PLoS One. 2025 Jan 28;20(1):e0317921. doi: 10.1371/journal.pone.0317921. eCollection 2025.

ABSTRACT

Severe acute respiratory syndrome coronavirus-1 (SARS-CoV-1) and -2 (SARS-CoV-2) are beta-coronaviruses (β-CoVs) that have caused significant morbidity and mortality worldwide. Therefore, a better understanding of host responses to β-CoVs would provide insights into the pathogenesis of these viruses to identify potential targets for medical countermeasures. In this study, our objective is to use a systems biology approach to explore the magnitude and scope of innate immune responses triggered by SARS-CoV-1 and -2 infection over time in pathologically relevant human lung epithelial cells (Calu-3/2B4 cells). Total RNA extracted at 12, 24, and 48 hours after β-CoVs or mock infection of Calu-3/2B4 cells were subjected to RNA sequencing and functional enrichment analysis to select genes whose expressions were significantly modulated post-infection. The results demonstrate that SARS-CoV-1 and -2 stimulate similar yet distinct innate antiviral signaling pathways in pathologically relevant human lung epithelial cells. Furthermore, we found that many genes related to the viral life cycle, interferons, and interferon-stimulated genes (ISGs) were upregulated at multiple time points. Based on their profound modulation upon infection by SARS-CoV-1, SARS-CoV-2, and Omicron BA.1, four ISGs, i.e., bone marrow stromal cell antigen 2 (BST2), Z-DNA Binding Protein 1 (ZBP1), C-X-C Motif Chemokine Ligand 11 (CXCL11), and Interferon Induced Transmembrane Protein 1 (IFITM1), were identified as potential drug targets against β-CoVs. Our findings suggest that these genes affect both pathogens directly and indirectly through the innate immune response, making them potential targets for host-directed antivirals. Altogether, our results demonstrate that SARS-CoV-1 and SARS-CoV-2 infection induce differential effects on host innate immune responses.

PMID:39874350 | DOI:10.1371/journal.pone.0317921

Proc Natl Acad Sci U S A. 2025 Feb 4;122(5):e2408582122. doi: 10.1073/pnas.2408582122. Epub 2025 Jan 28.

ABSTRACT

The formation of superoxide dismutase 1 (SOD1) filaments has been implicated in amyotrophic lateral sclerosis (ALS). Although the disulfide bond formed between Cys57 and Cys146 in the active state has been well studied, the role of the reduced cysteine residues, Cys6 and Cys111, in SOD1 filament formation remains unclear. In this study, we investigated the role of reduced cysteine residues by determining and comparing cryoelectron microscopy (cryo-EM) structures of wild-type (WT) and C6A/C111A SOD1 filaments under thiol-based reducing and metal-depriving conditions, starting with protein samples possessing enzymatic activity. The C6A/C111A mutant SOD1 formed filaments more rapidly than the WT protein. The mutant structure had a unique paired-protofilament arrangement, with a smaller filament core than that of the single-protofilament structure observed in WT SOD1. Although the single-protofilament form developed more slowly, cross-seeding experiments demonstrated the predominance of single-protofilament morphology over paired protofilaments, regardless of the presence of the Cys6 and Cys111 mutations. These findings highlight the importance of the number of amino acid residues within the filament core in determining the energy requirements for assembly. Our study provides insights into ALS pathogenesis by elucidating the initiation and propagation of filament formation, which potentially leads to deleterious amyloid filaments.

PMID:39874287 | DOI:10.1073/pnas.2408582122

J Med Chem. 2025 Jan 28. doi: 10.1021/acs.jmedchem.4c02415. Online ahead of print.

ABSTRACT

Molecular glue degraders (MGDs) are small molecules that facilitate proximity between a target protein and an E3 ubiquitin ligase, thereby inducing target protein degradation. Glutarimide-containing compounds are MGDs that bind cereblon (CRBN) and recruit neosubstrates. Through explorative synthesis of a glutarimide-based library, we discovered a series of molecules that induce casein kinase 1 alpha (CK1α) degradation. By scaffold hopping and rational modification of the chemical scaffold, we identified an imidazo[1,2-a]pyrimidine compound that induces potent and selective CK1α degradation. A structure-activity relationship study of the lead compound, QXG-6442, identified the chemical features that contribute to degradation potency and selectivity compared to other frequently observed neosubstrates. The glutarimide library screening and structure-activity relationship medicinal chemistry approach we employed is generally useful for developing new molecular glue degraders toward new targets of interest.

PMID:39873536 | DOI:10.1021/acs.jmedchem.4c02415

Bio Protoc. 2025 Jan 20;15(2):e5163. doi: 10.21769/BioProtoc.5163. eCollection 2025 Jan 20.

ABSTRACT

Nicotinic acetylcholine receptors (nAChRs) are a family of ligand-gated ion channels expressed in nervous and non-nervous system tissue important for memory, movement, and sensory processes. The pharmacological targeting of nAChRs, using small molecules or peptides, is a promising approach for the development of compounds for the treatment of various human diseases including inflammatory and neurogenerative disorders such as Alzheimer's disease. Using the Aplysia californica acetylcholine binding protein (Ac-AChBP) as an established structural surrogate for human homopentameric α7 nAChRs, we describe an innovative protein painting mass spectrometry (MS) method that can be used to identify interaction sites for various ligands at the extracellular nAChR site. We describe how the use of small molecule dyes can be optimized to uncover contact sites for ligand-protein interactions based on MS detection. Protein painting MS has been recently shown to be an effective tool for the identification of residues within Ac-AChBP involved in the binding of know ligands such as α-bungarotoxin. This strategy can be used with computational structural modeling to identify binding regions involved in drug targeting at the nAChR. Key features • Identify binding ligands of nicotinic receptors based on similarity with the acetylcholine binding protein. • Can be adapted to test various ligands and binding conditions. • Mass spectrometry identification of specific amino acid residues that contribute to protein binding. • Can be effectively coupled to structural modeling analysis.

PMID:39872720 | PMC:PMC11769746 | DOI:10.21769/BioProtoc.5163

Bio Protoc. 2025 Jan 20;15(2):e5169. doi: 10.21769/BioProtoc.5169. eCollection 2025 Jan 20.

ABSTRACT

Primary neuronal culture and transient transfection offer a pair of crucial tools for neuroscience research, providing a controlled environment to study the behavior, function, and interactions of neurons in vitro. These cultures can be used to investigate fundamental aspects of neuronal development and plasticity, as well as disease mechanisms. There are numerous methods of transient transfection, such as electroporation, calcium phosphate precipitation, or cationic lipid transfection. In this protocol, we used electroporation for neurons immediately before plating and cationic lipid transfection for neurons that have been cultured for a few days in vitro. In our experience, the transfection efficiency of electroporation can be as high as 30%, and cationic lipid transfection has an efficiency of 1%-2%. While cationic lipid transfection has much lower efficiency than electroporation, it does offer the advantage of a higher expression level. Therefore, these transfection methods are suitable for different stages of neurons and different expression requirements. Key features • Culture of primary neurons from the CNS. • Electroporation for freshly isolated neurons in suspension. • Cationic lipid transfection for adherent neurons.

PMID:39872712 | PMC:PMC11769751 | DOI:10.21769/BioProtoc.5169

Life Med. 2024 Nov 25;3(6):lnae039. doi: 10.1093/lifemedi/lnae039. eCollection 2024 Dec.

NO ABSTRACT

PMID:39872152 | PMC:PMC11761737 | DOI:10.1093/lifemedi/lnae039

bioRxiv [Preprint]. 2025 Jan 17:2025.01.15.633240. doi: 10.1101/2025.01.15.633240.

ABSTRACT

Deep learning sequence models trained on personalized genomics can improve variant effect prediction, however, applications of these models are limited by computational requirements for storing and reading large datasets. We address this with GenVarLoader, which stores personalized genomic data in new memory-mapped formats with optimal data locality to achieve ~1,000x faster throughput and ~2,000x better compression compared to existing alternatives.

PMID:39868273 | PMC:PMC11761601 | DOI:10.1101/2025.01.15.633240

bioRxiv [Preprint]. 2025 Jan 13:2025.01.13.632696. doi: 10.1101/2025.01.13.632696.

ABSTRACT

Autophagy is an essential cellular process which functions to maintain homeostasis in response to stressors such as starvation or infection. Here, we report that a subset of autophagy factors including ATG-3 play an antiviral role in Orsay virus infection of Caenorhabditis elegans. Orsay virus infection does not modulate autophagic flux, and re-feeding after starvation limits Orsay virus infection and blocks autophagic flux, suggesting that the role of ATG-3 in Orsay virus susceptibility is independent of its role in maintaining autophagic flux. atg-3 mutants phenocopy rde-1 mutants, which have a defect in RNA interference (RNAi), in susceptibility to Orsay virus infection and transcriptional response to infection. However, atg-3 mutants do not exhibit defects in RNAi. Additionally, atg-3 limits viral infection at a post-entry step, similar to rde-1 mutants. Differential expression analysis using RNA sequencing revealed that antiviral sqt-2, which encodes a collagen trimer protein, is depleted in naïve and infected atg-3 mutants, as well as in infected WT animals, as are numerous other collagen genes. These data suggest that ATG-3 has a role in collagen organization pathways that function in antiviral defense in C. elegans.

PMID:39868230 | PMC:PMC11761658 | DOI:10.1101/2025.01.13.632696

bioRxiv [Preprint]. 2025 Jan 14:2025.01.13.632860. doi: 10.1101/2025.01.13.632860.

ABSTRACT

Success of phage therapies is limited by bacterial defenses against phages. While a large variety of anti-phage defense mechanisms has been characterized, how expression of these systems is distributed across individual cells and how their combined activities translate into protection from phages has not been studied. Using bacterial single-cell RNA sequencing, we profiled the transcriptomes of ~50,000 cells from cultures of a human pathobiont, Bacteroides fragilis, infected with a lytic bacteriophage. We quantified the asynchronous progression of phage infection in single bacterial cells and reconstructed the infection timeline, characterizing both host and phage transcriptomic changes as infection unfolded. We discovered a subpopulation of bacteria that remained uninfected and determined the heterogeneously expressed host factors associated with protection. Each cell's vulnerability to phage infection was defined by combinatorial phase-variable expression of multiple genetic loci, including capsular polysaccharide (CPS) biosynthesis pathways, restriction-modification systems (RM), and a previously uncharacterized operon likely encoding fimbrial genes. By acting together, these heterogeneously expressed phase-variable systems and anti-phage defense mechanisms create a phenotypic landscape where distinct protective combinations enable the survival and re-growth of bacteria expressing these phenotypes without acquiring additional mutations. The emerging model of complementary action of multiple protective mechanisms heterogeneously expressed across an isogenic bacterial population showcases the potent role of phase variation and stochasticity in bacterial anti-phage defenses.

PMID:39868116 | PMC:PMC11761130 | DOI:10.1101/2025.01.13.632860

Clin Transl Med. 2025 Feb;15(2):e70201. doi: 10.1002/ctm2.70201.

NO ABSTRACT

PMID:39871108 | DOI:10.1002/ctm2.70201

Nat Methods. 2025 Jan 27. doi: 10.1038/s41592-024-02571-5. Online ahead of print.

NO ABSTRACT

PMID:39870863 | DOI:10.1038/s41592-024-02571-5

Nat Commun. 2025 Jan 27;16(1):1085. doi: 10.1038/s41467-025-56164-7.

NO ABSTRACT

PMID:39870666 | DOI:10.1038/s41467-025-56164-7

J Neurosci. 2025 Jan 27:e0053212025. doi: 10.1523/JNEUROSCI.0053-21.2025. Online ahead of print.

ABSTRACT

Neurons in the cerebral cortex and hippocampus discharge synchronously in brain state-dependent manner to transfer information. Published studies have highlighted the temporal coordination of neuronal activities between the hippocampus and a neocortical area, however, how the spatial extent of neocortical activity relates to hippocampal activity remains partially unknown. We imaged mesoscopic neocortical activity while recording hippocampal local field potentials in anesthetized and unanesthetized GCaMP-expressing transgenic mice. We found that neocortical activity elevates around hippocampal sharp wave ripples (SWR). SWR-associated neocortical activities occurred predominantly in vision-related regions including visual, retrosplenial and frontal cortex. While pre-SWR neocortical activities were frequently observed in awake and natural sleeping states, post-SWR neocortical activity decreased significantly in the latter. Urethane anesthetized mice also exhibited SWR-correlated calcium elevation, but in longer time scale than observed in natural sleeping mice. During hippocampal theta oscillation states, phase-locked oscillations of calcium activity were observed throughout the entire neocortical areas. In addition, possible environmental effects on neocortico-hippocampal dynamics were assessed in this study by comparing mice reared in ISO (isolated condition) and ENR (enriched environment). In both SWR and theta oscillations, mice reared in ISO exhibited clearer brain state-dependent dynamics than those reared in ENR. Our data demonstrate that the neocortex and hippocampus exhibit heterogeneous activity patterns that characterize brain states, and postnatal experience plays a significant role in modulating these patterns.Significant Statement The hippocampus is a center for memory formation. However, the memory formed in the hippocampus is not stored forever, but gradually transferred into the cerebral cortex synchronized activities between the neocortex and hippocampus has been hypothesized (for hippocampus-independent memory see (Sutherland and Rudy, 1989)). However, spatio-temporal dynamics between hippocampus and whole neocortical areas remains partially unexplored. We measured cortical calcium activities with hippocampal electroencephalogram (EEG) simultaneously and found that the activities of widespread neocortical areas are temporally associated with hippocampal EEG. The neocortico-hippocampal dynamics is primarily regulated by animal awake/sleep state. Even if similar EEG patters were observed, temporal dynamics between the neocortex and hippocampus exhibit distinct patterns between awake and sleep period. In addition, animals' postnatal experience modulates the dynamics.

PMID:39870530 | DOI:10.1523/JNEUROSCI.0053-21.2025

Am J Cardiol. 2025 Jan 25:S0002-9149(25)00039-6. doi: 10.1016/j.amjcard.2025.01.015. Online ahead of print.

ABSTRACT

Advances in personalized medicine and Systems Biology have introduced probabilistic models and error discovery to cardiovascular care, aiding disease prevention and procedural planning. However, clinical application faces cultural, technical, and methodological hurdles. Patient autonomy remains essential, with shared decision-making (SDM) gaining importance in managing complex cardiovascular treatment options. Effective SDM relies on collaboration between providers and patients, guided by P5 Medicine principles, which combine psycho-cognitive considerations with predictive, personalized, preventive, and participatory care. Here we propose a three-step methodological proposal for implementing SDM and enhancing consent acquisition in cardiovascular care. The approach emphasizes personalized patient engagement and the need for clear, comprehensive consent processes. It identifies and addresses significant gaps in current practices, including the complexity of consent language, information dispersion, and the specific needs of vulnerable populations. Issues of Medical Responsibility and/or Liability may raise in the case of absence of consent acquisition or invalid consent due to insufficient/incorrect information. The International Guidelines on Medico-Legal Methods of Ascertainment and Evaluation Criteria are reported. In conclusion, the paper proposes practical solutions, including the use of artificial intelligence (AI) to enhance decision-making and patient counseling, and strategies to ensure that consent processes are both thorough and legally sound and respectful to the individual's autonomy.

PMID:39870321 | DOI:10.1016/j.amjcard.2025.01.015

Brain Behav Immun. 2025 Jan 25:S0889-1591(25)00025-X. doi: 10.1016/j.bbi.2025.01.016. Online ahead of print.

ABSTRACT

This study investigated the neural correlates of perceiving visual contagion cues characteristic of respiratory infections through functional magnetic resonance imaging (fMRI). Sixty-two participants (32f/ 30 m; ∼25 years on average) watched short videos depicting either contagious or non-contagious everyday situations, while their brain activation was continuously measured. We further measured the release of secretory immunoglobulin A (sIgA) in saliva to examine the first-line defensive response of the mucosal immune system. Perceiving sneezing and sick individuals compared to non-contagious individuals triggered increased activation in the anterior insula and other regions of the neuroimmune axis, that have been implicated in the somatosensory representation of the respiratory tract, and further led to increased release of sIgA. In line with predictions, this contagion cue-related activation of the insula was positively correlated with both perceived contagiousness and disgust evoked by the videos, as well as with the mucosal sIgA response. In contrast, the amygdala exhibited heightened activation to all videos featuring humans, regardless of explicit signs of contagion, indicating a nonspecific alertness to human presence. Nevertheless, amygdala activation was also correlated with the disgust ratings of each video. Collectively, these findings outline a neuroimmune mechanism for the processing of respiratory contagion cues. While the insula coordinates central and peripheral immune activation to match the perceived contagion threat, supposedly by triggering both increased sIgA release and contagion-related cognitions, the amygdala may rather act as an alerting system for social situations with a heightened transmission risk. This proactive neuroimmune response may help humans to manage contagion risks, that are difficult to avoid, by activating physiological and cognitive countermeasures in reaction to typical symptoms of respiratory infection, which prepares the organism for subsequent pathogen exposure.

PMID:39870198 | DOI:10.1016/j.bbi.2025.01.016

PLoS Genet. 2025 Jan 27;21(1):e1011577. doi: 10.1371/journal.pgen.1011577. Online ahead of print.

ABSTRACT

Some animals can regenerate large missing regions of their nervous system, requiring mechanisms to restore the pattern, numbers, and wiring of diverse neuron classes. Because injuries are unpredictable, regeneration must be accomplished from an unlimited number of starting points. Coordinated regeneration of neuron-glia architecture is thus a major challenge and remains poorly understood. In planarians, neurons and glia are regenerated from distinct progenitors. We found that planarians first regenerate neurons expressing a Delta-encoding gene, delta-2, at key positions in the central and peripheral nervous systems. Planarian glia are specified later from dispersed Notch-1-expressing mesoderm-like phagocytic progenitors. Inhibition of delta-2 or notch-1 severely reduced glia in planarians, but did not affect the specification of other phagocytic cell types. Loss of several delta-2-expressing neuron classes prevented differentiation of the glia associated with them, whereas transplantation of delta-2-expressing photoreceptor neurons was sufficient for glia formation at an ectopic location. Our results suggest a model in which patterned delta-2-expressing neurons instruct phagocytic progenitors to locally differentiate into glia, presenting a mechanism for coordinated regeneration of numbers and pattern of cell types.

PMID:39869602 | DOI:10.1371/journal.pgen.1011577

Int J Syst Evol Microbiol. 2025 Jan;75(1). doi: 10.1099/ijsem.0.006648.

ABSTRACT

An obligately anaerobic, spore-forming sulphate-reducing bacterium, strain SB140T, was isolated from a long-term continuous enrichment culture that was inoculated with peat soil from an acidic fen. Cells were immotile, slightly curved rods that stained Gram-negative. The optimum temperature for growth was 28 °C. Strain SB140T grew at pH 4.0-7.5 with an optimum pH of 6.0-7.0 using various electron donors and electron acceptors. Yeast extract, sugars, alcohols and organic acids were used as electron donors for sulphate reduction. SB140T additionally used elemental sulphur and nitrate as electron acceptors but not sulphite, thiosulphate or iron(III) provided as ferrihydrite and fumarate. The 16S rRNA gene sequence placed strain SB140T in the genus Desulfosporosinus of the phylum Bacillota. The predominant cellular fatty acids were iso-C15 : 0 (52.6%) and 5,7 C15 : 2 (19.9%). The draft genome of SB140T (5.42 Mbp in size) shared 77.4% average nucleotide identity with the closest cultured relatives Desulfosporosinus acididurans M1T and Desulfosporosinus acidiphilus SJ4T. On the basis of phenotypic, phylogenetic and genomic characteristics, SB140T was identified as a novel species within the genus Desulfosporosinus, for which we propose the name Desulfosporosinus paludis sp. nov. The type strain is SB140T (=DSM 117342T=JCM 39521T).

PMID:39869511 | DOI:10.1099/ijsem.0.006648

J Virol. 2025 Jan 27:e0171724. doi: 10.1128/jvi.01717-24. Online ahead of print.

ABSTRACT

The imperative for developing robust tools to detect, analyze, and characterize viruses has become increasingly evident as they continue to threaten human health. In this review, we focus on recent advancements in studying human viruses with flow virometry (FV), an emerging technique that has gained considerable momentum over the past 5 years. These advancements include the application of FV in viral surface phenotyping, viral protein functionality, virus sorting, vaccine development, and diagnostics. With examples illustrated using primary data from our recent studies, we demonstrate that FV is a powerful yet underutilized methodology that, when employed with best practices and experimental rigor, can be highly valuable for studying individual virion heterogeneity, virus phenotypes, and virus-antibody interactions. In this review, we also address the current challenges when performing FV studies, propose strategies to overcome these obstacles, and outline best practices for both new and experienced researchers. Finally, we discuss the promising future prospects of FV within the broader context of virology research.

PMID:39868829 | DOI:10.1128/jvi.01717-24

Biol Aujourdhui. 2024;218(3-4):91-98. doi: 10.1051/jbio/2024009. Epub 2025 Jan 27.

ABSTRACT

The advent of high-throughput omics data and the generation of new algorithms provide the biologists with the opportunity to explore living processes in the context of systems biology aiming at revealing the gene interactions, the networks underlying complex cellular functions. In this article, we discuss two methods for gene network reconstruction, WGCNA (Weighted Gene Correlation Network Analysis) developed by Steve Horvath and collaborators in 2008, and MIIC (Multivariate Information-based Inductive Causation) developed by Hervé Isambert and his team in 2017 and 2024. These two methods are complementary, WGCNA generating undirected networks in which most gene-to-gene interactions are indirect, while MIIC reveals direct interactions and some causal links. We illustrate these aspects according to our own work aiming at identifying the gene interactions underlying the hematopoietic stem cell supportive activity of mesenchymal stromal cells at an early developmental stage.

PMID:39868708 | DOI:10.1051/jbio/2024009

Plant J. 2025 Jan;121(2):e17220. doi: 10.1111/tpj.17220.

ABSTRACT

The traditional Chinese medicinal plant Prunella vulgaris contains numerous triterpene saponin metabolites, notably ursolic and oleanolic acid saponins, which have significant pharmacological values. Despite their importance, the genes responsible for synthesizing these triterpene saponins in P. vulgaris remain unidentified. This study used a comprehensive screening methodology, combining phylogenetic analysis, gene expression assessment, metabolome-transcriptome correlation and co-expression analysis, to identify candidate genes involved in triterpene saponins biosynthesis. Nine candidate genes - two OSCs, three CYP716s and four UGT73s - were precisely identified from large gene families comprising hundreds of members. These genes were subjected to heterologous expression and functional characterization, with enzymatic activity assays confirming their roles in the biosynthetic pathway, aligning with bioinformatics predictions. Analysis revealed that these genes originated from a whole-genome duplication (WGD) event in P. vulgaris, highlighting the potential importance of WGD for plant metabolism. This study addresses the knowledge gap in the biosynthesis of triterpene saponins in P. vulgaris, establishing a theoretical foundation for industrial production via synthetic biology. Additionally, we present an efficient methodological protocol that integrates evolutionary principles and bioinformatics techniques in metabolite biosynthesis research. This approach holds significant value for studies focused on unraveling various biosynthetic pathways.

PMID:39868644 | DOI:10.1111/tpj.17220