Biology subjects

Garcia, F.

Publications and source records attributed to Garcia, F..

At least 19 recordsLinked to original sources

bioRxiv2026

Nmur1 and Cckar fail to support functional genetic access in adult dopamine neurons and challenge GPCR atlas assignments

Apuschkin et al. (2024) proposed a GPCR-based transcriptomic atlas for midbrain dopamine (DA) neuron subpopulations, including candidates such as Nmur1, Cckar, and Ffar4. To guide genetic targeting, these markers must reflect functional expression in adult DA neurons. Using in situ hybridization, Cre-dependent reporter lines, and both intracranial and systemic viral approaches, we find no evidence of adult Nmur1-mediated recombination in DA neurons, while Cckar-driven recombination is consistent with developmental expression only. Notably, Ffar4 expression overlaps extensively with Ntsr1 midbrain populations, indicating that it does not define a distinct DA neuron class. Furthermore, analysis of independent spatial transcriptomic datasets together with our MERFISH data shows that many proposed GPCR markers are not detectably expressed in adult DA neurons. These findings demonstrate that transcriptomic enrichment does not always yield reliable adult markers and highlight the need for functional validation prior to use in circuit targeting.

neuroscience↗

bioRxiv2026

Genetic Identification of Dopamine Neurons Required for Circadian Food Anticipatory Activity in Mice

Anticipating daily food availability is a conserved circadian behavior that persists even in animals lacking the suprachiasmatic nucleus, yet its neural substrates remain poorly defined. Previous studies implicated dopamine signaling in food anticipatory activity (FAA) but lacked the resolution to identify the responsible neuronal population. Here, we conditionally deleted tyrosine hydroxylase (Th) from molecularly defined dopamine neuron populations in mice. Broad deletion of Th in dopamine transporter-expressing neurons nearly abolished FAA, whereas restoration of Th in substantia nigra dopamine neurons rescued anticipatory locomotion. Surprisingly, deletion of Th from several large dopamine neuron populations had little effect on FAA. In contrast, deletion using Calb1Cre, targeting only [~]25% of substantia nigra dopamine neurons, produced a profound FAA deficit. Notably, these mice exhibited a profound loss of anticipatory locomotion while retaining substantial anticipatory food-seeking behavior. These findings identify a small Calbindin1+ dopamine population required for anticipatory locomotion and demonstrate that distinct behavioral components of food anticipation can be genetically dissociated.

neuroscience↗

bioRxiv2026

A Knock-in Ntsr1-Flp Driver Enables Intersectional and Systemic Targeting of Heterogeneous Midbrain Dopamine Circuits

Precise genetic access to molecularly defined neuronal subpopulations is essential for dissecting circuit heterogeneity. We developed and validated a knock-in neurotensin receptor 1 (Ntsr1)Flpmouse line for intersectional targeting of Ntsr1-expressing neurons. Following delivery of Flp-dependent adeno-associated viral (AAV) reporters, robust recombination was observed throughout the the midbrain and several other brain regions. A subset of Ntsr1+ neurons in the substantia nigra and ventral tegmental area lacked dopaminergic markers, indicating that midbrain Ntsr1 populations comprise both dopaminergic and non-dopaminergic neurons. Systemic delivery of a Cre and Flp-dependent reporter in complementary dual-recombinase configurations revealed configuration-dependent differences in dopaminergic targeting. Cis-gene controls (DatCre;DatFlp) defined the maximal dopaminergic targeting ceiling and helped distinguish true non-dopaminergic targeting from recombinase-dependent off-target labeling. Finally, a dual-recombinase-dependent taCaspase-3 construct enabled selective ablation of midbrain dopamine neurons in vivo, establishing Ntsr1Flp as a versatile driver for scalable Boolean targeting.

neuroscience↗

bioRxiv2026

Systemic AAV delivery of a calcium indicator in marmosets: functional validation in visual area MT

Functional optical imaging in nonhuman primates provides an important complement to electrophysiological approaches in neuroscience research, but its broader use has been limited by challenges in achieving large-scale, homogeneous expression of genetically encoded reporters, and imaging accessibility in species with gyrencephalic brains with sulci and fissures (e.g., rhesus macaques). Specifically, conventional local intracortical viral injections are invasive and often produce spatially restricted or heterogeneous expression, constraining population-level analyses. Here, we show that systemic intravenous delivery of an adeno-associated virus (AAV) capsid engineered for enhanced blood-brain barrier crossing, AAV.CAP-B10, supports robust and widespread expression of a calcium indicator CAaMP8s in the common marmoset. Intravenous delivery in two marmosets resulted in widespread cortical expression. Using a large cranial window over extrastriate visual area MT (and its satellite areas), we performed widefield single-photon imaging and two-photon cellular-resolution imaging in awake,behaving marmosets to functionally validate activity in this well studied primate visual-motion sensitive cortical area. Population level responses to visual motion and spatial organization measured with widefield imaging, as well as single-cell level motion direction tuning measured with two-photon imaging, were consistent with canonical properties of MT reported in previous electrophysiological studies. Quantitative analyses of lightsheet imaging after whole hemisphere brain clearing further confirmed the broad expression of GCaMP in both cortical and subcortical areas. Together, these results indicate that systemic delivery using AAV.CAP-B10 provides a minimally invasive approach for robust multi-scale functional optical imaging in awake, behaving marmosets.

neuroscience↗

bioRxiv2025

High-throughput phenomics of global ant biodiversity

The big data era in biology is underway, but the study of organismal form has been slow to capitalize on advances in imaging and computation. Modern imaging can digitize whole organisms, but low throughput has limited the effort to document morphological diversity. Within the open science initiative Antscan, we applied high-throughput synchrotron X-ray microtomography to capture phenotypes across a diverse and ecologically dominant insect group -- ants. We provide 2193 whole-body 3D ant datasets from 792 species to broadly cover the ant phylogeny with a global scope, also pairing phenomic data with genome sequencing projects. Scans acquired with standardized parameters facilitate automated analysis and free access to data can broaden the audience and incentivize methods development. Antscan presents a scalable approach to create libraries of diverse anatomies, heralding a new era of studies on the evolution, structure, and function of organismal phenotypes.

zoology↗

bioRxiv2025

High-Throughput Multiomics Profiling of Model Systems Using the AVITI24 Platform

We present a multiomics platform comprising Teton, a detection assay system, and AVITI24, a dual-flowcell instrument that performs both cellular imaging and sequencing readout. Teton integrates a compartmentalized flowcell for cell culture with methods to measure morphology, RNA, and protein at subcellular resolution. The platform quantifies morphological features through cell painting of 6 cellular components, RNA expression of up to 350 transcripts via sequencing of oligonucleotides hybridized to mRNA, and protein expression of up to 200 targets using antibody-linked oligonucleotide sequencing. The flow cell accommodates >1 million cells in a 10 cm squared open-well format or can be subdivided into 12 or 48 wells to support experiments with multiple conditions or time points. We describe and validate the detection methods of the platform and showcase its capabilities by co-culturing three cancer cell lines and elucidating the cellular pathways triggered by various drug treatments as a function of time. Using multiple time points enables us to capture the dynamics of cellular processes including receptor activation and signaling cascades. The results demonstrate how different cancer cells evade TNF-induced apoptosis by activating compensatory signaling programs that maintain survival despite pro-apoptotic cues. Our model system replicates previously published results and highlights the versatility of the platform in enabling rapid, high-throughput analysis of complex cellular responses in varied biological contexts.

genomics↗

bioRxiv2024

HDAC Inhibitors recapitulate Human Disease-Associated Microglia Signatures in vitro

Disease-associated microglia (DAM), initially described in mouse models of neurodegenerative diseases, have been classified into two related states; starting from a TREM2-independent DAM1 state to a TREM2 dependent state termed DAM2, with each state being characterized by the expression of specific marker genes1. Recently, single-cell (sc)RNA-Seq studies have reported the existence of DAMs in humans2-6; however, whether DAMs play beneficial or detrimental roles in the context of neurodegeneration is still under debate7,8. Here, we present a pharmacological approach to mimic human DAM in vitro by exposing different human microglia models to selected histone deacetylase (HDAC) inhibitors. We also provide an initial functional characterization of our model system, showing a specific increase of amyloid beta phagocytosis along with a reduction of MCP-1 secretion. Additionally, we report an increase in MITF expression, a transcription factor previously described to drive expression towards the DAM phenotype. We further identify CADM1, LIPA and SCIN as DAM- marker genes shared across various proposed DAM signatures and in our model systems. Overall, our strategy for targeted microglial polarization bears great potential to further explore human DAM function and biology.

neuroscience↗

bioRxiv2024

Autoregulation of cluster root and nodule development by white lupin CCR1 receptor-like kinase

Root development is controlled by local and systemic regulatory mechanisms that optimize mineral nutrient uptake and carbon allocation. The Autoregulation of Nodulation (AoN) pathway defines a negative regulation of nodule development in Legumes as a way to regulate the costly production of nitrogen-fixing organs. This pathway is defined as a response to symbiotic interaction and has been shown to also control root formation to some extent. However, it remains unclear if root and nodule development are under coordinated genetic regulation. Here, we identified mutants with altered root development in white lupin, constitutively producing specialized lateral roots called cluster roots. We showed that the CCR1 receptor-kinase negatively regulates cluster root and nodule development and targets common molecular modules such as NIN/LBD16-NFYA, defining a novel pathway that we named Autoregulation of Development (AoDev). AoDev defines a negative systemic pathway controlling several types of root organ development, independently of symbiotic partners and nutrient availability.

plant biology↗

bioRxiv2024

Synchronization of the prefrontal cortex with the hippocampus and posterior parietal cortex is navigation strategy-dependent during spatial learning

1.During goal-directed spatial learning, subjects progressively change their navigation strategies to increase their navigation efficiency, an operation supported by the medial prefrontal cortex (mPFC). However, how the mPFC may integrate relevant information in a wider memory networks involving the hippocampus (HPC) and the posterior parietal cortex (PPC) is poorly understood. We recorded local-field potential and neuronal firing simultaneously from the mPFC, HPC and PPC in mice subjected to spatial memory acquisition in the Barnes maze. During navigation trials, animals demonstrated two consecutive behavioral stages: searching and exploration. Throughout training, mice gradually switched from less efficient (non-spatial) to more efficient (spatial) goal-oriented strategies exclusively during the searching stage. 4-Hz and theta (6-12 Hz) oscillations were detected during spatial navigation in the three recorded areas associated with episodes of immobility and locomotion, respectively. The entrainment of prefrontal gamma oscillations (60-100 Hz) by hippocampal and parietal 4-Hz and theta oscillations, as well as the incidence of prefrontal gamma, was higher when mice implemented spatial strategies during the searching stage. Interestingly, 4-Hz and theta from HPC and PPC also synchronized the spike-timing of prefrontal neurons, which was maximum during spatial strategies in the searching stage. Finally, neurons recorded in the mPFC increased their task stage firing selectivity when they used spatial strategy. Altogether, these results provide evidence for the neural mechanisms underlying the prefrontal large-scale coordination with distributed neural networks during spatial learning.

neuroscience↗

bioRxiv2024

"Out of sight, out of mind". The antagonistic role of the transcriptional memory associated with repeated acoustic stimuli on the priming of plant defense.

BackgroundPriming plant immunity offers a powerful and sustainable strategy for crop protection, enabling plants to respond faster and more efficiently to threats. This increased readiness is driven by transcriptional memory--molecular mechanisms that store and recall stress responses, including protein accumulation, transcription factor activity, and epigenetic modifications. However, the interplay among transcriptional stress memory, its stability, and its broader impact on plant resistance remain poorly understood. ResultsHere, we reveal a tight link between transcriptional memory and defense priming in Arabidopsis thaliana exposed to repeated acoustic stimulations. Using a combination of experiments and computational modeling, we show that enhanced resistance to Sclerotinia sclerotiorum after three stimulations arises from three key mechanisms: (1) preemptive activation of defense pathways in noninoculated plants, (2) increased diversification of defense-related genes, and (3) gene priming. This heightened defense state is sustained by transcriptional stress memory across thousands of genes, which is likely orchestrated by transcription factor cascades. Challenging the conventional view that priming involves stepwise activation of distinct pathways, our findings suggest that priming instead results from the simultaneous modulation of a broad spectrum of defense pathways. This built-in redundancy enhances resilience, shielding primed plants from the genetic variability-driven resistance loss observed in naive plants. However, this same redundancy imposes strict limits on further enhancing the resistance. More frequent acoustic stimulations did not amplify the protective effect, and transcriptional memory faded within 1.5 days after stimulation ceased. ConclusionsBy integrating experimental and computational approaches, we present a genome-scale quantitative model of stress-induced gene regulation. Our results highlight the trade-offs inherent in transcriptional memory-driven priming, revealing both its potential and its limitations in optimizing plant immunity.

plant biology↗

bioRxiv2024

SIEGA the integrated genomic surveillance system of Andalusia, a One Health regional resource connected with the clinic

The One Health approach, recognizing the interconnectedness of human, animal, and environmental health, has gained significance amid emerging zoonotic diseases and antibiotic resistance concerns. This paper aims to demonstrate the utility of a collaborative tool, the SIEGA, for monitoring infectious diseases across domains, fostering a comprehensive understanding of disease dynamics and risk factors, highlighting the pivotal role of One Health surveillance systems. Raw whole-genome sequencing is processed through different species-specific open software that additionally reports the presence of genes associated to anti-microbial resistances and virulence. The SIEGA application is a Laboratory Information Management System, that allows customizing reports, detect transmission chains, and promptly alert on alarming genetic similarities. The SIEGA initiative has successfully accumulated a comprehensive collection of more than 1900 bacterial genomes, including Salmonella enterica, Listeria monocytogenes, Campylobacter jejuni, Escherichia coli, Yersinia enterocolitica and Legionella pneumophila, showcasing its potential in monitoring pathogen transmission, resistance patterns, and virulence factors. SIEGA enables customizable reports and prompt detection of transmission chains, highlighting its contribution to enhancing vigilance and response capabilities. Here we show the potential of genomics in One Health surveillance when supported by an appropriate bioinformatic tool. By facilitating precise disease control strategies and antimicrobial resistance management, SIEGA enhances global health security and reduces the burden of infectious diseases. The integration of health data from humans, animals, and the environment, coupled with advanced genomics, underscores the importance of a holistic One Health approach in mitigating health threats.

microbiology↗

bioRxiv2024

BPTF cooperates with MYCN and MYC to link neuroblastoma cell cycle control to epigenetic cellular states

The nucleosome remodeling factor BPTF is required for the deployment of the MYC-driven transcriptional program. Deletion of one Bptf allele delays tumor progression in mouse models of pancreatic cancer and lymphoma. In neuroblastoma, MYCN cooperates with the transcriptional core regulatory circuitry (CRC). High BPTF levels are associated with high-risk features and decreased survival. BPTF depletion results in a dramatic decrease of cell proliferation. Bulk RNA-seq, single-cell sequencing, and tissue microarrays reveal a positive correlation of BPTF and CRC transcription factor expression. Immunoprecipitation/mass spectrometry shows that BPTF interacts with MYCN and the CRC proteins. Genome-wide distribution analysis of BPTF and CRC in neuroblastoma reveals a dual role for BPTF: 1) it co-localizes with MYCN/MYC at the promoter of genes involved in cell cycle and 2) it co-localizes with the CRC at super-enhancers to regulate cell identity. The critical role of BPTF across neuroblastoma subtypes supports its relevance as a therapeutic target.

genomics↗

bioRxiv2024

The relationship between gut and nasopharyngeal microbiome composition can predict the severity of COVID-19

Coronavirus disease 2019 (COVID-19) is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that displays great variability in clinical phenotype. Many factors have been described to be correlated with its severity, and microbiota could play a key role in the infection, progression, and outcome of the disease. SARS-CoV-2 infection has been associated with nasopharyngeal and gut dysbiosis and higher abundance of opportunistic pathogens. To identify new prognostic markers for the disease, a multicenter prospective observational cohort study was carried out in COVID-19 patients divided into three cohorts based on symptomatology: mild (n=24), moderate (n=51), and severe/critical (n=31). Faecal and nasopharyngeal samples were taken, and the microbiota was analyzed. Linear discriminant analysis identified M. salivarium, P. dentalis, and H. parainfluenzae as biomarkers of severe COVID-19 in nasopharyngeal microbiota, while P. bivia and P. timonensis were defined in faecal microbiota. Additionally, a connection between faecal and nasopharyngeal microbiota was identified, with a significant ratio between P. timonensis (faeces) and P. dentalis and M. salivarium (nasopharyngeal) abundances found in critically ill patients. This ratio could serve as a novel prognostic tool for identifying severe COVID-19 cases.

microbiology↗

bioRxiv2023

Molecular and phylogenetic characterization of the monkeypox outbreak in the South of Spain

Until the May 2022 Monkeypox outbreak, which spread rapidly to many non-endemic countries, the virus was considered a viral zoonosis limited to some African countries. The Andalusian circuit of genomic surveillance was rapidly applied to characterize the Monkeypox outbreak in the South of Spain. Whole genome sequencing was used to obtain the genomic profiles of samples collected across the south of Spain, representative of all the provinces of Andalusia. Phylogenetic analysis was used to study the relationship of the isolates and the available sequences of the 2022 outbreak. Whole genome sequencing of a total of 160 monkeypox viruses from the different provinces that reported cases were obtained. Interestingly, we report the sequences of monkeypox viruses obtained from two patients who died. While one of the isolates bore no noteworthy mutations that explain a potential heightened virulence, in another patient the second consecutive genome sequence, performed after the administration of tecovirimat, uncovered a mutation within the A0A7H0DN30 gene, known to be a prime target for tecovirimat in its Vaccinia counterpart. In general, a low number of mutations were observed in the sequences reported, which were very similar to the reference of the 2022 outbreak (OX044336), as expected from a DNA virus. The samples likely correspond to several introductions of the circulating monkeypox viruses from the last outbreak. The virus sequenced from one of the two patients that died presented a mutation in a gene that bears potential connections to drug resistance. This mutation was absent in the initial sequencing prior to treatment.

microbiology↗

bioRxiv2022

Viroscope: plant viral diagnosis from NGS data using biologically-informed genome assembly coverage

Next-generation sequencing (NGS) methods are transforming our capacity to detect pathogens and perform disease diagnosis. Although sequencing advances have enabled accessible and point-of-care NGS, data analysis pipelines have yet to provide robust tools for precise and certain diagnosis, particularly in cases of low sequencing coverage. Lack of standardized metrics and harmonized detection thresholds confound the problem further, impeding the adoption and implementation of these solutions in real-world applications. In this work, we tackle these issues and propose biologically-informed viral genome assembly coverage as a method to improve diagnostic certainty. We use the identification of viral replicases, an essential function of viral life cycles, to define genome coverage thresholds in which biological functions can be described. We validate the analysis pipeline, Viroscope, using field samples, synthetic and published datasets and demonstrate that it provides sensitive and specific viral detection. Furthermore, we developed Viroscope.io a web-service to provide on-demand NGS data viral diagnosis to facilitate adoption and implementation by phytosanitary agencies to enable precise viral diagnosis.

microbiology↗

bioRxiv2022

New distribution data and phylogenetic approach reveal bioregionalization of the western Palearctic ants

AimBiogeographic regionalization has fascinated biogeographers and ecologists for centuries and is endued with new vitality by evolutionary perspectives. However, progress is scant for most insect groups due to shortfalls in distribution and phylogenetic information, namely Wallacean and Darwinian shortfalls respectively. Here, we used the western Palearctic ants as the case to tackle these shortfalls and test their biogeographic structure through novel distribution data and phylogenetic approaches. LocationWestern Palearctic realm. TaxonAnts (Formicidae). MethodsFirstly, we developed a refined database integrating the occurrences of 747 ant species across 207 regions of the western Palearctic realm, based on newly expert-validated records derived from the existing global ant biodiversity informatics. Using range estimates for these species derived from polygons and species distribution modelling, we produced species assemblages in 50 x 50 km grid cells. We calculated taxonomic and phylogenetic turnover of ant assemblages, performing hierarchical clustering analysis using the Simpson dissimilarity index to delineate biogeographic structure. ResultsAt both the regional list- and grid assemblage-levels, the Mediterranean has higher turnover and more biogeographic regions than northern Europe, both taxonomically and phylogenetically. Delineations based on grid assemblages detected more detailed biogeographic transitions, while those based on regional lists showed stronger insularity in biogeographic structure. The phylogenetic regionalization suggested closer but varied affinities between assemblages in comparison to the taxonomic approach. Main conclusionsHere, we integrated expert-validated regional lists, species distribution modelling, and a recent phylogeny to tackle Wallacean and Darwinian shortfalls for an important insect group by developing a next-generation map of biogeographic regionalization for the western Palearctic ants. The results of this study suggest strong constraints from geographic barriers and potential effects of climatic history on ant distributions and evolutionary history, and also provide baseline spatial information for future investigations of regional insect distributions.

zoology↗

bioRxiv2021

Pathogen-derived mechanical cues regulate the spatio-temporal implementation of plant defense

How immune responses are activated and regulated is a central question in immunology. In addition to molecular signaling, recent work has shown that physical forces regulate the immune response of vertebrates by modifying transmembrane protein conformation and cell contact. Mechanical stress and strain produced by forces constitute physical cues perceived by cells instructing gene expression. Whether mechanical cues generated by pathogens during host colonization can trigger adaptive responses in plant cells remains elusive. We found that local and progressive variations of plant cell wall tension caused by fungal pathogen attacks are transmitted to neighboring healthy tissue around the infection site and trigger immunity in distal cells. This thigmoimmunity process requires the reorganization of cortical microtubules and contributes strongly to Arabidopsis disease resistance. One-Sentence SummaryActivation of plants immunity depends on fluctuations of mechanical tension caused by a fungal pathogen.

plant biology↗

bioRxiv2021

NFIC regulates ribosomal biology and ER stress in pancreatic acinar cells and suppresses PDAC initiation

Tissue-specific differentiation is driven by specialized transcriptional networks. Pancreatic acinar cells crucially rely on the PTF1 complex, and on additional transcription factors, to deploy their transcriptional program. Here, we identify NFIC as a novel regulator of acinar differentiation using a variety of methodological strategies. NFIC binding sites are found at very short distances from NR5A2-bound genomic regions and both proteins co-occur in the same complex. Nfic knockout mice show reduced expression of acinar genes and, in ChIP-seq experiments, NFIC binds the promoters of acinar genes. In addition, NFIC binds to the promoter of, and regulates, genes involved in RNA and protein metabolism; in Nfic knockout mice, p-RS6K1 and p-IEF4E are down-regulated indicating reduced activity of the mTOR pathway. In 266-6 acinar cells, NFIC dampens the ER stress program through its binding to ER stress gene promoters and is required for complete resolution of Tunicamycin-mediated ER stress. Normal human pancreata from subjects with low NFIC mRNA levels display reduced epxression of genes down-regulated in Nfic knockout mice. Consistently, NFIC displays reduced expression upon induced acute pancreatitis and is required for proper recovery after damage. Finally, expression of NFIC is lower in samples of mouse and human pancreatic ductal adenocarcinoma and Nfic knockout mice develop an increased number of mutant Kras-driven pre-neoplastic lesions.

cell biology↗