Biology subjects

Rodriguez, N.

Publications and source records attributed to Rodriguez, N..

11 recordsLinked to original sources

bioRxiv2026

Dissociable species-specific impact of Aβ on static and dynamic functional connectomes

Temporal dynamics in functional connectomes offer a physiologically grounded signature of hidden pathologies during preclinical stages of Alzheimers disease (AD). We evaluated the effect of beta-amyloid (A{beta}) on dynamic functional connectomes in transgenic mice and human subjects. Functional magnetic resonance images (fMRI) were collected in two strains of A{beta} mice. fMRI-derived connectomes were segmented into discrete states using a hidden Markov model and network strength, efficiency, and transitivity were analyzed per state. Human fMRI-derived connectome measures were analyzed across 3 states. Static network measures were significantly different between A{beta} mice and controls, the former having high values for strength, efficiency and clustering coefficient in anterior cingulate, hippocampus and retrosplenium. Dynamic network measures were stable within-states in A{beta} mice. Similarly, human subjects with high A{beta} had high node strength in precuneus and temporoparietal areas compared to low A{beta}. In contrast, however, high A{beta} was associated with high state switch rates, high fractional occupancy and state dwell times. Also, global strength, efficiency, and transitivity were less stable within states in the high A{beta} group. Our results indicate that static, but not dynamic, connectome strength, efficiency and network integration are increased in A{beta} mice, while dynamic network states appear less stable in human functional connectomes. This data supports a dissociable, species-specific impact of A{beta}, with dynamic network alterations present in humans but not in A{beta} mouse models, suggesting additional non-A{beta}-driven influences on dynamic functional connectivity in preclinical AD. SIGNIFICANT STATEMENTDetecting Alzheimers disease before symptoms appear remains a critical challenge. This study reveals that beta-amyloid -- a hallmark Alzheimers protein -- disrupts brain network dynamics differently across species. While both transgenic mice and humans with elevated amyloid show stronger static brain connectivity, only humans exhibit unstable, rapidly shifting brain network states. This dissociation suggests that the dynamic network disruptions seen in preclinical Alzheimers patients are not solely driven by amyloid accumulation, but likely reflect additional biological factors absent in mouse models. These findings highlight an important translational gap between animal models and human disease, with implications for how we design and interpret preclinical Alzheimers research and develop early diagnostic biomarkers.

neuroscience↗

bioRxiv2026

Covalently linked peptides and membrane potential enable CyaA segment translocation

The adenylate cyclase toxin (CyaA) from Bordetella pertussis intoxicates host cells by directly translocating its N-terminal catalytic domain across the plasma membrane; however, the forces driving this unique process remain poorly defined. Here, we dissect the membrane translocation mechanisms of two peptide segments derived from CyaA: P233 and P454 from the catalytic domain and the translocation region, respectively. Both P454 and P233 are calmodulin-binding segments that are sequentially involved in the translocation and activation of the catalytic domain. Using a newly developed Droplet Interface Bilayer (DIB) approach, called DIB-Pipette, which enables direct visualization of peptide transport under controlled membrane potentials, we show that P454 translocates across membranes independently of membrane potential, whereas P233 translocation requires a negative electric membrane potential. Strikingly, covalent coupling of P233 and P454 enables efficient translocation of the resulting peptide even in the absence of a membrane potential. Together, these results suggest that two distinct membrane-active segments within CyaA act cooperatively to promote translocation at the peptide level, revealing an intrinsic mechanism that may contribute to membrane potential-dependent translocation. These findings provide new mechanistic insights into CyaA cell intoxication process and reveal a multifunctional strategy for protein delivery across membranes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/716334v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@750ab3org.highwire.dtl.DTLVardef@11a980org.highwire.dtl.DTLVardef@18f2b27org.highwire.dtl.DTLVardef@5a3a59_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

A lightweight, physics-based, sensor-fusion filter for real-time EEGdenoising and improved downstream AI classification

Physiological time-series data, like electroencephalography (EEG), are vulnerable to motion, ocular, and muscle artifacts that hinder real-time inference and bias offline analyses. We present the Minds AI Filter: a lightweight, physics-based, sensor-fusion method that exploits multichannel spatial structure and band-aware synchrony to enhance neural activity while suppressing non-neural noise. The nomenclature "AI" reflects integration within a larger artificial-intelligence pipeline; the filter itself requires no prior training or deep learning. A single tuning parameter controls filter strength. The design supports streaming windows ({approx}1 s) with minimal added latency and extends naturally to longer offline segments; leveraging a sensor-fusion design across channels, it suggests applicability to other neurophysiological time-series, such as MEG and ECoG, pending further validation; exploratory incorporation of EOG/ECG as auxiliary signals is a potential avenue for future filter advancements. We evaluate the approach across multiple devices and public datasets, assessing both down-stream AI classification performance and real-time signal-quality metrics. In both real-time and offline settings, the filter performed better on dynamic artifacts and noise than baseline and commonly used alternatives in our evaluations. When applied in conjunction with other methods, it was only observed to improve downstream accuracy, never reduce it, when any effect was present. Denoising is quantified using SNR-like measures, and ablations isolate the roles of spatial coupling and band weighting. Artifact-specific analyses (ocular bursts, head tilt, jaw clench) and latency profiling on commodity hardware are included. These results indicate that a lightweight, synchrony-aware filter can robustly stabilize real-time EEG and systematically improve downstream AI classification. The method is compatible with standard preprocessing but does not depend on it.

neuroscience↗

bioRxiv2025

Asymmetric phosphoinositide lipid bilayers generated by spontaneous lipid insertion

Phosphatidylinositol phosphate (PIP) lipids, enriched on the cytoplasmic leaflet of the plasma membrane, are key regulators of diverse cellular processes, often through interactions with partner proteins that regulate actin assembly. Supported lipid bilayers (SLBs) provide a powerful model system to study the interactions of PIP lipids with their partner proteins. However, despite advances in SLB preparation methods, it remains a challenge to robustly obtain fluid SLBs in which PIP lipids are both mobile and asymmetrically distributed. In this study, we report a simple and robust method to generate asymmetric SLBs containing tunable amounts of PI(4,5)P2. By dissolving PI(4,5)P2 below its critical micelle concentration (CMC), we enable its spontaneous insertion into the upper leaflet of SLBs exposed to bulk solution. The mobility of PI(4,5)P2 is confirmed using fluorescence recovery after photobleaching (FRAP). Furthermore, we demonstrate that PI(4,5)P2 incorporated using this method retains its functionality, recruiting binding partners, actin-membrane linker ezrin, and myosin 1 motors capable of sliding actin filaments on the SLBs. Our method offers a straightforward strategy to generate asymmetric PI(4,5)P2-containing SLBs and is applicable to other lipid species with high CMC values.

biophysics↗

bioRxiv2024

Key roles of the zona pellucida and perivitelline space in promoting gamete fusion and fast block to polyspermy inferred from the choreography of spermatozoa in mice oocytes

Mammalian fertilization is still lacking a comprehensive understanding of gamete fusion and block to polyspermy mechanisms. One reason is that they are highly dynamic processes involving transient events that can only be revealed and characterized by direct observation. To extend while challenging existing knowledge, this study applies real time brightfield and confocal imaging to inseminated ZP-intact mouse oocytes and statistical analyses to establish an accurate dynamic picture of the cascade of events leading to fusion and prevention of polyspermy in conditions as close to physiology as possible. These observations allow to characterize the roles of the different components of the oocyte (i.e. zona pellucida (ZP), perivitelline space (PVS), oocyte plasma membrane (OPM)) and the spermatozoon (i.e. head, flagellum) in promoting fertilization and preventing polyspermy. The kinetics we have determined challenge dogmas by showing that: (i) the first sperm is not necessarily the one that fertilizes in mice pointing to the existence of other post-penetration fertilization factors, (ii) the ZP block resulting from the cortical reaction is too slow to contribute to the prevention of polyspermy in mice. On the other hand, it evidences that the ZP directly contributes to polyspermy block in two other ways: (a) as a naturally effective entry barrier for the spermatozoon (independent of any block caused by fertilization), (b) as an effective exit barrier for components released by the OPM, which may contribute to a fast PVS block to polyspermy through the neutralizing of unwanted spermatozoa in the PVS. Moreover, our observations reveal that the ZP plays a key role in fertilization itself by channeling the flagellar oscillations of spermatozoa in the PVS to make them conducive to fusion.

cell biology↗

bioRxiv2024

Gene Therapy Mediates Therapeutic Improvement in Cardiac Hypertrophy and Survival in a Murine Model of MYBPC3-Associated Cardiomyopathy

BackgroundHypertrophic cardiomyopathy (HCM) affects an estimated 600,000 people in the U.S. and is the leading cause of sudden cardiac arrest in those under 18. Loss-of-function mutations in Myosin Binding Protein C3, MYBPC3, are the most common genetic cause of HCM. The majority of MYBPC3 mutations causative for HCM result in truncations. The sarcomeric pathophysiology of the majority of HCM patients with MYBPC3 mutations appears to be due to haploinsufficiency, as the total amount of MYBPC3 protein incorporated into sarcomeres falls significantly below normal. MethodsA clear path for the treatment of haploinsufficiency is the restoration of the insufficient gene product; in this case wild-type MYBPC3. To achieve this, we engineered an AAV vector (TN-201) with superior properties for mediating cardiomyocyte-selective expression of MYBPC3 after systemic delivery. ResultsWe have demonstrated for the first time with AAV gene therapy the ability of both a mouse surrogate and TN-201, which encodes human MYBPC3 to reverse cardiac hypertrophy and systolic dysfunction and to improve diastolic dysfunction and survival in a symptomatic MYBPC3-deficient murine model of disease. Dose-ranging efficacy studies exhibited restoration of wild-type MYBPC3 protein levels and saturation of cardiac improvement at the clinically relevant dose of 3E13 vg/kg, outperforming a previously published construct. Further, we have established stable cardiac benefit for greater than one year post-injection, as well as reversal of cardiac dysfunction even in late-stage models of disease. ConclusionsOur data suggest that by restoring MYBPC3 to the sarcomere, TN-201 has the potential to slow and even reverse the course of the disease in patients with MYBPC3-associated HCM.

genetics↗

bioRxiv2021

Orthogonal control of gene expression in plants using synthetic promoters and CRISPR-based transcription factors

BackgroundThe construction and application of synthetic genetic circuits is frequently improved if gene expression can be orthogonally controlled, relative to the host. In plants, orthogonality can be achieved via the use of CRISPR-based transcription factors that are programmed to act on natural or synthetic promoters. The construction of complex gene circuits can require multiple, orthogonal regulatory interactions, and this in turn requires that the full programmability of CRISPR elements be adapted to non-natural and non-standard promoters that have few constraints on their design. Therefore, we have developed synthetic promoter elements in which regions upstream of the minimal 35S CaMV promoter are designed from scratch to interact via programmed gRNAs with dCas9 fusions that allow activation of gene expression. ResultsA panel of three, mutually orthogonal promoters that can be acted on by artificial gRNAs bound by CRISPR regulators were designed. Guide RNA expression targeting these promoters was in turn controlled by either Pol III (U6) or ethylene-inducible Pol II promoters, implementing for the first time a fully artificial Orthogonal Control System (OCS). Following demonstration of the complete orthogonality of the designs, the OCS was tied to cellular metabolism by putting gRNA expression under the control of an endogenous plant signaling molecule, ethylene. The ability to form complex circuitry was demonstrated via the ethylene-driven, ratiometric expression of fluorescent proteins in single plants. ConclusionsThe design of synthetic promoters is highly generalizable to large tracts of sequence space, allowing Orthogonal Control Systems of increasing complexity to potentially be generated at will. The ability to tie in several different basal features of plant molecular biology (Pol II and Pol III promoters, ethylene regulation) to the OCS demonstrates multiple opportunities for engineering at the system level. Moreover, given the fungibility of the core 35S CaMV promoter elements, the derived synthetic promoters can potentially be utilized across a variety of plant species.

synthetic biology↗

bioRxiv2021

3D-mapping of human lymph node and spleen reveals integrated neuronal, vascular, and ductal cell networks

The spleen and lymph node represent important hubs for both innate and adaptive immunity1,2. Herein, we map immune, endothelial, and neuronal cell networks within these tissues from "normal"/non-diseased organ donors, collected through the NIH Human BioMolecular Atlas Program (HuBMAP)3, using highly multiplexed CODEX (CO-Detection by indEXing) imaging and 3D light sheet microscopy of cleared tissues. Building on prior reports4-6, we observed the lymph node subcapsular sinus expressing podoplanin, smooth muscle actin, and LYVE1. In the spleen, LYVE1 was expressed by littoral cells lining venous sinusoids, whereas podoplanin was restricted to arteries and trabeculae. 3D visualization of perivascular innervation revealed a subset of axonal processes expressing choline acetyl transferase in both tissues, in contrast with prior literature on human spleen7. We further report our novel observations regarding the distinct localization of GAP43 and {beta}3-tubulin within the vascular anatomy of both lymph node and spleen, with Coronin-1A+ cells forming a dense cluster around {beta}3-tubulin positive GAP43 low/negative segments of large vessels in spleen. These data provide an unprecedented 2D and 3D visualization of cellular networks within secondary lymphoid tissues, laying the groundwork for future disease-specific and system-wide studies of neural regulation of immunity in human lymphatics.

immunology↗

bioRxiv2020

A high-affinity calmodulin-binding site in the CyaA toxin translocation domain is essential for invasion into eukaryotic cells

The molecular mechanisms and forces involved in the translocation of bacterial toxins into host cells have thus far remained elusive. The adenylate cyclase (CyaA) toxin from Bordetella pertussis displays a unique intoxication pathway in which its catalytic domain is directly translocated across target cell membranes. We have previously identified a translocation region in CyaA that contains a segment, P454 (residues 454-484), exhibiting membrane-active properties related to antimicrobial peptides. Herein, we show that this peptide is able to translocate across membranes and interact with calmodulin. Structural and biophysical analyses have revealed the key residues of P454 involved in membrane destabilization and calmodulin binding. Mutational analysis demonstrated that these residues play a crucial role in CyaA translocation into target cells. We have also shown that calmidazolium, a calmodulin inhibitor, efficiently blocks CyaA internalization. We propose that after CyaA binding to target cells, the P454 segment destabilizes the plasma membrane, translocates across the lipid bilayer and binds calmodulin. Trapping of the CyaA polypeptide chain by the CaM:P454 interaction in the cytosol may assist the entry of the N-terminal catalytic domain by converting the stochastic process of protein translocation into an efficient vectorial chain transfer into host cells.

biophysics↗

bioRxiv2020

Specific interaction of Penetratin with cell surface partners measured with biomembrane force probe

Penetratin is a Cell Penetrating Peptide able to cross the cell plasma membrane possibly bound to a cargo molecule to be delivered into the cell. The mechanism of its entry is poorly known. A key to a molecular description of this mechanism is to identify the partners of Penetratin at the cell surface during its adhesion and internalization. We used the Biomembrane Force Probe to identify the partners during the first second of adhesion of Penetratin on the cell plasma membrane. We evidenced that heparan sulfates are the first partners after contact as well as unknown partners hidden by sialic acids. Experiments of binding of Penetratin on vesicles bearing charged or sulfated lipids showed no adhesion pointing that a negatively charged partner is not enough and there is a specificity for certain chemical groups bearing the charges. A model of the measured forces of interaction enabled to determine the adhesion energy of a Penetratin with heparan sulfates on a cell to be in the range 18 to 22 kBT.

biophysics↗

bioRxiv2019

pumilio regulates sleep homeostasis in response to chronic sleep deprivation in Drosophila melanogaster

Recent studies have identified the Drosophila brain circuits involved in the sleep/wake switch and have pointed to the modulation of neuronal excitability as one of the underlying mechanisms triggering sleep need. In this study we aimed to explore the link between the homeostatic regulation of neuronal excitability and sleep behavior in the circadian circuit. For this purpose, we selected the neuronal homeostasis protein Pumilio (Pum), whose main function is to repress protein translation and has been linked to modulation of neuronal excitability during chronic patterns of altered neuronal activity. Here we explore the effects of Pum on sleep homeostasis in Drosophila melanogaster, which shares most of the major features of mammalian sleep homeostasis. Our evidence indicates that Pum is necessary for sleep rebound and that its effect is more pronounced during chronic sleep deprivation (84 hours) than acute deprivation (12 hours). Knockdown of pum, results in a reduction of sleep rebound during acute sleep deprivation and the complete abolishment of sleep rebound during chronic sleep deprivation. These behavioral changes were associated with accompanying changes in the expression of genes involved in the regulation of neuronal excitability. Interestingly, pum knockdown also increased baseline daytime sleep, suggesting that Pum differentially regulates rebound and normal sleep. Based on these findings, we propose that Pum is a critical regulator of sleep homeostasis through neural adaptations triggered during sleep deprivation and induces rebound sleep by altering neuronal excitability.

neuroscience↗