Biology subjects

Saeedi, A.

Publications and source records attributed to Saeedi, A..

8 recordsLinked to original sources

bioRxiv2026

Absence of the Earths magnetic field activates stress-related brain circuits in a mammal

The Earths magnetic field is a constantly available cue for animals with a magnetic sense. While magnetic navigation is best studied in migratory birds, a magnetic sense is also found in some mammals. Among these, it is most thoroughly studied in African mole-rats of the genus Fukomys, subterranean mammals that navigate in kilometre-long dark tunnel systems. Our understanding of the neural pathways involved in magnetoreception remains incomplete. To address this, we here performed an unbiased whole-brain screen for magnetically induced neuronal activity in the mole-rat brain. We set up MoBI-DisC (Mole-rat Brain Imaging with iDISCO and ClearMap), an experimental pipeline that combines global c-Fos immunolabelling, tissue clearing, light-sheet microscopy, and mapping to a novel 3D brain atlas. To identify brain areas involved in magnetosensation, we exposed mole-rats to a changing magnetic field and compared their brain activity to that of control animals exposed to a near-zero magnetic field. Unexpectedly, we found that the near-zero magnetic field exposure activated many brain areas, predominantly those involved in stress and anxiety responses. These included the amygdala, the bed nucleus of the stria terminalis, the substantia innominata, and the periaqueductal grey. This suggests that magnetic field deprivation acts as a physiological stressor in mole-rats. To test this, we conducted a place-preference test and found that mole-rats avoid entering a zone with a near-zero magnetic field, consistent with the hypothesis that this condition is not neutral for these animals. In summary, we present a novel pipeline for unbiased mapping of neural activity in subterranean mole-rats and uncover evidence of stress and avoidance responses to the absence of an Earth-strength magnetic field.

neuroscience↗

bioRxiv2025

Neuronal recordings in head-fixed and freely-moving mole-rats

Mole-rats are subterranean rodents that have evolved remarkable sensory adaptations to life in underground tunnel systems, yet their neural mechanisms remain largely unexplored. Here, we present a protocol for in vivo electrophysiological recordings in awake, head-fixed, and freely moving African mole-rats (Fukomys anselli/micklemi), overcoming unique challenges of studying the neurobiology of subterranean species. For example, we find that mole-rat brain physiology impacts survival after surgeries, with higher carbon dioxide concentrations required for recovery compared to other rodents, likely due to a mutation in the chloride-potassium symporter KCC2. Having addressed the challenges, we used tetrodes and Neuropixels probes to record single-unit activity and local field potentials (LFP) across several cortical and subcortical regions for several weeks. We observed single units responsive to auditory and visual stimuli in the superior colliculus, and hippocampal recordings in freely moving mole-rats revealed prominent theta rhythms at frequencies lower than those observed in any other rodent species to date. Finally, we performed integrated three-dimensional and two-dimensional probe-track analysis within the same brain using tissue clearing, light sheet imaging, rehydration, and vibratome sectioning, and we present a newly developed stereotaxic brain atlas for implantation and histological alignment. The established methodology will guide future studies in comparative rodent neurobiology, providing further insights into neurobiological adaptations to subterranean environments. Given their phylogenetic and ecological similarities, we expect our protocols to be transferable to other subterranean species, including the widely studied naked mole-rat (Heterocephalus glaber). HighlightsO_LIProtocols for chronic and acute electrode implantations in mole-rats C_LIO_LIStereotaxic brain atlas for the Ansells mole-rat (https://doi.org/10.17617/3.UNDKRO) C_LIO_LINeuropixels and tetrode single-unit recordings in head-fixed and freely moving mole-rats C_LIO_LIIntegrated 3D (tissue clearing) and 2D (histology) probe-track analysis within the same brain C_LIO_LIDiscovery of low-frequency hippocampal theta rhythm in Ansells mole-rats C_LI

neuroscience↗

bioRxiv2022

Engineering non-cytotoxic delivery of proteins by T cells via fusion to NPC2

Engineering cellular therapeutics by programming T cells has great potential in immunology. The primary mechanism employed by T cells for the specific transfer of proteins at the immunological synapse is via the lysosomal perforin pathway that facilitates the transfer of cytotoxic granzymes leading to apoptosis in target cells. Facilitating the delivery of non-cytotoxic proteins through perforin oligomers will dramatically expand the range of protein cargos that T cells can traffic to the target cells. Here, we have identified the intralysosomal protein, NPC2, as a chaperone that can facilitate the delivery of T-cell derived reporter proteins through perforin pores at the immunological synapse. Structural and biophysical considerations suggested that NPC2 could traverse through perforin pores and in vitro experiments confirmed the transport of purified NPC2 through perforin pores on cell membranes. To characterize the ability of NPC2 to facilitate the transfer of payloads in T cells, we constructed NPC2-mCherry fusion proteins in T cells. Using confocal microscopy and flow cytometry, we confirmed the colocalization of the NPC2 fused protein with lytic granules and the transfer of the fluorescent protein payload from T cells to target cells in co-culture experiments. The NPC2 fusion enabled the localization of mCherry to secretory lysosomes in mouse TCR CD8+ T cells and human CD4+ and CD8+ chimeric antigen receptor (CAR) T cells. These results illustrate that by using NPC2 as a molecular chaperone, the NPC2-perforin pathway can be exploited as a programmable molecular delivery system for cell-based therapies.

immunology↗

bioRxiv2022

Mouse primary visual cortex neurons respond to the illusory ''darker than black'' in neon color spreading.

Illusions are a powerful tool for studying the single neuron correlates of perception. Here, we introduce the neon color spreading (NCS) illusion in mice and report the neuronal correlates of illusory brightness, which has heretofore only been studied using human fMRI. We designed a novel NCS paradigm to evoke the percept of an illusory drifting grating and analyzed the activity of 520 single units in the mouse primary visual cortex (V1). A substantial proportion of V1 single units (60.5%) responded to illusory gratings with direction tuning matched to their preferred direction, which was determined using physically presented luminance-defined gratings (LDG). Moreover, by presenting LDG gratings with a 180{degrees} phase shift relative to NCs gratings, we show that spatial phase tuning shifted 180{degrees} for most single units. This finding conclusively demonstrates that V1 single units respond to illusory brightness. Using this novel mouse paradigm, we show that responses to illusory gratings have a lower magnitude and are delayed relative to physical gratings. We determined where V1 single units fell in the V1 cellular hierarchy (based on their susceptibility to surround suppression, their putative classification as interneuron or pyramidal neuron, and designation as a simple or complex cell) and found that higher-level V1 single units are more responsive to NCS stimuli. These findings resolve the debate of whether V1 is involved in illusory brightness processing and reveal a V1 hierarchical organization in which higher-level neurons are pivotal to the processing of illusory qualities, such as brightness.

neuroscience↗

bioRxiv2022

Ending transmission of SARS-CoV-2: sterilizing immunity using an intranasal subunit vaccine

Immunization programs against SARS-CoV-2 with commercial intramuscular (IM) vaccines prevent disease but not infections. The continued evolution of variants of concern (VOC) like Delta and Omicron has increased infections even in countries with high vaccination coverage. This is due to commercial vaccines being unable to prevent viral infection in the upper airways and exclusively targeting the spike (S) protein that is subject to continuous evolution facilitating immune escape. Here we report a multi-antigen, intranasal vaccine, NanoSTING-NS that yields sterilizing immunity and leads to the rapid and complete elimination of viral loads in both the lungs and the nostrils upon viral challenge with SARS-CoV-2 VOC. We formulated vaccines with the S and nucleocapsid (N) proteins individually to demonstrate that immune responses against S are sufficient to prevent disease whereas combination immune responses against both proteins prevents viral replication in the nasal compartment. Studies with the highly infectious Omicron VOC showed that even in vaccine-naive animals, a single dose of NanoSTING-NS significantly reduced transmission. These observations have two implications: (1) mucosal multi-antigen vaccines present a pathway to preventing transmission and ending the pandemic, and (2) an explanation for why hybrid immunity in humans is superior to vaccine-mediated immunity by current IM vaccines.

immunology↗

bioRxiv2022

T-cell potential for CD19-expressing malignancies revealed by multi-dimensional single-cell profiling

Adoptive immunotherapy with T cells expressing chimeric antigen receptors (CARs) for B-cell malignancies serves as a model for identifying subsets with superior clinical activity. We profiled the infusion products (IP) of 16 patients with large B-cell lymphoma (LBCL) using an integrated suite of single-cell assays to reveal the therapeutic potential of CD19-specific CAR+ T cells. Timelapse imaging microscopy in nanowell grids (TIMING) profiling revealed that T cells from responders showed migration (persistent motion for at least one body length), and migration was associated with serial killing capacity. In addition, confocal microscopy revealed that migration is linearly correlated with both mitochondrial volume and lysosomal volume; and scRNA-seq demonstrated that T cells from responders were enriched in pathways related to T-cell killing, migration and actin cytoskeleton, and TCR clustering. A marker-free sorting strategy enriched T cells with migratory capacity and validated serial killing, bioenergetics, and in vivo efficacy. In aggregate, we demonstrate that migration is a cell-intrinsic biomarker independent of CAR design or biomanufacturing, desired in the bioactivity of CAR+ T cells associated with clinical antitumor efficacy.

immunology↗

bioRxiv2022

An intranasal nanoparticle STING agonist has broad protective immunity against respiratory viruses and variants

Respiratory viral infections, especially Influenza (endemic) or SARS-CoV-2 (pandemic since 2020), cause morbidity and mortality worldwide. Despite remarkable progress in the development and deployment of vaccines, they are clearly impacted by the rapid emergence of viral variants. The development of an off-the-shelf, effective, safe, and low-cost drug for prophylaxis against respiratory viral infections is a major unmet medical need. Here, we developed NanoSTING, a liposomally encapsulated formulation of the endogenous STING agonist, 2-3 cGAMP, to function as an immunoantiviral. NanoSTING rapidly activates the bodys innate immune system to facilitate a broad-spectrum antiviral response against SARS-CoV-2 and influenza variants in hamsters and mice. We demonstrate that a single intranasal dose of NanoSTING can: (1) treat infections throughout the respiratory system and minimize clinical symptoms, (2) protect against highly pathogenic strains of SARS-CoV-2 (alpha and delta), (3) provide durable protection against reinfection from the same strains without the need for retreatment, (4) prevent transmission of the highly infectious SARS-CoV-2 Omicron strain, and (5) provide protection against both oseltamivir-sensitive and resistant strains of influenza. Mechanistically, administration of NanoSTING rapidly upregulated interferon-stimulated and antiviral pathways in both the nasal turbinates and lung. Our results support using NanoSTING as a thermostable, immunoantiviral with broad-spectrum antiviral properties making it appealing as a therapeutic for prophylactic or early post-exposure treatment.

immunology↗

bioRxiv2020

Mesoscopic Liquid Clusters Represent a Distinct Condensate of Mutant p53

The oncogenic properties of mutant p53 have been ascribed to destabilization of the p53 conformation, followed by aggregation into insoluble fibrils. Here we combine immunofluorescent 3D confocal microscopy of breast cancer cells expressing the p53 mutant Arg248Gln (R248Q) with light scattering from solutions of the purified protein and molecular simulations to probe the mechanisms that govern phase behaviors of the mutant across multiple length scales, from cellular to molecular. We establish that p53 R248Q forms mesoscopic protein-rich clusters, an anomalous liquid phase with several unique properties. We demonstrate that the clusters host and facilitate the nucleation of amyloid fibrils. The distinct characteristics of the clusters of R248Q and wild-type p53 and theoretical models indicate that p53 condensation into clusters is driven by the structural destabilization of the core domain and not by interactions of its extensive disordered region. Two-step nucleation of mutant p53 amyloids suggests means to control fibrillization and the associated pathologies through modifying the cluster behaviors. In a broader context, our findings exemplify interactions between distinct protein phases that activate complex physicochemical mechanisms operating in biological systems.

biophysics↗