Biology subjects

Du, L.

Publications and source records attributed to Du, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Salmonella hijacks a host glucose transporter for intravacuolar proliferation

AbstractsSalmonella is an intracellular pathogen that resides within a vacuole, which protects it from cytosolic host defenses at the expense of limited nutrient access. Glucose serves as a critical carbon source supporting Salmonellas intracellular replication. However, the molecular mechanisms driving glucose enhancement and the pathways by which cytosolic glucose becomes accessible to intravacuolar Salmonella remain poorly understood. Here, we elucidate a sophisticated three-pronged strategy through which Salmonella hijacks GLUT1 to co-opt host glucose metabolism for pathogenic advantage. Firstly, Salmonella infection upregulates the glucose transporter GLUT1 by activating the MAPK signaling cascade, enhancing host glucose uptake, and accelerating glycolytic flux. Secondly, Salmonella redirects GLUT1 to the bacterial vacuolar membrane to establish a glucose-import conduit that facilitates bacterial acquisition of cytosolic glucose. Thirdly, K29-linked ubiquitination modifications on bacterial vacuolar membranes are a previously unrecognized regulatory mechanism that potentiates GLUT1 transporter activity. Inhibition of GLUT1 potentiates Salmonella-triggered innate immune responses and attenuates bacterial virulence in vitro (RAW264.7 macrophages) and in vivo (murine infection model). Collectively, these findings delineate a novel paradigm of metabolic hijacking, wherein Salmonella systematically rewires host glucose metabolic networks to support intracellular proliferation, providing new insights into host-directed antimicrobial interventions.

microbiology↗

bioRxiv2025

Cell type-specific contributions to impaired blood-brain barrier and cerebral metabolism in presymptomatic 5XFAD mice

Altered cerebral metabolism and blood-brain barrier (BBB) dysfunction are emerging as critical contributors to the preclinical phase of Alzheimers disease (AD), underscoring their role in early pathogenesis. To identify sensitive biomarkers before irreversible neuronal loss and cognitive decline, we examined 5XFAD mice at 3 months of age by applying multiple advanced MRI techniques. Arterial spin tagging based MRI revealed increased BBB permeability and water extraction fraction, indicating compromised BBB integrity at the early stage of pathogenesis in 5xFAD mice. Despite preserved cerebral blood flow, a decreased unit mass cerebral metabolic rate of oxygen (CMRO2) was evident in the same cohorts of 5XFAD mice. Interestingly, a region-specific decrease of tissue pH values was detected in the hippocampus of these 5XFAD mice by creatine chemical exchange saturation transfer MRI. Elevated neuronal H4K12 lactylation in the hippocampus supports the reduced pH values. To further dissect the cellular and molecular mechanisms underlying these MRI-detectable changes in 5XFAD mice, we conducted single-nucleus RNA sequencing (snRNA-Seq) with optimized blood vessel enrichment protocols. Our results revealed cell type-specific transcriptomic changes in the hippocampus of 3-month-old 5XFAD mice, including downregulation of synaptogenesis and synaptic transmission genes in the CA1 and dentate gyrus excitatory neurons, impaired endothelial gene expression linked to brain barrier function and angiogenesis, altered innate immune response genes in astrocytes, as well as upregulation of cholesterol biosynthesis and metabolism genes in the CA1 excitatory neurons. These findings underlie the intricate interplay between BBB disruption and metabolic dysregulation before the onset of cognitive decline in AD. Our study demonstrates that BBB dysfunction and cerebral metabolic alterations preceded brain hypoperfusion and cognitive decline, emphasizing potential molecular pathways for early intervention. These findings, once validated in human studies, could significantly enhance early diagnosis and inform novel therapeutic strategies targeting early AD pathogenesis.

neuroscience↗

bioRxiv2025

MF-PENS: An Efficient and Versatile Nuclear Extraction Method for Plant Single-Cell Sequencing

The widespread adoption of single-cell transcriptomics in plants remains constrained by the challenges of isolating high-quality nuclei from tissues with rigid cell walls and complex metabolomes. Here, we present methanol fixation and Percoll-enriched nuclei sorting (MF-PENS), a robust strategy designed to tackle these limitations. Distinct from conventional protocols, MF-PENS circumvents the need for fluorescence activated cell sorting (FACS) and effectively reduce RNA leakage, consistently yielding high-quality single-nucleus RNA sequencing (snRNA-seq) data. MF-PENS has been validated across various plant tissues, including fresh and frozen rice roots and leaves, as well as recalcitrant samples such as soybean root nodules, soybean seeds, and tomato fruits. Benchmarking results demonstrate that MF-PENS significantly enhances gene capture efficiency, cell clustering performance, and cell type annotation accuracy. With its broad applicability and superior performance, MF-PENS represents a robust and versatile tool for plant single-cell research, facilitating deeper insights into plant development and biology processes.

plant biology↗

bioRxiv2025

Effects of Lamina-Chromatin Attachment on Super Long-Range Chromatin Interactions

The interactions between chromatin and lamin proteins localized on the nuclear envelope play a crucial role in the three-dimensional (3D) organization of the genome. This study investigates the influence of lamin associated domains (LADs) on genome organization at the chromosome level using 3D polymer models of mouse embryonic fibroblasts (MEFs) and embryonic stem cells (mESCs). By integrating genome-wide LAD maps from DamID assays, we simulated chromatin conformations with and without LAD attachment to the nuclear envelope. Our results show that incorporating LAD-lamin interactions yields a radial chromatin distribution consistent with experimental observations. Moreover, LAD-lamin interactions induce significant super long-range chromatin contacts across distant genomic regions. These findings suggest two distinct mechanisms driving induction of chromatin interactions by LAD-lamin attachment.

genomics↗

bioRxiv2025

Cisternostomy facilitates clearance of metabolic waste from cerebrospinal fluid in patients with traumatic brain injury

Decompressive craniotomy, a common intervention for traumatic brain injury (TBI), can fail to effectively alleviate patient symptoms. Cisternostomy, reported for cistern drainage in TBI patients, has shown efficacy in reducing intracranial pressure and clearing detritus resulting from brain hemorrhage. However, the mechanisms underlying its effectiveness remain largely unknown. Here, we utilized non-targeted metabolomics to analyze cerebrospinal fluid from cisterns alongside peripheral blood samples from TBI patients undergoing cisternostomy. Through a systematic comparison of the cisternal cerebrospinal fluid and blood plasma metabolomes, we identified multiple blood-enriched metabolites, including betaine, triethanolamine, and proline, that were efficiently cleared during the acute stage of TBI. Notably, two metabolites linked to arginine metabolism and the urea cycle, N8-acetylspermidine and N-acetylputrescine, showed significant reductions that correlated with improvements in the Glasgow Coma Scale. Our findings indicate that cisternostomy effectively removes blood-derived substances and aids the recovery of patients with acute-stage TBI.

neuroscience↗

bioRxiv2025

Roles of Cro2 and CI2 binding to OR operators in controlling lysogeny stability during prophage induction

The lysogeny-lysis switch in bacteriophage lambda serves as a model for understanding cell fate decisions. The molecular network controlling this switch has been explored through extensive experimental and computational studies. Yet, the specific role of protein-DNA interactions, like the binding of CI2 and Cro2 proteins to operator sites, in regulating lysogeny stability during prophage induction remains less under-stood. This study employs a minimalistic model and the Accurate Chemical Master Equation (ACME) method to construct detailed probability landscapes of the networks behavior under varying conditions, such as different dissociation and CI2 degradation rates which simulate UV irradiation effects. Our findings indicate that Cro2 binding at OR3 and CI2 at OR1 significantly influence lysogeny stability, with the former destabilizing and the latter stabilizing it. Conversely, interactions at OR1 by Cro2 and OR3 by CI show minimal impact on this stability. Through the ACME approach, we could examine the networks global behavior under conditions unapproachable by conventional stochastic simulations. This study highlights the critical roles of specific protein-DNA interactions in maintaining lysogeny and provides insight into the broader dynamics of the lysogeny-lysis switch under various physiological stresses.

systems biology↗

bioRxiv2024

Deciphering the thiolactonization mechanism in thiolactomycin biosynthesis

Thiolactomycin (1), which features a unique{gamma} -thiolactone ring, is a promising antibiotic candidate that specifically targets bacterial type II fatty acid synthase. Despite extensive studies on its pharmacological activities, modes of action, and chemical synthesis, the enzymatic processes responsible for forming the activity-determining{gamma} -thiolactone ring have remained largely unknown. Here, we resolve this problem by revealing that the condensation and heterocyclization (Cy) domain of the nonribosomal peptide synthetase (NRPS) TlnC (TlnCCy), along with the cytochrome P450 enzyme TlnA, cooperatively enable the{gamma} -thiolactone assembly. TlnCCy mediates an unusual sulfurtransfer reaction to sulfurate the polyketide intermediate, generating a thiocarboxylate intermediate. Subsequently, TlnA acts as a{gamma} -thiolactone synthase, converting the linear thiocarboxylate intermediate into 1 via a distal radical-based cyclization mechanism. These findings not only expand the functional and catalytic repertoires of NRPS Cy domains and P450 enzymes, but also highlight a special enzymatic strategy for{gamma} -thiolactone biosynthesis in nature. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/629141v2_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@7e0ad2org.highwire.dtl.DTLVardef@f86b80org.highwire.dtl.DTLVardef@159d136org.highwire.dtl.DTLVardef@1b633ff_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

ABA increases fatty acids levels in apple roots to boost colonization by arbuscular mycorrhizal fungi

The roots of most land plants are in symbiosis with arbuscular mycorrhizal (AM) fungi. The fungus promotes nutrient uptake from the soil while receiving plant photosynthate as lipids and sugars. Nutrient exchange must be regulated by both partners, but the mechanisms underlying the regulation of lipid supplement from the plant to the AM fungus remain elusive. Here, we conducted a molecular study on the role of increased abscisic acid (ABA) levels during AM fungus infection in the roots of apple (Malus spp.). AM fungus induced the expression of two ABA synthesis genes, MdNCED3.1 and 3.2, in apple roots and increased the ABA content, which promoted the growth of the AM fungus. The effect of ABA on symbiosis was confirmed in transgenic apple roots either overexpressing or silencing MdNCED3.1 or MdNCED3.2. Transcriptome analysis and transgenic manipulation revealed that the transcription factor MdABF2 played a key role in the ABA-mediated formation of symbiosis during AM infection and that MdABF2 could regulate the expression levels of genes related to fatty acid (FA) synthesis (e.g., MdKASIII) and translocation (such as MdSTR2) in apple roots. Activation of these genes boosted the levels of available fatty acids in the roots and increased the AM fungal colonization and arbuscule development in the roots. These results revealed a molecular pathway in which positive regulation of FA synthesis and transport by the ABA signaling pathway increases supplementation to AM fungi and promotes AM symbiosis.

molecular biology↗

bioRxiv2024

Pan-Prediction of MHC-II Restricted Epitopes Across Species via an Alphafold-based Quantification Scheme

Predicting MHC-II restricted epitopes across species used to be challenging, but Alphafold (AF) may provide a structure-based pan-prediction solution. In this study, we established the new tool AF-pred with a clear standard for quantitative prediction results. Compared to the sequence-based tools heavily trained with human ligandome, AF-pred does not show advantage in predicting the binding patterns of human HLA-II but has far better performance in predicting binding patterns of other animals MHC-II. Using recently resolved bat MHC-II structures, we analyzed AF-preds prediction capability, logic and limitation. In addition, we also explored the impact of AF algorithm iterations on the prediction of MHC-II restricted epitopes. The results demonstrated that AF-pred is capable of cross-species prediction of MHC-II restricted epitopes and is conducive to the development of novel veterinary vaccines.

immunology↗

bioRxiv2024

Tim-3 promotes viral infection by suppressing USP25-TRAF3-IRF7 signaling pathway

Tim-3, an immune checkpoint inhibitor, plays key roles in maintaining immune homeostasis and is involved in viral evasion. However, the precise role of Tim-3 in viral infection remains to be determined. USP25 is one of the deubiquitinating enzymes that serves to initiate antiviral immunity by deubiquitinating TRAF3 and triggering the anti-viral signaling pathway. Here we found that Tim-3 specific knockout in myeloid cells leads to enhanced anti-viral immunity in mice with VSV encephalitis by increasing type I interferon response. Mechanistically, Tim-3 inhibits the expression of USP25 via STAT1, interacts with USP25 but does not regulate its post-translational modification, and as a result, Tim-3 inhibits USP25 mediated deubiquitination of TRAF3, promotes k48-linked ubiquitination and degradation of TRAF3, and then inhibits the phosphorylation of IRF7, finally down-regulates the interferon response. These findings provide new insights into the function of Tim-3 in antiviral immunity and its related clinical significance.

immunology↗

bioRxiv2024

Competition and Compromise between Exogenous Probiotics and Native Microbiota

Probiotic interventions are effective strategies to modulate the gut microbiome, but how exogenous probiotics compete with native gut microbiota remains elusive. Here, we use a mouse model and a well-documented probiotic Bifidobacterium animalis subsp. lactis V9 (BV9) to mechanistically investigate its competitive strategies. We perform metagenomic and whole genome sequencing of stool samples and isolated BV9, longitudinally collected from 24 mice orally administered with BV9 and different diets. Results show that a high-fiber diet most effectively supports the colonization of BV9, where BV9 selectively competes with Parabacteroides distasonis (P. distasonis), rather than extensively with other gut bacteria. By comparing the genomic structures of BV9 and P. distasonis isolated during the washout period, we infer their co-evolution mechanisms, highlighting their competition and compromise in utilizing inulin-derived glucose. Finally, our in vitro co-culture experiments validate such competitive dynamics. This study fills a critical gap in our understanding of niche competition in colonization.

microbiology↗

bioRxiv2024

Structural Basis of Differential Gene Expression at eQTLs Loci from High-Resolution Ensemble Models of 3D Single-Cell Chromatin Conformations

MotivationTechniques such as high-throughput chromosome conformation capture (Hi-C) have provided a wealth of information on the organization of the nucleus and the genome important for understanding gene expression regulation. Additionally, Genome-Wide Association Studies (GWASs) have uncovered thousands of loci related to complex traits. Expression quantitative trait loci (eQTL) studies have further linked the genetic variants to alteration in expression levels of associated target genes across individuals. However, the functional roles of many eQTLs located in non-coding regions are unclear. Current joint analyses of Hi-C and eQTLs data lack advanced computational tools, limiting what can be learned from these data. ResultIn this work, we developed a computational method for simultaneous analysis of Hi-C and eQTL data. Our method can identify a small set of non-random interactions from all Hi-C interactions. Using these non-random interactions, we reconstruct large ensemble (x105) of high-resolution single-cell 3D chromatin conformations with thorough sampling, which accurately replicate Hi-C measurements. Our results revealed the presence of many-body interactions in chromatin conformation at single-cell level in eQTL locus, offering detailed view into how three-dimensional structures of chromatin form the physical foundation for gene regulation, including how genetic variants of eQTLs affect the expression level of their associated eGenes. Furthermore, our method can deconvolve chromatin heterogeneity and investigate the spatial associations of eQTLs and eGenes at subpopulation level to reveal their regulatory impacts on gene expression. Together, ensemble modeling of thoroughly sampled single cell chromatin conformations from Hi-C, along with eQTL data, helps to decipher how chromatin 3D structures provide the physical basis for gene regulation, expression control, and aid in understanding of the overall structure-function relationships of genome organization. Availability and implementation: It is available at https://github.com/uic-liang-lab/3DChromFolding-eQTL-Loci

bioinformatics↗

bioRxiv2024

A New Approach for Discovering Functional Links Connecting Non-Coding Regulatory Variants to Gene Targets

Genome-wide association studies (GWAS) have linked thousands of genetic variants to various complex traits or diseases. However, most identified variants have weak individual effects, are correlated with nearby polymorphisms due to linkage disequilibrium (LD), and are located in non-coding cis-regulatory elements (CREs). These characteristics complicate the assessment of the direct impact of each variant on tissue specific gene expression and phenotype. To address this challenge, we have developed a novel algorithm that leverages polymer folding and 3D chromatin interactions to prioritize and identify putative causal variants and their target genes. From the millions of eQTL-Gene pairs identified by GTEx in human somatic tissues, we classify only [~]10-20% as putative functional eQTL-Gene pairs supported by phenotypic associations confirmed through CRISPR deletion experiments. Our findings show that unlike most variants, functional eQTL-Gene pairs predominantly reside within the same topologically associating domain (TAD) and have strong associations with cell-type specific cis-regulatory elements (CREs), enriched for binding sites of tissue-specific transcription factors. Unlike most approaches that rely on linear distance or other chromatin features (histone code, accessibility), our algorithm emphasizes the importance of physical interactions and 3D chromatin folding in gene regulation, as the identified eQTL-Gene pairs are all among the small fraction of physical chromatin interactions sufficient for chromatin locus folding. Overall, our algorithm reduces false positive associations between DNA variants and genes identified by eQTL analysis and uncovers novel variant-gene pair associations. These findings suggest a mechanism where a small number of regulatory variants control tissue specific gene expression via their physical association with target genes confined within the same TAD. Our approach provides new insights into the molecular mechanisms driving GWAS phenotypes.

genomics↗

bioRxiv2024

Elucidating Electronic Structure Variations in Nucleic Acid-Protein Complexes Involved in Transcription Regulation Using a Tight-Binding Approach

Transcription factor (TF) are proteins that regulates the transcription of genetic information from DNA to messenger RNA by binding to a specific DNA sequence. Nucleic acid-protein interactions are crucial in regulating transcription in biological systems. This work presents a quick and convenient method for constructing tight-binding models and offers physical insights into the electronic structure properties of transcription factor complexes and DNA motifs. The tight binding Hamiltonian parameters are generated using the random forest regression algorithm, which reproduces the given ab-initio level calculations with reasonable accuracy. We present a library of residue-level parameters derived from extensive electronic structure calculations over various possible combinations of nucleobases and amino acid side chains from high-quality DNA-protein complex structures. As an example, our approach can reasonably generate the subtle electronic structure details for the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta within a few seconds on a laptop. This method potentially enhances our understanding of the electronic structure variations of gene-protein interaction complexes, even those involving dozens of proteins and genes. We hope this study offers a powerful tool for analyzing transcription regulation mechanisms at an electronic structural level. Topic of ContentTranscription factors that bind to DNA modulate gene expression, with the stability and reactivity of their interactions elucidated by eigenvalues derived from the tight-binding model. Visualization of these interactions reveals the Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO), the gap between which determines the reactivity and stability of the molecular complex. This approach advances our understanding of gene regulation by revealing the dynamics of charge transfer and electronic states within transcription factor-DNA complexes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=123 SRC="FIGDIR/small/589549v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@c61734org.highwire.dtl.DTLVardef@11d629aorg.highwire.dtl.DTLVardef@348085org.highwire.dtl.DTLVardef@e1da71_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

Thymidine Phosphorylase Promotes the Formation of Abdominal Aortic Aneurysm in Mice Fed a Western Diet

AimsThe precise molecular drivers of abdominal aortic aneurysm (AAA) remain unclear. Thymidine phosphorylase (TYMP) contributes to increased platelet activation, thrombosis, and inflammation, all of which are key factors in AAA development. Additionally, TYMP suppresses the proliferation of vascular smooth muscle cells (VSMCs), which are central to the development and progression of AAA. We hypothesize that TYMP plays a key role in AAA development. Methods and ResultsWe conducted a histological study using human AAA samples and normal abdominal aortas, revealing heightened levels of TYMP in human AAA vessel walls. To validate this observation, we utilized an Ang II perfusion-induced AAA model in wild-type C57BL/6J (WT) and Tymp-/-mice, feeding them a Western diet (TD.88137) starting from 4 weeks of age. We found that Tymp-/-mice were protected from Ang II perfusion-induced AAA formation. Furthermore, by using TYMP-expressing VSMCs as well as primarily cultured VSMCs from WT and Tymp-/- mice, we elucidated the essential role of TYMP in regulating MMP2 expression and activation. TYMP deficiency or inhibition by tipiracil, a selective TYMP inhibitor, led to reduced MMP2 production, release, and activation in VSMCs. Additionally, TYMP was found to promote pro-inflammatory cytokine expression systemically, and its absence attenuates TNF--stimulated activation of MMP2 and AKT. By co-culturing VSMCs and platelets, we observed that TYMP-deficient platelets had a reduced inhibitory effect on VSMC proliferation compared to WT platelets. Moreover, TYMP appeared to enhance the expression of activated TGF{beta}1 in cultured VSMCs in vitro and in human AAA vessel walls in vivo. TYMP also boosted the activation of thrombospondin-1 type 1 repeat domain-enhanced TGF{beta}1 signaling, resulting in increased connective tissue growth factor production. ConclusionOur findings collectively demonstrated that TYMP serves as a novel regulatory force in vascular biology, exerting influence over VSMC functionality and inflammatory responses that promote the development of AAA. Translational PerspectiveThymidine phosphorylase (TYMP) is increased in the vessel walls of patients with abdominal aortic aneurysm (AAA), and TYMP deficiency in mice reduces the incidence of AAA, suggesting that TYMP plays a crucial role in AAA development. This could be attributed to TYMPs role in enhancing systemic inflammation and thrombosis, inhibiting vascular smooth muscle cell function, increasing the activation of matrix metalloproteinase and AKT, as well as enhancing the expression of TGF{beta}1 and connective tissue growth factor. Tipiracil is an FDA-approved drug known to inhibit TYMP-enhanced thrombosis. Targeting TYMP with tipiracil could represent a promising new therapeutic strategy for AAA development.

cell biology↗

bioRxiv2024

GTPase-activating protein ARAP1 regulates circular dorsal ruffles as a nutrient uptake mechanism in the Hep3B hepatocellular carcinoma cell line

Circular dorsal ruffles (CDRs), large-scale rounded membrane ruffles, function as precursors of macropinocytosis. We recently reported that CDRs are exposed in the Hep3B hepatocellular carcinoma cell line, while not in other hepatocellular carcinoma cell lines, indicating that the CDRs in Hep3B are associated with malignant potential. In this study, we investigated the cellular function of CDRs in Hep3B cells by focusing on the molecular mechanisms of the GTPase-activating protein ARAP1. ARAP1 was localized to the CDRs, the sizes of which were reduced by deletion of this protein. High-resolution scanning electron micrographs revealed that CDRs comprise small vertical lamellipodia, the expression pattern of which was disrupted in ARAP1 KO cells. Extracellular solute uptake, rate of cell growth, and malignant potential were attenuated in the KO cells. ARAP1 is also localized in Hep3B cell mitochondria, although not in those of the Huh7 hepatocellular carcinoma cell line. On the basis of these findings, we propose that the aberrant expression of ARAP1 in Hep3B cells modulates CDRs, thereby resulting in an excess uptake of nutrients as an initial event in cancer development. SUMMARY STATEMENTARAP1 regulates circular dorsal ruffles (CDRs) in the Hep3B HCC cell line and deletion of this protein attenuates malignant potential, thereby indicating the involvement of CDRs in cancer development.

cell biology↗

bioRxiv2023

Enhanced K Na 1.1 Channel Underlies Cortical Hyperexcitability and Seizure Susceptibility after Traumatic Brain Injury

Pathogenic variants of the sodium-activated potassium channel KNa1.1, have been reported in multiple epileptic disorders. However, whether and how KNa1.1 channel is involved in epileptogenesis after traumatic brain injury (TBI) remains unknown. Firstly, we used behavioral monitoring and EEG recording to examine physiological property, spontaneous seizure activity, and seizure susceptibility after TBI. We explored the changes of KNa1.1 channel following TBI, including changes of subcellular distribution and expression pattern. Meanwhile, we performed patch-clamp recording to detect the neuronal excitability. Furthermore, we built TBI model using kcnt1-/- mice and compared seizure activity with those on wild- type mice. We found severity-dependent seizure susceptibility in different degree of injured mice. Meanwhile, increased neuronal expression of KNa1.1 channel, especially in inhibitory neurons, around the lesion was also observed following TBI with increased neuronal excitability including reduced firing rate of interneurons and imbalanced excitation and inhibition (E/I). Although the maximum frequency of action potential of kcnt1-/- neurons was increased, kcnt1-/- mice displayed decreased seizure susceptibility to the pentylenetetrazole (PTZ) after TBI. Taken together, this study suggests that pathologically enhanced expression and abnormally distributed KNa1.1 channel after TBI contribute to disputed E/I and seizure susceptibility, which might provide a potential therapeutic target on the epileptogenesis after TBI.

neuroscience↗

bioRxiv2023

Optimal Transport Method-Based Gene Filter (GF) Denoising Algorithm for Enhancing Spatially Resolved Transcriptomics Data

The recent advancements in spatially resolved transcriptomics (SRT) technology have enabled the acquisition of gene expression data at near- or sub-single-cell resolution, along with simultaneous imaging of physical locations. Nevertheless, necessary experimental procedures such as tissue fixation, permeabilization, and tissue removal inevitably induce the diffusion of transcribed molecules. Consequently, this leads to the partial capture of ex-situ transcripts in SRT data, thereby introducing a considerable amount of noise into the dataset. To address this issue, in this study, we focused on evaluating the diffusion pattern of individual genes within tissue regions and quantitatively calculating their signal-to-noise ratio (SNR). Through this analysis, we successfully identified "invalid genes" exhibiting widespread expression across tissue regions. Then by filtering out these genes, we effectively reduced the high noise level present in SRT data. To achieve this, we developed the gene filter denoising (GF) algorithm, which utilizes the optimal transport method to compute the gene diffusion coefficient and generate denoised SRT data. One notable advantage of our GF algorithm is its ability to fully "respect" the raw sequencing data, thereby avoiding the introduction of false positives often associated with traditional interpolation and modification denoising methods. Furthermore, we conducted comprehensive validation of GF, and the GF-denoised SRT data demonstrated substantial improvements in clustering, identification of differentially expressed genes (DEGs), and cell type annotation. Taken together, we believe that the GF denoising technique will serve as an essential and crucial step in exploring SRT data and investigating the underlying biological processes.

bioinformatics↗