Biology subjects

Li, D.

Publications and source records attributed to Li, D..

At least 181 records · Page 10Linked to original sources

bioRxiv2025

Extrusion-modulated DnaA activity oscillations coordinate DNA replication with biomass growth

Robust control of DNA replication is fundamental to bacterial proliferation. In Escherichia coli, replication initiation is thought to be regulated by oscillations in DnaA activity, driven by DnaA-chromosome interactions that differ among leading models. However, direct evidence linking these oscillations to replication initiation has been lacking, and existing models fail to explain the observed decoupling of replication initiation from dnaA expression. Here, we establish a direct link between DnaA activity and replication initiation by demonstrating robust oscillations in DnaA activity, which peak precisely at replication initiation across diverse growth conditions and genetic perturbations. Notably, these oscillations persist even when dnaA transcription remains constant, suggesting a regulatory mechanism that modulates DnaA activity independently of its expression. Additionally, we propose an extrusion model in which DNA-binding proteins sense biomass-DNA imbalance and extrude DnaA from the chromosome to trigger replication, overcoming limitations of existing models. Consistent with this model, perturbation of the nucleoid-associated protein H-NS modulates DnaA activity and replication timing, supporting its mechanistic validity.

microbiology↗

bioRxiv2025

A census of anti-CRISPR proteins reveals AcrIE9 as an inhibitor of Escherichia coli K12 Type IE CRISPR-Cas system

CRISPR-Cas adaptive immunity systems provide defense against mobile genetic elements and are often countered by diverse anti-CRISPR (Acr) proteins. The Type IE CRISPR-Cas of Escherichia coli K12 has been a model for structural and functional studies and is a part of the species core genome. However, this system is transcriptionally silent, which has fueled questions about its true biological function. To clarify the role of this system in defense, we carried out a census of Acr proteins found in Enterobacterales and identified AcrIE9 as a potent inhibitor of the E. coli K12 Type IE CRISPR-Cas system. While sharing little sequence identity, AcrIE9 proteins from Pseudomonas and Escherichia both interact with the Cas7 subunit of the Cascade complex, thus preventing its binding to DNA. We further show that AcrIE9 is genetically linked to AcrIE10, forming the most widespread anti-CRISPR cluster in Enterobacterales, and this module often co-occurs with a novel HTH-like protein with unusual architecture.

microbiology↗

bioRxiv2025

Incorporating LLM-Derived Information into Hypothesis Testing for Genomics Applications

We propose strategies for incorporating the information in large language models (LLMs) into statistical hypothesis tests in genomics studies. Using gene embeddings derived from text inputs to OpenAIs GPT-3.5 model, we show that biological signals in a variety of genomics datasets reside near the principal subspace spanned by the embeddings. We then use a frequentist and Bayesian (FAB) framework to propose several hypothesis tests that are either optimal or approximately optimal with respect to prior information based on the gene embedding subspace. In four real-world genomics examples, the FAB tests guided by the LLM-derived information achieve more power than classical counterparts.

bioinformatics↗

bioRxiv2025

Digital Twin Brain Predicts rTMS Effects on Brain State Dynamics in Chronic Tinnitus

Predicting repetitive transcranial magnetic stimulation (rTMS) effects on whole-brain dynamics in clinical populations is crucial for developing personalized therapies and advancing precision medicine in brain disorders. This study provides the first proof-of-concept demonstrating that the Digital Twin Brain (DTB) can forecast rTMS effects on brain state dynamics in individuals with brain disorders (chronic tinnitus). First, we identified two aberrant brain states that predominantly overlapped with the somatomotor and default mode networks, respectively. Subsequently, we developed DTB for patients and derived regional responses for each brain region, revealing distinct roles of the parieto-occipital and frontal regions. Mechanistically, we examined the biological plausibility using tinnitus-specific risk genes and investigated the multi-scale neurobiological relevance. Clinically, we found that DTB can predict rTMS effects in an independent, longitudinal dataset (all r > 0.78). Particularly, the predictive capacity exhibits a state-specific nature. Overall, this work proposes a novel DTB-based framework for predicting rTMS effects in clinical populations and provides the first empirical evidence supporting its clinical utility. This approach may be generalizable to other brain disorders and neuromodulation techniques, promoting broader advancements in brain health.

neuroscience↗

bioRxiv2025

A Cross-Species Generative Cell Atlas Across 1.5 Billion Years ofEvolution: The TranscriptFormer Single-cell Model

Single-cell transcriptomics has revolutionized our understanding of cellular diversity, yet our understanding of the transcriptional programs across the tree of life remains limited. Here we present TranscriptFormer, a family of generative foundation models trained on up to 112 million cells spanning 1.53 billion years of evolution across 12 species. By jointly modeling gene identities and expression levels using a novel generative architecture, TranscriptFormer encodes multi-scale biological structure, functioning as a queryable virtual cell atlas. We demonstrate state-of-the-art performance on both in-distribution and out-of-distribution cell type classification, with robust performance even for species separated by over 685 million years of evolution. TranscriptFormer can also perform zero-shot disease state identification in human cells and accurately transfers cell state annotations across species boundaries. As a generative model, TranscriptFormer can be prompted to predict cell type-specific transcription factors and gene-gene interactions that align with independent experimental observations. Developmental trajectories, phylogenetic relationships and cellular hierarchies emerge naturally in TranscriptFormers representations without any explicit training on these annotations. This work establishes a powerful framework for quantitative single-cell analysis, and comparative cellular biology, thus demonstrating that universal principles of cellular organization can be learned and predicted across the tree of life.

systems biology↗

bioRxiv2025

BLTP2 orchestrates lysobisphosphatidic acid synthesis and exosome biogenesis via SCAMP3-dependent ER contacts in tumorigenesis

Multivesicular bodies (MVBs) contain intraluminal vesicles (ILVs) designated for degradation in lysosomes or release as exosomes for cell-to-cell communication. The mechanisms governing ILV/exosome formation are not fully understood. Here, we show that the integral endoplasmic reticulum (ER) membrane protein bridge-like lipid transfer protein 2 (BLTP2; KIAA0100) is indispensable in ILV/exosome formation and that secretory carrier membrane protein 3 (SCAMP3) recruits BLTP2 to ER-MVB membrane contact sites (MCSs) in a Rab5-dependent manner. Our results indicate that this recruitment is hindered by NEDD4-mediated ubiquitination of SCAMP3. Depletion of BLTP2 was found to impede ILV/exosome formation and selectively diminish the levels of cone-shaped phospholipids, including bis(monoacylglycero)phosphate (BMP) and the BMP precursor phosphatidylglycerol (PG) within endosomes. BLTP2 knockout also hampered cell proliferation and tumorigenicity, which could be restored to a significant extent by supplementation with exosomes from wild-type cells. Since BLTP2 is associated with acute monocytic leukemia and is highly expressed in breast cancer, our findings suggest that BLTP2 transfers the BMP/LBPA precursor PG to MVBs for BMP/LBPA synthesis and promotes ILV/exosome formation at SCAMP3-dependent ER-MVB MCSs, a process crucial for cell proliferation and tumorigenesis.

cell biology↗

bioRxiv2025

Arcuate Fasciculus: Evolutionary Convergence in Marmosets and Humans

The marmoset is a highly vocal platyrrhine monkey that shares key anatomical and functional features with humans, offering insights into the evolution of brain connectivity. Although similarities in vocalization features with humans have been reported, it remains unclear whether marmosets possess an arcuate fasciculus (af) homolog. This study delineated white matter tracts in marmosets, establishing homologies with those observed in other primates, including macaques, chimpanzees, and humans. The presence of an af homolog in marmosets was confirmed by tracer and ultra-high-resolution diffusion magnetic resonance imaging datasets. We compared cortical connectivity patterns across these species and found the af in marmosets terminates in the ventral frontal cortex, with greater similarity to humans than macaques. Furthermore, we linked af connectivity with vocalization-related brain activation in both marmosets and humans. Collectively, our findings suggest that a dorsal pathway, which emerged early in marmoset evolution, has evolved convergently with humans, despite their distant phylogenetic kinship.

neuroscience↗

bioRxiv2025

Molecular insights into early malignant transition of hepatocellular carcinoma

The molecular continuum of premalignant-to-malignant transition remains elusive in carcinogenesis, primarily due to the difficulty in sampling transitional lesions. Here, we present comprehensive genomic and immunological profiling of 21 very early hepatocellular carcinomas (veHCCs) arising within 17 cancer-prone DNs. Surprisingly, 82% of cancer-prone DNs harbored TERT alterations, suggesting a predisposing rather than causative role in malignancy transition. A substantial increase in CNA burden, rather than SNV, was noted, indicating a role of chromosome instability in malignancy transition. Additionally, veHCC-originating DNs showed immune inactivity, not falling into the prevailing paradigm that HCCs develop in a context of chronic inflammation. 43% of veHCCs showed an inflamed phenotype with relatively mild CNA burden but already exhibited immune evasion features. Two major evolutionary scenarios were thus proposed: 1) CNA-dominant progression and 2) early immune evasion of those with mild CNA burden. Collectively, our findings illustrate previously unexplored molecular paradigms in HCC initiation, highlighting the therapeutic potential of immunotherapy for early intervention.

cancer biology↗

bioRxiv2025

Stress Granule Formation Drives ZBP1-dependent Necroptosis in Non-obstructive Azoospermia and Aging testes

Male infertility and age-related reproductive decline remain major unmet medical challenges, with limited understanding of the underlying mechanisms. Here, we identify a stress granule-driven necroptosis pathway involving ZBP1 and RIPK3 as a central driver of non-obstructive azoospermia (NOA), a severe form of male infertility marked by loss of spermatogenesis. We show that heat stress or environmental insults activate eIF2 kinases, inducing stress granules that recruit ZBP1 and RIPK3 to form a signaling complex. This leads to RIPK3 activation, MLKL phosphorylation, and necroptotic death of spermatogonia and Sertoli cells. Genetic ablation of Zbp1 or Ripk3 protects mice from heat-induced testicular atrophy, highlighting their essential role in testicular cell death. Notably, this same necroptosis pathway is also activated in aged human testes, suggesting a shared mechanism driving both male infertility and age-related testicular degeneration.

molecular biology↗

bioRxiv2025

Helicon: Helical indexing and 3D reconstruction from one image

Helical symmetry is a common structural feature of many biological macromolecules. However, helical indexing and de novo 3D reconstruction remain challenging. We have developed a computational method, Helicon, which poses helical reconstruction as a linear regression problem with the projection matrix parameterized by the helical twist, rise, and axial symmetry. A sparse search of the twist and rise parameters would allow helical indexing and 3D reconstruction directly from one 2D class average or a raw cryo-EM image. The Helicon method has been validated with simulation tests and experimental cryo-EM images of helical tubes, non-amyloid filaments, and amyloid fibrils. Imaging stitching and L1 regularization of linear regression were shown to improve the robustness for low-twist amyloids and noisy raw cryo-EM images. Using Helicon, we could successfully index the helical parameters and perform de novo reconstruction of a previously unreported, low abundance tau amyloid structure from a publicly available dataset. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/647385v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@165119borg.highwire.dtl.DTLVardef@66d9e1org.highwire.dtl.DTLVardef@6a5a93org.highwire.dtl.DTLVardef@609b5f_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIHelicon enables helical indexing and 3D reconstruction from a single 2D image C_LIO_LIFormulates helical reconstruction as a linear regression problem C_LIO_LITackles low-twists and raw cryo-EM images with image stitching and regularization C_LIO_LIValidated with diverse experimental data and a previously unreported tau filament C_LI

biophysics↗

bioRxiv2025

The impact of artificial linear features on the pollination of plant communities

Linear features, such as road verges, hedgerows can function as corridors for species dispersal. Previous studies showed that these features could enhance movement of pollinators such as bees, increasing pollination success of bee pollinated plants. However, it remains unclear if these effects extend to communities of plants pollinated by other pollinators. We conducted a field experiment where we measured the pollination of phytometer plant communities linked by linear features. We constructed six 30m artificial linear features in both urban and rural meadows in the Southwest UK, and placed plant communities on either end of these linear features, comparing these to phytometers without linking linear features. Plant communities were assembled with seven species known to attract different groups of insect pollinators including bees, flies, and moths. We tested self-incompatibility of plant species and used their seed set to measure pollination. We found that linear features significantly improved the pollination success of three bee pollinated species, whilst the seed production of fly and moth pollinated species were either unaffected or less affected. Overall, it is likely that linear features benefit the pollination of some plant species more than others. Our results suggest that linear features play an important role in maintaining pollination for some plant species, highlighting the importance of evaluating community-level impacts of corridors on pollination. Given the importance of bees as pollinators, linear features can provide a practical strategy to conserve and improve pollination, but where species are fly or moth pollinated, alternative strategies may need to be considered.

ecology↗

bioRxiv2025

Conformational Changes of Surfactant Protein B Due to the Alveolar Air/Liquid Interface Using Molecular Dynamics

Surfactant Protein B (SP-B) is a critically important component of pulmonary surfactant (PS), responsible for much of the lipid restructuring activity necessary to maintain proper respiratory function. Despite its functional and biological importance, there is a significant lack of knowledge regarding the structural characteristics of SP-B, exacerbated by a lack of a complete experimentally determined structure. Comparative modeling with homologous Saposin-family proteins was used to generate predicted structures for SP-B in both an open (hydrophobic residues exposed) and closed (hydrophobic residues buried) conformation. These structures were then used for further study with Molecular Dynamics. Five replicate simulation systems were prepared for both conformations in different solvent conditions, including water and chloroform, a hydrophobic solvent. For each system, a minimum of 900 ns production time per simulation was collected in 5 replicate simulations. Overall RMSD, per-residue RMSF, specific geometric parameters, and solvent distribution information were collected over the course of the simulations and analyzed. Results of these analyses indicate the relative stability of the closed conformation protein in water, with the open conformation structure undergoing a large conformational change due to hydrophobic forces in water quantified by relevant intramolecular distances. Solvent distribution analysis elucidated the varying affinity of different regions of the protein to hydrophobic and hydrophilic environments, providing insight into the structural-functional characteristics of SP-B in the varied PS environment. Helix 3 was identified as a region of particular interest, demonstrating structure-dependent increased affinity to hydrophobic solvent molecules.

biochemistry↗

bioRxiv2025

Imputation Disparities Driven by Recent Selectionand Their Impact on Disease Risk Estimation in East and Southeast Asian Populations

Using genotype data consisting of 8,316 individuals, we systematically evaluated imputation performance across six state-of-the-art reference panels for Chinese and Thai populations. A substantial proportion of variants identified through whole-genome sequencing, especially low-frequency variants, remained undetected by existing reference panels. In the Chinese population, the TOPMed panel required an R2 threshold of 0.60-0.70 to achieve comparable imputation accuracy of the ChinaMAP panel without R2 filtering, challenging the standard practice of applying a fixed R2 threshold for downstream analyses. Regional analysis highlighted the role of recent selection in imputation discrepancies and revealed an enrichment of immune-related genes in poorly imputed regions. In addition, we showed that the selection of reference panels and R2 thresholds could significantly influence estimation of polygenic risk score for disease prediction. These findings underscore the importance of developing ancestrally diverse reference panels and provide valuable guidelines for improving genotype imputation in East and Southeast Asian populations.

genomics↗

bioRxiv2025

An unrecognized and crucial role of chloroplast division in leaf variegation in Arabidopsis thaliana

Leaf variegation provides a valuable model for elucidating the molecular mechanisms that underlie chloroplast biogenesis, including both chloroplast development and division. While there has been notable advancement in comprehending the role of the Arabidopsis Yellow Variegated2 (VAR2), which encodes the AtFtsH2 subunit of the thylakoid FtsH metalloprotease complex, the exact mechanism governing leaf variegation formation remains elusive. In this study, time-course microscopy analyses of chloroplast number per cell from the first leaf pair revealed that most var2 cells lack chloroplasts. Interestingly, chloroplast biogenesis in the green sector of var2 leaves is significantly delayed but prolonged compared to the wild type (WT), leading to increased heterogeneity in chloroplast number and size among cells. These results suggest that chloroplast biogenesis in the green sector can partially compensate for the defect in the white sector. Additionally, approximately 15% of cells in var2 white sectors are devoid of plastids, and chloroplast number in guard cells is significantly lower in var2 than in WT, indicating that VAR2 mutations impair chloroplast division. Consistently, the var2 phenotype is exacerbated by knocking out key plastid division genes, including Paralog of Accumulation and Replication of Chloroplasts6 (PARC6) and Plastid Division1 (PDV1), but is fully rescued by overexpressing PDV1 or PDV2. Furthermore, VAR2 mutations inhibit etioplast development, while accelerating chloroplast biogenesis by knocking out Constitutively Photomorphogenic1 (COP1) rescues the var2 phenotype. Together, our findings reveal a novel role for VAR2 in plastid division and its essential function in chloroplast biogenesis, providing new insights into the mechanism underlying variegated leaf formation.

plant biology↗

bioRxiv2025

Restoration of Susceptibility of blaNDM-bearing Escherichia. coli to Carbapenem Antibiotics by Exogenous N-acetylcysteine

The global spread of the New Delhi metallo-{beta}-lactamase (NDM) -producing carbapenem-resistant Enterobacteriaceae pose a serious threat to public health, as NDM and its variants enzymes efficiently hydrolyze almost {beta}-lactam antibiotics. The development of novel antibiotics or antibiotic adjuvants capable of eradicating antibiotic-resistance bacteria through multiple mechanisms represents a promising strategy for reversing antibiotic resistance and preventing the emergence of new resistance. In this study, we utilized high-performance liquid chromatography (HPLC) to demonstrate that N-acetylcysteine (NAC) is a prominent reducing metabolite in bacteria harboring NDM-5. Notably, NAC was able to restore carbapenem susceptibility in NDM-producing bacteria in vitro. Subsequently, we further investigated the underlying mechanisms involved. Our findings revealed that NAC exerts its effect through multiple mechanisms that collectively contribute to reversing meropenem resistance. Firstly, NAC may inhibit biofilm formation and reduces polysaccharide production in NDM-positive Escherichia coli. and this potential mechanism was verified by transcriptomic analysis, reverse transcription PCR (RT-PCR) and a biofilm restoration experiment involving the addition of citrate cycle intermediate metabolites. Secondly, RT-PCR analysis demonstrated that NAC significantly downregulates the expression of blaNDM-5. Additionally, NAC exhibited competitive inhibition of NDM activity in vitro. Thirdly, NAC was found to enhance the intracellular accumulation of meropenem, therapy increasing its bactericidal efficacy. These three independent mechanisms offer valuable insights for developing adjuvants. The discovery offers a promising prospect for combating the antibiotic resistance concern. This study paves the way for further exploration and potential clinical applications in the fight against antibiotic-resistant bacterial infections.

pharmacology and toxicology↗

bioRxiv2025

Development and Clinical Evaluation of a Multiplexed Health Surveillance Panel Using Ultra High-Throughput PRM-MS in an Inflammatory Bowel Disease Cohort.

Despite advances in clinical proteomics, translating protein biomarker discoveries into clinical use remains challenging due to the technical complexity of the validation process. Targeted MS-based proteomics approaches such as parallel reaction monitoring (PRM) offer sensitive and specific assays for biomarker translation. In this study, we developed a multiplex PRM assay using the Stellar mass spectrometry platform to quantify 57 plasma proteins, including 21 FDA-approved proteins. Loading curves (11-points) were performed at 4 sample throughputs (100, 144, 180, and 300 samples per day) using independent, optimized, and scheduled PRM methods. Following optimization, an inflammatory bowel disease (IBD) cohort of plasma samples (493 IBD, 509 matched controls) was analyzed at a throughput of 180 SPD. To monitor system performance, the study also included 1,000 additional injections for system suitability tests, low-, middle-, and high-quality controls, washes, and blanks. Using this approach, we observed high quantifiability (linearity, sensitivity, reproducibility) in the PRM assay and consistent in data acquisition across a large cohort. We also validated the candidate IBD markers, C-reactive protein and orosomucoid protein, identified in a recent discovery experiment.

biochemistry↗

bioRxiv2025

Mapping the coupling between tract reachability and cortical geometry of the human brain

The study of cortical geometry and connectivity is prevalent in research on the human brain. However, these two aspects of brain structure are usually examined separately, leaving the essential connections between the brains folding patterns and white matter connectivity unexplored. In this study, we aimed to elucidate fundamental links between cortical geometry and white matter tract connectivity. We developed the concept of tract-geometry coupling (TGC) by optimizing the alignment between tract connectivity to the cortex and multiscale cortical geometry. Specifically, spectral analyses of the cortical surface yielded a set of geometrical eigenmodes, which were then used to explain the locations on the cortical surface reached by specific white matter tracts, referred to as tract reachability. In two independent datasets, we confirmed that tract reachability was well characterized by cortical geometry. We further observed that TGC had high test-retest ability and was specific to each individual. Interestingly, low-frequency TGC was found to be heritable and more informative than the high-frequency components in behavior prediction. Finally, we found that TGC could reproduce task-evoked cortical activation patterns. Collectively, our study provides a new approach to mapping coupling between cortical geometry and connectivity, highlighting how these two aspects jointly shape the connected brain.

neuroscience↗

bioRxiv2025

Loss of Kmt2c/d promotes gastric cancer initiation and confers vulnerability to mTORC1 inhibition and anti-PD1 immunotherapy

KMT2C and KMT2D (KMT2C/D) are frequently mutated in gastric adenocarcinoma, yet their function in cancer initiation remains poorly understood. In this study, based on the observation that loss-of-function mutations of KMT2C and KMT2D are enriched and co-occur in gastric adenocarcinoma, we developed genetically engineered mouse models to selectively knock out Kmt2c and Kmt2d in gastric epithelial cells with Tmprss2-CreERT2. Through histological staining and single-cell RNA sequencing, we observed that Kmt2c/d loss led to nuclear dysplasia and expansion of cells with mixed gastric lineage markers. When combined with Pten deletion, Kmt2c/d loss drove rapid development of muscle-invasive gastric adenocarcinoma as early as 3 weeks post Cre-mediated gene deletion. The adenocarcinoma exhibited decreased expression of gastric lineage markers and increased expression of intestinal differentiation markers, phenocopying human gastric adenocarcinoma. Kmt2c/d knockout reduced protein synthesis but upregulated transcription of ribosomal proteins, rendering sensitivity to mTORC1 inhibitors. Additionally, Kmt2c/d knockout increased MHC-I molecule expression and enhanced antigen presentation. Combination of mTROC1 inhibition and anti-PD1 immunotherapy significantly suppressed tumor growth in immune-competent mice. Together, these findings reveal the role of Kmt2c/d loss in gastric cancer initiation and suggest the potential therapeutic strategies for KMT2C/D-deficient gastric cancer.

cancer biology↗