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This 23-color mouse immunophenotyping panel was designed and developed by the Virginia Commonwealth University’s (VCU) flow cytometry shared resource (FCSR) to easily bring new use to our high-parameter spectral cytometers. Our method is broadly applicable to multiple tissue types, is modifiable, and provides a reproducible, cost-effective option for utilizing high-parameter flow cytometry. To facilitate the mouse immunophenotyping panel, researchers can be provided with optimized reagents, a step-by-step staining protocol, instrument training, pre-run single-color controls, and acquisition and analysis templates to streamline the workflow. Data analysis is generally done with a traditional manual gating strategy, but t-stochastic neighbor embedding (tSNE) and uniform manifold approximation projection (uMAP) generation can be performed, as desired. In an FCSR, this panel requires only light preparation work for shared resource (SR) staff with maximum benefit for researchers. Overall, this publication describes how SR facilities can provide additional benefits and services to their clientele by reducing costs, increasing reproducibility, and lowering the barriers of entry for researchers into the field of high parameter spectral flow cytometry. The panel described is used as an example of the application of the included methods, as well as a complete resource for other institutions to utilize themselves.

Mouse behavioral genetic mapping studies can identify genomic intervals modulating complex traits under well-controlled environmental conditions and have been used to study ethanol behaviors to aid in understanding genetic risk and the neurobiology of alcohol use disorder (AUD). However, historically such studies have produced large confidence intervals, thus complicating identification of potential causal candidate genes. Diversity Outbred (DO) mice offer the ability to perform high-resolution quantitative trait loci (QTL) mapping on a very genetically diverse background, thus facilitating identification of candidate genes. Here, we studied a population of 636 male DO mice with four weeks of intermittent ethanol access via a three-bottle choice procedure, producing a progressive ethanol consumption phenotype. QTL analysis identified 3 significant (Chrs 3, 4, and 12) and 13 suggestive loci for ethanol-drinking behaviors with narrow confidence intervals (1–4 Mbp for significant QTLs). Results suggested that genetic influences on initial versus progressive ethanol consumption were localized to different genomic intervals. A defined set of positional candidate genes were prioritized using haplotype analysis, identified coding polymorphisms, prefrontal cortex transcriptomics data, human GWAS data and prior rodent gene set data for ethanol or other misused substances. These candidates included Car8 , the lone gene with a significant cis-eQTL within a Chr 4 QTL for week four ethanol consumption. These results represent the highest-resolution genetic mapping of ethanol consumption behaviors in mice to date, providing identification of novel loci and candidate genes for study in relation to the neurobiology of AUD.

Background Post-hemorrhagic hydrocephalus (PHH) is a severe complication in premature infants following intraventricular hemorrhage (IVH). It is characterized by abnormal cerebrospinal fluid (CSF) accumulation, disrupted CSF dynamics, and elevated intracranial pressure (ICP), leading to significant neurological impairments. Objective This review provides an overview of recent molecular insights into the pathophysiology of PHH and evaluates emerging therapeutic approaches aimed at addressing its underlying mechanisms. Methods Recent studies were reviewed, focusing on molecular and cellular mechanisms implicated in PHH, including neuroinflammatory pathways, immune mediators, and regulatory genes. The potential of advanced technologies such as whole genome/exome sequencing, proteomics, epigenetics, and single-cell transcriptomics to identify key molecular targets was also analyzed. Results PHH has been strongly linked to neuroinflammatory processes triggered by the degradation of blood byproducts. These processes involve cytokines, chemokines, the complement system, and other immune mediators, as well as regulatory genes and epigenetic mechanisms. Current treatments, primarily surgical CSF diversion, do not address the underlying molecular pathology. Emerging therapies, such as mesenchymal stem cell-based interventions, show promise in modulating immune responses and mitigating neurological damage. However, concerns about the safety of these novel approaches in neonatal populations and their potential effects on brain development remain unresolved. Conclusions Advanced molecular tools and emerging therapies have the potential to transform the treatment of PHH by targeting its underlying pathophysiology. Further research is needed to validate these approaches, enhance their safety profiles, and improve outcomes for infants with PHH. Impact statement This review elucidates the molecular complexities of post-hemorrhagic hydrocephalus (PHH) by examining specific immune pathways and their impact on disease pathogenesis and progression. It outlines the application of genomic, epigenomic, and proteomic technologies to identify critical molecular targets in PHH, setting the stage for innovative, targeted therapeutic approaches that could improve the outcomes of neonates affected by PHH. It discusses the potential of gene and stem cell therapies in treating PHH, offering non-surgical alternatives and focusing on the underlying neuroinflammatory mechanisms.

Traditional genetic mapping studies using inbred crosses are a powerful tool for identifying chromosomal regions associated with ethanol-related traits, but typically have very large confidence intervals which make identification of specific and potentially causal candidate genes difficult. Diversity Outbred (DO) mice offer the ability to map quantitative trait loci (QTLs) associated with ethanol-drinking behaviors at a high resolution that allows for easier identification of candidate genes. Here, we exposed a population of 636 male DO mice to four weeks of intermittent ethanol access via a three-bottle choice paradigm, identifying 3 significant (Chrs 3, 4, and 12) and 12 suggestive loci for ethanol-drinking behaviors. The confidence intervals for these loci were narrow (1-4 Mbp for significant QTLs). We then further analyzed positional candidate genes using transcriptomics data from prefrontal cortex samples taken from 220 of these animals, as well as human GWAS data and prior gene set data for ethanol or other drugs of abuse. These results represent the highest-resolution genetic mapping of ethanol consumption behaviors in mice to date, providing for the identification of novel loci and candidate genes for progressive ethanol consumption, including Car8 --the lone gene with a significant cis-eQTL in strong linkage disequilibrium with our QTL for last week ethanol consumption on Chr 4.Competing Interest StatementThe authors have declared no competing interest.