Biology subjects

Fan, S.

Publications and source records attributed to Fan, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Chlamydia-induced ex vivo activation of B cells from mice, nonhuman primates, and humans produces large numbers of uniformly activated antigen presenting cells

Chlamydia trachomatis (Ct) is a clinically important pathogen that causes ocular and genital infections. While genital Ct infection in women is typically persistent and asymptomatic, the host responses that dampen inflammation while gradually eradicating this bacterium are only partially defined. Herein, we show that Ct promotes human B cell activation via TLR2-mediated signaling of MyD88-dependent pathways and non-antigen-specific B cell receptor signaling that engages the CD19 and CD79a/b complex. We also found that ex vivo Chlamydia-induced activation of B cells from the peripheral blood of humans or rhesus macaques (RM), or from murine splenocytes, generates cells with a phenotype characteristic of an activated antigen presenting cell (APC). Consistent with this phenotype, intravenous injection of Chlamydia-activated B cells (CAB) loaded with various cognate antigens (Ag) elicited robust Ag-specific T cell immunity in several experimental models. Specifically, RM injected with CAB loaded with a model Ag developed Ag-specific CD8+ T cell immunity and mice injected with Ag-loaded CAB formed CD8+ T cell immune responses that protected against virus challenge and tumor development. As Chlamydia nonspecifically activated B cells to form large numbers of uniformly activated APC readily loaded with cognate Ag, our studies suggest that CAB may offer foundation for a cellular vaccine platform that elicits robust Ag-specific CD8+ T cell immunity against a variety of tumors and microbial pathogens.

immunology↗

bioRxiv2025

Compositionality of social gaze in the prefrontal-amygdala circuits

Social gaze underpins primate communication, yet the neural principles enabling its flexibility remain unknown. Each social gaze can be deconstructed into three primitives: gaze content, social state, and gaze duration. To reduce dimensionality and facilitate generalization, the brain needs to represent these primitives in an abstract format. Here we show that social gaze is governed by a compositional code built from these primitives in the brain. In male and female macaques (neural recordings in two males) engaged in real-life social gaze interaction, behavior analyses revealed that partner responses were determined by how primitives were combined, rather than by their independent sums, providing evidence for behavioral compositionality. The basolateral amygdala and the anterior cingulate gyrus represented content and state in an abstract format and orthogonally to one another, whereas the dorsomedial prefrontal and orbitofrontal cortices exhibited limited generalization. Linear mixed-selective neurons encoding both content and state in the basolateral amygdala and the anterior cingulate gyrus, but not in the other two areas, facilitated the abstraction underlying generalization. Moreover, distinct channels routed content and state information across prefrontal-amygdala circuits to minimize interference, which was mediated by linear mixed selectivity neurons. These findings identify a neural grammar for social gaze, revealing compositional computations as a principle of flexible social communication.

neuroscience↗

bioRxiv2025

Towards the Development of Isoenergetic Peptide Nucleic Acid Based Probes Targeting Double-Stranded RNAs Through Enhancing Sequence-Specific Stacking Interactions

Peptide nucleic acid (PNA), a synthetic nucleic acid analog, exhibits substantial potential in biotechnology and therapeutic applications due to its high binding affinity and nuclease/protease resistance. Chemically modified PNAs capable of forming stable triplex structures with double-stranded RNAs (dsRNAs) under near-physiological conditions further expand their utility by enabling sequence-specific precise targeting and probing of functional RNA structural motifs. However, the presence of inverted Watson-Crick pairs (C-G and U-A) may significantly weaken the triplex formation of the dsRNA-binding PNAs (dbPNAs). Our previous work demonstrated that dbPNA P3 (composed of L, T, and Q monomers for the recognition of G-C, A-U, and C-G base pairs, respectively) can stimulate ribosomal frameshifting by binding to rHP2, a model RNA hairpin structure in an mRNA, albeit with suboptimal efficiency, due to its significantly weakened Q*C-G triple formation. We hypothesize that incorporating s2U adjacent to Q may offer unique stacking and hydrogen bonding interactions facilitating the development of isoenergetic dbPNA-based probes binding toward dsRNAs with varied sequences. In this study, we investigate how incorporating s2U adjacent to Q residues in P3 influences its binding to rHP2. Bio-layer interferometry (BLI) and non-denaturing polyacrylamide gel electrophoresis (PAGE) analyses demonstrate that substituting T with s2U at the N-terminal position adjacent to Q (P3-2QT) enhances binding affinity by [~]10-fold compared to unmodified P3, whereas C-terminal substitution (P3-TQ2) yields only a 2-fold improvement. Consistent with these findings, a cell-free dual-luciferase reporter assay reveals that P3-2QT significantly increases ribosomal frameshifting efficiency compared to P3 and P3-TQ2. Molecular dynamics simulations further indicate that P3-2QT maintains enhanced PNA-PNA stacking stability, particularly between s2U3 and Q4, suggesting a structural basis for its superior activity. Intriguingly, analogous s2U substitution in the P5 oligomer with the Q replaced by L does not confer a comparable enhancement in binding to the target RNA (rHP1) and frameshifting stimulation, highlighting the context-dependent nature of this modification. To assess the broader applicability of the s2U-Q motif, we examined its effect in dbPNAs targeting the RNA panhandle structure of influenza virus A and precursor microRNA-21, respectively. Both PAGE and BLI data confirm that s2U incorporation improves binding affinity, reinforcing the generality of this strategy. These findings underscore the potential of sequence-dependent uracil thiolation in optimizing triplex-forming dsRNA-binding PNAs, warranting further exploration of modified nucleobase designs to enhance their binding and functional properties. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/662161v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@15d86aborg.highwire.dtl.DTLVardef@1347369org.highwire.dtl.DTLVardef@852040org.highwire.dtl.DTLVardef@84b0a_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThiolation of uracil upstream of Q base in PNA markedly enhances triplex binding affinity and enables isoenergetic and orthogonal targeting/activation. C_LIO_LIN-terminal s2U modification adjacent to Q residues increases PNA-dsRNA binding by [~]10-fold and significantly boosts ribosomal frameshifting efficiency. C_LIO_LIBiophysical assays and molecular dynamics simulations reveal that thiolation improves PNA stacking stability and slows dissociation, thereby enhancing functional activity toward structured RNA targets. C_LIO_LIThe general applicability of s2U modification is demonstrated with influenza A virus RNA panhandle structure and precursor micoRNA-21 targets, underscoring its broad potential for optimizing PNA-based therapeutics and biotechnological tools. C_LI

biochemistry↗

bioRxiv2025

Towards Unified Neural Decoding with Brain Functional Network Modeling

Recent achievements in implantable brain-computer interfaces (iBCIs) have demonstrated the potential to decode cognitive and motor behaviors with intracranial brain recordings; however, individual physiological and electrode implantation heterogeneities have constrained current approaches to neural decoding within single individuals, rendering interindividual neural decoding elusive. Here, we present Multi-individual Brain Region-Aggregated Network (MIBRAIN), a neural decoding framework that constructs a whole functional brain network model by integrating intracranial neurophysiological recordings across multiple individuals. MIBRAIN leverages self-supervised learning to derive generalized neural prototypes and supports group-level analysis of brain-region interactions and inter-subject neural synchrony. To validate our framework, we recorded stereoelectroencephalography (sEEG) signals from a cohort of individuals performing Mandarin syllable articulation. Both real-time online and offline decoding experiments demonstrated significant improvements in both audible and silent articulation decoding, enhanced decoding accuracy with increased multi-subject data integration, and effective generalization to unseen subjects. Furthermore, neural predictions for regions without direct electrode coverage were validated against authentic neural data. Overall, this framework paves the way for robust neural decoding across individuals and offers insights for practical clinical applications.

neuroscience↗

bioRxiv2025

Click chemistry-based quantification of extracellular matrix turnover for drug screening and regenerative medicine

This study presents a sensitive and cost-efficient method to quantify extracellular matrix (ECM) synthesis and degradation using copper-free click chemistry reactions to fluorescently label new ECM components. The approach enables spatial visualization and longitudinal measurement of specific ECM turnover in vitro. We validated the method across multiple platforms, including native cartilage explants and monolayer cultures of human mesenchymal stem cells and breast cancer cells. The technique also proved effective for osteoarthritis drug screening by detecting compounds that mitigate inflammation-induced ECM degradation. Compared to traditional biochemical or histological assays, this click chemistry-based technique offers higher sensitivity, lower sample requirements, and improved temporal resolution. Its versatility supports broad applications in tissue engineering, regenerative medicine, disease modeling, and high-throughput drug evaluation.

bioengineering↗

bioRxiv2025

Mechanisms of resistance to active state selective tri-complex RAS inhibitors

Tri-complex inhibitors (TCIs) act as molecular glues to recruit cyclophilin A (CYPA) to the active (GTP-bound or ON) conformation of RAS, which in turn prevents the activation of downstream effector proteins like RAF and PI3K. Emerging data demonstrate clinical activity, including tumor regressions, in patients with RAS driven cancers. Despite being promising therapeutic interventions, the mechanisms of resistance in patients treated with these inhibitors remain unknown. Here we studied matched baseline and post-progression specimens from patients treated with the RAS(ON) multi-selective inhibitor daraxonrasib (RMC-6236). Tissue or cell-free DNA specimens were collected from 40 patients with RAS-mutant non-small cell lung, colorectal, or other cancers. Eighteen patients (45%) were found to have acquired alterations in RAS signaling intermediates, including recurrent alterations in KRAS, BRAF, RAF1, MAP2K1/2 and PIK3CA. Preclinical resistance models mirrored the alterations observed in patients. We found that secondary KRAS Y64X mutations caused resistance by disrupting an important pi-pi interaction between KRAS and the indole ring of daraxonrasib, which lowers the affinity of the daraxonrasib:CYPA binary complex for active KRAS. We also identified kinase-dead and low-activity BRAF mutations in samples with acquired resistance. This is puzzling, because TCIs are expected to prevent the interaction between RAS and BRAF, which is needed for hypoactive mutants to dimerize and signal. We now show that RAF dimers are harder to displace from active RAS, as compared to their monomeric forms. Indeed, enhanced RAF dimerization attenuated the ability of TCIs to recruit CYPA to active RAS, resulting in diminished inhibition of oncogenic signaling and tumor growth. Thus, several clinical resistance alterations converge at attenuating the formation of the RAS:daraxonrasib:CYPA tri-complex, either by preventing daraxonrasib binding or by inducing RAF dimers.

cancer biology↗

bioRxiv2025

Characterization of the gut mycobiome in patients with non-alcoholic fatty liver disease and correlations with serum metabolome

BackgroundThe relationship between the gut mycobiome and non-alcoholic fatty liver disease (NAFLD) is largely unexplored. MethodsIn this study, we used a publicly available shotgun metagenomic sequencing dataset of fecal samples to compare the gut fungal communities of 90 NAFLD patients with those of 90 healthy controls. We examined their correlations with gut bacterial communities, host serum metabolite s, and the interactions of key taxa within these networks. ResultsOur results revealed a remarked dysbiosis in the gut mycobiome of NAFLD patients, cha racterized by a significant increase in four fungal taxa, including Pseudopithomyces sp. c174, Muc or sp. c176, Aspergillus sp. c25, and uncultured Ascochyta c213. Multi-omics analysis showed that the gut mycobiome significantly contributes to the host serum metabolome. Pseudopithomyces s p. c174 was notably associated with some beneficial blood metabolites, such as glycoursodeoxycholic acid and alpha-linolenic acid, whereas the NAFLD-enriched pro-inflammatory phenylacetic acid was linked to Aureobasidium sp. c170 and Basipetospora sp. c193. Network analysis revealed significant alterations in the gut microbiome of NAFLD patients, highlighting the potential roles of Alternaria alternata c42, Penicillium sp. c5, and uncultured Malassezia c303. Moreover, predictive models that integrated both bacterial and fungal taxa improved prediction accuracy, emphasizing the crucial role of gut fungi in NAFLD. ImportanceNon-alcoholic fatty liver disease (NAFLD) is a widespread liver condition with limited treatments. While gut bacteria have been extensively studied in NAFLD, the role of gut fungi (the mycobiome) remains poorly understood. This study fills that gap by characterizing gut fungal communities in NAFLD patients and linking these changes to their blood metabolite profiles. We found that NAFLD patients show distinct fungal imbalances, which correlate with key metabolic alterations in the host. These findings expand our understanding of NAFLD by spotlighting gut fungi as important contributors to disease progression. This insight opens new avenues for potential biomarkers and therapies targeting the gut-liver axis. ConclusionsOur findings provide a comprehensive understanding of the link between the gut mycobiome and NAFLD progression, which is essential for guiding future therapeutic research.

microbiology↗

bioRxiv2025

Improving American chestnut resistance to two invasive pathogens through genome-enabled breeding

Over a century after two introduced pathogens decimated American chestnut populations, breeding programs continue to incorporate resistance from Chinese chestnut to recover self-sustaining populations. Due to complex genetics of chestnut blight resistance, it is challenging to obtain trees with sufficient resistance and competitive growth. We developed high quality reference genomes for Chinese and American chestnut and leveraged large disease phenotype and genotype datasets to develop accurate genomic selection. Inoculation and simulation results indicate that resistance may be substantially increased in trees that inherited 70% to 100% of their genome from American chestnut. To facilitate gene editing, we integrated multiple lines of evidence to discover candidate alleles for blight resistance and susceptibility. These genomic resources provide a strong foundation to accelerate restoration of this iconic tree.

genomics↗

bioRxiv2025

Inhibition of cathepsin B blocks amyloidogenesis in the mouse models of neurological lysosomal diseases mucopolysaccharidosis type IIIC and sialidosis

Neuronal accumulation of amyloid aggregates is a hallmark of brain pathology in neurological lysosomal storage diseases (LSDs) including mucopolysaccharidoses (MPS), however, the molecular mechanism underlaying this pathology has not been understood. We demonstrate that elevated lysosomal cathepsin B (CTSB) levels and CTSB leakage to the cytoplasm triggers amyloidogenesis in two neurological LSDs. CTSB levels were elevated 3-5-fold in the cortices of mouse models of MPS IIIC (Hgsnat-Geo and HgsnatP304L) and sialidosis (Neu1{Delta}Ex3), as well as in cortical samples of MPS I, IIIA, IIIC and IIID patients. CTSB was found in the cytoplasm of pyramidal layer IV-V cortical neurons containing Thioflavin-S-positive, {beta}-amyloid-positive aggregates consistent with pro-senile phenotype. In contrast, CTSB-deficient MPS IIIC (HgsnatP304L/Ctsb-/-) mice as well as HgsnatP304L and Neu1{Delta}Ex3 mice chronically treated with irreversible brain-penetrable CTSB inhibitor, E64, showed a drastic reduction of neuronal Thioflavin-S-positive/APP-positive deposits. Neurons of HgsnatP304L/Ctsb-/- mice and E64-treated HgsnatP304L mice also showed reduced levels of P62/LC3-positive puncta, GM2 ganglioside and misfolded subunit C of mitochondrial ATP synthase (SCMAS) consistent with restored autophagy. E64 treatment also rescued hyperactivity and reduced anxiety in HgsnatP304L mice implying that CTSB may become a novel pharmacological target for MPS III and similar LSDs.

genetics↗

bioRxiv2025

Crb3 and NF2: A dynamic duo that controls assembly of the apical junctions and barrier function via Rho/ROCK signaling

The gastrointestinal epithelium serves as a critical barrier separating intestinal lumen contents from the underlying tissue environment. Structure and function of the apical junctional complex (AJC), comprising tight and adherens junctions, are essential for establishing and maintaining a polarized and functional epithelial barrier. In this study, we investigated mechanisms by which an apical polarity protein Crumbs homolog 3 (CRB3) regulates AJC assembly and barrier function in primary murine intestinal epithelial cells. Using primary colonic epithelial cells (colonoids) derived from inducible and conditional Crb3 knockdown (Crb3ER{Delta}IEC) and control mice (Crb3fl/fl), we demonstrate that Crb3 loss leads to compromised epithelial barrier function that was associated with hypercontractile perijunctional actomyosin and defective assembly of the AJC. We identified CRB3 associates with the Band 4.1 family of cytoskeletal linker proteins, Merlin (NF2) via FERM (band4.1/ezrin/radixin/moesin) binding domain (FBD) of CRB3. Interestingly, NF2 knockdown in cultured intestinal epithelial cells phenocopied the effect of CRB3 deletion, supporting a coordinated role in AJC formation and barrier assembly. Moreover, increased active Rho was detected in assembling junctions of Crb3-null cells and inhibition of ROCKII and myosin II alleviated the hypercontractile phenotype, highlighting involvement of Rho/ROCK signaling. Additionally, increased vinculin localization at the AJC seen in Crb3-null epithelial cells indicates elevated tension at junctions. Our findings underscore the important role of Crb3 and NF2 in regulating contractility of the perijunctional actomyosin ring, mechanical tension at the AJC and barrier function via Rho/ROCK signaling during junctional assembly in intestinal epithelial cells.

cell biology↗

bioRxiv2024

MethylQUEEN: A Methylation Encoded DNA Foundation Model

DNA 5-methylcytosine (5mC) modification plays a pivotal role in many biological processes, yet 5mC information and pattern hidden behind remains to be explored. Here, we develop Methylation Language Model based on Quintuple Bidirectional Transformer (MethylQUEEN), a novel pre-trained DNA methylation foundation model capable of sensing methylation states and covering the genome-wide methylation landscape. Through tailored methylation-prone pre-training, MethylQUEEN effectively captured epigenetics information hidden within the DNA sequences: it accurately traces DNAs tissue-of-origin, and successfully recovers the expression profile through methylation states. Integrative analysis on MethylQUEENs attention scores also enables us to reveal the unique methylation status of a tissue for precise disease detection, and identifying key regulatory 5mC sites for disease intervention. As a result, MethylQUEEN signifies a new paradigm in methylation analysis for various biological problems. Besides, our study demonstrates the effectiveness of directly integrating methylation information into pre-training, offering new perspectives and methodologies for a range of methylation-related biological processes. It serves as an initial exploration for the development of more comprehensive epigenomic models.

genomics↗

bioRxiv2024

A novel and robust method for assessing mitochondrial (dys)function in healthy and diseased frozen cardiac tissue

Cardiovascular diseases are often associated with impairment in mitochondrial function detected by reduced mitochondrial oxygen consumption using high-resolution respirometry. However, existing respirometry protocols are limited by the necessity for fresh tissue samples. This study developed a method with tailored substrate-inhibitor titration (TSIT) of mitochondrial electron transport complexes (ETC) to measure mitochondrial function in frozen cardiac samples using high-resolution respirometry. Briefly, acetyl-CoA was added to fuel the tricarboxylic acid (TCA) cycle for NADH production, enabling complex I (CI)-linked respiratory assessment. NADH was then added to measure maximum CI-linked respiratory capacity, followed by rotenone and succinate to assess complex II (CII)-linked respiratory capacity. TSIT detected mitochondrial functional differences between frozen atrial and ventricular tissue, with comparable results as measured in fresh samples. It also detected cardiac mitochondrial dysfunction across various (patho)physiological mouse models (including aging, ischemia reperfusion, obesity, and CI deficiency) as well as in frozen human donor samples, highlighting its clinical potential. Furthermore, we showed the first evidence for supercomplexes (SCs) formation between ETC-SCs and the TCA cycle metabolon, underpinning TSIT feasibility. In conclusion, we established a novel, robust, sensitive and translational method (TSIT) for assessing mitochondrial (dys)function in frozen cardiac samples from various species, enabling flexible analysis of mitochondrial function in both laboratory and clinical settings.

physiology↗

bioRxiv2024

A comprehensive foundation model for cryo-EM image processing

Cryogenic electron microscopy (cryo-EM) has become a premier technique for high-resolution structural determination of biological macromolecules1-4. However, its widespread adoption is hampered by the need for specialized expertise. We introduce the Cryo-EM Image Evaluation Foundation (Cryo-IEF) model, pre-trained on an extensive dataset of approximately 65 million cryo-EM particle images using unsupervised learning. Cryo-IEF excels in various cryo-EM data processing tasks, such as classifying particles from different structures, clustering particles by pose, and assessing the quality of particle images. Upon fine-tuning, the model effectively ranks particle images by quality at high efficiency, enabling the creation of CryoWizard--a fully automated single-particle cryo-EM data processing pipeline. This pipeline has successfully resolved high-resolution structures of diverse properties and proven adept at mitigating the prevalent preferred orientation challenge in many cryo-EM samples. The Cryo-IEF model and CryoWizard pipeline collectively represent a significant advancement in rendering cryo-EM technology more accessible, efficient, and robust, with substantial implications for life sciences research.

bioinformatics↗

bioRxiv2024

Amyloid Beta Pathology Accelerates Alterations in the Visual Pathway of the 5xFAD Mouse

Alzheimers disease (AD) is a neurodegenerative disorder characterized by the formation of amyloid beta plaques and neurofibrillary tangles that leads to decreased quality of life due to behavioral, motor, and cognitive impairments. Due to the widespread pathological nature of AD, many brain regions are affected by amyloid beta plaques including regions important for vision such as the lateral geniculate nucleus (LGN) of the thalamus which is critical for relaying signals from the retina to the primary visual cortex. Using a wide range of techniques including electrophysiological approaches, in vivo and ex vivo imaging methods, and immunohistochemistry in a mouse model with progressing amyloidosis (5xFAD), the goal of this study was to determine whether AD-like pathology disrupts neuronal and synaptic structure and function in the visual system. In vivo electroretinogram recordings revealed photoreceptor dysfunction in the 6- and 9-month-old 5xFAD mice, while optical coherence tomography indicated no changes in retinal thickness. In the dorsolateral geniculate nucleus (dLGN), the rodent homolog of the primate LGN, we identified decreased densities of retinal ganglion cell axon terminals and fewer thalamocortical (TC) neuron cell bodies. No detectable deficits in excitatory synaptic function or TC neuron dendritic structure were seen in the dLGN, and reflexive visual behavior was also found to be normal in the 5xFAD mice. These results indicate relatively modest amyloid-triggered dysfunction in these stages of the visual system suggesting that amyloid beta plaque formation may play only a small role in the visual system dysfunction seen in AD patients. These results may also point to potential compensatory mechanisms that preserve function of visual pathways in the 5xFAD visual system.

neuroscience↗

bioRxiv2024

Zinc and Metformin Co-Functionalized Polyetheretherketone: A Novel Dental Implant Material Tailored for the Elderly

This study focuses on addressing the challenges of dental implants in the geriatric population by enhancing the bioactivity of polyetheretherketone (PEEK) through surface modification. PEEK, with its elastic modulus close to alveolar bone, mitigates stress shielding but faces limitations in osseointegration due to low bioactivity. We introduced zinc (Zn) and metformin (MF) onto PEEK surfaces via a dopamine-assisted physical adhesion method, creating a functionalized derivative called ZnMF@PEEK. This combination targets diminished osteogenic potential, persistent inflammation, and cell senescence, which are common issues in elderly patients. Comprehensive physicochemical characterizations confirmed the successful preparation of ZnMF@PEEK, and in vitro and in vivo experiments systematically evaluated its biocompatibility and bioactivity. The results indicate that ZnMF@PEEK holds promise as a dental implant material tailored to the specific needs of the elderly, addressing multifaceted challenges in osseointegration.

bioengineering↗

bioRxiv2024

Early to Middle Pleistocene transition shapes the evolution of human-specific mutations associated with height and basal metabolic rate

Understanding the genetic basis of modern-human-specific traits is essential for elucidating the formation of anatomically modern humans (AMHs). Here, we studied the genetic underpinnings of height and basal metabolic rate (BMR), which have undergone extensive modifications in AMHs compared to other Homo species and apes. The results revealed a significant genetic correlation between the two traits. The evolution of the variants associated with height and BMR was heavily influenced by environmental factors, marked by two bursts during the Early to Middle Pleistocene transition and one afterward, accounting for 37.4% of the inferred causal variants for height and BMR. We identified an AMH-specific mutation, rs34590044-A, which emerged around 981,916 years ago, coinciding with the first burst of variants associated with increased height and BMR. rs34590044-A upregulates the expression of ACSF3 via increasing its enhancer activity, leading to increased mitochondrial function, body length, and BMR exclusively in mice fed essential amino acids, specifically threonine-enriched diets, which are characteristic of meat-based diets. Therefore, the emergence of rs34590044-A may contribute to the shift from an herbivorous to a carnivorous diet in AMHs. Our results underscore the complex interplay between genetics and environment in shaping the crucial phenotypes and physiological traits of AMHs.

genetics↗

bioRxiv2024

Recognition of RNA secondary structures with a programmable peptide nucleic acid-based platform

RNA secondary structures comprise double-stranded (ds) and single-stranded (ss) regions. Antisense peptide nucleic acids (asPNAs) enable the targeting of ssRNAs and weakly formed dsRNAs. Nucleobase-modified dsRNA-binding PNAs (dbPNAs) allow for targeting of relatively stable dsRNAs. A programmable RNA structure-specific targeting strategy is needed for simultaneous recognition of dsRNAs and ssRNAs. Here, we report on combining dbPNAs and asPNAs (designated as daPNAs) for the targeting of dsRNA-ssRNA junctions. Our binding and modeling data suggest that combining traditional asPNA (with a 4-letter code: T, C, A, and G) and dbPNA (with a 4-letter code: T or s2U, L, Q, and E) scaffolds facilitates RNA structure-specific tight binding (nM to M) under physiologically-relevant conditions. We further applied our daPNAs in substrate specific inhibition of Dicer acting on pre-miR-198 in a cell-free assay and regulating ribosomal frameshifting induced by model hairpins in both cell-free and cell culture assays. daPNAs would be a useful platform for developing chemical probes and therapeutic ligands targeting RNA. HighlightO_LIWe demonstrated that sequence- and structure-specific targeting of RNA can be facilitated by nucleobase-modified dsRNA-binding PNAs (dbPNAs) platform in combination with antisense PNAs (asPNAs). We name the novel PNAs as daPNAs. C_LIO_LIdaPNAs can be used in a programmable way for targeting RNAs by formation of a short triplex next to a short duplex at a dsRNA-ssRNA junction. C_LIO_LIWe applied our daPNAs in substrate specific inhibition of Dicer acting on pre-miR-198 in a cell-free assay and regulating ribosomal frameshifting induced by model hairpins in both cell-free and cell culture assays. C_LIO_LIThe daPNAs platform would serve as useful junction-specific molecular glues for the targeting of many biologically important RNA structures in transcriptomes. C_LI

biochemistry↗

bioRxiv2024

An unbiased method to partition diverse neuronal responses into functional ensembles reveals interpretable population dynamics during innate social behavior

In neuroscience, understanding how single-neuron firing contributes to distributed neural ensembles is crucial. Traditional methods of analysis have been limited to descriptions of whole population activity, or, when analyzing individual neurons, criteria for response categorization varied significantly across experiments. Current methods lack scalability for large datasets, fail to capture temporal changes and rely on parametric assumptions. Theres a need for a robust, scalable, and non-parametric functional clustering approach to capture interpretable dynamics. To address this challenge, we developed a model-based, statistical framework for unsupervised clustering of multiple time series datasets that exhibit nonlinear dynamics into an a-priori-unknown number of parameterized ensembles called Functional Encoding Units (FEUs). FEU outperforms existing techniques in accuracy and benchmark scores. Here, we apply this FEU formalism to single-unit recordings collected during social behaviors in rodents and primates and demonstrate its hypothesis-generating and testing capacities. This novel pipeline serves as an analytic bridge, translating neural ensemble codes across model systems.

neuroscience↗