Prognostic gene expression profile of colorectal cancer

Colorectal cancer is a major global health burden, with significant heterogeneity in clinical outcomes among patients. Identifying robust prognostic gene expression signatures can help stratify patients, guide treatment decisions, and improve clinical management. This review provides an overview of current prognostic gene expression profiles in colorectal cancer research. We have synthesized evidence from numerous published studies investigating the association between tumor gene expression patterns and patient survival outcomes. The reviewed literature reveals several promising gene signatures that have demonstrated the ability to predict disease-free survival and overall survival in CRC patients, independent of standard clinicopathological risk factors. These genes are crucial in fundamental biological processes, including cell cycle control, epithelial-mesenchymal transition, and immune regulation. The implementation of prognostic gene expression tests in clinical practice holds great potential for enabling more personalized management strategies for colorectal cancer.

Exploring the intricacies of antimicrobial resistance: Understanding mechanisms, overcoming challenges, and pioneering innovative solutions

Antimicrobial resistance (AMR) poses a growing global threat. This review examines AMR from diverse angles, tracing the story of antibiotic resistance from its origins to today's crisis. It explores the rise of AMR, from its historical roots to the urgent need to counter this escalating menace. The review explores antibiotic classes, mechanisms, resistance profiles, and genetics. It details bacterial resistance mechanisms with illustrative examples. Multidrug-resistant bacteria spotlight AMR's resilience. Modern AMR control offers hope through precision medicine, stewardship, combination therapy, surveillance, and international cooperation. Converging traditional and innovative treatments presents an exciting frontier as novel compounds seek to enhance antibiotic efficacy. This review calls for global unity and proactive engagement to address AMR collectively, emphasizing the quest for innovative solutions and responsible antibiotic use. It underscores the interconnectedness of science, responsibility, and action in combatting AMR. Humanity faces a choice between antibiotic efficacy and obsolescence. The call is clear: unite, innovate, and prevail against AMR.

Targeted delivery systems of siRNA based on ionizable lipid nanoparticles and cationic polymer vectors

As an emerging therapeutic tool, small interfering RNA (siRNA) had the capability to down-regulate nearly all human mRNAs via sequence-specific gene silencing. Numerous studies have demonstrated the substantial potential of siRNA in the treatment of broad classes of diseases. With the discovery and development of various delivery systems and chemical modifications, six siRNA-based drugs have been approved by 2024. The utilization of siRNA-based therapeutics has significantly propelled efforts to combat a wide array of previously incurable diseases and advanced at a rapid pace, particularly with the help of potent targeted delivery systems. Despite encountering several extracellular and intracellular challenges, the efficiency of siRNA delivery has been gradually enhanced. Currently, targeted strategies aimed at improving potency and reducing toxicity played a crucial role in the druggability of siRNA. This review focused on recent advancements on ionizable lipid nanoparticles (LNPs) and cationic polymer (CP) vectors applied for targeted siRNA delivery. Based on various types of targeted modifications, we primarily described delivery systems modified with receptor ligands, peptides, antibodies, aptamers and amino acids. Finally, we discussed the challenges and opportunities associated with siRNA delivery systems based on ionizable LNPs and CPs vectors.

Fingerprint of ubiquitin coupled enzyme UBC13 in health and disease

Ubiquitination is one of the most well-known post-translational modifications in eukaryotes. UBC13 is an E2 ubiquitin coupling enzyme, which interacts with different E3 ligases and exerts ubiquitination activity to assemble and synthesize lysine-63-linked (Lys63) ubiquitin strands, thus playing an important role in cell homeostasis, various diseases caused by inflammation, and the occurrence and development of cancer. In this paper, we review the structure and function of UBC13, summarize the diverse pathways it mediates, and discuss its involvement in bacterial and non-bacterial inflammatory diseases. Additionally, we explore UBC13's role in physiological damage repair mechanisms, cancer development, DNA damage repair, immune cell maturation, and function. Furthermore, We also elucidate the progress of the discovery of small molecule inhibitors targeting UBC13 and summarize their structure, which suggests that targeting UBC13 may be a potential disease treatment strategy.

CmARF3-CmTCP7 module regulates flowering time in chrysanthemum (Chrysanthemum morifolium)

The precise timing of flowering in response to environment plays a crucial role in the reproductive processes of plants. The FLOWERING LOCUS T (FT)-FD module is a well-established key node in the photoperiod-mediated pathway. However, the identity of novel partners involved in this network and its regulatory mechanisms remain elusive in most nonmodel species. Here, we found that TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR7 (CmTCP7) functions as a floral repressor in Chrysanthemum morifolium. Its upstream transcriptional regulator AUXIN RESPONSE FACTOR3 (CmARF3) promotes flowering by directly repressing CmTCP7 expression. The expression levels of both genes are short-day inducible. Interestingly, FLOWERING LOCUS T-like3 (CmFTL3) interacts with FD-like1 (CmFDL1), which activates flowering-accelerating gene Chrysanthemum Dendrathema MADS111-like (CmCDM111L). Meanwhile, CmTCP7 interacts with CmFTL3 and CmFDL1, delaying the CmFTL3 and CmFDL1 complex-promoted flowering in chrysanthemum "Jinba." These findings reveal a novel regulatory module controlling photoperiod-dependent flowering in chrysanthemum.

Hijacking the autophagy-apoptosis crosstalk: African swine fever virus orchestrates immune evasion via host remodeling for viral pathogenesis

African swine fever (ASF) is an acute, highly fatal hemorrhagic disease of domestic and wild pigs caused by African swine fever virus (ASFV). ASFV, a large double-stranded DNA virus of the Asfarviridae family, is highly infectious and pathogenic. Through modulation of host apoptosis and autophagy pathways, the virus subverts innate immune surveillance to promote its replication and dissemination. Following ASFV infection, domestic pigs may exhibit 100 % morbidity and mortality rates with highly virulent strains, constituting a major threat to the global pork industry. Nowadays, ASF is listed as a notifiable terrestrial animal disease by the World Organisation for Animal Health (WOAH). Therefore, elucidating ASFV's pathogenic mechanisms, particularly its molecular regulation of apoptosis and autophagy, is crucial for developing effective ASF control and prevention strategies. This review comprehensively summarizes the pathogenic mechanisms of ASFV, with particular focus on the autophagy-apoptosis crosstalk and viral manipulation of these cellular processes. These insights not only improve our understanding of ASFV-mediated immune evasion mechanisms but also provide valuable references for developing ASF control strategies targeting apoptosis and autophagy pathways.

Alpha-ketoacid decarboxylases: Diversity, structures, reaction mechanisms, and applications for biomanufacturing of platform chemicals and fuels

In living cells, alpha-ketoacid decarboxylases (KDCs, EC 4.1.1.-) are a class of enzymes that convert alpha-ketoacids into aldehydes through decarboxylation. These aldehydes serve as either drop-in chemicals or precursors for the biosynthesis of alcohols, carboxylic acids, esters, and alkanes. These compounds play crucial roles in cellular metabolism and fitness and the bioeconomy, facilitating the sustainable and renewable biomanufacturing of platform chemicals and fuels. This review explores the diversity and classification of KDCs, detailing their structures, mechanisms, and functions. We highlight recent advancements in repurposing KDCs to enhance their efficiency and robustness for biomanufacturing. Additionally, we present modular KDC-dependent metabolic pathways for the microbial biosynthesis of aldehydes, alcohols, carboxylic acids, esters, and alkanes. Finally, we discuss recent developments in the modular cell engineering technology that can potentially be applied to harness the diversity of KDC-dependent pathways for biomanufacturing platform chemicals and fuels.

Recent advances in CRISPR-Cas system for Saccharomyces cerevisiae engineering

Yeast Saccharomyces cerevisiae (S. cerevisiae) is a crucial industrial platform for producing a wide range of chemicals, fuels, pharmaceuticals, and nutraceutical ingredients. It is also commonly used as a model organism for fundamental research. In recent years, the CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) system has become the preferred technology for genetic manipulation in S. cerevisiae owing to its high efficiency, precision, and user-friendliness. This system, along with its extensive toolbox, has significantly accelerated the construction of pathways, enzyme optimization, and metabolic engineering in S. cerevisiae. Furthermore, it has allowed researchers to accelerate phenotypic evolution and gain deeper insights into fundamental biological questions, such as genotype-phenotype relationships. In this review, we summarize the latest advancements in the CRISPR-Cas toolbox for S. cerevisiae and highlight its applications in yeast cell factory construction and optimization, enzyme and phenotypic evolution, genome-scale functional interrogation, gene drives, and the advancement of biotechnologies. Finally, we discuss the challenges and potential for further optimization and applications of the CRISPR-Cas system in S. cerevisiae.

An informed machine learning based environmental risk score for hypertension in European adults

BACKGROUND

The exposome framework seeks to unravel the cumulated effects of environmental exposures on health. However, existing methods struggle with challenges including multicollinearity, non-linearity and confounding. To address these limitations, we introduce SEANN (Summary Effect Adjusted Neural Network) a novel approach that integrates pooled effect sizes-a form of domain knowledge-with neural networks to improve the analysis and interpretation of hypertension risk factors.

METHODS

Based on data from 18,337 adults aged 40-65y participants in the GCAT cohort in Catalonia, covering a diverse selection of 53 environmental factors, we computed two environmental risk scores for hypertension prevalence using deep neural networks. An informed risk score using SEANN, integrating 11 different pooled effect size estimates from meta-analyses, and an agnostic counterpart for comparison. For each score, we computed Shapley values to extract and compare the learnt exposure-outcome relationships from each neural network model.

RESULTS

The obtained predictive performances were similarly good for the agnostic NN and SEANN (AUC 0.7). However, we demonstrate substantial improvements in the scientific validity of the informed risk score captured relationships. Directly informed variables were closer to their corresponding relationships observed in literature and other non-informed variables were successfully adjusted with their direction of associations more in line with previous studies. The mean delta SHAP distance averaged over all variables of the relationships extracted with both models and those observed in the literature, was 6 times lower with SEANN compared with the agnostic NN. The most influential environmental variables within the informed risk score included smoking intensity, Mediterranean diet adherence, coffee consumption and sedentary behaviour.

CONCLUSIONS

This study demonstrates the added value of SEANN over conventional, purely data-driven machine learning approaches. By aligning learned relationships with established literature-based effect sizes, SEANN improves the disentanglement of exposure effects on hypertension.

Overexpressed Rv0222 in M. smegmatis suppresses host innate immunity by downregulating miR-9 target SIRT1

Tuberculosis (TB) remains one of the most fatal infectious diseases, the pathogenic bacterium Mycobacterium tuberculosis (Mtb) has a thick wall to resist the invasion of extracellular substances and secretes a variety of virulence proteins to antagonize host innate immunity. Rv0222, a protein encoded by the gene Rv0222 in the RD4 region of Mtb, is a critical virulence factor in the pathogenicity of Mtb. However, the mechanism of its regulation of miRNAs during bacterial infection is unclear. We used Rv0222 gene and Mycobacterium smegmatis (M. smegmatis), which is highly homologous to Mtb, to construct Rv0222 recombinant M. smegmatis Ms_Rv0222. Ms_Rv0222 induced down-regulation of miR-9 expression and up-regulation of SIRT1 in RAW264.7 cells and mice post-infection. Up-regulation of SIRT1 caused down-regulation of p65 activity and decreased the expression of pro-inflammatory cytokine, which increased the intracellular survival of M. smegmatis. Si-SIRT1 induced up-regulation of p65 activity and increased the expression of pro-inflammatory cytokine, then decreased the intracellular survival of M. smegmatis. This study reveals that Mtb Rv0222 mediates the suppression of host innate immunity by miR-9 and its target SIRT1, and may provide a potential site for the development of new anti-TB drugs targeting Rv0222.

Retina-directed gene therapy: Achievements and remaining challenges

Gene therapy is an innovative medical approach that offers new treatment options for congenital and acquired diseases by transferring, correcting, inactivating or regulating genes to supplement, replace or modify a gene function. The approval of voretigene neparvovec (Luxturna), a gene therapy for RPE65-associated retinopathy, has marked a milestone for the field of retinal gene therapy, but has also helped to accelerate the development of gene therapies for genetic diseases affecting other organs. Voretigene neparvovec is a vector based on adeno-associated virus (AAV) that delivers a functional copy of RPE65 to supplement the missing function of this gene. The AAV-based gene delivery has proven to be versatile and safe for the transfer of genetic material to retinal cells. However, challenges remain in treating additional inherited as well as acquired retinopathies with this technology. Despite the high level of activity in this field, no other AAV gene therapy for retinal diseases has been approved since voretigene neparvovec. Ongoing research focuses on overcoming the current restraints through innovative strategies like AAV capsid engineering, dual-AAV vector systems, or CRISPR/Cas-mediated genome editing. Additionally, AAV gene therapy is being explored for the treatment of complex acquired diseases like age-related macular degeneration (AMD) and diabetic retinopathy (DR) by targeting molecules involved in the pathobiology of the degenerative processes. This review outlines the current state of retinal gene therapy, highlighting ongoing challenges and future directions.

Expanded insights into the mechanisms of RNA-binding protein regulation of circRNA generation and function in cancer biology and therapy

RNA-binding proteins (RBPs) regulate the generation of circular RNAs (circRNAs) by participating in the reverse splicing of circRNA and thereby influencing circRNA function in cells and diseases, including cancer. Increasing evidence has demonstrated that the circRNA-RBP network plays a complex and multifaceted role in tumor progression. Thus, a better understanding of this network may provide new insights for the discovery of cancer drugs. In this review, we discuss the characteristics of RBPs and circRNAs and how the circRNA-RBP network regulates tumor cell phenotypes such as proliferation, metastasis, apoptosis, metabolism, immunity, drug resistance, and the tumor environment. Moreover, we investigate the factors that influence circRNA-RBP interactions and the regulation of downstream pathways related to tumor development, such as the tumor microenvironment and N6-methyladenosine modification. Furthermore, we discuss new ideas for targeting circRNA-RBP interactions using various RNA technologies.

Mitochondrial DNA editing: Key to the treatment of neurodegenerative diseases

Neuronal death is associated with mitochondrial dysfunction caused by mutations in mitochondrial DNA. Mitochondrial DNA becomes damaged when processes such as replication, repair, and nucleotide synthesis are compromised. This extensive accumulation of damaged mitochondrial DNA subsequently disrupts the normal function of mitochondria, leading to aging, degeneration, or even death of neurons. Mitochondrial dysfunction stands as a pivotal factor in the development of neurodegenerative diseases, including Parkinson's disease, Alzheimer's disease, Huntington's disease, and amyotrophic lateral sclerosis. Recognizing the intricate nature of their pathogenesis, there is an urgent need for more effective therapeutic interventions. In recent years, mitochondrial DNA editing tools such as zinc finger nucleases, double-stranded DNA deaminase toxin A-derived cytosine base editors, and transcription activator-like effector ligand deaminases have emerged. Their emergence will revolutionize the research and treatment of mitochondrial diseases. In this review, we summarize the advancements in mitochondrial base editing technology and anticipate its utilization in neurodegenerative diseases, offering insights that may inform preventive strategies and therapeutic interventions for disease phenotypes.

A predictive model for MGMT promoter methylation status in glioblastoma based on terahertz spectral data

O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation is a crucial biomarker in glioblastoma (GBM) that influences response to temozolomide. Traditional detection methods, such as gene sequencing, are time-consuming and limited to postoperative analysis. This study explores the use of terahertz time-domain spectroscopy (THz-TDS) combined with machine learning to predict MGMT methylation status intraoperatively. By analyzing 180 GBM tissue samples, a Random Forest model was developed, achieving an AUC of 0.862. The findings suggest that THz spectroscopy offers a rapid, intraoperative alternative to traditional MGMT methylation detection methods, potentially enhancing surgical decision-making and personalized treatment strategies in GBM.

NRDN: A novel nuclear degradation tag for targeted protein regulation in Arabidopsis

The regulation of protein levels in plants is essential for improving agricultural productivity. Recent studies have explored inducible degradation systems in plants, with some showing promising advancements. This study introduces the NRDN degradation tag as a novel tool for regulating protein stability within the nucleus in Arabidopsis thaliana. Unlike traditional gene knockout methods, NRDN offers real-time, dynamic control over protein degradation, enabling precise studies of nuclear-localized proteins. This discovery provides a valuable tool for regulating protein stability in specific cellular compartments, which presents a versatile approach for dissecting complex cellular processes and offers broad applications in functional genomics and cellular research.

The nature of complex structural variations in tomatoes

Structural variations (SVs) in repetitive sequences could only be detected within a broad region due to imprecise breakpoints, leading to classification errors and inaccurate trait analysis. Through manual inspection at 4532 variant regions identified by integrating 14 detection pipelines between two tomato genomes, we generated an SV benchmark at base-pair resolution. Evaluation of all pipelines yielded F1-scores below 53.77% with this benchmark, underscoring the urgent need for advanced detection algorithms in plant genomics. Analyzing the alignment features of the repetitive sequences in each region, we summarized four patterns of SV breakpoints and revealed that deviations in breakpoint identification were primarily due to copy misalignment. According to the similarities among copies, we identified 1635 bona fide SVs with precise breakpoints, including substitutions (223), which should be taken as a fundamental SV type, alongside insertions (780), deletions (619), and inversions (13), all showing preferences for SV occurrence within AT-repeat regions of regulatory loci. This precise resolution of complex SVs will foster genome analysis and crop improvement.

Effect of in vivo and in vitro heat stress on DNA methylation and DNA hydroxymethylation of bovine oocytes and early embryos

In the bovine commercial industry, reduced reproductive performance in response to heat stress is one of the main factors causing economic losses. Several studies have shown that heat stress negatively affects oocytes and embryos at the morphological, biochemical, transcriptional, and developmental levels. Yet, there is limited information on the effect of heat stress on the epigenetic modifications of bovine oocytes and embryos. Therefore, the objective of this study was to evaluate the effect of in vivo and in vitro heat stress on the developmental competence, DNA methylation, and DNA hydroxymethylation of bovine oocytes and early embryos. Oocytes were collected through ovum pick-up from non-lactating, non-pregnant Bos taurus beef cows in February and August under Louisiana environmental conditions. The treatments evaluated were: in vivo heat stress (oocytes collected in August), in vitro heat stress (oocytes collected in February and subjected to in vitro heat stress), and control (oocytes collected in February and not subjected to in vitro heat stress). Developmental rates, DNA methylation and DNA hydroxymethylation of metaphase II oocytes (MII), 2-pronucleus embryos (2 PN) and 2-4 cell embryos were evaluated. Global DNA methylation and DNA hydroxymethylation were evaluated through fluorescence immunostaining. No differences between treatments was detected in developmental rates of MII oocytes, 2 PN embryos and 2-4 cell embryos. Similarly, no differences between treatments was detected in global DNA methylation and DNA hydroxymethylation of MII oocytes, 2 PN embryos, and 2-4 cell embryos. Importantly, no differences in global DNA methylation or DNA hydroxymethylation of paternal or maternal pronucleus was detected, indicating that the demethylation process during the 2 PN embryo stage was not altered at the global level. The results of our study showed that under our experimental conditions, in vivo and in vitro heat stress did not affect developmental rates, DNA methylation and DNA hydroxymethylation of MII oocytes and early embryos produced from oocytes obtained from non-lactating, non-pregnant Bos taurus beef cows.

Exploring the molecular mechanisms through which overexpression of TET3 alleviates liver fibrosis in mice via ferroptosis in hepatic stellate cells

Hepatic stellate cell (HSC) activation is crucial in the onset and progression of liver fibrosis, and inhibiting or eliminating activated HSCs is a key therapeutic strategy. Ferroptosis may help eliminate activated HSCs; however, its role and regulatory pathways in liver fibrosis remain unclear. As a DNA demethylase, TET3 regulates gene expression via DNA demethylation. We previously demonstrated that TET3 overexpression alleviates CCL4-induced liver fibrosis in mice; however, the specific mechanisms, including whether TET3 affects ferroptosis in HSCs, remain unexplored. Thus, we aimed to explore the molecular mechanisms wherein TET3 overexpression improves liver fibrosis in mice via ferroptosis in HSCs. Our in vivo observations showed that overexpression of TET3 ameliorate liver fibrosis in mice, and is associated with increased levels of malondialdehyde (MDA) and Fe2+ in liver tissue, as well as decreased protein expression of SLC7A11, GPX4, and FTH1. Further in vitro studies on HSCs showed that TET3 overexpression inhibits the expression of SLC7A11, GPX4, and FTH1, and reduces intracellular GSH levels, leading to accumulation of MDA and iron ions. This induces ferroptosis in HSC-LX2 cells, while simultaneously decreasing ECM accumulation in HSCs. Furthermore, hMeDIP-SEQ and ChIP-qPCR analyses revealed that TET3 directly interacts with the promoter regions of GPX4 and FTH1 to regulate their transcriptional expression. We propose that overexpression of TET3 modulates the gene methylation status of ferroptosis-related proteins, thereby regulating HSC ferroptosis, reducing activated HSCs, and decreasing ECM deposition in the liver. This may represent one of the molecular mechanisms wherein TET3 overexpression ameliorates liver fibrosis in mice.

Function of intramitochondrial melatonin and its association with Warburg metabolism

Warburg metabolism (aerobic glycolysis) is accompanied by high mitochondrial reactive oxygen species (ROS) generation from the electron transport chain; this is a "Hallmark of Cancer". The elevated ROS sustain the growth and proliferation of the cancer cells. Melatonin is a potent and functionally diverse free radical scavenger and antioxidant that is synthesized in the mitochondria of non-pathological cells and normally aids in keeping mitochondrial ROS levels low and in maintaining redox homeostasis. Because the glucose metabolite, pyruvate, does not enter mitochondria of Warburg metabolizing cells due to the inhibition of pyruvate dehydrogenase complex (PDH), acetyl coenzyme A production is diminished. Acetyl coenzyme A is a necessary co-substrate with serotonin for melatonin synthesis; thus, intramitochondrial melatonin levels become reduced in cancer cells. The hypothesis is that the depressed melatonin levels initiate aerobic glycolysis and allow the exaggerated ROS concentrations to go uncontested; the authors speculate that the elevated mtROS upregulates hypoxia inducible factor 1α (HIF-1α)/pyruvate dehydrogenase kinase (PDK) axis which inhibits PDH, thereby supporting cancer cell proliferation and stimulating cancer biomass. Exposing Warburg metabolizing cancer cells to melatonin elevates intramitochondrial melatonin, thereby reducing mtROS and concurrently interrupting aerobic glycolysis and inhibiting tumor cell proliferation. Mechanistically, higher mitochondrial melatonin levels by supplementation directly upregulates the sirtuin 3 (SIRT3)/FOXO/PDH axis, allowing pyruvate entry into mitochondria and enhancing intrinsic mitochondrial melatonin production as in non-pathological cells. Additionally, melatonin inhibits HIF1α, thereby decreasing PDK activity and disinhibiting PDH, so pyruvate enters mitochondria and is metabolized to acetyl coenzyme A, resulting in reversal of Warburg metabolism.

Systems biology of Haemonchus contortus - Advancing biotechnology for parasitic nematode control

Parasitic nematodes represent a substantial global burden, impacting animal health, agriculture and economies worldwide. Of these worms, Haemonchus contortus - a blood-feeding nematode of ruminants - is a major pathogen and a model for molecular and applied parasitology research. This review synthesises some key advances in understanding the molecular biology, genetic diversity and host-parasite interactions of H. contortus, highlighting its value for comparative studies with the free-living nematode Caenorhabditis elegans. Key themes include recent developments in genomic, transcriptomic and proteomic technologies and resources, which are illuminating critical molecular pathways, including the ubiquitination pathway, protease/protease inhibitor systems and the secretome of H. contortus. Some of these insights are providing a foundation for identifying essential genes and exploring their potential as targets for novel anthelmintics or vaccines, particularly in the face of widespread anthelmintic resistance. Advanced bioinformatic tools, such as machine learning (ML) algorithms and artificial intelligence (AI)-driven protein structure prediction, are enhancing annotation capabilities, facilitating and accelerating analyses of gene functions, and biological pathways and processes. This review also discusses the integration of these tools with cutting-edge single-cell sequencing and spatial transcriptomics to dissect host-parasite interactions at the cellular level. The discussion emphasises the importance of curated databases, improved culture systems and functional genomics platforms to translate molecular discoveries into practical outcomes, such as novel interventions. New research findings and resources not only advance research on H. contortus and related nematodes but may also pave the way for innovative solutions to the global challenges with anthelmintic resistance.

Characterization, microRNA profiling, and immunomodulatory role of plasma-derived exosomes from olive flounder (Paralichthys olivaceus) in response to viral hemorrhagic septicemia virus

Viral hemorrhagic septicemia virus (VHSV) is a highly pathogenic virus that frequently infects olive flounder (Paralichthys olivaceus), causing viral hemorrhagic septicemia (VHS), and posing a significant threat to global aquaculture. This study characterizes plasma-derived exosomes from olive flounder following VHSV challenge (VHSV-Exo) or phosphate buffered saline (PBS) injection (PBS-Exo), comparing their morphology, physicochemical properties, molecular profiles, and immunomodulatory functions. Both PBS-Exo (118.3 ± 8.6 nm) and VHSV-Exo (82.6 ± 5.9 nm) exhibited the typical cup-shaped morphology of exosomes. The successful isolation and purity of exosomes were confirmed by the presence of exosome markers (CD81, CD9, and CD63) and the absence of albumin. High-throughput sequencing identified 13 differentially expressed (DE) microRNAs (miRNAs) between PBS-Exo and VHSV-Exo, including six upregulated and seven downregulated miRNAs (log2 fold change ≥1 or ≤ -1). Toxicity assessments revealed that neither PBS-Exo nor VHSV-Exo were toxic to murine macrophage Raw 264.7 cells or zebrafish larvae at tested doses (up to 100 and 400 μg/mL, respectively). The absence of green fluorescence at 96 h post-treatment of VHSV-Exo indicated minimal reactive oxygen species generation, further supporting exosome safety. Functional studies demonstrated that both in vitro (Raw 264.7 cells) and in vivo (adult zebrafish) treatments with exosomes regulated immune-related genes and proteins expression. Notabaly, VHSV-Exo exhibited superior immunomodulatory effects, as evidenced by enhanced immune gene and protein expression. To our knowledge, this is the first study demonstrating the immunomodulatory potential of VHSV-Exo. These findings highlight VHSV-Exo as a promising immunomodulatory agent, with potential applications as a prophylactic vaccine candidate against VHSV infection in aquaculture.

Neural tube defects induce abnormal astrocyte development by activation and epigenetic permissiveness of STAT3

The open neural tube defect, myelomeningocele (MMC), is a debilitating congenital defect of the central nervous system, characterized by impaired spinal cord development. The pathological development of MMC spinal cord involves enhanced astrogenesis. However, the mechanisms underlying the abnormal generation of astrocytes in MMC spinal cord are poorly understood. Using a fetal rat model of this defect, we discovered that neural progenitor cells (NPCs) in the developing spinal cord undergo the accelerated acquisition of astrocytic competency and the abnormal induction of GFAP expression, resulting in the enhanced generation of astrocytes. We identified that the activation of signal transducer and activator of transcription 3 (STAT3) in NPCs, accompanied by the early epigenetic modifications at the consensus STAT3 binding site within the Gfap promoter, induces this pathological process. Furthermore, we demonstrated that the amniotic fluid exposure is the stimulator of STAT3 activation in MMC spinal cord NPCs, promoting GFAP expression and differentiation of NPCs into astrocytes. To validate this mechanism, we showed that elimination of Stat3 expression from NPCs using CRISPR/Cas9 inhibited GFAP expression and the emergence of astrocytes. Thus, our study provides a novel mechanism that drives abnormal astrogenesis in the developing MMC spinal cord.

Pleiotropic effects of APOE variants on a sleep-based adult epidemiological cohort

OBJECTIVES

Phenome Wide Association study (PheWAS) approach was applied in a sleep-based adult epidemiological cohort to address pleiotropic effects of APOE variants in sleep patterns.

METHODS

PheWAS analysis was performed on the São Paulo Epidemiologic Sleep Study (EPISONO), an adult epidemiological sample (1042 individuals) submitted to objective and subjective sleep evaluations, laboratory tests, clinical scales, anthropomorphic measurements and sociodemographic inquiries (1182 traits per individual). We determined APOE alleles using SNP-array and qPCR data. PheWAS was performed with an additive genetic model for the variant rs7412, using age, age2, sex, principal components, socioeconomic classification and body mass index as covariates. Validation analysis was performed for combinations of APOE full haplotypes (ε3ε3, ε2ε2, ε4ε4, ε2ε3, ε2ε4, and ε3ε4).

RESULTS

When all covariates were applied, nominal associations (p < 0.05 in PheWAS) between the rs7412 genotype and 5 continuous traits were identified and confirmed by non-parametric tests: LDL and total cholesterol blood concentrations, Morningness-Eveningness Questionnaire (MEQ) score, power of gamma and beta electroencephalographic (EEG) frequency bands in N1 and N3, respectively. The association with LDL levels remained significant after Bonferroni correction. All these 5 traits were significantly associated at nominal level with at least 1 of the APOE haplotype combinations. Lower LDL and cholesterol levels were associated with ε2ε3 genotype, higher MEQ scores were observed in ε2ε2 individuals, higher power of gamma waves in N1 was associated with ε2ε2, ε2ε3 and ε4ε4 (with indication of putative dosage effect for ε2 haplotype), and higher power of beta waves in N3 was associated with the ε2ε3 genotype.

CONCLUSIONS

Extensive APOE associations with lipid metabolism were replicated in an admixed cohort, despite sample size limitations. Suggestive associations of APOE genotype with diurnal preference scores and variables derived from sleep EEG spectral analysis present preliminary evidence of the effect of these variants over sleep patterns and individual differences in circadian typology.

Convergent evolution in nuclear and mitochondrial OXPHOS subunits underlies the phylogenetic discordance in deep lineages of Squamata

The order Squamata is a good candidate for detecting unusual patterns of mitochondrial evolution. The lineages leading to the snake and agamid clades likely experienced convergent evolution in mitochondrial OXidative PHOSphorylation (OXPHOS) genes, which provides strong support for the sister relationship of these two groups. The OXPHOS subunits are encoded by both the nuclear and mitochondrial genomes, which are subject to distinct evolutionary pressures. Nevertheless, the cooperation between OXPHOS subunits is essential for proper OXPHOS function, as incompatibilities between subunits can be highly deleterious. In the present study, we annotated OXPHOS genes of 56 Squamata species. The nuclear OXPHOS subunits that physically interact with mitochondrial proteins also support the clade sister relationship between snakes and agamids. Additionally, we found a significant number of convergent amino acid changes between agamids and snakes, not only in mitochondrial OXPHOS genes, but also in nuclear ones, with a higher rate of convergence in the nuclear OXPHOS subunits that play central roles in the OXPHOS complexes, like COX4 and NDUFA4. Overall, the common selective pressures in two distinct lineages can lead two sets of genes, encoded by two different genomes, to exhibit similar patterns of convergent evolution, as well as similar evolutionary rates. As a consequence, the coevolution of interdependent subunits and their adaptation to specific evolutionary pressures can heavily influence the molecular structure of cytonuclear enzyme complexes and blur phylogenetic signals.

NEK2 supports porcine embryonic development by modulating the AKT signaling pathway

AIMS

Serine/threonine kinase NIMA-related kinase 2 (NEK2) plays a crucial role in regulating the cell cycle and DNA damage response. This study explored the mechanisms by which NEK2 inhibition affects porcine embryonic development.

MATERIALS AND METHODS

To explore the role of NEK2 in porcine embryonic development, we used the NEK2 inhibitor JH295 and the AKT activator SC79. Various staining methods, including EdU, EU, OPP, TUNEL assay, real-time PCR, immunocytochemistry, and Western blotting, were used to identify the effects of NEK2 inhibition on developmental competence, DNA damage, and the related mechanisms in porcine embryos.

KEY FINDINGS

NEK2 inhibition significantly reduced the cleavage rate and blastocyst formation rate. Abnormal development was associated with decreased expression of genes related to zygotic genome activation and significantly reduced the levels of EdU, EU, and OPP. Notably, NEK2 inhibition decreased the levels of p-AKT and AKT, as well as their transcript levels. While NEK2 inhibition reduced the rates of cleavage and blastocyst formation as well as total cell number, all of these effects were reversed by SC79 co-treatment. The proportions of expanded blastocyst and cell survival and the trophectoderm cell numbers were similarly restored to control levels following combined treatment with SC79. Furthermore, the reduced levels of EdU, EU, and OPP by NEK2 inhibition were completely restored by SC79 co-treatment. NEK2 inhibition had a negative impact on DNA integrity, and this effect was inhibited by SC79 co-treatment.

SIGNIFICANCE

Together, these results suggest that NEK2 plays a crucial role in porcine embryonic development by regulating the AKT signaling pathway.

A panomics-driven framework for the improvement of major food legume crops: advances, challenges, and future prospects

Food legume crops, including common bean, faba bean, mungbean, cowpea, chickpea, and pea, have long served as vital sources of energy, protein, and minerals worldwide, both as grains and vegetables. Advancements in high-throughput phenotyping, next-generation sequencing, transcriptomics, proteomics, and metabolomics have significantly expanded genomic resources for food legumes, ushering research into the panomics era. Despite their nutritional and agronomic importance, food legumes still face constraints in yield potential and genetic improvement due to limited genomic resources, complex inheritance patterns, and insufficient exploration of key traits, such as quality and stress resistance. This highlights the need for continued efforts to comprehensively dissect the phenome, genome, and regulome of these crops. This review summarizes recent advances in technological innovations and multi-omics applications in food legumes research and improvement. Given the critical role of germplasm resources and the challenges in applying phenomics to food legumes-such as complex trait architecture and limited standardized methodologies-we first address these foundational areas. We then discuss recent gene discoveries associated with yield stability, seed composition, and stress tolerance and their potential as breeding targets. Considering the growing role of genetic engineering, we provide an update on gene-editing applications in legumes, particularly CRISPR-based approaches for trait enhancement. We advocate for integrating chemical and biochemical signatures of cells ('molecular phenomics') with genetic mapping to accelerate gene discovery. We anticipate that combining panomics approaches with advanced breeding technologies will accelerate genetic gains in food legumes, enhancing their productivity, resilience, and contribution to sustainable global food security.

Bioprinting spatially guided functional 3D neural circuits with agarose-xanthan gum copolymer hydrogels

Engineered three-dimensional (3D) tissue models are being used as predictive human in vitro assays for drug discovery and development. Tissue engineering technologies such as bioprinting are now available which use mixtures of polymeric hydrogels and cells for the construction of biomimetic engineered 3D tissue models. Many of the polymeric hydrogels used for bioprinting require post-printing processing steps which might hinder their application directly in multi-well plate platforms, thus limiting their utility in a drug screening setting. Here we describe an agarose and xanthan gum copolymer hydrogel (AG-XG) that has optimal rheological properties for high shape fidelity with extrusion-based printing, has long term stability in cell culture conditions, and is "ready-to-use" after printing, not requiring post-printing processing treatments, making it ideal for applications in multi-well plate format. This AG-XG hydrogel is non-degradable and has non-cell permissive features which makes it ideal to create customized spatially guided cellular patterns to enhance relevant tissue geometry and function. As a proof-of-concept, we show that a bioprinted AG-XG hydrogel casting mold significantly enhances functional connectivity of an engineered 3D neural circuit model made using human iPSC-derived GABAergic and dopaminergic neurons and astrocytes. The bioprinted AG-XG mold promotes the formation of strong functional synaptic connections between two spatially separated neuronal regions, as measured with calcium and optogenetic-based fluorescent biosensors with a customized fiber photometry device. The high shape fidelity of the AG-XG hydrogels described here enables the biofabrication of precisely positioned and spatially designed cellular models, in muti well-based platforms used for drug screening. The process of printing these AG-XG hydrogels uses commercially available extrusion-based bioprinters and can therefore be easily implemented in translational laboratories doing tissue modeling and drug screening without the need of additional specialized bioengineering equipment.

Identification and functional analysis of wheat lincRNAs in response to Fusarium graminearum infection

Intergenic long non-coding RNAs (lincRNAs) have recently been recognized as pivotal regulators in plant-pathogen interactions. However, the specific regulatory mechanisms of lincRNAs responding to Fusarium graminearum (F. graminearum) infection remain largely unexplored. Here, we performed time-series transcriptome profiling (0, 24, 48, and 72 h post-inoculation) and systematic identification of lincRNAs. A total of 1238 expressed lincRNAs were identified, among which 548 were differentially expressed lincRNAs during the time course of F. graminearum infection. We further predicted cis-regulatory lincRNA-mRNA pairs, comprising 347 lincRNAs and potential 1015 target genes, which were found to be mainly involved in amino acid metabolism and biosynthetic pathways. Moreover, 19 lincRNAs were predicted as putative precursors or endogenous target mimics of miRNAs. Subsequently, we verified that two lincRNAs, MSTRG.6494 and MSTRG.32080, showed strong transcriptional responses to F. graminearum infection by quantitative real-time PCR (qPCR) screening. Silencing MSTRG.6494 reduced the expression level of defense-related genes, resulting in reduced resistance to fungal pathogenicity. Meanwhile, the expression level of the potential target gene ATP synthase subunit beta (TaATP2) was significantly decreased in MSTRG.6494-silenced plants infected with F. graminearum. Overall, we performed the genome-wide identification of lincRNAs and their possible regulatory networks during F. graminearum infection-related process, confirming that MSTRG.6494 participates in wheat resistance to F. graminearum, may be via targeting TaATP2 to enhance defense responses. Our findings provide new insights into the regulatory mechanism of lincRNAs for Fusarium head blight (FHB) resistance, suggesting this mechanism as an essential strategy for protecting wheat from F. graminearum.

NAT10 mediated polycystic ovary syndrome through the ac4C modification of CXCL14

Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder among women of reproductive age, underscoring the critical importance of investigating its regulatory mechanisms. N-Acetyltransferase 10 (NAT10) is a crucial enzyme involved in mRNA acetylation modification, mediating target genes expression through N4-acetylcytidine (ac4C) modification to regulate the biological function of various diseases. Nonetheless, the specific role of NAT10 in PCOS regulation remains undisclosed. Ac4C dot hybridization experiment was conducted to determine ac4C expression in PCOS tissues. RT-qPCR was employed to assess the expression levels of NAT10 and CXCL14 in PCOS tissues and KGN cells. Cells viability was assessed using the CCK-8 method, while cell proliferation capacity was evaluated through the colony formation assay and EDU assay. Flow cytometry analysis was utilized to measure the apoptosis rate. The ac4C modification level was determined by acrp-qPCR analysis. RIP and luciferase reporter experiments confirmed the target binding relationship. The rat experiments confirmed the specific regulatory role of NAT10 in polycystic ovary syndrome in vivo. This study highlighted reduced levels of NAT10 and ac4C in PCOS, where silencing NAT10 boosts KGN cell proliferation and suppresses apoptosis. Additionally, NAT10-mediated ac4C modification governed the chemokine CXCL14 expression. Our research unveiled that NAT10 modulated PCOS occurrence and progression by enhancing the CXCL14 mRNA stability through acetylation, presenting potential novel insights into the mechanisms of mRNA acetylation in PCOS.

Turning sour into sweet: Lactylation modification as a promising target in cardiovascular health

Lactylation, a recently identified posttranslational modification (PTM), has emerged as a critical regulatory mechanism in cardiovascular diseases (CVDs). This PTM involves the addition of lactyl groups to lysine residues on histones and nonhistone proteins, influencing gene expression and cellular metabolism. The discovery of lactylation has revealed new directions for understanding metabolic and immune processes, particularly in the context of CVDs. This review describes the intricate roles of specific lactylated proteins and enzymes, such as H3K18, HMGB1, MCT1/4, and LDH, in the regulation of cardiovascular pathology. This study also highlights the unique impact of lactylation on myocardial hypertrophy and distinguishes it from other PTMs, such as SUMOylation and acetylation, underscoring its potential as a therapeutic target. Emerging drugs targeting lactate transporters and critical enzymes involved in lactylation offer promising avenues for novel CVD therapies. This review calls for further research to elucidate the mechanisms linking lactylation to CVDs, emphasizing the need for comprehensive studies at the molecular, cellular, and organismal levels to pave the way for innovative preventive, diagnostic, and treatment strategies in cardiovascular medicine.

Taking the 3Rs to a higher level: replacement and reduction of animal testing in life sciences in space research

Human settlements on the Moon, crewed missions to Mars and space tourism will become a reality in the next few decades. Human presence in space, especially for extended periods of time, will therefore steeply increase. However, despite more than 60 years of spaceflight, the mechanisms underlying the effects of the space environment on human physiology are still not fully understood. Animals, ranging in complexity from flies to monkeys, have played a pioneering role in understanding the (patho)physiological outcome of critical environmental factors in space, in particular altered gravity and cosmic radiation. The use of animals in biomedical research is increasingly being criticized because of ethical reasons and limited human relevance. Driven by the 3Rs concept, calling for replacement, reduction and refinement of animal experimentation, major efforts have been focused in the past decades on the development of alternative methods that fully bypass animal testing or so-called new approach methodologies. These new approach methodologies range from simple monolayer cultures of individual primary or stem cells all up to bioprinted 3D organoids and microfluidic chips that recapitulate the complex cellular architecture of organs. Other approaches applied in life sciences in space research contribute to the reduction of animal experimentation. These include methods to mimic space conditions on Earth, such as microgravity and radiation simulators, as well as tools to support the processing, analysis or application of testing results obtained in life sciences in space research, including systems biology, live-cell, high-content and real-time analysis, high-throughput analysis, artificial intelligence and digital twins. The present paper provides an in-depth overview of such methods to replace or reduce animal testing in life sciences in space research.

A comprehensive view of muscle glucose uptake: regulation by insulin, contractile activity, and exercise

Skeletal muscle is the main site of glucose deposition in the body during meals and the major glucose utilizer during physical activity. Although in both instances the supply of glucose from the circulation to the muscle is of paramount importance, in most conditions the rate-limiting step in glucose uptake, storage, and utilization is the transport of glucose across the muscle cell membrane. This step is dependent upon the translocation of the insulin- and contraction-responsive glucose transporter GLUT4 from intracellular storage sites to the sarcolemma and T tubules. Here, we first analyze how glucose can traverse the capillary wall into the muscle interstitial space. We then review the molecular processes that regulate GLUT4 translocation in response to insulin and muscle contractions and the methodologies utilized to unravel them. We further discuss how physical activity and inactivity, respectively, lead to increased and decreased insulin action in muscle and touch upon sex differences in glucose metabolism. Although many key processes regulating glucose uptake in muscle are known, the advent of newer and bioinformatics tools has revealed further molecular signaling processes reaching a staggering level of complexity. Much of this molecular mapping has emerged from cellular and animal studies and more recently from application of a variety of -omics in human tissues. In the future, it will be imperative to validate the translatability of results drawn from experimental systems to human physiology.

Advances in gene editing-led route for hybrid breeding in crops

With the global demand for sustainable agriculture on the rise, RNA-guided nuclease technology offers transformative applications in crop breeding. Traditional hybrid breeding methods, like three-line and two-line systems, are often labor-intensive, transgenic, and economically burdensome. While chemical mutagens facilitate these systems, they not only generate weak alleles but also produce strong alleles that induce permanent sterility through random mutagenesis. In contrast, RNA-guided nuclease system, such as clustered regularly interspaced short palindromic repeats (CRISPR)- associated protein (Cas) system, facilitates more efficient hybrid production by inducing male sterility through targeted genome modifications in male sterility genes, such as MS8, MS10, MS26, and MS45 which allows precise manipulation of pollen development or pollen abortion in various crops. Moreover, this approach allows haploid induction for the rapid generation of recombinant and homozygous lines from hybrid parents by editing essential genes, like CENH3, MTL/NLD/PLA, and DMP, resulting in high-yield, transgene-free hybrids. Additionally, this system supports synthetic apomixis induction by employing the MiMe (Mitosis instead of Meiosis) strategy, coupled with parthenogenesis in hybrid plants, to create heterozygous lines and retain hybrid vigor in subsequent generations. RNA-guided nuclease-induced synthetic apomixis also enables genome stacking for autopolyploid progressive heterosis via clonal gamete production for trait maintenance to enhance crop adaptability without compromising yield. Additionally, CRISPR-Cas-mediated de novo domestication of wild relatives, along with recent advances to circumvent tissue culture- recalcitrance and -dependency through heterologous expression of morphogenic regulators, holds great promise for incorporating diversity-enriched germplasm into the breeding programs. These approaches aim to generate elite hybrids adapted to dynamic environments and address the anticipated challenges of food insecurity.

Citrullination in health and disease: From physiological function to gene regulation

Protein citrullination involves the deimination of arginine or methylarginine residues in peptide chains to form citrulline by peptidyl arginine deiminases. This process is an important protein post-translational modification that affects molecular structure and function of various proteins, including histones. In recent years, protein citrullination has attracted widespread attention for its influence on gene transcription. Studies on the impact of protein citrullination modification on chromatin structure remodeling and the establishment of gene regulatory networks have made rapid progress. In this review, we briefly summarize the physiological functions of protein citrullination modification. Specifically, we comprehensively outline the latest progress in the study of the role of protein citrullination modification in gene transcription regulation, focusing on the interaction of protein citrullination with other post-translational modifications.

In silico prospecting of ADH activating peptides from Pacific oyster (Crassostrea gigas) and protective effect on ethanol-induced damage in HepG2 cells

Alcoholic liver disease (ALD) is becoming a major health threat in the world today. Alcohol dehydrogenase (ADH) plays an important role in alcohol metabolism. Pacific oyster (Crassostrea gigas) has been identified as a food-borne hepatoprotective agent. For the first time, we integrated in silico strategy, including simulated hydrolysis, bioinformatic prediction and molecular docking to screen ADH activating peptides from C. gigas. In vitro ADH activation activity and surface plasmon resonance (SPR) results showed that this strategy could stably screen ADH activating peptides. We selected six of them to further verify their protective effect on EtOH-induced HepG2 cells. Among them, peptide LQPPR (Leu-Gln-Pro-Pro-Arg) pretreatment increased cell viability, can effectively resist EtOH-induced cytotoxicity. And the transaminase (ALT, AST) in the cell supernatant decreased, indicating the cell damage was improved. The results also showed that the antioxidant capacity (SOD, GSH) of LQPPR pretreated cells increased, and the oxidative stress (MDA) decreased.

TAK-901, a novel EPHA2 inhibitor as a therapeutic strategy against prostate cancer

Prostate cancer is the most common cancer and remains a leading cause of cancer-related deaths among men worldwide. Androgen deprivation therapy continues to be the cornerstone of treatment for prostate cancer. However, the efficacy of this treatments is often limited, leading to the emergence of drug resistance and tumor recurrence. TAK-901, an inhibitor of Aurora kinase B, has been shown to inhibit tumor growth both in vitro and in vivo models. To date, the effect of TAK-901 on prostate cancer and the underlying mechanism remain unknown. In this study, we found that TAK-901 could inhibit proliferation, colony formation and migration, while also inducing apoptosis in prostate cancer cells. We further demonstrated that TAK-901 activates the CHK1 signaling pathway, leading to G2/M-phase arrest in these cells. Additionally, we identified EPHA2 as a novel therapeutic target of TAK-901. By mutating the binding sites between EPHA2 and TAK-901, we discovered that these mutations could reverse the anti-proliferative effects of TAK-901 in prostate cancer models. Our study is the first to reveal that TAK-901 induces apoptosis in prostate cancer cells and inhibits cell growth by targeting EPHA2. These findings provide valuable insights into the underlying mechanisms of TAK-901 and may develop its therapeutic applications in prostate cancer.

Surveillance of Escherichia coli antimicrobial resistance in pig farms in Zhejiang province, China: High prevalence of multidrug resistance and risk-associated genes

OBJECTIVES

The global rise in antimicrobial resistance (AMR) poses a critical threat to public health, with the overuse of antibiotics in livestock being a key driver of this escalating problem. However, research on livestock-associated AMR remains limited, with few systematic monitoring efforts. This study addresses this gap by presenting findings from our surveillance of Escherichia coli resistance in pig farms in Zhejiang Province, China.

METHODS

The minimum inhibitory concentrations were determined via broth microdilution-based antimicrobial susceptibility testing. The complete genome sequence was acquired using both Illumina NovaSeq 6000 platforms. In the plasmid conjugation experiment, sodium azide-resistant E. coli strain J53 served as the recipient. The E. coli genomes were analyzed for AMR genes, multi-locus sequence typing (MLST) types, plasmid types, and virulence genes using the ABRicate.

RESULTS

A total of 51 E. coli strains from 90 fecal samples collected across six farms. Resistance rates for amoxicillin/clavulanic acid and sulfamethoxazole exceeded 90 %, while resistance to ampicillin, florfenicol, tetracycline, and trimethoprim/sulfamethoxazole was above 80 %. The prevalence of multidrug-resistant strains was 89.24 %. Whole-genome sequencing revealed 58 acquired AMR genes and 17 virulence-associated genes, notably including the astA gene. Two strains exhibited meropenem resistance and carried blaNDM-5, located on IncI1-I plasmids. These strains shared an identical genetic context, characterized by an "IS26-IS30-blaNDM-5-bleMBL-dsdD-IS91″ structure, which may promote horizontal gene transfer of blaNDM-5. Additionally, six strains harbored the tet(X4) gene.

CONCLUSIONS

Despite ongoing antibiotic reduction efforts, the high prevalence of resistant E. coli in pigs underscores the urgent need for sustained surveillance of AMR in animal populations to mitigate the threat of resistance.

Unveiling the spatiotemporal strategies of plants in response to biotic and abiotic stresses:A comprehensive review

Plant functions are governed by complex regulatory mechanisms that operate across diverse cell types in various tissues. However, the challenge of dissecting plant tissues has hindered the widespread application of single-cell technologies in plant research. Recent advancements in single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) have propelled the field forward. scRNA-seq enables the examination of gene expression at the single-cell level, while ST preserves the spatial context of cellular organization. While previous reviews have discussed the breakthroughs of scRNA-seq and ST in plants, none have comprehensively addressed the use of these technologies to study plant responses to environmental stress at the cellular level. This review provides an in-depth analysis of the development, advantages, and limitations of single-cell and spatial transcriptomics, highlighting their critical role in unraveling plant strategies for coping with biotic and abiotic stresses. We also explore the challenges and future prospects of integrating scRNA-seq and ST in plant research. Understanding cell-specific responses and the complex interactions between cellular entities within the plant under stress is essential for advancing our knowledge of plant biology.

Cancer-treatment-induced accelerated aging in older adult cancer survivors: A call for actions for future perspectives in geriatric oncology

Cancer treatment has significantly improved survival rates, but older adult cancer survivors remain at risk of cancer-treatment-induced late effects such as cardiac complications and second primary cancers. A new hypothesis emerged in the literature suggesting that such late effects can indeed be the manifestation of an accelerated aging process induced by cancer treatments. The cancer-treatment-induced accelerated aging could first arise from clinical and biological manifestations such as frailty, sarcopenia, cognitive impairments, cellular senescence, telomere attrition, and chronic inflammation, paralleling hallmarks of aging. Older adult cancer survivors frequently demonstrated early-onset frailty, sarcopenia, osteoporosis, cognitive impairments, diminished physical function, and increased levels of aging biomarkers compared to cancer-free age-matched older adults. However, existing studies are limited by their narrow focus on specific cancers, the use of single aging outcome measures, and short follow-up durations. A holistic research approach, incorporating comprehensive geriatric assessments and aging biomarkers, is crucial for describing the induced health burden and the mechanisms underlying these induced aging vulnerabilities. Addressing these gaps through large-scale longitudinal studies could lead to personalized interventions, improved treatment protocols, and supportive care strategies in older adult cancer survivors. Such efforts will enhance quality of life, promote healthy aging trajectories, and mitigate societal and economic burdens. To this end, concrete actions, such as establishing international consortia that include patient advocacy, are encouraged. Efforts should also include developing a centralized, registry-based repository for clinical and biological aging outcomes.

Nicotinamide N-methyltransferase as a potential therapeutic target for neurodegenerative disorders: Mechanisms, challenges, and future directions

Neurodegenerative diseases (NDs), including Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD), are characterized by progressive neuronal loss and functional decline, posing significant global health challenges. Emerging evidence highlights nicotinamide N-methyltransferase (NNMT), a cytosolic enzyme regulating nicotinamide (NAM) methylation, as a pivotal player in NDs through its dual impact on epigenetic regulation and metabolic homeostasis. This review synthesizes current knowledge on NNMT's role in disease pathogenesis, focusing on its epigenetic modulation via DNA hypomethylation and histone modifications, alongside its disruption of NAD+ synthesis and homocysteine (Hcy) metabolism. Elevated NNMT activity depletes NAD+, exacerbating mitochondrial dysfunction and impairing energy metabolism, while increased Hcy levels drive oxidative stress, neuroinflammation, and aberrant protein aggregation (e.g., Aβ, tau, α-synuclein). Notably, NNMT overexpression in AD and PD correlates with neuronal hypomethylation and neurotoxicity, as observed in postmortem brain studies and transgenic models. Mechanistically, NNMT consumes S-adenosylmethionine (SAM), limiting methyl donor availability for DNA methyltransferases (DNMTs) and histone methyltransferases (HMTs), thereby altering gene expression patterns critical for neuronal survival. Concurrently, NNMT-mediated NAD+ depletion disrupts sirtuin activity (e.g., SIRT1) and mitochondrial biogenesis, accelerating axonal degeneration. Therapeutic strategies targeting NNMT, such as RNA interference (RNAi), small-molecule inhibitors and exercise therapy, show promise in preclinical models by restoring NAD+ levels and reducing Hcy toxicity. However, challenges persist in achieving cellular specificity, optimizing blood-brain barrier penetration, and mitigating off-target effects. This review underscores NNMT's potential as a multifactorial therapeutic target, bridging metabolic and epigenetic dysregulation in NDs. Future research should prioritize elucidating tissue-specific NNMT interactions, refining inhibitor pharmacokinetics, and validating translational efficacy in clinical trials. Addressing these gaps could pave the way for novel disease-modifying therapies to combat the rising burden of neurodegeneration.

DNA Methylation in Long-Term Memory

Understanding the neural mechanisms of memory has been one of the key questions in biology. Long-term memory, specifically, allows one to travel mentally without constraints of time and space. A long-term memory must have gone through a series of temporal processes: encoding, consolidation, storage, and retrieval. Decades of studies have revealed cellular and molecular mechanisms underlying each process. In this article, we first review the emerging concept of memory engrams and technologies of engram labeling, as these methods provide a new avenue to study the molecular mechanisms for memory. Then, we focus on DNA methylation and its role in long-term memory. Finally, we discuss some key remaining questions in this field and their implications in memory-related disease.

Perilipin-2 mediates ferroptosis in oligodendrocyte progenitor cells and myelin injury after ischemic stroke

JOURNAL/nrgr/04.03/01300535-202507000-00024/figure1/v/2024-09-09T124005Z/r/image-tiff Differentiation of oligodendrocyte progenitor cells into mature myelin-forming oligodendrocytes contributes to remyelination. Failure of remyelination due to oligodendrocyte progenitor cell death can result in severe nerve damage. Ferroptosis is an iron-dependent form of regulated cell death caused by membrane rupture induced by lipid peroxidation, and plays an important role in the pathological process of ischemic stroke. However, there are few studies on oligodendrocyte progenitor cell ferroptosis. We analyzed transcriptome sequencing data from GEO databases and identified a role of ferroptosis in oligodendrocyte progenitor cell death and myelin injury after cerebral ischemia. Bioinformatics analysis suggested that perilipin-2 (PLIN2) was involved in oligodendrocyte progenitor cell ferroptosis. PLIN2 is a lipid storage protein and a marker of hypoxia-sensitive lipid droplet accumulation. For further investigation, we established a mouse model of cerebral ischemia/reperfusion. We found significant myelin damage after cerebral ischemia, as well as oligodendrocyte progenitor cell death and increased lipid peroxidation levels around the infarct area. The ferroptosis inhibitor, ferrostatin-1, rescued oligodendrocyte progenitor cell death and subsequent myelin injury. We also found increased PLIN2 levels in the peri-infarct area that co-localized with oligodendrocyte progenitor cells. Plin2 knockdown rescued demyelination and improved neurological deficits. Our findings suggest that targeting PLIN2 to regulate oligodendrocyte progenitor cell ferroptosis may be a potential therapeutic strategy for rescuing myelin damage after cerebral ischemia.

Autophagy-targeting modulation to promote peripheral nerve regeneration

Nerve regeneration following traumatic peripheral nerve injuries and neuropathies is a complex process modulated by diverse factors and intricate molecular mechanisms. Past studies have focused on factors that stimulate axonal outgrowth and myelin regeneration. However, recent studies have highlighted the pivotal role of autophagy in peripheral nerve regeneration, particularly in the context of traumatic injuries. Consequently, autophagy-targeting modulation has emerged as a promising therapeutic approach to enhancing peripheral nerve regeneration. Our current understanding suggests that activating autophagy facilitates the rapid clearance of damaged axons and myelin sheaths, thereby enhancing neuronal survival and mitigating injury-induced oxidative stress and inflammation. These actions collectively contribute to creating a favorable microenvironment for structural and functional nerve regeneration. A range of autophagy-inducing drugs and interventions have demonstrated beneficial effects in alleviating peripheral neuropathy and promoting nerve regeneration in preclinical models of traumatic peripheral nerve injuries. This review delves into the regulation of autophagy in cell types involved in peripheral nerve regeneration, summarizing the potential drugs and interventions that can be harnessed to promote this process. We hope that our review will offer novel insights and perspectives on the exploitation of autophagy pathways in the treatment of peripheral nerve injuries and neuropathies.

NMD-mediated posttranscriptional regulation fine-tunes the NLR-WRKY regulatory module to modulate bacterial defense response

Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic surveillance system that maintains transcriptome integrity by degrading aberrant RNA transcripts. NMD ensures proper growth and development by preventing autoimmunity through the direct regulation of nucleotide-binding, leucine-rich repeat (NLR) genes. Whether NMD directly regulates WRKY genes remains unclear, despite their upregulation in NMD-deficient plants, and potential feedback between NLRs and WRKYs is also poorly understood. In this study, we showed that NMD also directly regulates a subset of WRKY (WRKY15, 18, 25, 33, 46, 60, and 70) genes, particularly at lower temperatures (16°C). NMD signature-containing transcripts of WRKY46 and WRKY70, selected as representative NMD-regulated WRKY genes, showed increased half-lives in NMD-deficient mutants. Transcriptome analyses showed that these seven NMD-regulated WRKY genes are induced in response to bacterial infection. Potential homologues of these seven NMD-regulated WRKY genes in maize and rice showed similar induction in response to bacterial pathogen infection. Furthermore, these NMD-regulated WRKY genes are induced in plants overexpressing RESISTANT TO P. SYRINGAE 4 (RPS4) in a temperature-dependent manner. By using ChIP-seq and DAP-seq data of WRKY transcription factors, we showed that WRKYs potentially regulate a significant number of NLR genes by directly binding to the W-box in their promoter regions. Taken together, our findings revealed that in addition to the NLRs, the NMD machinery also regulates WRKY genes to keep the basal defense levels in check and the WRKY transcription factors directly regulate NLR genes to constitutes a positive feedback regulatory loop to optimize the plant response to invading pathogens.

Threshold sensitivity analysis for HIV-1 transmission cluster detection using different genomic regions and subtypes

HIV-1 cluster analysis has been widely used in characterizing HIV-1 transmission and some countries have implemented such molecular epidemiology as part of their prevention strategy. However, HIV-1 sequences derive from varying genome regions, which affects phylogenetic clustering outputs. Here, we apply different tools to run a sensitivity analysis for assessing which threshold give the most cohesive clustering outputs for different data sources. We used a dataset of 174 full-length sequences of subtype B from the Swiss HIV Cohort Study and publicly available subtype C from South Africa. Each dataset was divided into sub-genomic sub-datasets covering gag, pol, and env. pol was further subdivided into regions commonly used in HIV-1 genotyping laboratories (pr-rt, rt-int, and pr-rt-int). Cluster analyses for each sub-genomic region was performed specifying varying distance thresholds of 0.5 %-4.5 % and tree branch support of 70 %, 90 % and 99 % in ClusterPicker. Tree topologies and clustering outputs were compared against each other to assess cluster similarity. Pylogenies using pol, pr-rt-int, or rt-int had more robust tree topologies compared to gag and env. Cluster composition changed with increasing genetic distance threshold but was not affected by branch support. Cluster identity was most similar around genetic distances of 2.5 (±0.5)% for all sub-genomic regions and for both subtype B and C. Our study demonstrated the value of performing a sensitivity analysis before setting a genetic distance threshold for clustering output and that the pol region is appropriate for clustering outputs and can be used for near real-time HIV-1 cluster detection.

DriverMEDS: Cancer driver gene identification using mutual exclusivity from embeded features and driver mutation scoring

Efficiently identifying cancer driver genes plays a key role in the cancer development, diagnosis and treatment. Current unsupervised driver gene identification methods typically integrate multi-omics data into gene function networks and employ network embedding algorithms to learn gene features. Additionally, they consider mutual exclusivity and mutation frequency as crucial concepts in identifying driver genes. However, existing approaches neglect the possible important implications of mutual exclusivity in the embedding space. Furthermore, they simply assume that all driver genes exhibit high mutation frequencies. Fortunately, we explored the mutual exclusivity implanted in the learned features and have verified that the Euclidean distances between learned features are strongly related to the mutual exclusivity and they can reveal more information for the mutual exclusivity. Thus, we designed an unsupervised driver gene predicting framework DriverMEDS based on the above idea and a novel driver mutation scoring strategy. First, we design a feature clustering algorithm to generate gene modules. In each module, the Euclidean distances of learned features are used to calculate a module importance score for each gene based on the related mutual exclusivity. Then, following the fact that most of driver genes have intermediate mutation frequencies, a driver mutation scoring function is designed for each gene to optimize the existing mutation frequency scoring strategy. Finally, the weighted sum of the module importance score and the driver mutation score is used to prioritize the genes. The experiment results and analysis show that DriverMEDS could detect novel cancer driver genes and relevant function modules, and outperforms other five state-of-the-art methods for cancer driver identification.

Nonlocal models in biology and life sciences: Sources, developments, and applications

Mathematical modeling is one of the fundamental techniques for understanding biophysical mechanisms in developmental biology. It helps researchers to analyze complex physiological processes and connect like a bridge between theoretical and experimental observations. Various groups of mathematical models have been studied to analyze these processes, and the nonlocal models are one of them. Nonlocality is important in realistic mathematical models of physical and biological systems when local models fail to capture the essential dynamics and interactions that occur over a range of distances (e.g., cell-cell, cell-tissue adhesions, neural networks, the spread of diseases, intra-specific competition, nanobeams, etc.). This review illustrates different nonlocal mathematical models applied to biology and life sciences. The major focus has been given to sources, developments, and applications of such models. Among other things, a systematic discussion has been provided for the conditions of pattern formations in biological systems of population dynamics. Special attention has also been given to nonlocal interactions on networks, network coupling and integration, including brain dynamics models that provide an important tool to understand neurodegenerative diseases better. In addition, we have discussed nonlocal modeling approaches for cancer stem cells and tumor cells that are widely applied in the cell migration processes, growth, and avascular tumors in any organ. Furthermore, the discussed nonlocal continuum models can go sufficiently smaller scales, including nanotechnology, where classical local models often fail to capture the complexities of nanoscale interactions, applied to build biosensors to sense biomaterial and its concentration. Piezoelectric and other smart materials are among them, and these devices are becoming increasingly important in the digital and physical world that is intrinsically interconnected with biological systems. Additionally, we have reviewed a nonlocal theory of peridynamics, which deals with continuous and discrete media and applies to model the relationship between fracture and healing in cortical bone, tissue growth and shrinkage, and other areas increasingly important in biomedical and bioengineering applications. Finally, we provided a comprehensive summary of emerging trends and highlighted future directions in this rapidly expanding field.

The role of the multiplicity of circadian clocks in mammalian systems

Circadian clocks regulate rhythmic biological processes in nearly every tissue, aligning physiology and behavior with the 24-h light-dark cycle. While the central circadian clock in the suprachiasmatic nucleus (SCN) has been extensively studied, emerging evidence indicates that virtually every cell in the body possesses its own locally autonomous circadian clock. This raises a fundamental question: why do multicellular organisms utilize multiple circadian clocks instead of a single master clock broadcasting time cues? Here, we examine how distributed local clocks differ from phase-resettable cycles and ensure robust temporal scheduling of physiological processes. We discuss how internal entrainment among local clocks governs self-sustained, yet flexible, circadian organization of tissue-specific responses to environmental changes. We also examine how the organization of clocks contributes to seasonal homeostasis, and the implications for disease when coordination among these clocks is disrupted.

Diagnostic tools in respiratory medicine (Review)

Recent advancements in diagnostic technologies have significantly transformed the landscape of respiratory medicine, aiming for early detection, improved specificity and personalized therapeutic strategies. Innovations in imaging such as multi-slice computed tomography (CT) scanners, high-resolution CT and magnetic resonance imaging (MRI) have revolutionized our ability to visualize and assess the structural and functional aspects of the respiratory system. These techniques are complemented by breakthroughs in molecular biology that have identified specific biomarkers and genetic determinants of respiratory diseases, enabling targeted diagnostic approaches. Additionally, functional tests including spirometry and exercise testing continue to provide valuable insights into pulmonary function and capacity. The integration of artificial intelligence is poised to further refine these diagnostic tools, enhancing their accuracy and efficiency. The present narrative review explores these developments and their impact on the management and outcomes of respiratory conditions, underscoring the ongoing shift towards more precise and less invasive diagnostic modalities in respiratory medicine.

The role of RNA binding proteins in cancer biology: A focus on FMRP

RNA-binding proteins (RBPs) act as crucial regulators of gene expression within cells, exerting precise control over processes such as RNA splicing, transport, localization, stability, and translation through their specific binding to RNA molecules. The diversity and complexity of RBPs are particularly significant in cancer biology, as they directly impact a multitude of RNA metabolic events closely associated with tumor initiation and progression. The fragile X mental retardation protein (FMRP), as a member of the RBP family, is central to the neurodevelopmental disorder fragile X syndrome and increasingly recognized in the modulation of cancer biology through its influence on RNA metabolism. The protein's versatility, stemming from its diverse RNA-binding domains, enables it to govern a wide array of transcript processing events. Modifications in FMRP's expression or localization have been associated with the regulation of mRNAs linked to various processes pertinent to cancer, including tumor proliferation, metastasis, epithelial-mesenchymal transition, cellular senescence, chemotherapy/radiotherapy resistance, and immunotherapy evasion. In this review, we emphasize recent findings and analyses that suggest contrasting functions of this protein family in tumorigenesis. Our knowledge of the proteins that are regulated by FMRP is rapidly growing, and this has led to the identification of multiple targets for therapeutic intervention of cancer, some of which have already moved into clinical trials or clinical practice.