review on RNA-based drugs in modern medicine

RNA therapies have evolved into a revolutionary approach in contemporary medicine for treating various diseases by directly targeting RNA molecules engaged in disease pathogenesis. These therapeutic agents regulate biological processes through diverse mechanisms, including modulation of RNA function and gene expression. Medical applications of RNA are greatly enhanced by its structure, adaptability, and capacity for targeted binding. Among these traits is its ability to bind to certain molecules unique to those chemicals. RNA-based treatments have emerged from advancements in the production, modification, and cellular transport of RNA molecules. Several RNA drugs have been approved whereas some are under trial for few diseases. RNA therapeutics can function at the level of RNAs, DNAs and proteins. The evolution of mRNA vaccines during the COVID-19 epidemic emphasizes the exciting potential of RNA therapies in the treatment of diseases. This article provides a comprehensive overview of the several forms of RNA therapies, including small-interfering RNA (siRNA), messenger RNA (mRNA), and antisense-oligonucleotides (ASOs), together with information on their action mechanisms and delivery strategies that improve cellular absorption and shield RNA molecules from degradation. Further, CRISPR-based editing of the genome can be employed for modification of target RNA sequences for various disorders. Development of RNA aptamers have also been identified as pivotal RNA-therapeutic candidate. Additionally, we have explained mechanistic details and examples of drugs approved for RNA therapy. Emphasizing their potential to enhance patient outcomes and fulfil unmet medical requirements, we also highlight the clinical development of RNA therapies in treating cancer and other infectious diseases.

Cross-Model Uncertainty-Aware Minimal Editing of Cis-Regulatory Elements for Cell-Type-Selective Design

Background/Objectives: Cis-regulatory elements (CREs) help mediate cell-type-selective gene expression, yet sequence-to-activity models are rarely converted into compact, experimentally tractable variant panels that retain natural regulatory scaffolds. We developed SafeEdit-CRE to select minimal edits that preserve cross-model specificity while reducing predictive uncertainty, yielding an auditable CRE variant library for reporter-screening prioritization. Methods: SafeEdit-CRE combines the published Malinois sequence–activity predictor with an architecture-distinct reviewer ensemble, validation-calibrated uncertainty, sequence-domain controls, and constrained beam search. Natural 200 nt CREs were edited under fixed substitution budgets of 1, 5, 10, or 20 nucleotides and evaluated by a separately trained multi-kernel ensemble kept entirely separate from candidate generation. Results: Across 600 held-out CRE parents in K562, HepG2, and SK-N-SH cells, SafeEdit-CRE achieved a mean cross-model specificity-margin gain of 0.877 versus 0.822 for greedy editing (paired difference 0.055; 95% CI 0.040–0.071). Relative to a compute-matched primary-model beam, SafeEdit-CRE yielded a similar cross-model specificity-margin gain (difference −0.004; 95% CI −0.011–0.004) with lower ensemble uncertainty (0.314 vs. 0.335). In a locked 90-parent benchmark, 60.6% of designs passed all nine prespecified sequence and model-agreement checks, compared with 38.8% for greedy and 13.1% for random substitution (paired difference 21.8 percentage points; 95% CI 18.3–25.3). Conclusions: SafeEdit-CRE reduced 3240 designs to 74 Tier A computational candidates prioritized for reporter screening across three cell types and four edit budgets. By separating search from cross-model audit and enforcing explicit edit budgets and sequence–domain safeguards, the framework provides a reproducible and auditable approach to computational CRE prioritization, regulatory-grammar studies, and synthetic regulatory-element design.

Supplementary code and analysis materials for "Reassessment of a fixed five-gene inflammatory score in cervical cancer"

This archive contains the frozen R analysis code, analysis-ready public-data derivatives, patient-level cohort audits, numerical result tables, figure-generation scripts, editable figure files, execution logs, and session information supporting the manuscript “Reassessment of a fixed five-gene inflammatory score in cervical cancer: survival association, CCL20 sensitivity, and cross-endpoint evaluation.” The work evaluates an unpublished legacy CCL20/IL16/IL1B/RABGEF1/TRPV4 linear predictor in TCGA-CESC, evaluates its score–overall-survival association in a separate CGCI-HTMCP-CC cohort, and reports GSE44001 disease-free-survival sensitivities. The archive does not reconstruct the unavailable historical 20-to-5 feature-selection path and does not represent a clinically validated prognostic assay.

Functional analyses of histone methyltransferases in sea lamprey embryos undergoing programmed DNA elimination

ABSTRACT During early embryogenesis, the sea lamprey ( Petromyzon marinus ) undergoes a dramatic form of genome reprogramming wherein specific chromosomes are selectively eliminated from somatic progenitor cells. These programmatic elimination events effectively silence all genes on these chromosomes in all somatic cells. Previous studies in lamprey and other eliminating species have shown that epigenetic silencing marks are enriched on germline-specific chromosomes during programmed elimination. These silencing marks include the histone marks H3K9me3 and H4K20me3, which are respectively deposited by KMT1A/SUV39 and KMT5/SUV420 methyltransferases. To test whether lamprey homologs of these methyltransferases contribute to deposition of silencing marks on eliminated (micronucleated) chromatin and whether these marks contribute to the highly coordinated process of DNA elimination in sea lamprey, we used Cas9 gene editing, lightsheet imaging and RNA sequencing to investigate their potential roles in DNA elimination and more generally during early development. Analysis of knockout embryos for four histone methyltransferases show that these genes contribute to the deposition of repressive histone marks on elimination micronuclei, but are not essential for programmed DNA elimination per se . Analysis of later embryogenic stages suggests that these marks may contribute to interim silencing of germline-specific chromosomes, and reveals major impacts on post-blastula survival and development.