Biology subjects

Hernandez, A.

Publications and source records attributed to Hernandez, A..

At least 19 recordsLinked to original sources

bioRxiv2026

A framework for identifying transcript orthologs: the evolution of sex bias in alternative transcript structure in Drosophila

BackgroundRecent advances in long read technologies provide an unprecedented opportunity to study transcript evolution. However, comparative evolutionary studies, even in Drosophila, are limited by inconsistent and incomplete annotation, and the lack of annotated transcript homology. ResultsIn this study of five species spanning 28 million years (D. melanogaster, D. simulans, D. yakuba, D. santomea and D. serrata), we infer transcript homology using reciprocal liftover, and orthology using network analyses, with data validation from long read RNA-seq of male and female head tissue. We build the first genus level annotation, with 15,996 genes and 56,370 transcripts. Expressed transcripts are conserved, 73% of transcript orthologs are detected in all species. Even the improved annotation underestimates the number of genes with alternative transcripts, with 75% of genes expressing multiple structurally diverse transcripts. In a replicated quantitative evaluation of [~]10,000 genes, both male and female-biased transcripts are expressed in 410 (D. melanogaster), 608 (D. simulans), and 493 (D. serrata) genes and in 118 orthologous genes in the D. melanogaster - D. simulans species pair, indicating greater potential for resolution of sexual conflict by alternative transcription than previously appreciated. We identified 605 transcript orthologs conserved for sex bias in the D. melanogaster-D. simulans species pair and of these, 22 male and 19 female-biased transcripts were conserved in sex bias with the outgroup D. serrata, including transcripts of genes involved in brain development, Sxl target Glutamine synthetase 2 and ciboulot. ConclusionsConserved alternative transcripts suggest that transcriptional diversity is a pervasive driver of the evolution of functional diversity.

genomics↗

bioRxiv2026

Exposure of Men to PTSD-Promoting Trauma Elevates Levels of Sperm miRNAs with Anxiety and Depression-Inducing Activities

Chronically stressing male rodents can induce stress-specific epigenetic changes in sperm that contribute to altered offspring phenotypes. Whether similar phenomena occur in men is unclear. This study addresses this knowledge gap by analyzing sperm microRNAs (miRNAs) from 51 men exposed to various levels of adult trauma including crime, disaster, and physical or sexual violence, quantified by the Trauma History Questionnaire (THQ), a measure of risk for Post-Traumatic Stress Disorder (PTSD). Four sperm miRNAs, miR-532-3p, 491-5p, 375-3p and 361-3p correlated positively with mens THQ scores, showing 4X to 130X over expression in sperm from the most highly traumatized men. These changes were independent of mens adverse childhood experiences (ACEs), which we previously linked to decreased miR-34/449 in their sperm; and sperm miR-34/449 levels were not associated with THQ scores. Injecting these 4 miRNAs into fertilized mouse oocytes at levels comparable to those found in men reporting high THQ scores yielded offspring with elevated anxiety-and depression-like phenotypes. This finding differs from the stress related phenotypes we observed in offspring of mice fertilized by sperm with reduced levels of miR-34/449. Consistent with only a small subset of men with high THQ scores developing PTSD, we observed no statistically significant increase in overall anxiety or depression among this highly traumatized group, however there were indications of increased sleeplessness, appetite and concentration difficulties and negative self-concept among this group. Nevertheless, almost all men reporting high THQ scores had elevated levels of all 4 of these miRNAs in their sperm, suggesting these trauma-induced epigenetic changes may raise mental health risks in the offspring of men with only subtle mental health problems. Since [~]20 % of men report either THQ or ACE scores in the ranges linked here and in our earlier study to changes in sperm miRNAs that in mice lead to elevated levels of stress-related behaviors, a large human population with an elevated risk of transmitting stress-related traits to their offspring likely exists.

genetics↗

bioRxiv2026

Rescuing functional defects in a zebrafish model of CDKL5 deficiency disorder: Contribution to the identification of new therapeutic compounds

Mutations in the CDKL5 gene cause CDKL5 deficiency disorder (CDD), a severe neurodevelopmental encephalopathy characterized by a broad range of symptoms, including early-onset seizures, profound motor impairment and dysmorphic facial features. Current treatment options remain limited and largely focus on seizure management, which is often challenging to control, underscoring the critical need for new effective therapies. To identify potential novel candidate molecules for the treatment of CDD, we performed the first in vivo drug screening using a cdkl5 mutant zebrafish model. Recapitulating key features of the human disorder, cdkl5-/- larvae exhibit reduced locomotor behavior, providing a robust readout to assess therapeutic efficacy. By screening 170 compounds from MAPK Inhibitor and Histone Modification Libraries, both implicated in CDKL5 dysfunction, we identified 18 and 12 small molecules that partially or fully restored locomotor activity, respectively. Among these, fisetin, divalproex, resveratrol, and VX-702 were further evaluated for their capacity to rescue cdkl5-/- craniofacial defects and altered gene expression. Fisetin demonstrated the most consistent phenotypic improvement, including partial restoration of craniofacial abnormalities and normalization of gene expression levels. Future research aimed at elucidating the molecular mechanisms underlying the observed rescue effects will be critical to understand their mode of action. Overall, our study demonstrates the utility of this rapid and scalable zebrafish-based screening approach for therapeutic discovery in CDD and identifies promising therapeutic molecules that warrant further validation in complementary preclinical systems.

neuroscience↗

bioRxiv2026

Chronic Exposure to Nanoplastics Alters Stem Cell Type-Specific Mechanisms, Promoting Cancer Development

Increasing levels of nanoplastics (NPLs) in the environment raise concerns about their effects on human health. We investigated the impact of the most prevalent NPLs, namely polyethylene terephthalate (PET) and polystyrene (PS), on stem cells (SCs), which persist for decades, support tissue function, and are often implicated in cancer development. Long-term exposure to both NPLs similarly affected mammary SC features with an enhanced self-renewal and altered 3D organization, without impairing differentiation capacity. Moreover, both NPLs significantly increased invasiveness and anchorage-independent growth, albeit molecular profiling revealed distinct signatures and mechanisms, indicating a shift towards a more aggressive phenotype. NPLs also synergized with BMP2 signaling, known to be disrupted by pollutants. These findings highlight how NPLs may contribute to early pre-neoplastic changes through distinct and cooperative mechanisms.

cancer biology↗

bioRxiv2025

A foundational model for joint sequence-function multi-species modeling at scale for long-range genomic prediction

Genomic prediction and design require models that integrate local sequence features with long-range regulatory dependencies spanning hundreds of kilobases to megabases. Existing approaches have made substantial progress along complementary axes: supervised sequence-to-function models achieve high accuracy for specific assays and organisms, self-supervised genomic foundation models learn transferable representations from large-scale sequence data, and conditional generative models enable principled sequence design guided by functional objectives. However, these strengths are typically realized in isolation--across distinct model classes, architectures, and training regimes--limiting the ability to combine long-context, base-resolution prediction, functional modeling, and controllable generation within a single efficient framework that generalizes across organisms and modalities. Here we introduce Nucleotide Transformer v3 (NTv3), a multi-species foundation model that unifies representation learning, functional-track and genome-annotation prediction, and controllable sequence generation within a common backbone. NTv3 uses a U-Net-like architecture to enable single-base tokenization and efficient modeling of contexts up to 1 Mb. We pre-train NTv3 on 9 trillion base pairs from OpenGenome2 using base-resolution masked language modeling, followed by post-training with a joint objective that integrates continued self-supervision with supervised learning on [~]16,000 functional tracks and annotation labels from 24 animal and plant species. After post-training, NTv3 achieves state-of-the-art accuracy for functional-track prediction and genome annotation across species, outperforming leading sequence-to-function and foundation-model baselines on established benchmarks and on the new NO_SCPLOWTVC_SCPLOW 3 BO_SCPLOWENCHMARKC_SCPLOW, a controlled downstream fine-tuning suite in a standardized 32 kb input / base-resolution output setting. We further show that NTv3 consolidates a shared regulatory grammar across tasks, enabling coherent long-range genome-to-function inference and variant-associated remodeling. Finally, we fine-tune NTv3 into a controllable generative model via masked diffusion language modeling and use it to design enhancer sequences with specified activity levels and promoter selectivity. We validate these designs experimentally, showing that generated enhancers recapitulate the intended activity stratification and achieve the desired promoter-specific activation in cellulo. We release the NTv3 model family together with code and practical cookbooks for long-context training, multispecies post-training, fine-tuning, interpretation, and sequence design.

genomics↗

bioRxiv2025

Links Between Gut Microbiota of Uruguayan Infants, Breast Milk Composition, and Maternal Factors During Exclusive Breastfeeding

BackgroundGiven the links between early gut microbiota, breastfeeding, and maternal physiology, we characterized the intestinal microbiota of infants during exclusive breastfeeding (mean=5.4 months), examining its associations with breastmilk composition, fecal IgA, and maternal factors in Uruguayan primiparous mothers, with vaginal (V, n=20) or cesarean-section delivery (CS, n=14). MethodsWe analyzed fecal microbiota via 16S rRNA V4 sequencing and quantified stool IgA, breastmilk components (antibodies, hormones, macronutrients) using ELISA and standard biochemical methods. ResultsPrincipal Coordinates Analysis showed separation by delivery mode (PCo1:44.6%, PCo2:14.2%). Samples of CS-group displayed lower relative abundance (RA %) of Bacteroidetes/Firmicutes ratio, higher RA of Proteobacteria (50.7%vs35.5%), and decreased Bacteroides (2.5%vs31.8%) than V-group. Biochemical parameters didnt differ between groups. In the V-group, milk and fecal IgA correlated (r=+0.47), as did Bifidobacterium RA with milk IgA (r=+0.47). Fat content was associated with different microbial taxa in both groups. Only in CS-group milk carbohydrates correlated with Bifidobacterium (r=-0.679) and maternal stress with Flavonifractor in CS-group (r=+0.461). ConclusionResults indicate delivery mode can exert persistent impact on infant gut microbiota until the introduction of complementary feeding. Differences in correlation patterns between groups suggest distinct regulatory mechanisms of microbiota, possibly linked to physiological processes that differ according to delivery mode. ImpactO_LIThis is the first study to assess the gut microbiota composition of exclusively breastfed infants born to Uruguayan mothers, in parallel with analyses of breast milk composition and maternal perceived stress C_LIO_LIThe mode of delivery was associated with differences in gut microbiota composition at a mean age of 5.4 months. C_LIO_LIDifferent associations between milk composition and maternal perceived stress with predominant microbial taxa were found according to the type of delivery. C_LIO_LIThese findings provide a basis for studies on microbiota regulatory mechanisms influenced by maternal physiology according to delivery mode C_LI

genomics↗

bioRxiv2025

A unified genetic perturbation language for human cellular programming

Evolution simultaneously and combinatorially explores complex genetic changes across perturbation classes, including gene knockouts, knockdowns, overexpression, and the creation of new genes from existing domains. Separate technologies are capable of genetic perturbations at scale in human cells, but these methods are largely mutually incompatible. Here we present CRISPR-All, a unified genetic perturbation language for programming of any major type of genetic perturbation simultaneously, in any combination, at genome scale, in primary human cells. This is enabled by a standardized molecular architecture for each major perturbation class, development of a functional syntax for combining arbitrary numbers of elements across classes, and linkage to unique single cell compatible barcodes. To facilitate use, CRISPR-All converts high level descriptions of desired complex genetic changes into a single DNA sequence that can rewire genomic programs within a cell. Using the CRISPR-All language allowed for head-to-head functional comparisons across perturbation types in a comprehensive analysis of all previously identified genetic enhancements of human CAR-T cells. Combining CRISPR-All programs with single cell RNA sequencing revealed a greater diversity of phenotypic states, including improved functional performance, only accessible through distinct perturbation classes. Finally, CRISPR-All combinatorial genome scale screening of up to four distinct perturbations simultaneously revealed additive functional improvements in human T cells accessible only through iterative multiplexing of modifications across perturbation classes. CRISPR-All enables exploration of a combinatorial genetic perturbation space, which may be impactful for biological and clinical applications.

genetics↗

bioRxiv2025

Effects of true to life polyethylene terephthalate and polycaprolactone nanoparticles on macrophages under a repeated exposure mode.

Micro and nanoplastics are pollutants which concentration in different biotopes increases continuously over time, which poses the question of their potential effects on health. In animals, these micro and nanoplastics are recognized as particulate materials and thus handled by macrophages, either directly in the case of lung exposure, or after the particles have crossed the epithelial barriers in case of oral or dermal exposure. It is thus important to study the potential effects of micro and nanoplastics on macrophages. Most studies have used an experimental scheme in which the cells of interest are exposed to a single dose of plastics, and where the readout of the studied parameters is made immediately after exposure. However, this classical experimental scheme does not take into account the impact of biopersistence, nor the potential cellular adaptation that may take place when cells are exposed repeatedly to a low dose of plastics. We thus used a repeated exposure scheme, in order to better take into account these phenomena. Within this frame, we compared the macrophages responses to a persistent nanoplastic, i.e. true-to-life polyethylene terephthalate nanoparticles and to a biodegradable nanoplastic, i.e. polycaprolactone, by a combination of proteomic and targeted experiments. Our results show that under this repeated exposure scheme, the proteome changes were of a lesser extent than under the acute exposure mode, indicating cell adaptation. However, polyethylene terephthalate nanoparticles induced oxidative stress and a pro-inflammatory response, while polycaprolactone nanoparticles induced a depression of macrophages functions, indicating harmful effects even in the repeated exposure scheme.

pharmacology and toxicology↗

bioRxiv2025

Brucella abortus egresses from host cells in infective clumps through an actin-dependent mechanism

Brucella abortus is an intracellular pathogen whose cell cycle encompasses attachment, internalization, trafficking, replication, and egress from cells. While the intracellular life of Brucella has been extensively studied, the mechanisms underlying its exit from host cells are still unclear. In this work, we observed a significant increase in the formation of B. abortus containing vacuoles intracellular clumps (BCVIC) and abundant B. abortus containing vacuoles-derived extracellular clumps (BCVEC) after 72 h of infection. Membrane extensions protruding through the polymerization of actin filaments were evident in cells at later stages of infection. Purified BCVIC and BCVEC were of similar sizes and predominantly acidic. These vacuoles exhibited a compact arrangement of well-ordered bacteria, comprised of a heterogeneous population of dead and live bacteria and host components LAMP-1 and actin filaments. A proportion of BCVEC were naked, while others were enclosed within an impermeable host membrane. The actin cytoskeleton was implicated in the protrusion of BCVEC since the modulation of Rho GTPases affected the egress of BCVEC. The BCVEC protruding from cells were capable of invading non-infected cells, initiating a new cycle of infection. The topological structure and function of BCVEC underscore their significance in the Brucella life cycle as vehicles for bacterial dissemination to host cells and organs. ImportanceB. abortus is an intracellular pathogen that traffics to the endoplasmic reticulum, where it replicates. However, the mechanisms by which Brucella exits host cells and infects new ones are not fully understood. We found that protruding acidic autophagic-like vesicles containing compact, well-organized Brucella clusters are shed from cells via GTPase and actin filament recruitment. Through this process, the vesicles are impermeable to antibodies and other substances, like antibiotics, and are highly infectious to neighboring cells. This previously unreported mechanism enhances understanding of the well-known Brucella stealth strategy to evade the immune system and establish harmful, long-lasting infections.

microbiology↗

bioRxiv2025

IDBac: an open-access web platform and compendium for the identification of bacteria by MALDI-TOF mass spectrometry.

The identification and analysis of bacteria is central to the microbiological sciences. While gene sequencing methods have been the standard to achieve this, use of MALDI-TOF mass spectrometry (MS), particularly in clinical microbiology, provides high-throughput identification to the subspecies level. However, biotyping has yet to be adopted outside of clinical settings due to the lack of a centralized public database of MS protein signatures that would facilitate isolate identification via spectral comparison. Further, current platforms lack meaningful ways to compare multiple properties from large numbers of bacterial isolates. Herein we present the IDBac web platform, a crowd-sourced central knowledgebase of protein MS signatures of >1400 strains spanning 6 bacterial phyla. Accompanying the knowledgebase is analysis infrastructure to identify unknown isolates, probe relationships within culture collections using metadata integration, and visualize specialized metabolite differences within groups of closely related bacteria. To highlight this utility and encourage wide community contribution, examples of each are presented.

microbiology↗

bioRxiv2025

Differential effects of postpartum sleep restriction on maternal and offspring immunity in the rat

Backgroundsleep disturbances can trigger a wide range of physiological consequences, affecting hormonal regulation, metabolism, cognitive function, and immune responses. Human mothers worldwide frequently experience sleep restriction and fragmentation, a pattern also observed in other mammalian mothers, such as rats. These alterations may add to sleep disturbances unrelated to motherhood. Considering this, we wondered about the impact of sleep restriction in postpartum mother rats on their immunological status. Furthermore, given that early-life experiences can shape the immune system and that even subtle parental changes can influence offspring development, we hypothesized that maternal sleep loss might also exert detrimental effects on the pups. In this study, we investigated the effects of acute and chronic maternal sleep restriction during the postpartum period on immune parameters in both mother rats and their offspring by analyzing antibody titers and systemic inflammation. Methodsmother rats were surgically implanted with electrodes for polysomnographic recordings and for sleep deprivation (deep electrodes targeting the mesopontine wake-promoting area). From postpartum day 5 to day 9, lactating dams were randomly assigned to one of three groups: chronic sleep restriction (CSR; 6 h of sleep deprivation per day for five consecutive days), acute sleep restriction (ASR; 6 h of sleep deprivation only on postpartum day 9), or control (undisturbed). On postpartum day 9, mothers were milked, and blood samples from both mothers and pups were subsequently collected. ELISA assays quantified IL-17A, IL-6, IgG, and IgG2a in maternal serum; IgG and IgG2a in milk; and IgG in pup serum. Hematological parameters, including leukocyte profiles, were also assessed in peripheral blood of dams and pups. Resultsmaternal immune parameters analyzed remained unaffected by sleep restriction. IgG levels were lower in male pups from mothers subjected to ASR (5560 {+/-} 734 {micro}g/mL) compared with the control group (8666 {+/-} 463 {micro}g/mL; p = 0.025), whereas female pups showed no significant changes. Additionally, both female (4.10 {+/-} 0.58) and male (3.81 {+/-} 0.42) pups from dams subjected to CSR exhibited higher absolute lymphocytes counts relative to the control group (females: 2.28 {+/-} 0.25, p = 0.004; males: 2.44 {+/-} 0.25; p = 0.029). ConclusionsChronic and acute maternal sleep restriction had distinct impacts on offspring immunity, altering serum antibody and leukocyte profiles, while leaving maternal parameters unaffected. These results indicate that maternal sleep loss can influence the offspring even in the absence of detectable maternal immune alterations, with male pups being especially susceptible.

immunology↗

bioRxiv2025

3D multi-omic mapping of whole nondiseased human fallopian tubes at cellular resolution reveals a large incidence of ovarian cancer precursors

Uncovering the spatial and molecular landscape of precancerous lesions is essential for developing meaningful cancer prevention and early detection strategies. High-Grade Serous Carcinoma (HGSC), the most lethal gynecologic malignancy, often originates from Serous Tubal Intraepithelial Carcinomas (STICs) in the fallopian tubes, yet their minute size and our historical reliance on standard 2D histology contribute to their underreporting. Here, we present a spatially resolved, multi-omics framework that integrates whole-organ 3D imaging at cellular resolution with targeted proteomic, metabolomic, and transcriptomic profiling to detect and characterize microscopic tubal lesions. Using this platform, we identified a total of 99 STICs and their presumed precursors that harbor TP53 mutations in morphologically unremarkable tubal epithelium in all five specimens obtained from cancer-free organ donors with average-risk of developing ovarian cancer. Although these lesions comprised only 0.2% of the epithelial compartment, they displayed geographic diversity, immune exclusion, metabolic rewiring, and DNA copy number changes among lesions and normal fallopian tube epithelium discovered alterations in STIC-associated genes and the pathways they control. In sum, this platform provides a comprehensive 3D atlas of early neoplastic transformation, yielding mechanistic insights into tumor initiation and informing clinical screening strategies for detecting cancer precursors in whole organs at cellular resolution.

bioinformatics↗

bioRxiv2025

Seeing the forest and the trees: a workflow for automatic acquisition of ultra-high resolution drone photos of tropical forest canopies to support botanical and ecological studies

Tropical forest canopies contain many tree and liana species, and foliar and reproductive characteristics useful for taxonomic identification are often difficult to see from the forest floor. As such, taxonomic identification often becomes a bottleneck in tropical forest inventories. Here we present a drone-based workflow to automatically acquire large volumes of close-up, ultra-high resolution photos of selected tree crowns (or specific locations over the canopy) to support tropical botanical and ecological studies (https://youtu.be/80goMEifpc4). Our workflow is built around the small, easy-to-use DJI Mavic 3 Enterprise (M3E) drone, which is equipped with a wide-angle and a telephoto camera. On day one, the pilot maps a forest area of up to [~]200 ha with the wide-angle camera to generate a high-resolution digital surface model (DSM) and orthomosaic using structure-from-motion (SfM) photogrammetry. On subsequent days, the pilot acquires close-up photos with the telephoto camera from up to 300 selected canopy trees per day. These close-up photos are acquired from 6 m above the canopy and contain a high level of visual detail that allows botanists to reliably identify many tree and liana species. The photos are geolocated with survey-grade accuracy using RTK GNSS, thus facilitating spatial co-registration with other data sources, including the photogrammetry products. The primary operational challenge of our workflow is the need to maintain RTK corrections with the drone to ensure that close-up photos are acquired exactly at the predefined locations. The maximum operational range we achieved was 3 km, which would allow the pilot to reach any tree within a [~]2800 ha area from the take-off point. Although our workflow was developed to support taxonomic identification of tropical trees and lianas, it could be extended to any other forest or vegetation type to support botanical, phenological, and ecological studies. We provide harpia, an open-source Python library to program these automatic close-up photo missions with the M3E drone (https://github.com/traitlab/harpia). Data/code for peer review statementWe provide harpia, an open-source Python library to program these automatic close-up photo missions (https://github.com/traitlab/harpia). Drone imagery and labelled close-up photo data are not yet publicly available because they were acquired with the goal of publishing benchmark machine learning datasets and models for tree and liana species classification and prior publication of the data would jeopardize this future publication.

ecology↗

bioRxiv2025

4-Nitrobenzoate inhibits 4-hydroxybenzoate polyprenyltransferase in malaria parasites and enhances atovaquone efficacy

Ubiquinone (UQ) is a critical component of the electron transport chain in Plasmodium falciparum, the etiological agent of human malaria. The first step in UQ biosynthesis is the condensation of 4-hydroxybenzoate (4-HB) and an isoprenic chain by the enzyme 4-hydroxybenzoate polyprenyltransferase (4-HPT; COQ2 gene). Atovaquone (AV), an antimalarial drug, competes with ubiquinol (UQH2) for binding to the mitochondrial bc1 complex, preventing the redox recycling of UQ. In clinical practice, AV is combined with proguanil, a dehydrofolate reductase inhibitor, in a single formulation. However, parasitic resistance to this combination has been demonstrated, indicating the need for new pharmacological combinations to potentiate AV. Previously, 4-nitrobenzoate (4-NB) demonstrated the ability to inhibit UQ biosynthesis in P. falciparum parasites as well as potentiate AV efficacy in vitro. However, both its pharmacodynamics and whether this potentiation could be useful in vivo remained obscure. Here we show that 4-NB enhances AV antiplasmodial efficacy to kill parasites, increases its selectivity compared with animal cells, and preserves proguanil efficacy. 4-NB specifically inhibited the 4-HPT enzymatic activity in mutant strains of Saccharomyces cerevisiae complemented with PfCOQ2. Finally, 4-NB also improved AV antimalarial efficacy in mice infected with Plasmodium berghei parasites. Finally, work with various 4-HB analogs delineated the chemical requirements to potentiate AV activity. These findings clarify the importance of UQ biosynthesis for malaria parasites and suggest that PfCOQ2 could be a therapeutic target to enhance the efficacy of AV.

microbiology↗

bioRxiv2025

Telmisartan and Lisinopril Show Potential Benefits in Rescuing Cognitive-Behavioral Function Despite Limited Improvements in Neuropathological Outcomes in Tg-SwDI Mice

Cerebral amyloid angiopathy (CAA) is a cerebrovascular disease that results from beta-amyloid (A{beta}) accumulation in the vessel walls that is associated with cognitive impairment and other neurological pathologies. There are currently no medications approved to treat CAA. This study investigated whether renin-angiotensin system (RAS)-targeting drugs, commonly prescribed to treat hypertension, can be repurposed to treat CAA, and whether their effects differ by sex. Male and female Tg-SwDI mice were treated for 5 months with sub-depressor doses of either telmisartan [angiotensin II receptor blocker (ARB)] or lisinopril [angiotensin-converting enzyme (ACE) inhibitor] starting at 3 months of age. Blood pressure monitoring was performed 2 and 4 months after the start of treatment, followed by behavior testing at 7 months of age. Histochemical analyses were conducted to determine vasculopathy, A{beta} pathology, and neuroinflammation (microgliosis and astrogliosis). Outcomes in drug-treated and untreated Tg-SwDI mice were compared to each other and with wild-type (C57BL/6J) controls. Overall, both drugs were able to rescue some cognitive-behavioral functions; however, no reductions in A{beta} levels were observed, and only limited improvements in vascular density and neuroinflammatory markers were detected. Notably, some treatment effects varied with sex, the specific behavioral task, and the brain region analyzed. These findings support the hypothesis that RAS-targeting drugs exert neuroprotective effects through mechanisms beyond blood pressure control offering a promising therapeutic avenue for CAA.

neuroscience↗

bioRxiv2025

DIO3 coordinates photoreceptor development timing and fate stability in human retinal organoids

The mechanisms governing the generation of neuronal subtypes at distinct times and proportions during human retinal development are poorly understood. While thyroid hormone (TH) signaling specifies cone photoreceptor subtypes, how this regulation changes over time remains unclear. To address this question, we studied the expression and function of type 3 iodothyronine deiodinase (DIO3), an enzyme that degrades TH, in human retinal organoids. We show that DIO3 is a master regulator of human photoreceptor developmental timing and cell fate stability. DIO3 is highly expressed in retinal progenitor cells (RPCs) and decreases as these cells asynchronously differentiate into neurons, progressively reducing TH degradation and increasing TH signaling. DIO3 mutant organoids display precocious development of S cones, L/M cones, and rods, increased photoreceptor (PR) density, and adoption of L/M cone fate characteristics by S cones and rods. Our multiomics and chimeric organoid experiments show that cell autonomous and non-autonomous mechanisms locally coordinate and maintain DIO3 expression and TH signaling levels among cells. Computational modeling reveals a mechanism that couples TH levels and fate specification, providing robustness to photoreceptor development as compared to a probabilistic, cell-intrinsic mechanism. Based on our findings, we propose an hourglass hypothesis, in which the proportion of progenitors to neurons decreases over time to relieve TH degradation, which triggers development of PR subtypes at specific times. Our study identifies how local regulation of thyroid hormone signaling influences neural cell fate specification, which may be a consideration for designing regenerative therapies.

developmental biology↗

bioRxiv2025

Ketogenic Diet Enhances Cognitive-Behavioral Function and Hippocampal Neurogenesis While Attenuating Amyloid Pathology in Tg-SwDI Mice

The ketogenic diet (KD), characterized by high-fat, low-carbohydrate, and moderate protein intake, has gained attention for its therapeutic potential in patients with neurodegenerative diseases, including Alzheimers disease. Studies in Alzheimers rodent models report that KD and/or ketogenic supplements attenuate cognitive-behavioral impairments, neuroinflammation, amyloid-beta plaques and tau pathology. However, it is unknown whether KD can similarly benefit individuals with cerebral amyloid angiopathy (CAA), a prevalent condition in which amyloid accumulates in cerebral vessels. CAA is highly comorbid in patients with Alzheimers and, on its own, increases the risk of stroke, cognitive impairment, and dementia, yet no effective treatments currently exist. The objective of this study was to determine whether KD can improve cognitive-behavioral and neuropathological outcomes in a mouse model with CAA. Male Tg-SwDI mice were fed either a standard chow or KD from 3.5 to 7.5 months of age. Following [~]3 months of dietary intervention, glucose and ketone-body levels were assessed, then mice underwent a battery of behavioral tests to evaluate locomotor activity, anxiety-related behaviors, and cognition. Immunohistochemistry was performed to assess amyloid pathology, vascular density, neuroinflammation, white matter integrity, and hippocampal neurogenesis. In addition to KD inducing nutritional ketosis and achieving metabolic benefits, mice on KD exhibited increased activity, enhanced spatial learning and memory, and a trend toward improved spatial working memory. These cognitive benefits were accompanied by an attenuation of amyloid pathology and increased hippocampal neurogenesis. These findings suggest that a ketogenic diet may be safe and effective in Alzheimers and dementia patients with CAA.

neuroscience↗

bioRxiv2025

Odd-chain dicarboxylic acid feeding recapitulates the biochemical phenotype of glutaric aciduria type-1 in mice

Glutaric aciduria type-1 (GA1) is an inherited mitochondrial neurometabolic disorder with a poorly understood pathogenesis and unmet medical needs. GA1 can be diagnosed via its hallmark biochemical signature consisting of glutaric aciduria, 3-hydroxyglutaric aciduria, and increased plasma glutarylcarnitine. These glutaryl-CoA-derived metabolites are thought to originate solely in the mitochondria. Here, we demonstrate that wild-type mice fed an 11-carbon odd-chain dicarboxylic acid (undecanedioic acid, DC11) recreates the biochemical phenotype of GA1. Odd-chain dicarboxylic acids like DC11 are not present in food but can arise from several endogenous processes, such as lipid peroxidation and fatty acid {omega}-oxidation. DC11 is chain-shortened in peroxisomes to glutaryl (DC5)-CoA, which then gives rise to the GA1-like pattern of DC5 metabolites in urine, tissues, and blood. Glutaric acid released from peroxisomes during DC11 chain-shortening can enter mitochondria, be activated to CoA by the enzyme succinyl-CoA:glutarate-CoA transferase (SUGCT), and become substrate for glutaryl-CoA dehydrogenase (GCDH), the enzyme that is mutated in GA1. Our data provide proof-of-concept that the generation of dicarboxylic acids by {omega}-oxidation, which is stimulated during the same catabolic states known to trigger acute encephalopathy in GA1, may exacerbate disease by increasing the glutaryl-CoA substrate load in mitochondria.

biochemistry↗