BMC Ecol Evol. 2024 Oct 18;24(1):128. doi: 10.1186/s12862-024-02311-5.

ABSTRACT

BACKGROUND: With the advances in high-throughput sequencing and bioinformatic pipelines, mitochondrial genomes have become increasingly popular for phylogenetic analyses across different clades of invertebrates. Despite the vast rise in available mitogenomic datasets of molluscs, one class of aplacophoran molluscs - Solenogastres (or Neomeniomorpha) - is still neglected.

RESULTS: Here, we present six new mitochondrial genomes from five families of Solenogastres (Amphimeniidae, Gymnomeniidae, Proneomeniidae, Pruvotinidae, Simrothiellidae), including the first complete mitogenomes, thereby now representing three of the four traditional orders. Solenogaster mitogenomes are variable in size (ranging from approximately 15,000 bp to over 17,000 bp). The gene order of the 13 protein coding genes and two rRNA genes is conserved in three blocks, but considerable variation occurs in the order of the 22 tRNA genes. Based on phylogenetic analyses and reconstruction of ancestral mitochondrial genomes of Aculifera, the position of (1) trnD gene between atp8 and atp6, (2) trnT and P genes between atp6 and nad5, and (3) trnL1 gene between G and E, resulting in a 'MCYWQGL1E'-block of tRNA genes, are all three considered synapomorphies for Solenogastres. The tRNA gene block 'KARNI' present in Polyplacophora and several conchiferan taxa is dissolved in Solenogastres.

CONCLUSION: Our study shows that mitogenomes are suitable to resolve the phylogenetic relationships among Aculifera and within Solenogastres, thus presenting a cost and time efficient compromise to approach evolutionary history in these clades.

PMID:39425046 | DOI:10.1186/s12862-024-02311-5

Nat Commun. 2024 Oct 18;15(1):9000. doi: 10.1038/s41467-024-52942-x.

ABSTRACT

Macrophages adopt distinct phenotypes in response to environmental cues, with type-2 cytokine interleukin-4 promoting a tissue-repair homeostatic state (M2IL4). Glucocorticoids (GC), widely used anti-inflammatory therapeutics, reportedly impart a similar phenotype (M2GC), but how such disparate pathways may functionally converge is unknown. We show using integrative functional genomics that M2IL4 and M2GC transcriptomes share a striking overlap mirrored by a shift in chromatin landscape in both common and signal-specific gene subsets. This core homeostatic program is enacted by transcriptional effectors KLF4 and the glucocorticoid receptor, whose genome-wide occupancy and actions are integrated in a stimulus-specific manner by the nuclear receptor cofactor GRIP1. Indeed, many of the M2IL4:M2GC-shared transcriptomic changes were GRIP1-dependent. Consistently, GRIP1 loss attenuated phagocytic activity of both populations in vitro and macrophage tissue-repair properties in the murine colitis model in vivo. These findings provide a mechanistic framework for homeostatic macrophage programming by distinct signals, to better inform anti-inflammatory drug design.

PMID:39424780 | DOI:10.1038/s41467-024-52942-x

Inflammation. 2024 Oct 19. doi: 10.1007/s10753-024-02167-3. Online ahead of print.

ABSTRACT

Acute lung injury (ALI) is primarily driven by an intense inflammation in the alveolar epithelium. Key to this is the pro-inflammatory cytokine, Interleukin 17 (IL-17), which influences pulmonary immunity and modifies p53 function. The direct role of IL-17A in p53-fibrinolytic system is still unclear, it is important to evaluate this mechanism to regulate the ALI progression to idiopathic pulmonary fibrosis (IPF). C57BL/6 mice, exposed to recombinant IL-17A protein and treated with curcumin, provided insight into IL-17A mechanisms and curcumin's potential for modulating early pulmonary fibrosis stages. A diverse methodology, including proteomics, single-cell RNA sequencing (scRNA-seq) integration, molecular, and Schroedinger approach were utilized. In silico approaches facilitated the potential interactions between curcumin, IL-17A, and apoptosis-related proteins. A notable surge in the expression levels of IL-17A, p53, and fibrinolytic components such as Plasminogen Activator Inhibitor-1 (PAI-I) was discerned upon the IL17A exposure in mouse lungs. Furthermore, the enrichment of pathways and differential expression of proteins underscored the significance of IL-17A in governing downstream regulatory pathways such as inflammation, NF-kappaB signaling, Mitogen-Activated Protein Kinases (MAPK), p53, oxidative phosphorylation, JAK-STAT, and apoptosis. The integration of scRNA-seq data from 20 IPF and 10 control lung specimens emphasized the importance of IL-17A mediated downstream regulation in PF patients. A potent immuno-pharmacotherapeutic agent, curcumin, demonstrated a substantial capacity to modulate the lung pathology and molecular changes induced by IL-17A in mouse lungs. Human IPF single cell data integration confirmed the effects of IL-17A mediated fibrinolytic components in ALI to IPF progression.

PMID:39424752 | DOI:10.1007/s10753-024-02167-3

Nat Biotechnol. 2024 Oct 18. doi: 10.1038/s41587-024-02447-1. Online ahead of print.

ABSTRACT

Current methods for analyzing chromatin architecture are not readily scalable to heterogeneous tissues. Here we introduce Droplet Hi-C, which uses a commercial microfluidic device for high-throughput, single-cell chromatin conformation profiling in droplets. Using Droplet Hi-C, we mapped the chromatin architecture of the mouse cortex and analyzed gene regulatory programs in major cortical cell types. In addition, we used this technique to detect copy number variations, structural variations and extrachromosomal DNA in human glioblastoma, colorectal and blood cancer cells, revealing clonal dynamics and other oncogenic events during treatment. We refined the technique to allow joint profiling of chromatin architecture and transcriptome in single cells, facilitating exploration of the links between chromatin architecture and gene expression in both normal tissues and tumors. Thus, Droplet Hi-C both addresses critical gaps in chromatin analysis of heterogeneous tissues and enhances understanding of gene regulation.

PMID:39424717 | DOI:10.1038/s41587-024-02447-1

Antiviral Res. 2024 Oct 16:106022. doi: 10.1016/j.antiviral.2024.106022. Online ahead of print.

ABSTRACT

There is an ongoing need to expand the anti-SARS-CoV-2 armamentarium to include agents capable of suppressing replication of drug-resistant mutants emerging during monotherapy with approved direct-acting antivirals. Using a subgenomic SARS-CoV-2 replicon system, we studied the RNA replication capacity of nirmatrelvir (NTV)-resistant mutants and their susceptibility to next-generation Mpro inhibitors, including ibuzatrelvir (ITV), ensitrelvir (ETV), and ML2006a4. Our findings revealed that E166V Mpro mutants reduced viral RNA replication, whereas other Mpro mutations retained or increased the replication capacity, suggesting the potential of the latter to dominate under NTV selective pressure. Except for having an advantage against E166A mutants, ITV largely showed the same mutational sensitivity as NTV. ETV was more effective than NTV against E166V mutants but less effective against S144A, E166A, and L167F mutants. ML2006a4 demonstrated the most effective suppression across most mutants (S144A, E166V, S144A+L50F, E166A/V+L50F, L167F+L50F, and E166A+L167F+L50F). Thus, ML2006a4 represents an attractive investigational candidate against clinically relevant NTV-resistant SARS-CoV-2 mutants.

PMID:39424074 | DOI:10.1016/j.antiviral.2024.106022

Plant Sci. 2024 Oct 16:112295. doi: 10.1016/j.plantsci.2024.112295. Online ahead of print.

ABSTRACT

Photosynthesis is an essential process in plants that synthesizes sugars used for growth and development, highlighting the importance of establishing robust methods to monitor photosynthetic activity. Infrared gas analysis (IRGA) can be used to track photosynthetic rates by measuring plant CO2 assimilation and release. Although much progress has been made in the development of IRGA technologies, challenges remain when using this technique on small herbaceous plants such as Arabidopsis thaliana. The use of whole plant chambers can overcome the difficulties associated with applying bulky leaf clamps to small delicate leaves. However, respiration from the roots and from soil-based microorganisms may skew these gas exchange measurements. Here, we present a simple method to efficiently perform IRGA on A. thaliana plants using a whole plant chamber that removes the confounding effects of respiration from roots and soil-based microorganisms from the measurements. We show that this method can be used to detect subtle changes in photosynthetic rates measured at different times of day, under different growth conditions, and between wild-type and plants with deficiencies in the photosynthetic machinery. Furthermore, we show that this method can be used to detect changes in photosynthetic rates even at very young developmental stages such as 10 d-old seedlings. This method contributes to the array of techniques currently used to perform IRGA on A. thaliana and can allow for the monitoring of photosynthetic rates of whole plants from young ages.

PMID:39423916 | DOI:10.1016/j.plantsci.2024.112295

Stem Cell Reports. 2024 Oct 8:S2213-6711(24)00269-8. doi: 10.1016/j.stemcr.2024.09.007. Online ahead of print.

ABSTRACT

Brain tumor stem cells (BTSCs) are a population of self-renewing malignant stem cells that play an important role in glioblastoma tumor hierarchy and contribute to tumor growth, therapeutic resistance, and tumor relapse. Thus, targeting of BTSCs within the bulk of tumors represents a crucial therapeutic strategy. Here, we report that edaravone is a potent drug that impairs BTSCs in glioblastoma. We show that edaravone inhibits the self-renewal and growth of BTSCs harboring a diverse range of oncogenic mutations without affecting non-oncogenic neural stem cells. Global gene expression analysis revealed that edaravone significantly alters BTSC transcriptome and attenuates the expression of a large panel of genes involved in cell cycle progression, stemness, and DNA repair mechanisms. Mechanistically, we discovered that edaravone directly targets Notchless homolog 1 (NLE1) and impairs Notch signaling pathway, alters the expression of stem cell markers, and sensitizes BTSC response to ionizing radiation (IR)-induced cell death. Importantly, we show that edaravone treatment in preclinical models delays glioblastoma tumorigenesis, sensitizes their response to IR, and prolongs the lifespan of animals. Our data suggest that repurposing of edaravone is a promising therapeutic strategy for patients with glioblastoma.

PMID:39423824 | DOI:10.1016/j.stemcr.2024.09.007

Cancer Cell. 2024 Oct 15:S1535-6108(24)00362-3. doi: 10.1016/j.ccell.2024.09.014. Online ahead of print.

ABSTRACT

Cancer neuroscience is a rapidly growing multidisciplinary field that conceptualizes tumors as tissues fully integrated into the nervous system. Recognizing the complexity and challenges in this field is of fundamental importance to achieving the goal of translational impact for cancer patients. Our commentary highlights key scientific priorities, optimal training settings, and roadblocks to translating scientific findings to the clinic in this emerging field, aiming to formulate a transformative and cohesive path forward.

PMID:39423816 | DOI:10.1016/j.ccell.2024.09.014

Cell. 2024 Oct 10:S0092-8674(24)01093-6. doi: 10.1016/j.cell.2024.09.035. Online ahead of print.

ABSTRACT

Fertilization, the basis for sexual reproduction, culminates in the binding and fusion of sperm and egg. Although several proteins are known to be crucial for this process in vertebrates, the molecular mechanisms remain poorly understood. Using an AlphaFold-Multimer screen, we identified the protein Tmem81 as part of a conserved trimeric sperm complex with the essential fertilization factors Izumo1 and Spaca6. We demonstrate that Tmem81 is essential for male fertility in zebrafish and mice. In line with trimer formation, we show that Izumo1, Spaca6, and Tmem81 interact in zebrafish sperm and that the human orthologs interact in vitro. Notably, complex formation creates the binding site for the egg fertilization factor Bouncer in zebrafish. Together, our work presents a comprehensive model for fertilization across vertebrates, where a conserved sperm complex binds to divergent egg proteins-Bouncer in fish and JUNO in mammals-to mediate sperm-egg interaction.

PMID:39423812 | DOI:10.1016/j.cell.2024.09.035

Diagn Microbiol Infect Dis. 2024 Oct 9;110(4):116556. doi: 10.1016/j.diagmicrobio.2024.116556. Online ahead of print.

ABSTRACT

The genus Phytobacter (fam. Enterobacteriaceae) includes species like Phytobacter diazotrophicus and Phytobacter ursingii, which have emerged as opportunistic human pathogens, particularly affecting vulnerable populations such as pre-term infants and immunocompromised patients. Traditional biochemical and molecular methods have struggled to accurately identify Phytobacter species in clinical diagnostics. This study addresses the issue by developing and validating two quantitative PCR (qPCR) assays using SYBR® Green I and TaqMan® technologies, targeting the nitrogen fixation regulatory gene (nifL) of Phytobacter spp. The SYBR® Green I assay showed a detection limit of a single cell per reaction, while the TaqMan® assay was easier to interpret due to the absence of background noise. These assays, validated with clinical isolates from Brazil, identified multiple new Phytobacter isolates, including a potentially novel species, providing improved diagnostic tools for detecting Phytobacter spp. and aiding in better clinical management.

PMID:39423472 | DOI:10.1016/j.diagmicrobio.2024.116556

STAR Protoc. 2024 Oct 16;5(4):103395. doi: 10.1016/j.xpro.2024.103395. Online ahead of print.

ABSTRACT

Quantifying immediate early gene expression as a marker of cellular activity in single-nuclei RNA sequencing data allows for the identification of neurons involved in specific behaviors. Here, we present a protocol for generating single-nuclei libraries from the mouse brain and identifying active cell populations following social interactions. We describe steps for the dissection, preparation, and analysis of the prefrontal cortex, hippocampus, and cerebellum. This protocol has the potential to be modified for any brain region or behavior of interest. For complete details on the use and execution of this protocol, please refer to Walker and Frost.1.

PMID:39423127 | DOI:10.1016/j.xpro.2024.103395

Anal Chem. 2024 Oct 18. doi: 10.1021/acs.analchem.4c04239. Online ahead of print.

ABSTRACT

The identification and characterization of immune cell subpopulations are critical to reveal cell development throughout life and immune responses to environmental factors. Next-generation sequencing technologies have dramatically advanced single-cell genomics and transcriptomics for immune cell classification. However, gene expression is often not correlated with protein expression, and immunotyping is mostly accepted in protein format. Current single-cell proteomic technologies are either limited in multiplex capacity or not sensitive enough to detect the critical functional proteins. Herein, we present a single-cell cyclic multiplex in situ tagging (CycMIST) technology to simultaneously measure >400 proteins, a scale of >10 times than similar technologies. Such an ultrahigh multiplexity is achieved by reiterative staining of the single cells coupled with a MIST array for detection. This technology has been thoroughly validated through comparison with flow cytometry and fluorescence immunostaining techniques. Both peripheral blood mononuclear cells (PBMCs) and T cells are analyzed by the CycMIST technology, and almost the entire spectrum of cluster of differentiation (CD) surface markers has been measured. The landscape of fluctuation of CD protein expression in single cells has been uncovered by our technology. Further study found T cell activation signatures and protein-protein networks. This study represents the highest multiplexity of single immune cell marker measurement targeting functional proteins. With additional information from intracellular proteins of the same single cells, our technology can potentially facilitate mechanistic studies of immune responses under various disease conditions.

PMID:39422499 | DOI:10.1021/acs.analchem.4c04239

ISME Commun. 2024 Sep 23;4(1):ycae113. doi: 10.1093/ismeco/ycae113. eCollection 2024 Jan.

ABSTRACT

The continental deep biosphere contains a vast reservoir of microorganisms, although a large proportion of its diversity remains both uncultured and undescribed. In this study, the metabolic potential (metagenomes) and activity (metatranscriptomes) of the microbial communities in Fennoscandian Shield deep subsurface groundwaters were characterized with a focus on novel taxa. DNA sequencing generated 1270 de-replicated metagenome-assembled genomes and single-amplified genomes, containing 7 novel classes, 34 orders, and 72 families. The majority of novel taxa were affiliated with Patescibacteria, whereas among novel archaea taxa, Thermoproteota and Nanoarchaeota representatives dominated. Metatranscriptomes revealed that 30 of the 112 novel taxa at the class, order, and family levels were active in at least one investigated groundwater sample, implying that novel taxa represent a partially active but hitherto uncharacterized deep biosphere component. The novel taxa genomes coded for carbon fixation predominantly via the Wood-Ljungdahl pathway, nitrogen fixation, sulfur plus hydrogen oxidation, and fermentative pathways, including acetogenesis. These metabolic processes contributed significantly to the total community's capacity, with up to 9.9% of fermentation, 6.4% of the Wood-Ljungdahl pathway, 6.8% of sulfur plus 8.6% of hydrogen oxidation, and energy conservation via nitrate (4.4%) and sulfate (6.0%) reduction. Key novel taxa included the UBA9089 phylum, with representatives having a prominent role in carbon fixation, nitrate and sulfate reduction, and organic and inorganic electron donor oxidation. These data provided insights into deep biosphere microbial diversity and their contribution to nutrient and energy cycling in this ecosystem.

PMID:39421601 | PMC:PMC11484514 | DOI:10.1093/ismeco/ycae113

PeerJ. 2024 Oct 14;12:e18229. doi: 10.7717/peerj.18229. eCollection 2024.

ABSTRACT

Freshwater crayfish are amongst the largest macroinvertebrates and play a keystone role in the ecosystems they occupy. Understanding the global distribution of these animals is often hindered due to a paucity of distributional data. Additionally, non-native crayfish introductions are becoming more frequent, which can cause severe environmental and economic impacts. Management decisions related to crayfish and their habitats require accurate, up-to-date distribution data and mapping tools. Such data are currently patchily distributed with limited accessibility and are rarely up-to-date. To address these challenges, we developed a versatile e-portal to host distributional data of freshwater crayfish and their pathogens (using Aphanomyces astaci, the causative agent of the crayfish plague, as the most prominent example). Populated with expert data and operating in near real-time, World of Crayfish™ is a living, publicly available database providing worldwide distributional data sourced by experts in the field. The database offers open access to the data through specialized standard geospatial services (Web Map Service, Web Feature Service) enabling users to view, embed, and download customizable outputs for various applications. The platform is designed to support technical enhancements in the future, with the potential to eventually incorporate various additional features. This tool serves as a step forward towards a modern era of conservation planning and management of freshwater biodiversity.

PMID:39421415 | PMC:PMC11485098 | DOI:10.7717/peerj.18229

Brain Commun. 2024 Sep 19;6(5):fcae326. doi: 10.1093/braincomms/fcae326. eCollection 2024.

ABSTRACT

Creating a mouse model that recapitulates human tau pathology is essential for developing strategies to intervene in tau-induced neurodegeneration. However, mimicking the pathological features seen in human pathology often involves a trade-off with artificial effects such as unexpected gene insertion and neurotoxicity from the expression system. To overcome these issues, we developed the rTKhomo mouse model by combining a transgenic CaMKII-tTA system with a P301L mutated 1N4R human tau knock-in at the Rosa26 locus with a C57BL/6J background. This model closely mimics human tau pathology, particularly in the hippocampal CA1 region, showing age-dependent tau accumulation, neuronal loss and neuroinflammation. Notably, whole-brain 3D staining and light-sheet microscopy revealed a spatial gradient of tau deposition from the entorhinal cortex to the hippocampus, similar to the spatial distribution of Braak neurofibrillary tangle staging. Furthermore, [18F]PM-PBB3 positron emission tomography imaging enabled the quantification and live monitoring of tau deposition. The rTKhomo mouse model shows potential as a promising next-generation preclinical tool for exploring the mechanisms of tauopathy and for developing interventions targeting the spatial progression of tau pathology.

PMID:39420962 | PMC:PMC11483584 | DOI:10.1093/braincomms/fcae326

Plant Cell Environ. 2024 Oct 17. doi: 10.1111/pce.15234. Online ahead of print.

NO ABSTRACT

PMID:39420656 | DOI:10.1111/pce.15234

NPJ Syst Biol Appl. 2024 Oct 18;10(1):121. doi: 10.1038/s41540-024-00452-3.

ABSTRACT

The cell cycle of budding yeast is governed by an intricate protein regulatory network whose dysregulation can lead to lethal mistakes or aberrant cell division cycles. In this work, we model this network in a Boolean framework for stochastic simulations. Our model is sufficiently detailed to account for the phenotypes of 40 mutant yeast strains (83% of the experimentally characterized strains that we simulated) and also to simulate an endoreplicating strain (multiple rounds of DNA synthesis without mitosis) and a strain that exhibits 'Cdc14 endocycles' (periodic transitions between metaphase and anaphase). Because our model successfully replicates the observed properties of both wild-type yeast cells and many mutant strains, it provides a reasonable, validated starting point for more comprehensive stochastic-Boolean models of cell cycle controls. Such models may provide a better understanding of cell cycle anomalies in budding yeast and ultimately in mammalian cells.

PMID:39420008 | DOI:10.1038/s41540-024-00452-3

Life Sci Alliance. 2024 Oct 17;8(1):e202403053. doi: 10.26508/lsa.202403053. Print 2025 Jan.

ABSTRACT

Ischemic conditions such as hypoxia and nutrient starvation, together with interactions with stromal cells, are critical drivers of metastasis. These conditions arise deep within tumor tissues, and thus, observing nascent metastases is exceedingly challenging. We thus developed the 3MIC-an ex vivo model of the tumor microenvironment-to study the emergence of metastatic features in tumor cells in a 3-dimensional (3D) context. Here, tumor cells spontaneously create ischemic-like conditions, allowing us to study how tumor spheroids migrate, invade, and interact with stromal cells under different metabolic conditions. Consistent with previous data, we show that ischemia increases cell migration and invasion, but the 3MIC allowed us to directly observe and perturb cells while they acquire these pro-metastatic features. Interestingly, our results indicate that medium acidification is one of the strongest pro-metastatic cues and also illustrate using the 3MIC to test anti-metastatic drugs on cells experiencing different metabolic conditions. Overall, the 3MIC can help dissecting the complexity of the tumor microenvironment for the direct observation and perturbation of tumor cells during the early metastatic process.

PMID:39419548 | DOI:10.26508/lsa.202403053

Neuroscience. 2024 Oct 15:S0306-4522(24)00519-0. doi: 10.1016/j.neuroscience.2024.10.015. Online ahead of print.

ABSTRACT

Chronic pain is prevalent among aging adults. Epidemiologic evidence has demonstrated that individuals with chronic pain have accelerated memory decline and increased probability of dementia. Neurophysiologic, molecular, and pharmacologic hypotheses have been proposed to explain the relationship between chronic pain and cognitive decline, but there remains currently limited evidence supporting any of these. Here, we integrate multi-omic data across human cohorts and rodent species and demonstrate that methylation in the prefrontal cortex induced by chronic pain specifically targets transcriptional networks associated with cognitive ability, memory, and Alzheimer's disease in humans. We validate this with multiple independent data sets and identify cortical microglia as a likely mechanism by which chronic pain can increase dementia risk. Our analyses support the molecular hypothesis for the role of chronic pain in cognitive decline and identifies several potential therapeutic targets.

PMID:39419469 | DOI:10.1016/j.neuroscience.2024.10.015

Biochim Biophys Acta Rev Cancer. 2024 Oct 15:189199. doi: 10.1016/j.bbcan.2024.189199. Online ahead of print.

ABSTRACT

Bladder cancer (BCa) is the most common malignant tumor of the urinary system. Current treatments often have poor efficacy and carry a high risk of recurrence and progression due to the lack of consideration of tumor heterogeneity. Patient-derived organoids (PDOs) are three-dimensional tissue cultures that preserve tumor heterogeneity and clinical relevance better than cancer cell lines. Moreover, PDOs are more cost-effective and efficient to cultivate compared to patient-derived tumor xenografts, while closely mirroring the tissue and genetic characteristics of their source tissues. The development of PDOs involves critical steps such as sample selection and processing, culture medium optimization, matrix selection, and improvements in culture methods. This review summarizes the methodologies for generating PDOs from patients with BCa and discusses the current advancements in drug sensitivity testing, immunotherapy, living biobanks, drug screening, and mechanistic studies, highlighting their role in advancing personalized medicine.

PMID:39419296 | DOI:10.1016/j.bbcan.2024.189199