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Detecting a sex difference in response to a treatment or intervention, often reported as a 'sex-specific effect,' requires statistical comparison of the response across sex. Here, we investigated analytical approaches used to test for such effects in the behavioral and brain sciences. Of 200 recent articles containing terms such as 'sex-specific' or 'gender-dependent' in their titles, only 24% presented appropriate evidence supporting the claim: the effect was compared statistically across sex and results consistent with the claim were reported. In most articles (58%), no test was conducted that could have supported the title claim. Only 15% of studies on non-human animals supported the claim with appropriate evidence, which was significantly less frequently than studies on human participants (34%; p = 0.002). The use of appropriate analytical approaches was unrelated to journal rank or the citation impact of the article. We conclude that claims of sex/gender-dependent effects in the behavioral and brain sciences are only infrequently supported by appropriate evidence.

Niemann - Pick Disease Type C1 (NPC1) is a fatal, neurodegenerative disorder, characterized by lysosomal lipid accumulation and dysmyelination. Previous studies have documented some lipid abnormalities in the null mouse focused on the whole brain and liver. However, the specific lipidomic alterations in severely affected brain regions, such as cerebellum and isolated myelin remain understudied. We present a comprehensive LC - MS - based lipidomic analysis of the cerebellum and cortex of Npc1-/- mice during disease progression stages, along with the first comprehensive characterization of the myelin lipidome in NPC1 disease. Our results reveal that the cerebellum accumulates lipid species, including sphingolipids and glycerophospholipids progressively, while the cortex shows an overall decline in lipid levels, indicating region-specific lipid dysregulation. Notably, bis(monoacylglycero)phosphates and their precursors including lysophosphatidylglycerol and hemibismonoacylglycerophosphate exhibit significant accumulation, with a preference for docosahexaenoic acid (DHA) containing species. Despite known cholesterol storage defects in NPC1, we observed reduced free cholesterol levels in both regions, which we attribute to myelin loss. Myelin-specific lipidomics demonstrated extensive dysregulation, particularly in cortical myelin, including severe losses in sulfatides, ether-lipids, and acylcarnitine, alongside striking accumulation of hydroxy-ceramides. These findings identify novel lipid alterations in brain subregions and myelin, offering critical insight into the lipid perturbations under the loss of NPC1, and highlight lipid targets that may be crucial for therapeutic intervention and biomarker development.

The NS3 helicases from the Flaviviridae family of viruses exhibit nucleotide-hydrolysis-dependent, nucleic-acid-unwinding activity. The RNA unwinding activity for NS3 helicases from the Orthoflavivirus genus has not been fully explored and contrasts with NS3 helicase from Hepatitis C virus (HCV) of the Hepacivirus genus, which has thus far served as the prototypical model enzyme from this family of viruses. To begin to understand the functional differences between flavivirus NS3 helicases, we first developed an expression and purification system for full-length untagged NS3 protein from West Nile virus (WNV) and Zika virus (ZIKV). Both enzymes exhibit RNA-stimulated ATPase activity and are dependent on the nucleoside triphosphatase active site of the enzyme. Unlike HCV NS3, orthoflavivirus NS3s do not efficiently pre-assemble on a 3-ssRNA-tailed dsRNA substrate in the absence of ATP-Mg which is a prerequisite for formation of a productive HCV NS3-RNA complex that can exhibit a rapid burst of RNA unwinding. Instead, to observe RNA unwinding by WNV and ZIKV NS3s, low Mg-ATP concentrations are required at a time coincident when NS3 encounters the RNA substrate. In addition, we find that orthoflavivirus NS3s require translocation beyond the displaced strand to completely unwind a dsRNA substrate. Last, we find that orthoflavivirus NS5 stimulates the ability of NS3 to unwind dsRNA. These results suggest that functional differences exist between the flavivirus NS3 helicases and illuminate that orthoflavivirus NS3s require a functional interaction with the NS5 protein for coordination of its activity, as it is believed these two proteins constitute the viral replicase.

The ability for an organism to encode fear memories is necessary for survival. Once a threat is no longer present, organisms must suppress, or extinguish, this fear memory in favor of other adaptive behaviors. In rodents, the infralimbic cortex (IL) is a locus critical for the extinction of cued fear memory. While this role has been known for decades, the circuit mechanisms underlying its recruitment are largely unknown. By using a combination of immunohistochemistry, neural tagging, in vivo calcium imaging and optogenetics, and optogenetics-assisted brain slice electrophysiology, we revealed that the dynamic activity and plasticity of IL inhibitory interneurons is critical for encoding fear extinction. Specifically, after fear conditioning, IL parvalbumin interneurons exhibit increased activity and plasticity, driving enhanced freezing. After fear extinction, however, IL somatostatin interneurons exhibit extinction cue-associated activity and plasticity, and their activity facilitates extinction memory encoding through inhibition of parvalbumin interneuron activity and disinhibition of IL principal neurons. Further, glutamatergic projections from the basolateral amygdala undergo experience- and cell type-specific plasticity that is required to drive the dynamic recruitment of IL parvalbumin and somatostatin interneurons after fear conditioning and extinction, respectively. Overall, these results reveal the mechanisms of cued fear extinction encoding and highlight critical roles for local IL microcircuit computations in these roles.

Research on progeria not only contributes to treatments for the disease but also enhances our understanding of physiological ageing. Mouse models of progeria recapitulate pathological ageing phenotypes seen in patients, including cardiovascular defects, increased cellular senescence, systemic inflammation, DNA damage accumulation, and shortened lifespan. In cultured cells from Hutchinson-Gilford progeria syndrome (HGPS) patients, the human p53 isoform Δ133p53α was previously shown to inhibit p53-mediated cellular senescence, proinflammatory IL-6 production, and DNA damage accumulation, and to extend cellular replicative lifespan. Here we show that, in a heterozygous HGPS mouse model, transgenic expression of Δ133p53α reproduces these in vitro-observed effects across multiple organs in vivo and extends median lifespan by 11% (387 versus 349 days, P = 0.0379). In the aorta and skin, Δ133p53α abrogates progeria-characteristic pathological changes and preserves tissue integrity. Our data further suggest that Δ133p53α may promote a broad spectrum of ageing-counteracting mechanisms, including bone homeostasis, metabolic fitness, antioxidant defense, youthful epigenome, and tissue stemness. Together with the anti-inflammatory and tissue-preserving effects of Δ133p53α in naturally aged mice and its age-associated downregulation in human tissues, this study suggests that Δ133p53α-based therapeutic strategies may be applicable not only to HGPS but also as broader interventions for preventing or delaying ageing.

Class B scavenger receptors BI (SR-BI) and BII (SR-BII) internalize lipoproteins but also bind and internalize bacteria. Their roles in sepsis are unknown. We overexpressed human SR-BI and BII in the liver and kidney as well as bone marrow-derived macrophages, and then performed cecal ligation and puncture (CLP) surgery. SR-BI and BII transgenic mice had significantly worse survival compared to WT mice. 24 h after CLP, liver injury markers and histological damage were prominent in both SR-BI and BII transgenic mice, whereas kidney damage was similar. Systemic inflammatory cytokines were markedly increased in SR-BI and BII transgenic mice; parallel increases were seen in liver mRNA expression, not in the kidney. The highest degree of neutrophil infiltration was observed in the liver of SR-BI. Human SR-BI and BII dramatically decreased bacterial accumulation in the liver. Green fluorescence protein-labeled E. coli were efficiently phagocytosed in hepatic macrophages of SR-BI and BII transgenic mice; phagocytosis was more prominent in SR-BII transgenic mice. Finally, human SR-BI overexpression reduced systemic HDL-C level, eliminated adrenal cortex lipid droplets, and dampened the systemic increase of corticosterone after CLP. Supplementation with glucocorticoid and mineralocorticoid improved survival in SR-BI, but not SR-BII, transgenic mice after CLP. In summary, our findings suggest human SR-BI and BII overexpression contributes to higher mortality after CLP by excessive inflammatory response due to adrenal insufficiency (SR-BI) or hyperactive phagocytosis (SR-BII) in the liver.

Data in mice, nonhuman primates, and in humans demonstrate that exposure to maternal obesity increases the risk of multiple diseases in offspring. However, little is known about the aging effects of maternal obesity on the offspring. This study shows that maternal obesity significantly reduced the lifespan of both male and female mice born to obese dams despite being weaned onto a healthy diet at three weeks of age. This reduction in longevity was linked to an increase in age-related fibrotic pathology across multiple organs, e.g., liver, heart, and kidney. Gompertz analysis of the lifespan data showed that maternal obesity offspring have reduced lifespan due to detrimental changes established early during development rather than factors that modify aging later-in-life. These findings are translationally significant as they demonstrate that the growing prevalence of MO may lead to a decrease in overall lifespan and increase in age-related diseases in the next generation.

Retroviral integration into host genomes is central to both HIV-1 persistence and the safety and function of lentiviral vectors used in gene and cell therapies. However, existing integration site assays remain limited by sensitivity, input requirements, and analytical complexity, and none have been validated at the single-molecule detection limit. Here, we introduce PRISM-seq, an ultra-sensitive workflow for genome-wide recovery of lentiviral-host junctions, paired with BulkIntSiteR, an open-source, fully automated pipeline for integration site annotation. We show that PRISM-seq accurately identifies proviral insertions across diverse genomic contexts, including euchromatin, heterochromatin, and repeat-rich centromeric regions, and detects high-confidence integration events down to a single input template molecule. By systematically characterizing assay- and amplification-associated noise, we developed a five-step quality control framework that removes PCR- and sequencing-derived artifacts. PRISM-seq also enables quantitative clonal tracking through replicate-based sampling and achieves performance comparable to or exceeding high-input assays at substantially reduced cost.

Histone modifications underpin the cell-type-specific gene regulatory networks that drive the remarkable cellular heterogeneity of the adult mammalian brain. Here, we profiled four histone modifications jointly with transcriptome in 2.5 million nuclei across multiple adult mouse brain regions. By integrating these data with existing maps of chromatin accessibility, DNA methylation, and 3D genome organization, we established a unified regulatory framework for over 100 brain cell subclasses. This integrative epigenomic atlas annotates 81% of the genome, defining distinct active, primed, and repressive states. Notably, active chromatin states marked by combinatorial histone modifications more precisely identify functional enhancers than chromatin accessibility alone, while Polycomb- and H3K9me3-mediated repression contributes prominently to cell-type-specific regulation. Finally, this multi-modal resource enables deep learning models to predict epigenomic features and gene expression from DNA sequences. This work provides a comprehensive annotation of the mouse brain regulatory genome and a framework for interpreting non-coding variation in complex tissues.

Enhancers have been proposed to act as privileged loading sites for cohesin, raising the idea that they actively fold the genome to engage distal target promoters for transcription. Supporting this idea, NIPBL/MAU2, which is required for cohesin loading, binds at enhancers in mouse embryonic stem cells. However, we find that driving cohesin recruitment near an enhancer strongly inhibits transcription from its target distal promoter, indicating that strong focal cohesin loading at enhancers is not compatible with their long-range regulatory functions. Quantitative experiments and biophysical modeling further indicate that cohesin loading at enhancers does not make major contributions to genome-wide cohesin binding and chromosome folding patterns. Instead, cohesin must load throughout the genome to extrude it, regardless of enhancer proximity, with the major determinants of cohesin traffic being extrusion barriers such as transcription and clustered CTCF sites. These findings indicate that enhancer function is largely ancillary to the general mechanisms of chromosome folding, informing further study of the relationship between genome architecture and transcriptional regulation.