Biology subjects

Wu, D.

Publications and source records attributed to Wu, D..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Planetary-scale metagenomic search reveals new patterns of CRISPR targeting

Interactions between microbes and their mobile genetic elements (MGEs), including viruses and plasmids, are critical drivers of microbiome structures and processes. CRISPR-Cas systems are important regulators of these host-MGE interactions, but a global understanding of CRISPR loci diversity, activity, and roles across Earths biomes is still lacking. Here, we use an optimized computational approach to search short-read data and collect [~]800 million CRISPR spacers across [~]450,000 public metagenomes. From this extensive CRISPR spacer dataset, we identified 1.18 billion hits between 41 million spacers and 2.5 million viruses and plasmids. Focusing on the role of CRISPR as anti-phage defense, we observed an over-representation of prevalent and conserved spacers consistent with a positive selection pressure associated with phage targeting. Identification of sustained CRISPR targeting by microbes not expected to be viable hosts suggested that some phage genomes may frequently enter non-host microbial cells. Taken together, these results outline the extensive diversity of CRISPR loci across microbiomes, and highlight key parameters driving CRISPR targeting patterns likely to influence strain-level diversification and selection processes within microbial populations.

microbiology↗

bioRxiv2025

Human meibomian gland organoids to study epithelial homeostasis and dysfunction

Meibomian glands (MGs) are holocrine glands that secrete lipids to maintain the homeostasis of ocular surface, and their dysfunction leads to dry eye disease. Herein, we established long-term 3D organoid culture for murine and human MGs, which retained the cell lineages and lipid-producing ability. The organoids mimicked the drug treatment responses and generated functional MGs after orthotopic transplantation. Inspired by organoid cultures, we found FGF10 eye drops could rescue all-trans retinoic acid-induced MG dysfunction in mice. Besides, nicotinamide uniquely hampered the human MG organoid expansion by inhibiting FGF10 signaling. Single-cell atlas and lipidome not only aligned the delineated cell types and featured lipids between human MGs and organoids, but highlighting MAPK signaling inhibition enhanced acinar cell differentiation and functional maturation of MG organoids. In summary, this study established an organoid platform to explore epithelial homeostasis and dysfunction of MGs, facilitating drug development and regenerative medicine for dry eye disease.

cell biology↗

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

Peptides alleviate cognitive impairment by inhibiting and disassembling amyloid-beta aggregates in Alzheimer disease

Alzheimers disease (AD) is a devasting neurodegenerative disorder characterized by {beta}-amyloid formation, further exacerbated by RIPK1/RIPK3 necrosome-induced programmed necrosis (necroptosis). We previously showed that the RIPK1/RIPK3 necrosome forms a functional amyloid complex using its RIP homotypic interaction motifs (RHIMs). Here, we discovered that the core RIPK1/RIPK3 necrosome shares strikingly structural similarity to the C-terminal region of {beta}-amyloid (A{beta}42), and the RHIM-derived tetrapeptides (IQIG or VQVG) directly inhibit A{beta} aggregation, disassemble preformed A{beta} fibrils (PFFs), and reduce RIPK1 polymerization. Also, the peptides exhibit effective membrane permeability and could reduce A{beta}40 or A{beta}42-induced neural death and TNF-induced necroptosis in SH-SY5Y cells. IQIG and VQVG injected by ICV increase learning and memory abilities by reducing A{beta} plaques and hyperphosphorylated tau in the cortex and hippocampus of APP/PS1 double-transgenic mice. Mechanistically, the peptides directly interact with A{beta} to block A{beta} aggregation and alleviate microglia-mediated neuroinflammation. Strikingly, single-cell RNA sequencing revealed that the peptides-treated AD transgenic mice restored neuronal homeostasis with increased GABAergic neurons and decreased glutamatergic neurons. Furthermore, total cell-cell interaction strength increased while the AD risk gene Apoe expression decreased in the specific oligodendrocyte subtype of peptides-treated AD mice. Thus, our findings revealed that the peptides could improve cognition and memory capabilities and serve as promising structural templates for potential drugs against AD.

neuroscience↗

bioRxiv2025

Changing the initiation unit of nonribosomal peptide synthetases to access underexplored biosynthetic potential

Nonribosomal peptide synthases (NRPSs) are large multimodular enzymes, capable of synthesizing nonribosomal peptides (NRPs) with diverse structures and bioactivities. Genome sequencing revealed a large number of uncharacterized NRPS biosynthetic gene clusters (BGCs) and their products are underexplored. The majority of NRPSs remain silent potentially attributed to factors such as the low activity of the initiation unit or insufficient precursor supply. Exchanging the starter condensation (Cs) domains within initiation unit can change the length of acyl chains of NRPs, hinting at a promising strategy through swapping of a well-studied Cs domain to activate the initiation unit and harness primary metabolites as precursors, which may offer a new option to access silent BGCs. Here, we first pinpointed two highly efficient fusion sites for initiation unit exchanges. Subsequently, they were validated by replacing the initiation region of endopyrrole pathway with a Cs-containing initiation unit for generation of a lipo-endopyrrole derivate. We promptly leveraged this strategy of changing initiation unit to target six previously silent NRPS BGCs, three BGCs were successfully activated and five novel lipopeptides were identified, demonstrating its application to recover silent BGCs. Furthermore, we extended this strategy in more BGCs from different bacteria. Utilizing a heterologous Cs-containing unit to replace the initiation region of chitinimide biosynthetic pathway led to successful incorporation of N-terminal fatty acid chains into chitinimide to create artificial lipo-chitinimides. This study provides a feasible strategy to rationally recover silent BGCs and add fatty acid chains to NRPs, enriching the genome mining and combinatorial biosynthesis approach for bacterial natural products. SignificanceNonribosomal peptide synthetases (NRPSs) represent a valuable yet underexplored reservoir for bioactive natural products, but most of them are silent. This study introduces the concept that changing initiation unit to activate and optimize the functional expression of NRPSs, and successfully access three of six previously silent NRPS pathways, providing a feasible complement to the current genome mining approaches. Moreover, the N-terminal lipid chains are crucial for the activity of lipopeptides. We employed a heterologous Cs (starter condensation domain)-containing initiation unit to replace the original initiation region for creation of artificial nonribosomal lipopeptides, ultimately yielding three novel lipo-derivatives. This work presents a groundbreaking approach for activating and optimizing NRPSs and provides profound insight into the exploration of bacterial NRPS pathways.

synthetic biology↗

bioRxiv2025

IL-17A-driven Macrophage Disorder Promotes Plaque Instability in Psoriatic Atherosclerosis

Psoriasis is a common chronic inflammatory skin disease that predisposes individuals to cardiovascular diseases such as atherosclerosis. However, the underlying mechanisms linking these conditions have not yet been fully elucidated. Recent studies have indicated that the inflammatory cytokine IL-17A plays a significant role in both diseases. The aim of this study was to investigate how psoriasis affects the stability of atherosclerotic plaques via the IL-17A/IL-17RA pathway. We performed single-cell sequencing on patients with both psoriasis and atherosclerosis to analyze changes in the immune microenvironment within their carotid plaques and psoriatic lesions. We found that IL-17A significantly upregulated the expression of pro-inflammatory factors (e.g., CXCL8) in macrophages of psoriatic atherosclerosis patients, leading to weakening of the fibrous cap structure of plaques. Additionally, IL-17A further exacerbated plaque instability by interfering with macrophage lipid metabolism, particularly sphingolipid metabolism. Finally, using in vitro experiments and animal models, we demonstrated that IL-17A enhances pro-inflammatory and metabolic abnormalities in macrophages by downregulating PPAR{gamma}. Therapeutic strategies targeting IL-17A may contribute to the simultaneous mitigation of psoriasis and atherosclerosis-associated cardiovascular risk, providing new directions for clinical intervention.

cell biology↗

bioRxiv2025

Separable Spatial Single-cell Transcriptome Representation Learning via Graph Transformer and Hyperspherical Prototype Clustering

Spatial transcriptomics enables the exploration of cell types, spatial domain organization, and cell-cell communication at tissue scale, serving as a powerful link between tissue morphology and molecular function. However, existing methods still struggle with limited spatial resolution, poor robustness in multi-slice alignment, and suboptimal ligand-receptor (L-R) detection in complex tissues. To address these challenges, we propose S3RL (Separable Spatial Single-cell transcriptome Representation Learning via Graph Transformer and Hyperspherical Prototype Clustering), a unified framework that integrates gene expression, spatial coordinates, and histological image features via a graph neural network and hyperspherical prototype-based separable representation learning. In spatial clustering tasks, S3RL improves the average Adjusted Rand Index (ARI) by nearly 120% on the Nanostring lung cancer dataset and over 26% on the 10X DLPFC dataset compared to state-of-the-art methods. For multi-slice spatial alignment, S3RL achieves an average ARI improvement of over 65.4% in partial brain slices and over 48.3% in complete slices relative to GraphST, highlighting its superior robustness and alignment consistency across heterogeneous spatial inputs. Moreover, S3RL reveals more biologically meaningful ligand-receptor signaling relationships, enhancing the interpretability of cell-cell communication patterns. Together, these results demonstrate S3RLs effectiveness in enhancing spatial resolution, cell type identification, and biological insight across diverse spatial transcriptomics datasets.

bioinformatics↗

bioRxiv2025

Robust Prediction of Multiple Protein Conformations with Entropy Guidance

Deep learning approaches, exemplified by AlphaFold, have made enormous progress in addressing the grand challenge of protein structure prediction. However, these methods typically predict only a single conformation, while accurately predicting multiple conformations, which are essential for the functions and regulations of many protein classes, remains challenging. Here, we demonstrate that AlphaFold2 has internal knowledge of alternative protein conformations, which can be effectively extracted by learning modifications to its intermediate hidden states using a negative entropy loss. Our resulting method, Entropy Guided Fold (EGF), achieves a success rate of over 80% in accurately predicting two conformations of 37 tested membrane proteins within a 2.0 [A] RMSD threshold, with similar performance for proteins both within and outside AlphaFold2s training dataset. In addition, our method successfully reveals three or more conformational states in several cases. We have also developed a post-processing strategy to effectively select accurate predictions. Overall, our method provides an efficient and robust approach for predicting multiple conformations of target proteins, with broad potential applications in mechanistic studies and translational applications.

bioinformatics↗

bioRxiv2025

Evolution of a fuzzy ribonucleoprotein complex in viral assembly

Previously we showed that the genetic diversity of SARS-CoV-2 nucleocapsid (N) protein explores a wide range of biophysical properties facilitated by non-local impact of point mutations to its intrinsically disordered regions (Nguyen et al., 2024). This includes modulation of self-association, such as the creation of a de novo binding interface through the P13L mutation characteristic of Omicron variants. In the present work we focus on the key function of N condensing viral RNA into ribonucleoprotein particles (RNPs) for viral assembly. Lacking high-resolution structural information, biochemical and biophysical approaches have revealed architectural principles of RNPs, which involve cooperative interactions of several protein-protein and protein-RNA interfaces, initiated through oligomerization of conserved transient helices in the central disordered linker of N. Here we study the impact of defining N-protein mutations in variants of concern on RNP formation, using biophysical tools, a virus-like particle assay, and reverse genetics experiments. We find convergent evolution in repeated, independent introduction of amino acid substitutions strengthening existing binding interfaces, compensating for other substitutions that promote viral replication but decrease RNP stability. Furthermore, we show that the P13L mutation of Omicron variants enhances RNP assembly and increases viral fitness. Overall, our data reveal RNP complexes to be highly variable not only in sequence and conformations, but also in thermodynamic and kinetic stability, with its pleomorphism affecting basic architectural principles. We hypothesize that the formation of polydisperse, fuzzy N-RNA clusters with multiple distributed weak binding interfaces optimizes reversible RNA condensation, while supporting host adaptation and allowing for a large sequence space to be explored.

biophysics↗

bioRxiv2025

EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome Research

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/649266v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@14dd0b1org.highwire.dtl.DTLVardef@1c04a79org.highwire.dtl.DTLVardef@159894dorg.highwire.dtl.DTLVardef@1454a01_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG HighlightsO_LIEasyMultiProfiler provides unified integration of microbial multi-omics data C_LIO_LIEasyMultiProfiler enables natural language-style analytical workflows C_LIO_LIEasyMultiProfiler solves key challenges in standardization and reproducibility C_LIO_LIEasyMultiProfiler extracts meaningful biological insights efficiently C_LI Host-microbiome interactions are crucial in maintaining physiological homeostasis and influencing disease progression. While traditional microbiome research, focused on microbial diversity and abundance, provided essential frameworks, the integration of multi-omics approaches established a far more comprehensive, systems-level understanding of microbiome functionality. However, significant methodological challenges in multi-omics data integration remain, including inconsistent sample coverage, heterogeneous data formats, and complex downstream analytical workflows. These challenges impact the reproducibility and reliability of results and underscore the critical requirement for developing standardized, systematic workflows. Thus, we developed the EasyMultiProfiler (EMP) workflow, a streamlined and efficient analytical framework for multi-omics data analysis. EMP provides a comprehensive infrastructure based on the SummarizedExperiment and MultiAssayExperiment classes, creating a unified framework for storing and analyzing omics data. The frameworks architecture comprises five interconnected functional modules: data extraction, preparation, support, analysis, and visualization. These modules are smoothly integrated into natural language-style analytical workflows, offering users an efficient and standardized solution for multi-omics analysis. EMP addresses critical challenges in multi-omics data analysis, including data integration, workflow standardization, and result reproducibility. The platforms modular architecture and intuitive interface provide researchers and clinicians with a robust, flexible workflow to systematically extract biologically relevant insights from complex multi-omics datasets.

bioinformatics↗

bioRxiv2025

Dentification of the Sorghum TMCO Gene Family and Differential Expression Analysis Under Aphid Infestation

The three-domain multicopper oxidase (TMCO) family, the largest subfamily of multicopper oxidases, plays a crucial role in plant growth, development, and responses to biotic stresses. To investigate the expression characteristics of the SbTMCO gene family under aphid infestation, a genome-wide identification and analysis of TMCO family members in sorghum were conducted using bioinformatics methods. Transcriptome data and qRT-PCR were utilized to preliminarily examine sorghums responses to aphid stress. The results revealed 42 TMCO genes in the sorghum genome, distributed across 10 chromosomes and classified into five subgroups. Members within the same subgroup displayed similar physicochemical properties, gene structures, and conserved motifs. Collinearity analysis suggested that tandem duplication and segmental duplication were the primary drivers of TMCO gene expansion in sorghum. Cis-acting element analysis identified multiple jasmonic acid (MeJA) and abscisic acid (ABA) responsive elements among SbTMCO genes. Gene expression analysis, based on RNA-seq and qRT-PCR, confirmed the relative expression levels of TMCO genes under aphid stress. This study establishes a foundation for exploring the anti-aphid functions of SbTMCO genes and provides recommendations and directions for further research on this gene family.

molecular biology↗

bioRxiv2025

Optimal distributions of receptors on arbitrarily shaped cell surfaces

Efficient absorption of signaling molecules and carbohydrates through receptors on cell surfaces is crucial for various biological processes. While ubiquitous patterns of receptor distributions, including polar localization in rod-shaped cells, have been widely observed experimentally, their underlying evolutionary advantage is unclear. In this work, we study how spatial distributions of receptors on cell surfaces affect the total flux entering the cell. We innovate a method by which one can calculate the fluxes through all receptors using linear equations, which applies to arbitrarily shaped cells. Our theories recover previous results for spherical cells and further show that the flux through each receptor is spatially dependent in non-spherical cells. In particular, the fluxes are the highest near the poles in rod-shaped cells and the highest near the invagination in defective spherical cells. Surprisingly, we prove that the optimal receptor distribution on an arbitrarily shaped cell maximizing the total flux is precisely the charge density distribution on an ideal conductor of the same shape, which agrees with numerical simulations. Our work unveils the evolutionary origin of receptor localizations.

biophysics↗

bioRxiv2025

Humanizing a CD28 signaling domain affects CD8 activation, exhaustion and stem-like precursors

CD28 ligation provides critical signals that modulate activated T cell fate. In a human to mouse reverse-engineering approach, a single amino acid substitution adjacent to the C-terminal proline-rich domain created CD28A210P mice with enhanced signaling. CD28A210P mice experienced pro-inflammatory responses to CD28 superagonist antibody, analogous to severe cytokine storm induced in a human clinical trial, with a striking increase of activated CD8 T cells. In acute and chronic viral infections, early activation and expansion of CD28A210P CD8 effector T cells increased, with accelerated exhaustion in chronic infection. Mechanistically, CD28A210P enhanced JunB, IL-2, and inhibitory receptors driven by MEK1/2. Generation of CD28A210P stem-like progenitor (Tpex) cells was enhanced in acute and chronic infections, and further expanded by PD-L1 blockade in chronically-infected mice. Thus, humanized PYAP mice reveal key roles for CD28 signaling strength in CD8 activation, accelerating exhaustion during antigen persistence, while promoting and sustaining Tpex during acute and chronic viral infection. One sentence SummaryA single amino acid substitution adjacent to PYAP to humanize CD28 signaling enhances superagonist response, early CD8 activation and Tpex generation during viral infection while accelerating exhaustion and sustaining Tpex during chronic infection. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/642460v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@13fc9f9org.highwire.dtl.DTLVardef@e50762org.highwire.dtl.DTLVardef@47c8eeorg.highwire.dtl.DTLVardef@d892d7_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO Humanized CD28 PYAPP enhances numbers of CD8 T cell effectors and stem-like precursors during acute viral infection, and accelerates exhaustion while sustaining increased self-renewing Tpex cells that are favored during PD-L1 blockade. C_FIG

immunology↗

bioRxiv2025

AarMIXTAs: key factors of T-shaped non-glandular trichome development in Artemisia argyi

Trichomes are necessary for stress resistance and metabolite synthesis in plant. T-shaped non-glandular trichomes (TSTs) as the main component of moxa floss, which are the specific characteristics of A. argyi. Here, we observed that TSTs were at an extremely high density on the lower surfaces in A. argyi leaves. The key transcription factors (TFs) involved in regulation of TSTs development of A. argyi were identified through RNA sequencing of TSTs and non-TSTs. The core regulatory genes, AarMIXTAs showed allelic amplification and functional differentiation compared with A. annua, might contribute development of TSTs. The overexpression of AarMIXTA1.2 significantly increased the density of TSTs in transgenic Arabidopsis and may regulate trichome development by regulating the downstream genes, which played an important positively regulatory role in the development of TSTs. This study provides a good reference for the molecular mechanisms related to the development of TSTs and a theoretical basis for the high-yield moxa floss cultivation of A. argyi.

plant biology↗

bioRxiv2025

Cochliobolus miyabeanus species-specific identification using nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS)-encoding genes associated with virulence to rice

Cochliobolus miyabeanus causes brown spot disease of rice. For necrotrophic Cochliobolus spp., some small molecule products of nonribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) are known pathogenicity and/or virulence factors, often acting in a host-specific manner. Previous whole genome analyses across Cochliobolus species identified 11 NRPS- and 21 PKS-encoding genes in C. miyabeanus. First purpose of the current study was to examine the effect of deletion of ten of the discontinuously distributed genes (corresponding to JGI protein IDs 4446, 5802, 6546, 7015, 9064, 41693, 41753, 83551, 98843 and 107726) on virulence of C. miyabeanus to rice. A second purpose, based on results of the first, was to develop a PCR method to specifically identify C. miyabeanus and to distinguish it from other closely related Cochliobolus spp. We show that deletion of seven of the genes resulted in mutants that were reduced in virulence compared to the wild-type strain WK1C. Wild-type developed large dark brown necrotic lesions surrounded by chlorotic halos, while the mutants produced smaller, light brown spots with chlorosis. These results suggest that the products of these genes contribute to brown spot disease. In addition, we identified PKS and NPS SNPs that discriminate between C. miyabeanus and other species of Cochliobolus.

genetics↗

bioRxiv2025

Reproductive Adaptation of Astyanax mexicanus Under Nutrient Limitation

Reproduction is a fundamental biological process for the survival and continuity of species. Examining changes in reproductive strategies offers valuable insights into how animals have adapted their life histories to different environments. Since reproduction is one of the most energy-intensive processes in female animals, nutrient scarcity is expected to interfere with the ability to invest in gametes. Lately, a new model to study adaptation to nutrient limitation has emerged; the Mexican tetra Astyanax mexicanus. This fish species exists as two different morphs, a surface river morph and a cave-dwelling morph. The cave-dwelling morph has adapted to the dark, biodiversity, and nutrient-limited cave environment and consequently evolved an impressive starvation resistance. However, how reproductive strategies have adapted to nutrient limitations in this species remains poorly understood. Here, we compared breeding activities and maternal contributions between laboratory-raised surface fish and cavefish. We found that cavefish produce different clutch sizes of eggs with larger yolk compared to surface fish, indicating a greater maternal nutrient deposition in cavefish embryos. To systematically characterize yolk compositions, we used untargeted proteomics and lipidomics approaches to analyze protein and lipid profiles in 2-cell stage embryos and found an increased proportion of sphingolipids in cavefish compared to surface fish. Additionally, we generated transcriptomic profiles of surface fish and cavefish ovaries using a combination of single cell and bulk RNA sequencing to examine differences in maternal contribution. We found that genes essential for hormone regulation were upregulated in cavefish follicular somatic cells compared to surface fish. To evaluate whether these differences contribute to their reproductive abilities under natural-occurring stress, we induced breeding in starved female fish. Remarkably, cavefish maintained their ability to breed under starvation, whereas surface fish largely lost this ability. We identified insulin-like growth factor 1a receptor (igf1ra) as a potential candidate gene mediating the downregulation of ovarian development genes, potentially contributing to the starvation-resistant fertility of cavefish. Taken together, we investigated the female reproductive strategies in Astyanax mexicanus, which will provide fundamental insights into the adaptations of animals to environments with extreme nutrient deficit.

evolutionary biology↗

bioRxiv2025

Deep-learning-based interpolation of longitudinal microbiome data powers biologically informative discovery

The human microbiome is a foundational and dynamic foundation for several health-related functions and disease processes. Advances in microbiome sequencing have enabled the characterization of microbial communities in several niches. Longitudinal microbiome studies further strive to discover clinically informative microbial community trajectories. However, these data are fraught with dropout events, high noise, and irregular sampling that limit and prevent the use of many available longitudinal analysis tools. To address these challenges, we introduce Bidirectional GRU-ODE-Bayes (BGOB), a deep learning framework developed for longitudinal microbiome interpolation. BGOB combines bidirectional information flow and ODE-based continuous modeling to jointly interpolate and smoothen trends across individual participants, providing uniform, denoised time intervals across patients. BGOB enables vastly improved performance in differential abundance testing and time-to-event analysis, and makes possible longitudinal analyses requiring uniformity, such as lead-lag detection and temporal clustering. After interpolation, previously low-powered datasets are able to broadly recapitulate known microbiology and elucidate interacting microbial communities. We highlight several associations between microbial taxa and disease, including novel species associated with Early Childhood Caries and disruption of key healthy gut microbiota in Inflammatory Bowel Disease. The BGOB package is publicly available at https://github.com/Rachel-Lyu/BGOB_n_test.

microbiology↗

bioRxiv2025

A versatile miniature two-photon microscope enabling multicolor deep-brain imaging

Here we present the FHIRM-TPM 3.0, a 2.6 g miniature two-photon microscope capable of multicolor deep-brain imaging in freely behaving mice. The system was integrated with a broadband anti-resonant hollow-core fiber featuring low transmission loss, minimal dispersion from 700-1060 nm, and high tolerance of laser power. By correcting chromatic and spherical aberrations and optimizing the fluorescence collection aperture, we achieved cortical neuronal imaging at depths exceeding 820 m and, using a GRIN lens, hippocampal Ca2+ imaging at single dendritic spine resolution. Moreover, we engineered three interchangeable parfocal objectives, allowing for a tenfold scalable field-of-view up to 1x0.8 mm{superscript 2}, with lateral resolutions ranging from 0.68 to 1.46 m. By multicolor imaging at excitation wavelengths of 780 nm, 920 nm and 1030 nm, we investigated mitochondrial and cytosolic Ca2+ activities relative to the deposition of amyloid plaques in the cortex of awake APP/PS1 transgenic mice. Thus, the FHIRM-TPM 3.0 provides a versatile imaging system suitable for diverse brain imaging scenarios.

neuroscience↗