Haematopoietic gene therapy of non-conditioned patients with Fanconi anaemia-A: results from open-label phase 1/2 (FANCOLEN-1) and long-term clinical trials

BACKGROUND

Allogeneic haematopoietic stem-cell transplantation is the standard treatment for bone marrow failure (BMF) in patients with Fanconi anaemia, but transplantation-associated complications such as an increased incidence of subsequent cancer are frequent. The aim of this study was to evaluate the safety and efficacy of the infusion of autologous gene-corrected haematopoietic stem cells as an alternative therapy for these patients.

METHODS

This was an open-label, investigator-initiated phase 1/2 clinical trial (FANCOLEN-1) and long-term follow-up trial (up to 7 years post-treatment) in Spain. Mobilised peripheral blood (PB) CD34+ cells from nine patients with Fanconi anaemia-A in the early stages of BMF were transduced with a therapeutic FANCA-encoding lentiviral vector and re-infused without any cytotoxic conditioning treatment. The primary efficacy endpoint of FANCOLEN-1 was the engraftment of transduced cells, as defined by the detection of at least 0·1 therapeutic vector copies per nucleated cell of patient bone marrow (BM) or PB at the second year post-infusion, without this percentage having declined substantially over the previous year. The safety coprimary endpoint was adverse events during the 3 years after infusion. The completed open-label phase 1/2 and the ongoing long-term clinical trials are registered with ClinicalTrials.gov, NCT03157804; EudraCT, 2011-006100-12; and NCT04437771, respectively.

FINDINGS

There were eight evaluable treated patients with Fanconi anaemia-A. Patients were recruited between Jan 7, 2016 and April 3, 2019. The primary endpoint was met in five of the eight evaluable patients (62·50%). The median number of therapeutic vector copies per nucleated cell of patient BM and PB at the second year post-infusion was 0·18 (IQR 0·01-0·20) and 0·06 (0·01-0·19), respectively. No genotoxic events related to the gene therapy were observed. Most treatment-emergent adverse events (TEAEs) were non-serious and assessed as not related to therapeutic FANCA-encoding lentiviral vector. Nine serious adverse events (grade 3-4) were reported in six patients, one was considered related to medicinal product infusion, and all resolved without sequelae. Cytopenias and viral infections (common childhood illnesses) were the most frequently reported TEAEs.

INTERPRETATION

These results show for the first time that haematopoietic gene therapy without genotoxic conditioning enables sustained engraftment and reversal of BMF progression in patients with Fanconi anaemia.

FUNDING

European Commission, Instituto de Salud Carlos III, and Rocket Pharmaceuticals.

A face-off between Smaug and Caspar modulates primordial germ cell count and identity in Drosophila embryos

Proper formation and specification of Primordial Germ Cells (PGCs) is of special significance as they gradually transform into Germline Stem Cells (GSCs) that are ultimately responsible for generating the gametes. Intriguingly, not only the PGCs constitute the only immortal cell type but several specific determinants also underlying PGC specification such as Vasa, Nanos and Germ-cell-less are conserved through evolution. In Drosophila melanogaster, PGC formation and specification depends on two independent factors, the maternally deposited specialized cytoplasm (or germ plasm) enriched in germline determinants, and the mechanisms that execute the even partitioning of these determinants between the daughter cells. Prior work has shown that Oskar protein is necessary and sufficient to assemble the functional germ plasm, whereas centrosomes associated with the nuclei that invade the germ plasm are responsible for its equitable distribution. Our recent data suggests that Caspar, the Drosophila orthologue of human Fas-associated factor-1 (FAF1) is a novel regulator that modulates both mechanisms that underlie the determination of PGC fate. Consistently, early blastoderm embryos derived from females compromised for caspar display reduced levels of Oskar and defective centrosomes.

tRNA modifications: greasing the wheels of translation and beyond

Transfer RNA (tRNA) is one of the most abundant RNA types in cells, acting as an adaptor to bridge the genetic information in mRNAs with the amino acid sequence in proteins. Both tRNAs and small fragments processed from them play many nonconventional roles in addition to translation. tRNA molecules undergo various types of chemical modifications to ensure the accuracy and efficiency of translation and regulate their diverse functions beyond translation. In this review, we discuss the biogenesis and molecular mechanisms of tRNA modifications, including major tRNA modifications, writer enzymes, and their dynamic regulation. We also summarize the state-of-the-art technologies for measuring tRNA modification, with a particular focus on 2'-O-methylation (Nm), and discuss their limitations and remaining challenges. Finally, we highlight recent discoveries linking dysregulation of tRNA modifications with genetic diseases.

Exploring the versatility of Drosophila melanogaster as a model organism in biomedical research: a comprehensive review

Drosophila melanogaster is a highly versatile model organism that has profoundly advanced our understanding of human diseases. With more than 60% of its genes having human homologs, Drosophila provides an invaluable system for modelling a wide range of pathologies, including neurodegenerative disorders, cancer, metabolic diseases, as well as cardiac and muscular conditions. This review highlights key developments in utilizing Drosophila for disease modelling, emphasizing the genetic tools that have transformed research in this field. Technologies such as the GAL4/UAS system, RNA interference (RNAi) and CRISPR-Cas9 have enabled precise genetic manipulation, with CRISPR-Cas9 allowing for the introduction of human disease mutations into orthologous Drosophila genes. These approaches have yielded critical insights into disease mechanisms, identified novel therapeutic targets and facilitated both drug screening and toxicological studies. Articles were selected based on their relevance, impact and contribution to the field, with a particular focus on studies offering innovative perspectives on disease mechanisms or therapeutic strategies. Our findings emphasize the central role of Drosophila in studying complex human diseases, underscoring its genetic similarities to humans and its effectiveness in modelling conditions such as Alzheimer's disease, Parkinson's disease and cancer. This review reaffirms Drosophila's critical role as a model organism, highlighting its potential to drive future research and therapeutic advancements.

Analysis of somatic piRNAs in the malaria mosquito Anopheles coluzzii reveals atypical classes of genic small RNAs

Piwi-interacting small RNAs (piRNA) play a key role in controlling the activity of transposable elements (TEs) in the animal germline. In diverse arthropod species, including the pathogen vectors mosquitoes, the piRNA pathway is also active in nongonadal somatic tissues, where its targets and functions are less clear. Here, we studied the features of small RNA production in head and thorax tissues of an uninfected laboratory strain of Anopheles coluzzii focusing on the 24-32-nt-long RNAs. Small RNAs derived from repetitive elements constitute a minor fraction while most small RNAs process from long noncoding RNAs (lncRNAs) and protein-coding gene mRNAs. The majority of small RNAs derived from repetitive elements and lncRNAs exhibited typical piRNAs features. By contrast, majority of protein-coding gene-derived 24-32 nt small RNAs lack the hallmarks of piRNAs and have signatures of nontemplated 3' end tailing. Most of the atypical small RNAs exhibit female-biased expression and originate from mitochondrial and nuclear genes involved in energy metabolism. We also identified atypical genic small RNAs in Anopheles gambiae somatic tissues, which further validates the noncanonical mechanism of their production. We discuss a novel mechanism of small RNA production in mosquito somatic tissues and the possible functional significance of genic small RNAs.

Stage-specific modulation of Drosophila gene expression with muscle GAL4 promoters

The bipartite GAL4/UAS system is the most widely used method for targeted gene expression in Drosophila melanogaster and facilitates rapid in vivo genetic experimentation. Defining precise gene expression patterns for tissues and/or cell types under GAL4 control will continue to evolve to suit experimental needs. However, the precise spatial and temporal expression patterns for some commonly used muscle tissue promoters are still unclear. This missing information limits the precise timing of experiments during development. Here, we focus on three muscle-enriched GAL4 drivers (Mef2-GAL4, C57-GAL4 and G7-GAL4) to better inform selection of the most appropriate muscle promoter for experimental needs. Specifically, C57-GAL4 and G7-GAL4 turn on in the first or second instar larval stages, respectively, and can be used to bypass myogenesis for studies of muscle function after development.

Metagenomic driven isolation of poorly culturable species in food

Although isolating microorganisms from food microbiota may appear less challenging than from the gut or environmental sources, recovering all representative species from food remains a difficult task. Here, we showed by metagenomic analysis that several abundant species had escaped isolation in a previous study of ten cheeses, including several previously uncharacterized species. This highlights the ongoing challenge of achieving a comprehensive recovery of microbes from food. To address this gap, we designed a novel strategy integrating metagenomics-based probes targeting the species of interest, coupled with an incremental culturing approach using pooled samples. As proof of concept, we applied this strategy to two cheeses containing species that were not isolated in our previous study, with the objective of isolating all species present at levels above 2% and, in particular, potential novel food species. Through this approach, we successfully performed the targeted isolation of two Psychrobacter and two Vibrio species from the first cheese, and four Halomonas and two Pseudoalteromonas species from the second one. Notably, P. undina and V. litoralis represented, as far as we know, the first cheese isolates characterized for these species. However, we were unable to isolate a novel species of Pseudoalteromonas, with no characterized representative to date, and Marinomonas foliarum, previously isolated from marine environment. Using metagenome-assembled genomes (MAGs) and metagenomic analysis, we discussed the possible reasons for their non-recovery. Finally, this strategy offers a promising approach for isolating a set of strains representative of the microbial diversity present in food ecosystems. These isolates can serve as a basis for investigating their roles in the communities, their impact on product development, safety implications and their potential in the development of starter cultures.

Stresses in the food chain and their impact on antibiotic resistance of foodborne pathogens: A review

Antibiotic resistance in foodborne pathogens represents a major public health concern. The farm-to-fork continuum is recognized as a critical pathway for the development and spread of this resistance. Throughout the food chain, foodborne pathogens are exposed to diverse environmental stresses, including temperature extremes, osmotic pressure, food additives, and disinfectants, and others. These stress factors can influence antibiotic resistance, with effects varying based on the type and intensity of stress, the pathogen species and strain, and the specific antibiotic involved. Stress conditions can trigger bacterial adaptive responses, such as general stress response systems, the SOS response, and genetic mutations, which can confer cross-protection and enhance antibiotic resistance. Conversely, stress-induced injury or metabolic suppression may increase bacterial susceptibility to certain antibiotics. Understanding these complex interactions is crucial, as suboptimal food processing can inadvertently select for resistant strains. Investigating the molecular mechanisms underlying stress adaptation is essential for developing effective strategies to mitigate antibiotic resistance. Optimizing food processing protocols and implementing robust monitoring systems throughout the food chain are essential steps to reduce these risks. A comprehensive understanding of stress-induced antibiotic resistance will provide a scientific basis for improving food safety and safeguarding global public health.

Characterization and functional analysis of the small heat shock protein HSP19.5 in Bombyx mori in response to Nosema bombycis infection

Small heat shock proteins (sHSPs) are molecular chaperones known for their role in maintaining cellular homeostasis and protecting cells from various environmental stresses. This study focuses on the silkworm small heat shock protein HSP19.5 and its potential functions in the context of Nosema bombycis infection, a microsporidian pathogen causing severe disease in the sericulture industry. We cloned and characterized HSP19.5 and revealed its expression patterns in different silkworm tissues and developmental stages. Our results indicate that HSP19.5 expression is significantly up-regulated in response to N. bombycis infection, suggesting a role in the host stress response. Through a series of experiments, including RNA interference and overexpression analyses, we demonstrated that HSP19.5 promotes N. bombycis proliferation, possibly by inhibiting host cell apoptosis and regulating intracellular ROS levels. The cytoplasmic localization of HSP19.5 in silkworm cells is consistent with its function as a molecular chaperone. The results enhance our understanding of the complex host-pathogen interactions between silkworms and N. bombycis, and provides insights that may inform the development of novel strategies to control the pebrine disease.

Unveiling the effects of micro and nano plastics in embryonic development

The improper disposal and degradation of plastics causes the formation and spread of micro and nano-sized plastic particles in the ecosystem. The widespread presence of these micro and nanoplastics leads to their accumulation in the biotic and abiotic components of the environment, thereby affecting the cellular and metabolic functions of organisms. Despite being classified as xenobiotic agents, information about their sources and exposure related to reproductive health is limited. Micro and nano plastic exposure during early developmental stages can cause abnormal embryonic development. It can trigger neurotoxicity and inflammatory responses as well in the developing embryo. In embryonic development, a comprehensive study of their role in pluripotency, gastrulation, and multi-differentiation potential is scarce. Due to ethical concerns associated with the direct use of human embryos, pluripotent cells and its 3D in vitro models (with cell lines) are an alternative source for effective research. Thus, the 3D Embryoid body (EB) model provides a platform for conducting embryotoxicity and multi-differentiation potential research. Pluripotent stem cells such as embryonic and induced pluripotent stem cells derived embryoid bodies (EBs) serve as a robust 3D in vitro model that mimics characteristics similar to that of human embryos. Thus, the 3D EB model provides a platform for conducting embryotoxicity and multi-differentiation potential research. Accordingly, this review discusses the significance of 3D in vitro models in conducting effective embryotoxicity research. Further, we also evaluated the possible sources/routes of microplastic generation and analyzed their surface chemistry and cytotoxic effects reported till date.

A coarse-grained model for aqueous two-phase systems: Application to ferrofluids

Aqueous two-phase systems (ATPSs), phase-separating solutions of water soluble but mutually immiscible molecular species, offer fascinating prospects for selective partitioning, purification, and extraction. Here, we formulate a general Brownian dynamics based coarse-grained simulation model for an ATPS of two water soluble but mutually immiscible polymer species. Including additional solute species into the model is straightforward, which enables capturing the assembly and partitioning response of, e.g., nanoparticles (NPs), additional macromolecular species, or impurities in the ATPS. We demonstrate that the simulation model captures satisfactorily the phase separation, partitioning, and interfacial properties of an actual ATPS using a model ATPS in which a polymer mixture of dextran and polyethylene glycol (PEG) phase separates, and magnetic NPs selectively partition into one of the two polymeric phases. Phase separation and NP partitioning are characterized both via the computational model and experimentally, under different conditions. The simulation model captures the trends observed in the experimental system and quantitatively links the partitioning behavior to the component species interactions. Finally, the simulation model reveals that the ATPS interface fluctuations in systems with magnetic NPs as a partitioned species can be controlled by the magnetic field at length scales much smaller than those probed experimentally to date.

IL-33 exerts neuroprotective effects through activation of ST2/AKT signaling axis in microglia after subarachnoid hemorrhage in rats

BACKGROUND AND PURPOSE

ST2, a member of the interleukin-1 (IL-1) receptor family, along with its ligand IL-33, plays critical roles in immune regulation and inflammatory responses. This study investigates the roles of endogenous IL-33/ST2 signaling in subarachnoid hemorrhage (SAH) and elucidates the underlying mechanisms.

METHODS

Dynamic changes in endogenous IL-33 levels were examined following SAH induction in vivo. Rats underwent the endovascular perforation model of SAH and were randomly assigned to receive either recombinant IL-33 (rIL-33) or a vehicle, administered intranasally 1 h post-SAH. ST2 siRNA or an AKT selective inhibitor was administered intraperitoneally (i.p.) 48 h prior to SAH induction to explore the potential mechanisms of IL-33-mediated neuroprotection.

RESULTS

Endogenous IL-33 and ST2 levels were elevated in in vitro models of SAH. Exogenous IL-33 significantly alleviated neuronal apoptosis, reduced brain edema, and enhanced short-term neurofunction in a dose-dependent manner following SAH in rats.

CONCLUSION

Exogenous rIL-33 alleviates SAH-induced neurological deficits by promoting M2-like polarization of microglia post-SAH. These findings suggest a potential role of the microglial ST2/AKT axis in IL-33-related neuroprotection, which warrants further investigation.

Neurobiology, molecular pathways, and environmental influences in antisocial traits and personality disorders

Personality disorders (PDs) are psychiatric conditions characterized by enduring patterns of cognition, emotion, and behaviour that deviate significantly from cultural norms, causing distress or impairment. The aetiology of PDs is complex, involving both genetic and environmental factors. Genetic studies estimate the heritability of PDs at 30%-60%, implicating genes involved in neurotransmitter regulation, such as those for serotonin transporters and dopamine receptors. Environmental factors, including childhood trauma and chronic stress, interact with genetic predispositions to induce epigenetic modifications like DNA methylation and histone modifications, contributing to PD development. Neurobiological research has identified structural and functional abnormalities in brain regions related to emotional regulation and social cognition, such as the amygdala, prefrontal cortex, and limbic system. These abnormalities are linked to impaired emotion processing and interpersonal functioning in PDs. This review focuses on how environmental factors shape maladaptive behaviours and endophenotypes central to many PDs. It explores the interaction between the Ras-ERK, p38, and mTOR molecular pathways in response to environmental stimuli, and examines the role of oxidative stress and mitochondrial metabolism in these processes. Also reviewed are various types of PDs and existing animal models that replicate key endophenotypes, highlighting changes in neurotransmitters and neurohormones. Identifying molecular biomarkers can lead to the development of "enviromimetic" drugs, which mimic environmental influences to activate molecular pathways, facilitating targeted, personalized treatments based on the molecular profiles of individuals with PDs. Ultimately, understanding the molecular mechanisms of PDs promises to enhance diagnostic accuracy, prognosis, and therapeutic outcomes for affected individuals.

RBM10 loss promotes metastases by aberrant splicing of cytoskeletal and extracellular matrix mRNAs

RBM10 modulates transcriptome-wide cassette exon splicing. Loss-of-function RBM10 mutations are enriched in thyroid cancers with distant metastases. Analysis of transcriptomes and genes mis-spliced by RBM10 loss showed pro-migratory and RHO/RAC signaling signatures. RBM10 loss increases cell velocity. Cytoskeletal and ECM transcripts subject to exon inclusion events included vinculin (VCL), tenascin C (TNC), and CD44. Knockdown of the VCL exon inclusion transcript in RBM10-null cells reduced cell velocity, whereas knockdown of TNC and CD44 exon inclusion isoforms reduced invasiveness. RAC1-GTP levels were increased in RBM10-null cells. Mouse HrasG12V/Rbm1OKO thyrocytes develop metastases that are reversed by RBM10 expression or by combined knockdown of VCL, CD44, and TNC inclusion isoforms. Thus, RBM10 loss generates exon inclusion in transcripts regulating ECM-cytoskeletal interactions, leading to RAC1 activation and metastatic competency. Moreover, a CRISPR-Cas9 screen for synthetic lethality with RBM10 loss identified NFκB effectors as central to viability, providing a therapeutic target for these lethal thyroid cancers.

Polystyrene nanoplastics amplify the toxic effects of PFOA on the Chinese mitten crab (Eriocheir sinensis)

Nanoplastics (NPs), the final form of degraded microplastics in the environment, can adsorb PFOA (an emerging organic pollutant in recent years) in several ways. Current research on these has focused on bony fishes and mollusks, however, the combined toxicity of PFOA and NPs remains unknown in Eriocheir sinensis. Therefore, the effects of single or combined exposure to PFOA and NPs were investigated. The results showed that NPs aggravated PFOA exposure-induced oxidative stress, serum lipid disorders, immune responses, and morphological damage. DEGs altered by NPs-PFOA exposure were predominantly enriched in GO terms for cell lumen, and organelle structure, and KEGG terms for spliceosome and endocrine disorders-related diseases. Notably, the apoptotic pathway plays a central role enriched under different exposure modes. PFOA or NPs-PFOA exposure disrupted the levels of lipids molecules-related metabolites by mediating the glycerophospholipid pathway, and the NPs mediated the ferroptosis pathway to exacerbate PFOA-induced metabolic toxicity. In addition, NPs exacerbated the inflammatory response and metabolic imbalance by mediating Fusobacterium ulcerans in the intestinal. In conclusion, this study provides a valuable reference for the characterization of NPs-PFOA combined pollution and a scientific basis for the development of environmental protection policies and pollution management strategies.

Unexpected links between cancer and telomere state

Eukaryotes possess chromosome ends known as telomeres. As telomeres shorten, organisms age, a process defined as senescence. Although uncontrolled telomere lengthening has been naturally connected with cancer developments and immortalized state, many cancers are instead characterized by extremely short, genomically unstable telomeres that may hide cancer cells from immune attack. By contrast, other malignancies feature extremely long telomeres due to absence of 'shelterin' end cap protecting factors. The reason for rampant telomere extension in these cancers had remained elusive. Hence, while telomerase supports tumor progression and escape in cancers with very short telomeres, it is possible that different - transfer based or alternative - lengthening pathways be involved in the early stage of tumorigenesis, when telomere length is intact. In this Review, I hereby discuss recent discoveries in the field of telomeres and highlight unexpected links connecting cancer and telomere state. We hope these parallelisms may inform new therapies to eradicate cancers.

Disruption of mitochondrial DNA integrity in cardiomyocyte injury upon ischemia/reperfusion

Mitochondria serve as the energy provider and enable life activities, and they are the only organelles containing extra-chromosomal DNA. Each mitochondrion contains multiple copies of its genome, which is usually referred to as mitochondrial DNA (mtDNA). mtDNA encodes necessary electron transport chain complex subunits, as well as the essential RNAs for their translation within the organelle. Therefore, the precondition for intact mitochondrial function and cardiomyocyte survival is the integrity of mtDNA. Accumulating evidence suggests that the disruption of mtDNA integrity is involved in ischemia/reperfusion-induced mitochondrial dysfunction and cardiomyocyte injury. Here, we review the current opinions about the pathways of mtDNA integrity maintenance and discuss the role of mtDNA integrity in cardiomyocyte injury reacting to ischemia/reperfusion. We also discuss the mechanisms by which mtDNA mediates ischemia/reperfusion-induced cardiomyocyte injury, together with therapeutic strategies by targeting mtDNA.

A novel directed evolution approach for co-evolution of β-glucosidase activity and organic acid tolerance

Directed evolution is a potent tool for protein engineering; however, Error-prone PCR and DNA Shuffling often lead to a high frequency of negative and reverse mutations, especially in the case of large genes. This study introduces two innovative techniques to tackle these challenges: Segmental error-prone PCR (SEP) and Directed DNA shuffling (DDS). SEP involves averagely dividing large genes into small fragments, independently and randomly mutagenizing them in vitro, and reassembling them as well as other unmutated fragments in Saccharomyces cerevisiae. DDS selectively amplifies mutated fragments of positive variants from SEP and reassembles them in S. cerevisiae to produce complete genes with cumulative positive mutations. We have used these two techniques to simultaneously improve the activity of β-glucosidase and its tolerance to organic acids, which validates the effectiveness and feasibility of the approach.

Whole genome sequencing and In silico analysis of the safety and probiotic features of Lacticaseibacillus paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules

Lacticaseibacillus paracasei is widely used as a probiotic supplement and food additive in the medicinal and food industries. However, its application requires careful evaluation of safety traits associated with probiotic pathogenesis, including the transfer of antibiotic-resistance genes, the presence of virulence and pathogenicity factors, and the potential disruptions of the gut microbiome and immune system. In this study, we conducted whole genome sequencing (WGS) of L. paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules and performed genome annotation to assess its probiotic and safety attributes. Our comparative genomic analysis assessed this novel strain's genetic attributes and functional diversity and unraveled its evolutionary relationships with other L. paracasei strains. The assembly yielded three contigs: one corresponding to the chromosome and two corresponding to plasmids. Genome annotation revealed the presence of 2838 DNA-coding sequences (CDS), 78 ribosomal RNAs (rRNAs), 60 transfer RNAs (tRNAs), three non-coding RNAs (ncRNAs), and 126 pseudogenes. The strain lacked antibiotic resistance genes and pathogenicity factors. Two intact prophages, one Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, and three antimicrobial peptide gene clusters were identified, highlighting the genomic stability and antimicrobial potential of the strain. Furthermore, genes linked to probiotic functions, such as mucosal colonization, stress resistance, and biofilm formation, were characterized. The pan-genome analysis identified 3358 orthologous clusters, including 1775 single-copy clusters, across all L. paracasei strains. Notably, L. paracasei FMT2 contained many unique singleton genes, potentially contributing to its distinctive probiotic properties. Our findings confirm the potential of L. paracasei FMT2 for food and therapeutic applications based on its probiotic profile and safety.

Phylogenetic and structural analysis of Hydra ADAR

Adenosine deaminases acting on RNAs (ADARs) perform adenosine-to-inosine (A-to-I) RNA editing for essential biological functions. While studies of editing sites in diverse animals have revealed unique biological roles of ADAR editing including temperature adaptation and reproductive maturation, rigorous biochemical and structural studies of these ADARs are lacking. Here, we present a phylogenetic sequence analysis and AlphaFold computational structure prediction to reveal that medusozoan ADAR2s contain five dsRNA binding domains (dsRBDs) with several RNA binding residues in the dsRBDs and deaminase domain conserved. Additionally, we identified evolutionary divergence between the medusozoan (e.g. Hydra) and anthozoan cnidarian subphyla. The anthozoan ADAR deaminase domains more closely resemble human ADARs with longer 5' RNA binding loops, glutamate base-flipping residues, and a conserved TWDG dimerization motif. Conversely, medusozoan ADAR deaminase domains have short 5' binding loops, glutamine flipping residues, and non-conserved helix dimerization motif. We also report the direct detection of A-to-I RNA editing by an ADAR ortholog from the freshwater cnidarian Hydra vulgaris (hyADAR). We solved the crystal structure of the monomeric deaminase domain of hyADAR (hyADARd) to 2.0 Å resolution, showing conserved active site architecture and the presence of a buried inositol hexakisphosphate known to be required for ADAR activity. In addition, these data demonstrate that medusozoans have evolved novel ADAR structural features, however the physiological consequence of this remains unknown. In addition, these results provide a framework for biochemically and structurally characterizing ADARs from evolutionarily distant organisms to understand the diverse roles of ADAR editing amongst metazoans.

A network toxicology and molecular docking-based approach revealed shared hepatotoxic mechanisms and targets between the herbicide 2,4-D and its metabolite 2,4-DCP

The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) and its major environmental metabolite 2,4-dichlorophenol (2,4-DCP) are pollutants associated with hepatotoxicity, whose molecular mechanisms remain poorly understood. This study investigated the molecular pathways and targets involved in 2,4-D and 2,4-DCP-induced hepatotoxicity using protein-protein interaction (PPI) network analyses and molecular docking. Target genes were identified using PharmMapper and SwissTargetPrediction, and cross-referenced with hepatotoxicity-related genes from GeneCards and OMIM databases. The PPI network, constructed via STRING and visualized in Cytoscape, revealed 12 critical hub nodes, including HSP90AA1, RXRA, EGFR, SRC, CREBBP, PIK3R1, ESR1, AKT1, RAF1, IGF1R, MDM2, and MAPK14. Gene Ontology (GO) analysis indicated processes such as apoptosis, oxidative stress, mitochondrial dysfunction, and lipid metabolism impairment, while Reactome pathway analysis highlighted disruptions in PI3K/AKT and nuclear receptors signaling. Molecular docking confirmed significant interactions of 2,4-D and 2,4-DCP with key proteins, including SRC, AKT, RXRA, MDM2, and HSP90AA1. These results suggest that 2,4-D and 2,4-DCP share similar toxic mechanisms, providing new insights into their hepatotoxicity pathways for the first time.

Treatment of thymoma with low-dose glucocorticoids before surgery for significant tumor shrinkage: A case report

BACKGROUND

Thymic epithelial neoplasms are rare malignant neoplasms originating in the thymus gland. There have been case reports of patients with advanced thymomas treated with a methylprednisolone pulse or with glucocorticoid (GCs) shock before surgery, followed by surgical treatment, all of whom achieved good results. The effect of GCs on thymomas is related mainly to the action on GC receptors in thymic lymphocytes and epithelial cells. GC receptor expression has been associated with a better prognosis in patients with thymomas, including those with surgically removed thymomas.

CASE SUMMARY

We report a case of a patient with thymoma who had a significant response to preoperative low-dose GC therapy. A mediastinal tumor was detected in the patient via computerized tomography upon admission. The tumor was initially suspected to be a thymic tumor, but lymphoma could not be ruled out. The tumor shrank significantly after low-dose (5 mg/day) GC therapy. Thoracoscopic thymoma resection was performed after puncture pathology was confirmed. The patient recovered well after the operation and is currently performing well with no recurrence of the tumor.

CONCLUSION

This case highlights that low-dose GCs are effective in the treatment of thymomas, and we believe that GCs should be applied more frequently and studied more thoroughly in the treatment of thymomas.

Shotgun and targeted proteomics of Mycolicibacterium smegmatis highlight the role of arginine phosphorylation in the functional adaptation to its environment

Although the phosphorylation of serine (S), threonine (T), and tyrosine (Y) is well-established, arginine phosphorylation (pR) has recently garnered significant attention due to its crucial role in bacteria pathogenicity and stress response. Mycolicibacterium smegmatis, a nonpathogenic surrogate of Mycobacterium tuberculosis, serves as a model for studying mycobacterial pathogenesis. A recent proteomics study identified six pR proteins in M. smegmatis. To gain a more comprehensive understanding, we performed pR profiling using mass spectrometry in combination with two distinct phosphopeptide enrichment strategies: titanium-immobilized metal ion affinity chromatography (Ti4+-IMAC) and Fe-NTA cartridge purification. This approach led to the identification of 1192 shared pR peptides with 1553 pR sites in M. smegmatis following both competitive and non-competitive scoring assessments for pR and pS/T/Y. Further stringent filtering through manual verification resulted in 58 high-confident pR sites across 57 proteins. These confirmed pR-proteins are functionally related, particularly in DNA binding and ATP binding. Alterations in the modification of three pR sites during the logarithmic and stationary phases at the phosphorylation level, but not at the total cell protein level, further suggest the role of pR in the bacterium's functional adaptation to its environment. SIGNIFICANCE: Our findings reveal that pR proteins are prevalent and play roles in DNA-binding and ATP-binding activities, providing insights into the broader biological functions of pR peptides in other genetically diverse species. The reliable identification of bacterial pR events in M. smegmatis not only propels the study of pR within the realm of proteomics but also paves the way for exploring its detailed function in bacteria.

Decipher syntrophies and adaptive response towards enhancing conversion of propionate to methane under psychrophilic condition

Propionate is a key intermediate in anaerobic digestion (AD) under low operational temperatures, which can destabilize the process. In this study, the supplementation of syntrophic cold-tolerant consortia and trace elements significantly improved the performance of psychrophilic (20 °C) reactor, increasing methane production to 91 % of mesophilic reactor levels and reducing propionate concentrations to less than 2 % of those in untreated psychrophilic reactors. Multi-omics analyses revealed that psychrophilic conditions downregulated the methylmalonyl-CoA and aceticlastic methanogenesis pathways. Electron paramagnetic resonance analyses detected 2.6E-05mol/L reactive oxygen species as stress metabolites in the inhibited psychrophilic reactors. Conversely, supplementation with syntrophic cold-tolerant consortia and trace elements enhanced the abundance of Smithellaceae, Syntrophobacteraceae, and Methanothrix by fivefold in the bioenhanced reactors. This supplementation broadened the propionate degradation pathways from relying solely on the methylmalonyl-CoA pathway to also incorporating the dismutation pathway, while upregulating both pathways. These changes enhanced methanogenesis from propionate through improved activity of the syntrophic cold-tolerant consortia. Genome-centric metatranscriptomic analysis identified the upregulation of key antioxidant genes (sod, kat, grx), temperature regulation genes (cspA), and cryoprotective genes (pslF, pslH, cysE) within the syntrophic cold-tolerant consortia. Additionally, extracellular polymeric substance (EPS) yield per cell increased in the bioenhanced reactors by up to 1.07-fold compared to RC-P. These metabolic traits emphasize the critical roles in mitigating oxidative stress, adapting to low temperatures, and supporting efficient methanogenesis under psychrophilic conditions. These findings offer insights into the transcriptional responses and adaptive mechanisms of propionate-degrading consortia in response to psychrophilic stress.

Long non coding RNA function in epigenetic memory with a particular emphasis on genomic imprinting and X chromosome inactivation

Cells preserve and convey certain gene expression patterns to their progeny through the mechanism called epigenetic memory. Epigenetic memory, encoded by epigenetic markers and components, determines germline inheritance, genomic imprinting, and X chromosome inactivation. First discovered long non coding RNAs were implicated in genomic imprinting and X-inactivation and these two phenomena clearly demonstrate the role of lncRNAs in epigenetic memory regulation. Undoubtedly, lncRNAs are well-suited for regulating genes in close proximity at imprinted loci. Due to prolonged association with the transcription site, lncRNAs are able to guide chromatin modifiers to certain locations, thereby enabling accurate temporal and spatial regulation. Nevertheless, the current state of knowledge regarding lncRNA biology and imprinting processes is still in its nascent phase. Herein, we provide a synopsis of recent scientific advancements to enhance our comprehension of lncRNAs and their functions in epigenetic memory, with a particular emphasis on genomic imprinting and X chromosome inactivation, thus gaining a deeper understanding of the role of lncRNAs in epigenetic regulatory networks.

Research progress in DNA damage response (DDR)-targeting modulators: From hits to clinical candidates

In recent years, synthetic lethality has been regarded as a sound example of cancer treatment. Identifying a growing number of synthetic lethality targets has led to a substantial broadening of the application of synthetic lethality, well beyond the PAPR inhibitors employed for treating tumors with BRCA1/2 deficiencies. Especially, molecular targets within the DDR have furnished inhibitor sources and have rapidly advanced to clinical trials. In this review, we summarize the DDR-associated synthetic lethality targets such as WRN, USP1, PARP, ATR, DNA-PK, PRMT5, POLQ, and WEE1. These targets allow for the development of targeted modulators like inhibitors and degraders. Additionally, we emphasize the rational design, advantages, and potential limitations. Furthermore, we outline the promising future of DDR-targeted drug development.

AKT/mTOR mediated autophagy contributes to the self-replication of canine influenza virus in vivo and in vitro

The prevalence and spread of canine influenza virus (CIV) pose a threat to the health of dogs and humans. Some studies have shown that autophagy is closely related to virus replication, but the exact relationship between CIV replication and autophagy is still unclear. Therefore, this study investigated the effects of autophagy on CIV replication in vitro and in vivo. The data showed that CIV infection significantly caused respiratory tract damage in mice, upregulated the mRNA/protein levels of CIV replication-related genes and autophagy-related genes. In addition, the activation of autophagy by rapamycin (Rapa) significantly intensified the CIV replication and the respiratory tract damage of mice, while the inhibition of autophagy by 3-Methyladenine (3-MA) significantly alleviated these effects. Data of MDCK cells also demonstrated that CIV promoted self-replication through activating autophagy, and the upregulation of AKT/mTOR by insulin significantly inhibited the CIV replication. In summary, this study showed that CIV could promote self-replication by activating AKT/mTOR mediated autophagy, which provides new ideas for the prevention and treatment of canine influenza.

Using statistical analysis to explore the influencing factors of data imbalance for machine learning identification methods of human transcriptome m6A modification sites

RNA methylation, particularly through m6A modification, represents a crucial epigenetic mechanism that governs gene expression and influences a range of biological functions. Accurate identification of methylation sites is crucial for understanding their biological functions. Traditional experimental methods, however, are often costly and can be influenced by experimental conditions, making machine learning, especially deep learning techniques, a vital tool for m6A site identification. Despite their utility, current machine learning models struggle with unbalanced datasets, a common issue in bioinformatics. This study addresses the RNA methylation site data imbalance problem from three key perspectives: feature encoding representation, deep learning models, and data resampling strategies. Using the K-mer one-hot encoding strategy, we effectively extracted RNA sequence features and developed classification prediction models utilizing long short-term memory networks (LSTM) and its variant, Multiplicative LSTM (mLSTM). We further enhanced model performance by ensemble and weighted strategy models. Additionally, we utilized the sequence generative adversarial network (SeqGAN) and the synthetic minority resampling technique (SMOTE) to construct balanced datasets for RNA methylation sites. The prediction results were rigorously analyzed using the Wilcoxon test and multivariate linear regression to explore the effects of different K-mer values, model architectures, and sampling methods on classification outcomes. The analysis underscored the significant impact of feature selection, model architecture, and sampling techniques in addressing data imbalance. Notably, the optimal prediction performance was achieved with a K value of 5 using the mLSTM-ensemble model. These findings not only offer new insights and methodologies for RNA methylation site identification but also provide valuable guidance for addressing similar challenges in bioinformatics.

Can a microbial community become an evolutionary individual?

Microbial communities provide crucial services for human well-being, driving an interest in designing and controlling them towards optimised or novel functions. Unfortunately, promising strategies such as community breeding - sometimes referred to as 'directed evolution' or 'artificial community selection' - have shown limited success. A key issue is that microbial communities do not reliably exhibit heritable variation, limiting their capacity for adaptive evolution. In other words, microbial communities are not evolutionary individuals. Here, we provide an overview of the literature on evolutionary transitions in individuality and, with insights from paradigmatic organisms, build a multidimensional space in which the individuality of a multispecies community is characterised by three ecological traits: positive interactions, functional integration, and entrenchment. We then place microbial communities within this individuality space, explore how they can be directed toward increased individuality, and discuss how this perspective can help improve our approach to community breeding.

Synechism 2.0: Contours of a new theory of continuity in bioengineering

The methodological principle of synechism, the all-pervading continuity first proposed by Charles Peirce in 1892, is reinvigorated in the present paper to prompt a comprehensive reevaluation of the integrated concepts of life, machines, agency, and intelligence. The evidence comes from the intersections of synthetic bioengineering, developmental biology, and cognitive and computational sciences. As a regulative principle, synechism, "that continuity governs the whole domain of experience in every element of it", has been shown to infiltrate fundamental issues of contemporary biology, including cognition in different substrates, embodied agency, collectives (swarm and nested), intelligence on multiple scales, and developmental bioelectricity in morphogenesis. In the present paper, we make explicit modern biology's turn to this fundamental feature of science in its rejection of conceptual binaries, preference for collectives over individuals, quantitative over qualitative, and multiscale applicability of the emerging hypotheses about the integration of the first principles of the diversity of life. Specifically, synechism presents itself as the bedrock for research encompassing biological machines, chimaeras, organoids, and Xenobots. We then review a synechistic framework that embeds functionalist, information-theoretic, pragmaticist and inferentialist approaches to springboard to continuum-driven biosystemic behaviour.

Canonical and non-canonical PRC1 differentially contribute to regulation of neural stem cell fate

Neocortex development is characterized by sequential phases of neural progenitor cell (NPC) expansion, neurogenesis, and gliogenesis. Polycomb-mediated epigenetic mechanisms are known to play important roles in regulating the lineage potential of NPCs during development. The composition of Polycomb repressive complex 1 (PRC1) is highly diverse in mammals and was hypothesized to contribute to context-specific regulation of cell fate. Here, we have performed a side-by-side comparison of the role of canonical PRC1.2/1.4 and non-canonical PRC1.3/1.5, all of which are expressed in the developing neocortex, in NSC proliferation and differentiation. We found that the deletion of Pcgf2/4 in NSCs led to a strong reduction in proliferation and to altered lineage fate, both during the neurogenic and gliogenic phase, whereas Pcgf3/5 played a minor role. Mechanistically, genes encoding stem cell and neurogenic factors were bound by PRC1 and differentially expressed upon Pcgf2/4 deletion. Thus, rather than different PRC1 subcomplexes contributing to different phases of neural development, we found that canonical PRC1 played a more significant role in NSC regulation during proliferative, neurogenic, and gliogenic phases compared with non-canonical PRC1.

How to store the bone powder left after extraction for future analysis

Proper storage conditions are important for preservation of DNA. Bones are usually stored long term at -20 °C. When isolating DNA from bones, the bone powder obtained is not fully consumed. The value of retaining bone powder left after extracting DNA for future DNA analysis has been confirmed after storing bone powder for 10 years at -20 °C. Because long-term storage in a freezer is expensive and requires significant space, we were interested in whether bone powder could also be stored at room temperature without affecting the preservation of DNA. To explore this, 21 Second World War bones that generated full short tandem repeat (STR) profiles were selected, and their bone powder was stored in a freezer and at room temperature for up to 3 years. After each year, the DNA was extracted and analyzed from the stored bone powder samples. DNA was extracted using the full demineralization method employing a commercial forensic EZ1 & EZ2 DNA Investigator extraction kit (Qiagen), and automated DNA purification was performed in an EZ1 Advanced XL machine (Qiagen). Real-time PCR quantification was employed to determine the quantity and quality of DNA. The effect of different storage conditions on preservation of DNA was evaluated by determining the amount of DNA, its degradation rate, and after 3 years of storage also the success of STR genotyping. The results obtained showed no difference in the amount of DNA and degradation rate between samples stored in a freezer and at room temperature. In addition, highly informative STR profiles were obtained from all samples after 3 years of storage, regardless of whether they were stored at room temperature or were frozen. The results show no need for freezing bone powder for long-term storage, which makes it possible to save space in freezers and reduce costs.

Natural neopolyploids: a stimulus for novel research

Recently formed allopolyploid species offer unprecedented insights into the early stages of polyploid evolution. This review examines seven well-studied neopolyploids (we use 'neopolyploid' to refer to very recently formed polyploids, i.e. during the past 300 years), spanning different angiosperm families, exploring commonalities and differences in their evolutionary trajectories. Each neopolyploid provides a unique case study, demonstrating both shared patterns, such as rapid genomic and phenotypic changes, and unique responses to hybridization and genome doubling. While previous studies of these neopolyploids have improved our understanding of polyploidy, significant knowledge gaps remain, highlighting the need for further research into the varied impacts of whole-genome duplication on gene expression, epigenetic modifications, and ecological interactions. Notably, all of these neopolyploids have spontaneously arisen due to human activity in natural environments, underscoring the profound consequences of polyploidization in a rapidly changing world. Understanding the immediate effects of polyploidy is crucial not only for evolutionary biology but also for applied practices, as polyploidy can lead to novel traits, as well as stress tolerance and increased crop yields. Future research directions include investigating the genetic and epigenetic mechanisms underlying polyploid evolution, as well as exploring the potential of neopolyploids for crop improvement and environmental adaptation.

Responding to exogenous quorum-sensing signals promotes defense against phages by repressing OmpV expression in Pseudomonas syringae pv. actinidiae

Bacteriophages as viral predators can restrict host strains and shape the bacterial community. Conversely, bacteria also adopt diverse strategies for phage defense. Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of bacterial canker on kiwifruit. Though Psa lacks quorum sensing signaling molecule synthase LuxI, two (PsaR1 and PsaR3) of three LuxR homologous were confirmed to bind with exogenous N-acyl homoserine lactone (AHL), OXO-C8-HSL. The adsorption and infection efficiency of phage KBC54 to Psa significantly reduced by adding OXO-C8-HSL or heterologous expression of traI of Agrobacterium tumefaciens in Psa. By generating PsaR1 and PsaR3 mutants, as well as PsaR-AHL MST assays, we specified that the two PsaRs can recruit AHL to enhance bacterial resistance against phage. Absence of PsaR1 and PsaR3 resulted in up-regulation of the outer membrane protein OmpV, and knockout of ompV led to impaired phage adsorption efficiency. Given that OmpV specifically interacted with the phage tail fiber protein Tp3 in pull-down assay, we deduced that OmpV serves as a cell surface receptor recognized by phage. This study highlights the remarkable ability of Psa recruiting QS signals to inhibit phage infection. This may be a common strategy for non-AHL producing bacteria that evolved to take control of phage infection and promote host fitness by orchestrating QS signals in living niches.

Skeletal and dental tissue mineralization: The potential role of the endoplasmic reticulum/Golgi complex and the endolysosomal and autophagic transport systems

This paper presents a review of the potential role of the endoplasmic reticulum/Golgi complex and intracellular vesicles in mediating events leading to or associated with vertebrate tissue mineralization. The possible importance of these organelles in this process is suggested by observations that calcium ions accumulate in the tubules and lacunae of the endoplasmic reticulum and Golgi. Similar levels of calcium ions (approaching millimolar) are present in vesicles derived from endosomes, lysosomes and autophagosomes. The cellular level of phosphate ions in these organelles is also high (millimolar). While the source of these ions for mineral formation has not been identified, there are sound reasons for considering that they may be liberated from mitochondria during the utilization of ATP for anabolic purposes, perhaps linked to matrix synthesis. Published studies indicate that calcium and phosphate ions or their clusters contained as cargo within the intracellular organelles noted above lead to formation of extracellular mineral. The mineral sequestered in mitochondria has been documented as an amorphous calcium phosphate. The ion-, ion cluster- or mineral-containing vesicles exit the cell in plasma membrane blebs, secretory lysosomes or possibly intraluminal vesicles. Such a cell-regulated process provides a means for the rapid transport of ions or mineral particles to the mineralization front of skeletal and dental tissues. Within the extracellular matrix, the ions or mineral may associate to form larger aggregates and potential mineral nuclei, and they may bind to collagen and other proteins. How cells of hard tissues perform their housekeeping and other biosynthetic functions while transporting the very large volumes of ions required for mineralization of the extracellular matrix is far from clear. Addressing this and related questions raised in this review suggests guidelines for further investigations of the intracellular processes promoting the mineralization of the skeletal and dental tissues.

Reframing Formalin: A Molecular Opportunity Enabling Historical Epigenomics and Retrospective Gene Expression Studies

Formalin preservation of museum specimens has long been considered a barrier to molecular research due to extensive crosslinking and chemical modification. However, recent optimisation of hot alkaline lysis and proteinase K digestion DNA extraction methods have enabled a growing number of studies to overcome these challenges and conduct genome-wide re-sequencing and targeted locus-specific sequencing. The newest, and perhaps most unexpected utility of formalin preservation in archival samples is its ability to preserve in situ DNA-protein interactions at a molecular level. Retrieving this signal provides information about the relative compaction or accessibility of the genome to the transcriptional machinery required for gene expression. Thus, exposure to formalin essentially corresponds to taking a snapshot of organism-wide gene expression at the time of death. While DNA methylation and RNA-Seq analyses of dried tissues have provided glimpses into historical gene regulation, these techniques were previously limited to skeletal or desiccated remains, offering only partial insights. By examining fluid-preserved specimens, molecular tools can now be applied to a broader range of tissues, enabling more detailed tissue-specific gene regulation profiling across vertebrates. In this review, we chronicle the historical use of formaldehyde in collections and discuss how targeted chromatin profiling with assays like MNase-seq and FAIRE-seq are surmounting fixation challenges and unlocking invaluable insights into historical genomes and gene expression profiles. The deeper integration of molecular genetics with museum collections bridges the gap between past and present and provides a vital tool that could help us predict and mitigate some of the impacts of future environmental change, novel pathogens, or invasive species.

Amisulbrom induces mitochondrial dysfunction, leading apoptosis and cell cycle arrest in human trophoblast and endometrial cells

Amisulbrom, a triazole-based fungicide, is utilized in agriculture to increase agricultural production by controlling fungal infections. The long disappearance time of 50 % (DT50) and potential toxic effects of amisulbrom on nontarget organisms have been reported. However, the toxic effects on the pregnancy process remain unclear. This study aims to determine the cytotoxic responses of human trophoblast cells (HTR-8/SVneo) and human endometrial cells (T HESCs), which are associated with implantation upon amisulbrom exposure. Mitochondrial dysfunction and intracellular Ca2+ overload were determined in both cells that are exposed to amisulbrom. Additionally, amisulbrom arrested the cell cycle progression in the G2/M phase, causing apoptosis and reduced survival. Excessive reactive oxygen species (ROS) accumulation and dephosphorylation of PI3K/AKT signaling proteins by amisulbrom exposure mediated these toxic effects. Additionally, spheroid formation was inhibited by amisulbrom treatment in the three-dimensional hanging drop culture model. These results indicate that amisulbrom may pose an adverse effect on the implantation process. Further research is required to identify the toxicity of amisulbrom in vivo. This is the first study to raise concerns about possible toxicity mechanisms of amisulbrom in the implantation process.

Cell-free synthesis system: An accessible platform from biosensing to biomanufacturing

The fundamental aspect of cell-free synthesis systems is the in vitro transcription-translation process. By artificially providing the components required for protein expression, in vitro protein production alleviates various limitations tied to in vivo production, such as oxygen supply and nutrient constraints, thus showcasing substantial potential in engineering applications. This article presents a comprehensive review of cell-free synthesis systems, with a primary focus on biosensing and biomanufacturing. In terms of biosensing, it summarizes the recognition-response mechanisms and key advantages of cell-free biosensors. Moreover, it examines the strategies for the cell-free production of intricate proteins, including membrane proteins and glycoproteins. Additionally, the integration of cell-free metabolic engineering approaches with cell-free synthesis systems in biomanufacturing is thoroughly discussed, with the expectation that biotechnology will embrace greater prosperity.

Spatiotemporal control of cell ablation using Ronidazole with Nitroreductase in Drosophila

The ability to induce cell death in a controlled stereotypic manner has led to the discovery of evolutionary conserved molecules and signaling pathways necessary for tissue growth, repair, and regeneration. Here we report the development of a new method to genetically induce cell death in a controlled stereotypic manner in Drosophila. This method has advantages over other current methods and relies on expression of the E. coli enzyme Nitroreductase (NTR) with exogenous application of the nitroimidazole prodrug, Ronidazole. NTR expression is controlled spatially using the GAL4/UAS system while temporal control of cell death is achieved through timed feeding of Ronidazole supplied in the diet. In cells expressing NTR, Ronidazole is converted to a toxic substance inducing DNA damage and cell death. Caspase cell death is achieved in a range of NTR-expressing cell types with Ronidazole feeding, including epithelial, neurons, and glia. Removing Ronidazole from the diet restores cell death to normal unperturbed levels. Unlike other genetic ablation methods, temporal control is achieved through feeding not temperature, circumventing developmental complications associated with temperature changes. Ronidazole-NTR also requires only two transgenes, a GAL4 driver and UAS-NTR, which is generated as a GFP-NTR fusion allowing for easy setup of large-scale screening of UAS-RNAi lines. Altogether, Ronidazole-NTR provides a new streamlined method for inducing cell death in Drosophila with temperature-independent ON/OFF control.

More X's, more problems: how contributions from the X chromosomes enhance female predisposition for autoimmunity

Many autoimmune diseases exhibit a strong female bias. While sex hormones may influence sex bias in disease, recent studies suggest that the X chromosome itself directly contributes to female-biased susceptibility to autoimmunity. Females with two X chromosomes utilize X Chromosome Inactivation (XCI) to silence gene expression from one X chromosome, equalizing expression between the sexes. The X chromosome is highly enriched with immune-related genes, and recent work indicates that the fidelity of XCI maintenance in lymphocytes from female systemic lupus erythematosus patients is compromised, suggesting that aberrant X-linked gene expression contributes to autoimmune phenotypes. XCI is initiated and maintained by the long noncoding RNA XIST/Xist through its interactions with the inactive X chromosome and numerous interacting proteins, and recent studies also implicate XIST/Xist RNA in driving endosomal Toll-like receptor signaling and XIST/Xist RNA-protein complexes in serving as a source of autoantigens to respectively drive autoimmunity. Here, we will review these three distinct pathways that underscore the significance of X-linked genetics for understanding the origins of the female bias in autoimmune disease.

The role of tRNA-Derived small RNAs (tsRNAs) in pancreatic cancer and acute pancreatitis

tRNA-derived small RNAs (tsRNAs), encompassing tRNA fragments (tRFs) and tRNA-derived stress-induced RNAs (tiRNAs), represent a category of non-coding small RNAs (sncRNAs) that are increasingly recognized for their diverse biological functions. These functions include gene silencing, ribosome biogenesis, retrotransposition, and epigenetics. tsRNAs have been identified as key players in the progression of various tumors, yet their specific roles in pancreatic cancer (PC) and acute pancreatitis (AP) remain largely unexplored. Pancreatic cancer, particularly pancreatic ductal adenocarcinoma, is notorious for its high mortality rate and extremely low patient survival rate, primarily due to challenges in early diagnosis. Similarly, acute pancreatitis is a complex and significant disease. This article reviews the roles of 18 tsRNAs in PC and AP, focusing on their mechanisms of action and potential clinical applications in these two diseases. These tsRNAs influence the progression of pancreatic cancer and acute pancreatitis by modulating various pathways, including ZBP1/NLRP3, Hippo, PI3K/AKT, glycolysis/gluconeogenesis, and Wnt signaling. Notably, the dysregulation of tsRNAs is closely linked to critical clinical factors in pancreatic cancer and acute pancreatitis, such as lymph node metastasis, tumor-node-metastasis (TNM) stage, overall survival (OS), and disease-free survival (DFS). This article not only elucidates the mechanisms by which tsRNAs affect pancreatic cancer and acute pancreatitis but also explores their potential as biomarkers and therapeutic targets for pancreatic cancer. The insights provided here offer valuable references for future research, highlighting the importance of tsRNAs in the diagnosis and treatment of these challenging diseases.

Oogenesis involves a novel nuclear envelop remodeling mechanism in Schmidtea mediterranea

The cell nuclei of Ophisthokonts, the eukaryotic supergroup defined by fungi and metazoans, is remarkable in the constancy of their double-membraned structure in both somatic and germ cells. Such remarkable structural conservation underscores common and ancient evolutionary origins. Yet, the dynamics of disassembly and reassembly displayed by Ophisthokont nuclei vary extensively. Besides closed mitosis in fungi and open mitosis in some animals, little is known about the evolution of nuclear envelope remodeling dynamics during oogenesis. Here, we uncovered a novel form of nuclear envelope remodeling as oocytes are formed in the flatworm Schmidtea mediterranea. From zygotene to metaphase II, both nuclear envelope (NE) and peripheral endoplasmic reticulum (ER) expand notably in size, likely involving de novo membrane synthesis. 3-D electron microscopy reconstructions demonstrated that the NE transforms itself into numerous double-membraned vesicles similar in membrane architecture to NE doublets in mammalian oocytes after germinal vesicle breakdown. The vesicles are devoid of nuclear pore complexes and DNA, yet are loaded with nuclear proteins, including a planarian homologue of PIWI, a protein essential for the maintenance of stem cells in this and other organisms. Our data contribute a new model to the canonical view of NE dynamics and suggest important roles of NE remodeling in planarian oogenesis.

What Drosophila can tell us about state-dependent peptidergic signaling in insects

Plasticity in animal behavior and physiology is largely due to modulatory and regulatory signaling with neuropeptides and peptide hormones (collectively abbreviated NPHs). The NPHs constitute a very large and versatile group of signaling substances that partake at different regulatory levels in most daily activities of an organism. This review summarizes key principles in NPH actions in the brain and in interorgan signaling, with focus on Drosophila. NPHs are produced by neurons, neurosecretory cells (NSCs) and other endocrine cells in NPH-specific and stereotypic patterns. Most of the NPHs have multiple (pleiotropic) functions and target several different neuronal circuits and/or peripheral tissues. Such divergent NPH signaling ensures orchestration of behavior and physiology in state-dependent manners. Conversely, many neurons, circuits, NSCs, or other cells, are targeted by multiple NPHs. This convergent signaling commonly conveys various signals reporting changes in the external and internal environment to central neurons/circuits. As an example of wider functional convergence, 26 different Drosophila NPHs act at many different levels to regulate food search and feeding. Convergence is also seen in hormonal regulation of peripheral functions. For instance, multiple NPHs target renal tubules to ensure osmotic homeostasis. Interestingly, several of the same osmoregulatory NPHs also regulate feeding, metabolism and stress. However, for some NPHs the cellular distribution and functions suggests multiple unrelated functions that are restricted to specific circuits. Thus, NPH signaling follows distinct patterns for each specific NPH, but taken together they form overlapping networks that modulate behavior and physiology.

Effect of MisMatch repair deficiency on metastasis occurrence in a syngeneic mouse model

Mismatch repair deficiency leads to high mutation rates and microsatellite instability (MSI-H), associated with immune infiltration and responsiveness to immunotherapies. In early stages, MSI-H tumors generally have a better prognosis and lower metastatic potential than microsatellite-stable (MSS) tumors, especially in colorectal cancer. However, in advanced stages, MSI-H tumors lose this survival advantage for reasons that remain unclear. We developed a syngeneic mouse model of MSI cancer by knocking out the MMR gene Msh2 in the metastatic 4T1 breast cancer cell line. This model mirrored genomic features of MSI-H cancers and showed reduction in metastatic incidence compared to their MSS counterparts. In MSI-H tumors, we observed an enrichment of immune gene-signatures that negatively correlated with metastasis incidence. A hybrid epithelial-mesenchymal signature, related to aggressiveness was detected only in metastatic MSI-H tumors. Interestingly, we identified immature myeloid cells at primary and metastatic sites in MSI-H tumor-bearing mice, suggesting that MMR deficiency elicits specific immune responses beyond T-cell activation.

ClsC protein encoded by a stress-responsive operon in Escherichia coli functions as a trans-acting activator of RNase III

RNase III, an endoribonuclease that cleaves double-stranded RNAs (dsRNAs), significantly impacts Escherichia coli (E. coli) adaptation by regulating global RNA gene expression. YmdB from E. coli was characterized as a trans-acting regulator of RNase III. However, no protein encoded in E. coli has been characterized as an activator of RNase III. This study reports the discovery of ClsC protein, a phospholipase D (PLD) superfamily enzyme previously known as the third cardiolipin synthase (Cls) and a biofilm inhibitor in E. coli, as a novel RNase III activator. Overexpression of clsC in vivo stimulated the cleavage of RNase III-targeted lacZ fusions and antagonized the inhibition of RNase III by YmdB. Additional in vitro cleavage assays of RNase III-targeted RNAs using RNase III and ClsC confirmed this activity. Moreover, we identified multiple RNAs targeted by RNase III that are regulated dependently on cellular ClsC levels. Mechanistic investigations revealed that ClsC interacts with RNase III. Moreover, the isoleucine residue at the 466th position from the N-terminus of ClsC was identified as crucial for ClsC function. This study is the first to demonstrate that the ymdAB-clsC operon serves as an unexpected source for RNase III regulation in E. coli.

Deciphering the Vulnerability of Pollen to Heat Stress for Securing Crop Yields in a Warming Climate

Climate change is leading to more frequent and severe extreme temperature events, negatively impacting agricultural productivity and threatening global food security. Plant reproduction, the process fundamental to crop yield, is highly susceptible to heatwaves, which disrupt pollen development and ultimately affect seed-set and crop yields. Recent research has increasingly focused on understanding how pollen grains from various crops react to heat stress at the molecular and cellular levels. This surge in interest over the last decade has been driven by advances in genomic technologies, such as single-cell RNA sequencing, which holds significant potential for revealing the underlying regulatory reprogramming triggered by heat stress throughout the various stages of pollen development. This review focuses on how heat stress affects gene regulatory networks, including the heat stress response, the unfolded protein response, and autophagy, and discusses the impact of these changes on various stages of pollen development. It highlights the potential of pollen selection as a key strategy for improving heat tolerance in crops by leveraging the genetic variability among pollen grains. Additionally, genome-wide association studies and population screenings have shed light on the genetic underpinnings of traits in major crops that respond to high temperatures during male reproductive stages. Gene-editing tools like CRISPR/Cas systems could facilitate precise genetic modifications to boost pollen heat resilience. The information covered in this review is valuable for selecting traits and employing molecular genetic approaches to develop heat-tolerant genotypes.

Intracellular diffusion in the cytoplasm increases with cell size in fission yeast

Diffusion in the cytoplasm can greatly impact cellular processes, yet regulation of macromolecular diffusion remains poorly understood. There is increasing evidence that cell size affects the density and macromolecular composition of the cytoplasm. Here, we studied whether cell size affects diffusion at the scale of macromolecules tens of microns in diameter. We analyzed the diffusive motions of intracellular genetically-encoded multimeric 40 nm nanoparticles (cytGEMs) in the cytoplasm of the fission yeast Schizosaccharomyces pombe. Using cell size mutants, we showed that cytGEMs diffusion coefficients decreased in smaller cells and increased in larger cells. This increase in diffusion in large cells may be due to a decrease in the DNA-to-cytoplasm ratio, as diffusion was not affected in large multinucleate cytokinesis mutant cells. In investigating the underlying causes of altered cytGEMs diffusion, we found that the proteomes of large and small cells exhibited size-specific changes, including the subscaling of ribosomal proteins in large cells. Comparison with a similar dataset from human cells revealed that features of size-dependent proteome remodeling were conserved. These studies demonstrate that cell size is an important parameter in determining the biophysical properties and the composition of the cytoplasm.

A detailed review on the role of miRNAs in mitochondrial-nuclear cross talk during cancer progression

MicroRNAs (miRNAs) are a class of small non-coding RNAs that are associated with biochemical pathways through the post-transcriptional regulation of gene expression in different cell types. Based on their expression pattern and function, miRNAs can have oncogenic and tumor suppressor activities in different cancer cells. Altered mitochondrial function and bioenergetics are known hallmarks of cancer cells. Mitochondria play a central role in metabolic reprogramming during cancer progression. Cancer cells exploit mitochondrial function for cell proliferation, invasion, migration and metastasis. Genetic and epigenetic changes in nuclear genome contribute to altered mitochondrial function and metabolic reprogramming in cancer cells. Recent studies have identified the role of miRNAs as major facilitators of anterograde and retrograde signaling between the nucleus and mitochondria in cancer cells. Detailed analysis of the miRNA-mediated regulation of mitochondrial function in cancer cells may provide new avenues for the diagnosis, prognosis, and therapeutic management of the disease. Our review aims to discuss the role of miRNAs in nuclear-mitochondrial crosstalk regulating mitochondrial functions in different cancer types. We further discussed the potential application of mitochondrial miRNAs (mitomiRs) targeting mitochondrial biogenesis and metabolism in developing novel cancer therapy.

Visualization of mitochondrial molecular dynamics during mitophagy process by label-free surface-enhanced Raman scattering spectroscopy

BACKGROUND

Mitophagy is a selective way to eliminate dysfunctional mitochondria and recycle their constituents, which plays an important role in regulating and maintaining intracellular homeostasis. Real-time monitoring mitophagy process is of great importance for cellular physiological and pathological processes related to mitochondria. Howbeit, most of the current methods only focus on single-parameter detection of mitochondrial microenvironmental changes such as pH, viscosity and polarity. The mitochondrial molecular responses under mitophagy are not clear. Therefore, developing a new and simple method for molecular profiling is of great importance for accurately and comprehensively visualizing mitophagy.

RESULTS

In this work, Au NPs-based mitochondria-targeting nanoprobe was developed and the nanoprobe-based label-free surface enhanced Raman spectroscopy (SERS) method was proposed to track starvation induced mitophagy process at molecular level. The nanoprobe displayed good SERS performance and low cytotoxicity. Based on the developed strategy, the molecular response within mitochondria under mitophagy was validated. Meanwhile, the protein denaturation, conformational change, lipid degradation and DNA fragmentation within mitochondria under mitophagy were revealed for the first time, which provides molecular evidence for mitophagy. The changes in reactive oxygen species level and mitochondrial membrane potential further confirmed the damage of mitochondria. Moreover, the developed label-free SERS strategy was used to detect mitophagy in drug (cisplatin)-induced liver injury (DILI) cell model, and obvious mitophagy in DILI cells was observed.

SIGNIFICANCE

The molecular biochemical signature dynamic changes within mitochondria during mitophagy process were revealed by SERS for the first time. Moreover, compared with the current research, our study can provide new insights into mitophagy and mitophagy-involved diseases at molecular level. This study will provide new insights into the molecular mechanism of mitophagy and offer a simple and effective method for mitochondrial molecular event monitoring in mitophagy-involved cellular processes.

The spatial and temporal pattern of GPER/GPR30 reporter expression in the developing and mature forebrain of mice

Evidence suggest that estrogens play crucial roles in the regulation of neural development and function and the G protein-coupled estrogen receptor (GPER/GPR30) appears to be the predominant estrogen receptor in the brain. However, the distribution and functions of GPER in the developing and mature brain are not fully understood. The current study aimed to characterize the expression of GPER in the forebrain, using Gper gene reporter mice combined with fluorescent in situ hybridization (FISH/RNAscope) and immunohistochemistry (IHC). Two lines of Gper reporter mice were constructed by crossing the Gper-cre mice with Ai14(RCL-tdT)-D or R26-ZsGreen mice, which showed identical spatial distributions of the reporters in adult brain. In the forebrain, neurons, protoplasmic astrocytes, mural cells and ependymal cells of third ventricle, were found to express Gper reporters. GPER-expressing neurons were particularly enriched in the olfactory system and the salience network, including posteromedial nucleus of the cortical amygdala (PmCo), entorhinal cortex, insula cortex, prefrontal cortex and dentate gyrus of the hippocampus. RNAscope and neural tracing showed GPER-expressing cortical neurons were long-range excitatory pyramidal neurons. GPER-expressing astrocytes represented a minor population (<10 %) of astrocytes and were found to be closely associated with neurovascular units. GPER-expressing mural cells were not labelled by the common pericyte marker PDGFRβ. In the critical period of neural development (P1-P10), GPER expression appeared to be intimately associated with neurogenesis, proliferation and migration in the olfactory system and the salience network. Collectively, the spatial and temporal pattern of GPER/GPR30 expression in the forebrain implied it might play important roles regulating the development and functions of the olfactory system, the salience network and the cerebral vessels.