bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multifaceted Actions of Neurosteroids
Authors: Kumar Ajeet , Qian Mingxing , Xu Yuanjian , Benz Ann , Covey Douglas F. , Zorumski Charles F. , Mennerick Steven 
Published: January 2025

ABSTRACTBackground and purposeNeurosteroids modulate neuronal function and are promising therapeutic agents for neuropsychiatric disorders. Neurosteroid analogues are approved for treating postpartum depression and are of interest in other disorders. GABA-A receptors are well characterized targets of natural neurosteroids, but other biological pathways are likely relevant to therapeutic mechanisms and/or to off-target effects. We performed hypothesis-generatingin silicoanalyses and broadin vitrobiological screens to assess the range of actions of neurosteroids analogues of varying structural attributes.Key ResultsWe employedin silicomolecular similarity analysis and network pharmacology to elucidate likely targets. This analysis confirmed likely targets beyond GABA-A receptors. We then functionally screened 19 distinct neurosteroid structures across 78 targets representing interconnected signaling pathways, complemented with a limited screen of kinase activation. Results revealed unanticipated modulation of targets by neurosteroids with some structural selectivity. Many compounds-initiated androgen receptor translocation with little or no enantioselectivity. Modulation of multiple G-protein receptors was also unexpected.Conclusions and implicationsNeurosteroids are ascendant treatments in neuropsychiatry, but their full spectrum of actions remains unclear. This virtual and biological screening discovery approach opens new vistas for exploring mechanism of neurosteroids analogues. The multifaceted approach provides an unbiased, holistic exploration of the potential effects of neurosteroids across various molecular targets and provides a platform for future validation studies to aid drug discovery.
DUX4-stimulated genes define the antiviral response to herpesviruses in human trophoblasts
Authors: Hatterschide Joshua , Yang Liheng , Coyne Carolyn B. 
Published: January 2025

AbstractThe placenta serves as a barrier against the vertical transmission of viruses, due to the protective functions of fetal-derived trophoblasts. Although some antiviral programs of trophoblasts are well-documented, our understanding of how trophoblasts respond to teratogenic viruses remains incomplete. To address this, we profiled the transcriptional responses of human trophoblast organoids to seven teratogenic viruses. We discovered that herpesviruses including HSV-1, HSV-2, and HCMV did not trigger an interferon (IFN) response but instead induced the expression ofDUX4and downstream target genes, termed DUX4-stimulated genes (DSGs). This program was uniquely, highly expressed in trophoblasts. Through single-cell RNA sequencing, we defined the trophoblast response toDUX4and demonstrated that this program defines cells with low viral transcripts following HSV-1 infection. Similar to the IFN-stimulated genes, we observed that many DSGs with diverse predicted functions exhibited anti-herpesvirus activity. These findings establish DUX4 and DSGs as a critical antiviral defense mechanism in trophoblasts.
Macrophage depletion restores the DRG microenvironment and prevents axon degeneration in bortezomib-induced neuropathy
Authors: Thomsen Michael B. , Singh Abhishek , Thebeau Christina N. , Gao Vivian D. , Schulze Nicholas F. , Avraham Oshri , Yang Sarah X. , Koneru Shriya , Geier Sami S. , Landon Shannon M. , Pelea Aidan , Cavalli Valeria , Geisler Stefanie 
Published: January 2025

AbstractPeripheral neuropathy is a common and debilitating side effect of the chemotherapeutic bortezomib (BTZ). To explore the mechanisms underlying BTZ-induced neuropathy (BIPN), we developed a mouse model that replicates the route of administration and approximates the prolonged BTZ exposure experienced by patients. We find that male mice treated with BTZ experience more severe sensorimotor dysfunction and axon loss compared to females and observed similar results when analyzing human data. Using single cell RNA-sequencing, we reveal that BTZ significantly alters the dorsal root ganglia (DRG) microenvironment in mice, producing pronounced sex-specific changes in satellite glial cells (SGCs) in males and females and dysregulation of the extracellular matrix (ECM), particularly in males. These changes are accompanied by expansion of macrophages, which is more pronounced in males. We identify four macrophage subtypes in the DRG, including a pro-fibrotic population that is exclusively associated with BIPN. Depletion of macrophages via anti-CSF1R treatment in male mice prevents BTZ-induced SGC activation and aberrant collagen deposition in DRGs, potently preserves peripheral axons, and improves functional outcomes. These findings highlight SGCs, neuroinflammation and dysregulation of the ECM as drivers of sex-specific differences in BIPN and suggest that targeting neuroinflammation is a promising therapeutic strategy to treat this disease.One Sentence SummaryInflammation and neurofibrosis in DRGs underlie sex-specific differences in bortezomib-induced neuropathy and are promising treatment targets.
Accessible and accurate cytometry analysis using fluorescence microscopes
Authors: Foyt Daniel , Kuang Yiming , Rehem Samma , Yserentant Klaus , Huang Bo 
Published: January 2025

AbstractWe have developed a method along with a python-based analysis tool to capture images and produce flow cytometry like data utilizing simple accessible microscopes. Utilizing the recently developed generalist algorithms for cell segmentation, our approach easily segments semi-adherent or suspended cells facilitating quantification of fluorescent intensity similar to flow cytometry. We have shown that our approach exhibits similar speed and enhanced sensitivity when compared to typical flow cytometry. The utility of our approach is demonstrated by screening a set of 88 prime editing conditions utilizing the integration of mNeonGreen11as a reporter.
Construction of Multi-Modal Transcriptome-Small Molecule Interaction Networks from High-Throughput Measurements to Study Human Complex Traits
Authors: Akbary Moghaddam Vaha , Acharya Sandeep , Schwaiger-Haber Michaela , Liao Shu , Jung Wooseok J. , Thyagarajan Bharat , Shriver Leah P. , Warwick Daw E. , Saccone Nancy L. , An Ping , Brent Michael R. , Patti Gary J. , Province Michael A. 
Published: January 2025

AbstractSmall molecules (SMs) are integral to biological processes, influencing metabolism, homeostasis, and regulatory networks. Despite their importance, a significant knowledge gap exists regarding their downstream effects on biological pathways and gene expression, largely due to differences in scale, variability, and noise between untargeted metabolomics and sequencing-based technologies. To address these challenges, we developed a multi-omics framework comprising a machine learning-based protocol for data processing, a semi-supervised network inference approach, and network-guided analysis of complex traits. The ML protocol harmonized metabolomic, lipidomic, and transcriptomic data through batch correction, principal component analysis, and regression-based adjustments, enabling unbiased and effective integration. Building on this, we proposed a semi-supervised method to construct transcriptome-SM interaction networks (TSI-Nets) by selectively integrating SM profiles into gene-level networks using a meta-analytic approach that accounts for scale differences and missing data across omics layers. Benchmarking against three conventional unsupervised methods demonstrated the superiority of our approach in generating diverse, biologically relevant, and robust networks. While single-omics analyses identified 18 significant genes and 3 significant SMs associated with insulin sensitivity (IS), network-guided analysis revealed novel connections between these markers. The top-ranked module highlighted a cross-talk between fiber-degrading gut microbiota and immune regulatory pathways, inferred by the interaction of the protective SM, N-acetylglycine (NAG), with immune genes (FCER1A,HDC,MS4A2, andCPA3), linked to improved IS and reduced obesity and inflammation. Together, this framework offers a robust and scalable solution for multi-modal network inference and analysis, advancing SM pathway discovery and their implications for human health. Leveraging data from a population of thousands of individuals with extended longevity, the inferred TSI-Nets demonstrate generalizability across diverse conditions and complex traits. These networks are publicly available as a resource for the research community.
Dissecting pOXA-48 fitness effects in clinical enterobacteria using plasmid-wide CRISPRi screens
Authors: Calvo-Villamañán Alicia , Sastre-Dominguez Jorge , Barrera-Martín Álvaro , Costas Coloma , San Millan Álvaro 
Published: January 2025

AbstractConjugative plasmids are the main vehicle for the spread of antimicrobial resistance (AMR) genes in clinical bacteria. AMR plasmids allow bacteria to survive antibiotic treatments, but they also produce physiological alterations in their hosts that commonly translate into fitness costs. Despite the key role of plasmid-associated fitness effects in AMR evolution, their origin and molecular bases remain poorly understood. In this study, we introduce plasmid-wide CRISPR interference (CRISPRi) screens as a tool to dissect plasmid-associated fitness effects. We designed and performed CRISPRi screens targeting the globally distributed carbapenem resistance plasmid pOXA-48 in 13 different multidrug resistant clinical enterobacteria. Our results revealed that pOXA-48 gene-level effects are conserved across clinical strains, and exposed the key role of the carbapenemase-encoding gene,blaOXA-48, as the main responsible for pOXA-48 fitness costs. Moreover, our results highlighted the relevance of postsegregational killing systems in pOXA-48 vertical transmission, and uncovered new genes implicated in pOXA-48 stability. This study sheds new light on the biology and evolution of carbapenem resistant enterobacteria and endorses CRISPRi screens as a powerful method for studying plasmid-mediated AMR.
Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa
Authors: Ngwese Mirabeau M. , Adegbite Bayode R. , Zinsou Jeannot F. , Fitzstevens J. Liam , Schmidt Victor T. , Moure Alvyn N. , Maloum Moustapha M. , Tyakht Alexander V. , Huus Kelsey E. , Youngblut Nicholas D. , Kremsner Peter G. , Adegnika Ayola A. , Ley Ruth E. 
Published: January 2025

AbstractSoil-transmitted helminths (STH) are common in (sub)tropical regions and primarily affect impoverished populations. STHs reside in the gut, interacting both with the gut microbiota and host immunity. Clinical STH detection is laborious and often not performed within the context of gut microbiome studies. Here, we assessed whether fecal metagenome data could be used to assess STH infection, and to relate STH infection to microbiome diversity. We generated 310 gut metagenomes for mother-child pairs from two different locations in Gabon: one rural and one semi-urban. The presence and abundance of four STH parasites (Ascaris lumbricoides,Strongyloides stercoralis,Trichuris trichiura, andNecator americanus) were assessed using both microscopy and qPCR. Sequence data were used to characterize the microbiomes and to detect the presence of these four STH parasites. We found that metagenome data could accurately detect the presence of all four STHs, as reflected by high sensitivity and specificity compared to microscopy or qPCR detection. Furthermore, the number of STH species present in stool was associated with microbiome diversity and with the abundances of specific taxa, most notably in young children. We applied this approach to microbiome data from five other populations in Africa and corroborated our findings. Our results demonstrate that human intestinal parasites can be accurately detected via metagenomic sequencing, and highlight how infection with multiple STH parasites is linked to consistent features in the gut microbiome in populations in Africa.
Diet gel-based oral drug delivery system for controlled dosing of small molecules for microglia depletion and inducible Cre recombination in mice
Authors: Jovanovic Joel , Stone Megan L. , Dooyema Samantha R. , Tao Yuankai K. , Fuhrmann Sabine , Levine Edward M. 
Published: January 2025

AbstractSmall molecules like PLX5622 for microglia depletion and Tamoxifen for inducible Cre recombination are commonly used in mouse research. Traditional application methods, such as chow or oral gavage and injections, have limitations, including uncontrolled dosage and risk of injury. To address this issue, we have developed an alternative oral drug delivery system using a gel-based rodent maintenance diet that allows for controlled consumption and adjustment of dosage and is suitable for water-insoluble small molecules. We tested DietGel®93M (93M) infused with PLX5622 (0.8 mg/g and 2.0 mg/g) in theCx3cr1gfp/+retinal microglia reporter mouse and Tamoxifen-infused 93M (0.3125 mg/g) in the Rlbp1-CreERT2;Rosaai14mouse with an inducible tdTomato reporter in retinal Müller glia. Mice were single-caged and received daily batches of PLX5622-infused 93M over 14 days or Tamoxifen-infused 93M for one or three days followed by a 14-day observation period. Longitudinal scanning laser ophthalmoscopyin vivoand fixed tissue imaging were used to track GFP and tdTomato expression. Following evaluation of a suitable 93M consumption rate (g/d) to sustain body weight, the PLX5622-93M diet at both concentrations showed a 94% microglia depletion rate at 3 days and >99% after one and two weeks. The Tamoxifen-93M diet confirmed suitability for inducible Cre recombination, with significant treatment-time dependent efficacy and a positive correlation between total Tamoxifen dose and tdTomato expression. This study demonstrates that a diet gel-based drug delivery system offers a controllable and less invasive alternative to current drug application methods for PLX5622 and Tamoxifen.
Synergistic effects ofRetcoding and enhancer loss-of-function alleles cause progressive loss of inhibitory motor neurons in the enteric nervous system
Authors: Fries Lauren E , Grullon Gabriel , Berk-Rauch Hanna E , Chakravarti Aravinda , Chatterjee Sumantra 
Published: January 2025

AbstractCoding and enhancer variants of theRETreceptor tyrosine kinase gene contribute to ∼50% of Hirschsprung disease (HSCR) risk, a congenital disorder of disrupted enteric nervous system (ENS) development. The greatest contribution of this risk is from a common variant (rs2435357) in an ENS-active, SOX10-boundRETenhancer (MCS+9.7) that reducesRETgene expressionin vivoand triggers expression changes in other ENS genes in the human fetal gut. To uncover the cellular basis ofRET-mediated aganglionosis, we used CRISPR/Cas9 to delete (Δ) the homologous mouse enhancer (mcs+9.7). We used single cell RNA sequencing and high-resolution immunofluorescence to demonstrate four significant features of the developing E14.5 gut of Δmcs+9.7/Δmcs+9.7 embryos: (1) a small (5%) yet significant reduction inRetgene expression in only two major cell types – early differentiating neurons and fate-restricted inhibitory motor neurons; (2) no significant cellular loss in the ENS; and, (3) loss of expression of 19 cell cycle regulator genes suggesting a proliferative defect. To identify theRetfunctional threshold for normal ENS development, we also generated, in combination with theRetCFP null allele, (4) Δmcs+9.7/CFP double heterozygote mice which reducedRetgene expression in the ENS to 42% with severe loss of inhibitory motor neurons, an effect restricted to the hindgut and driven by proliferative loss. Thus,Retgene expression drives proliferation of ENS progenitor cells and hindgut-specific inhibitory motor neuron development, and that HSCR aganglionosis arises from a cascade of cellular defects triggered by >50% loss ofRetfunction.
Local traveling waves of cytosolic calcium elicited by defense signals or wounding are propagated by distinct mechanisms
Authors: Zhang Weiwei , Kumar Nilay , Helwig Jessica R. , Hoerter Alexis , Iyer-Pascuzzi Anjali S. , Umulis David M. , Pienaar Elsje , Staiger Christopher J. 
Published: January 2025

AbstractCytosolic Ca2+signatures with specific spatiotemporal patterns play crucial roles in plant responses to biotic and abiotic stresses. Perception of microbe- or damage-associated molecular patterns (MAMPs or DAMPs) initiates signaling cascades that represent the first layer of plant defense against pathogens known as pattern-triggered immunity (PTI). During PTI, MAMP/DAMP-induced cytosolic Ca2+fluxes serve as essential messengers in the initiation and transmission of defense signals at the cellular, whole organ, and systemic levels. However, the specific patterns of these Ca2+signatures in response to different pathogen cues, and the mechanisms that encode them, remain largely unexplored. In this study, we quantitatively assessed Ca2+signatures at the single-cell level as well as the local traveling Ca2+waves induced by global treatment of Arabidopsis cotyledons with MAMPs or DAMPs. We demonstrated that MAMPs induced distinct local spatiotemporal Ca2+responses in epidermal pavement cells, with Ca2+traveling waves consistently initiated from a subset of cells and spreading in an approximately radial pattern. These local traveling waves propagated at a slow but constant speed of approximately 1 µm/s and spread to a limited number of neighboring cells. In contrast, wound-induced traveling waves displayed a diffusion-like decay pattern that moved rapidly away from the wounded cell but with diminishing speed over time and distance. Mathematical modeling supported a calcium-induced calcium release mechanism that could recapitulate the constant wave speed induced by MAMPs. These findings contribute to a deeper understanding of plant defense-related Ca2+signaling mechanisms as well as how defense responses are spatially restricted within tissues.One Sentence SummaryA slow, local traveling wave of calcium is initiated from a subset of epidermal cells during plant immune signaling.
Dynamic activity ofErgpromotes aging of the hematopoietic system
Authors: Tanaka-Yano Mayuri , Sugden Wade W. , Wang Dahai , Badalamenti Brianna , Côté Parker , Chin Diana , Goldstein Julia , George Stephan , Rodrigues-Luiz Gabriela F. , da Rocha Edroaldo Lummertz , Li Hojun , North Trista E. , Gryder Berkley E. , Rowe R. Grant 
Published: January 2025

ABSTRACTHematopoiesis changes to adapt to the physiology of development and aging. Temporal changes in hematopoiesis parallel age-dependent incidences of blood diseases. Several heterochronic regulators of hematopoiesis have been identified, but how the master transcription factor (TF) circuitry of definitive hematopoietic stem cells (HSCs) adapts over the lifespan is unknown. Here, we show that expression of the ETS family TFErgis adult-biased, and that programmed upregulation ofErgexpression during juvenile to adult aging is evolutionarily conserved and required for complete implementation of adult patterns of HSC self-renewal and myeloid, erythroid, and lymphoid differentiation.Ergdeficiency maintains fetal transcriptional and epigenetic programs, and persistent juvenile phenotypes inErghaploinsufficient mice are dependent on deregulation of the fetal-biased TFHmga2. Finally,Erghaploinsufficiency in the adult results in fetal-like resistance to leukemogenesis. Overall, we identify a mechanism whereby HSC TF networks are rewired to specify stage-specific hematopoiesis, a finding directly relevant to age-biased blood diseases.SUMMARYThe hematopoietic system undergoes a process of coordinated aging from the juvenile to adult states. Here, we find that expression of ETS family transcription factor Erg is temporally regulated. Impaired upregulation ofErgduring the hematopoietic maturation results in persistence of juvenile phenotypes.
NRGSuite-Qt: A PyMOL plugin for high-throughput virtual screening, molecular docking, normal-mode analysis, the study of molecular interactions and the detection of binding-site similarities
Authors: Galdino Gabriel T. , DesCôteaux Thomas , Teruel Natalia , Najmanovich Rafael 
Published: January 2025

AbstractSummaryWe introduce NRGSuite-Qt, a PyMOL plugin that provides a comprehensive toolkit for protein modeling, virtual screening, normal mode analysis, and binding-site similarity calculations. Building on the original NRGSuite plugin for FlexAID, this updated version integrates five new functionalities: protein-protein and protein-ligand interaction analysis using Surfaces, ultra-massive virtual screening with NRGRank, binding-site similarity detection with IsoMIF, normal mode analysis using NRGTEN, and mutational studies through integration with the Modeller Suite. By merging these advanced tools into a cohesive platform, NRGSuite-Qt streamlines complex workflows and facilitates high-throughput computational studies within a single interface. Additionally, we benchmark a newer version of the Elastic Network Contact Model for normal mode analysis method ENCoM, utilizing the same 40 atom-type pairwise interaction matrix that is used in all other software. This version outperforms the default model in multiple benchmarking tests.AvailabilityThe Installation guide and tutorial is available athttps://nrg-qt.readthedocs.io/Contactrafael.najmanovich@umontreal.ca
Decaying and expanding Erk gradients process memory of skeletal size during zebrafish fin regeneration
Authors: Rich Ashley , Lu Ziqi , Simone Alessandro De , Garcia Lucas , Janssen Jacqueline , Ando Kazunori , Ou Jianhong , Vergassola Massimo , Poss Kenneth D. , Talia Stefano Di 
Published: January 2025

AbstractRegeneration of an amputated salamander limb or fish fin restores pre-injury size and structure, illustrating the phenomenon of positional memory. Although appreciated for centuries, the identity of position-dependent cues and how they control tissue growth are not resolved. Here, we quantify Erk signaling events in whole populations of osteoblasts during zebrafish fin regeneration. We find that osteoblast Erk activity is dependent on Fgf receptor signaling and organized into millimeter-long gradients that extend from the distal tip to the amputation site. Erk activity scales with the amount of tissue amputated, predicts the likelihood of osteoblast cycling, and predicts the size of regenerated skeletal structures. Mathematical modeling suggests gradients are established by the transient deposition of long-lived ligands that are transported by tissue growth. This concept is supported by the observed scaling of expression of the essential epidermal ligandfgf20awith extents of amputation. Our work provides evidence that localized, scaled expression of pro-regenerative ligands instructs long-range signaling and cycling to control skeletal size in regenerating appendages.