Biology subjects

Ma, L.

Publications and source records attributed to Ma, L..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

2D, or not 2D? Investigating Vertical Signal Integrity of Tissue Slices

Imaging-based spatially resolved transcriptomics can localize transcripts within tissue sections in 3D. Cell segmentation assigns transcripts to cells and precedes annotation of cell function. However, cell segmentation is usually performed in 2D, thus unable to deal with spatial doublets arising from overlapping cells, resulting in segmented cells containing transcripts originating from multiple cell types. Here we present a computational tool called ovrlpy that identifies overlapping cells, tissue folds, and inaccurate cell-segmentation by analyzing transcript localization in 3D.

bioinformatics↗

bioRxiv2025

A novel broad-spectrum antibiotic targets multiple-drug-resistant bacteria with dual binding targets and no detectable resistance

The rapid emergence of difficult-to-treat multidrug-resistant pathogens, combined with the scarcity of antibiotics possessing novel mechanisms, poses a significant threat to global public health. Here, we integrated the synthetic-bioinformatic natural product approach with peptide optimization to unveil the antibiotic-producing potential of Paenibacillaceae bacteria. Our culture-independent approach led to the discovery of paenimycin, a novel 11-mer depsi-lipopeptide featuring an unprecedented dual-binding mechanism. By sequestering the phosphate and hydroxyl groups of lipid A in Gram-negative bacteria, as well as the phosphate groups of teichoic acids in Gram-positive bacteria, paenimycin exhibited potent and broad-spectrum efficacy against MDR pathogens in vitro and in vivo models. Remarkably, paenimycin demonstrates no detectable resistance, favorable pharmacokinetics and low nephrotoxicity, positioning it as a promising candidate for treating serve and urgent MDR infections.

biochemistry↗

bioRxiv2025

AncestryHub: A web server for local ancestry analysis

SummaryAncestryHub is a web version of local ancestry analysis software. It contains four built-in software and a set of built-in population reference panels. AncestryHub will significantly reduce the efforts and requirements for the users on their personal computational skills and computational hardware environment for ancestry analysis. Availabilityhttps://www.ancestryhub.4dgenome.com Contact: lima@4dgenome.com

bioinformatics↗

bioRxiv2024

scRNA+TCR-seq Reveals the Proportion and Characteristics of Dual TCR Treg Cells in Mouse Lymphoid and Non-lymphoid Tissues

The rearrangement of TCR germline V(D)J genes during T cell development, including allelic exclusion and tolerance selection, ensures the clonal selection theory, which states that "a lymphocyte expresses only one type of antigen receptor" This forms the basis for T cell-specific responses. However, The existence of "dual TCR T cells" has consistently been supported by specific experimental evidence. detailed reports on the origin, proportion, tissue distribution, and CDR3 characteristics of "dual TCR Treg cells" are currently lacking. In this study, we utilized scRNA+TCR-seq technology to achieve in-depth analysis of single TCR T and dual TCR T pairings, along with their mRNA expressions, from over 5,000 T cells in each sample. Through comparative studies with shared databases, we provided a detailed analysis of the proportions and characteristics of dual TCR Tregs in mouse lymphoid and non-lymphoid tissues (such as iLN, mLN, blood, and skin). Our findings revealed a high proportion of dual TCR Tregs across various mouse tissues, with their TCR pairing patterns, V(D)J usage, and mRNA expression showing both homogeneity and certain differences compared to single TCR Tregs, as well as heterogeneity across different tissue sites. This research provides new insights and technical approaches for studying the origins, characteristics, effects, and mechanisms of Treg cells in different tissue locations.

immunology↗

bioRxiv2024

Endosome maturation is orchestrated by inside-out proton signaling through a Na+/H+ exchanger and pH-dependent Rab GTPase cycling

Endosome maturation requires progressive lumen acidification. To what extent is lumen acidification sensed by cytosolic-side molecules that drive endosome maturation? We show here that "inside-out" proton signaling through the endosomal Na+/H+ Exchanger 6 (NHE6) activates the late endosome master regulator Rab7. The mechanism involves potent inactivation of the Rab7 GTPase-activating protein (GAP) TBC1D5 with decreasing pH. NHE6 interacts with TBC1D5 in a complex with Rab7. Neurons from NHE6-null mice or mice engineered with a selective defect in NHE6 proton efflux exhibit blocked endosome maturation and decreased active Rab7, consistent with an overactive Rab7 GAP. Finally, epistatic knock-down of TBC1D5, thereby reducing Rab7 GAP activity, in NHE6-null neurons rescues Rab7 GTPase cycling and endosome maturation. Importantly, NHE6 is mutated in Christianson Syndrome underscoring the significance of these mechanisms to neurodegeneration. We conclude that lumen acidification regulates pH-dependent Rab GTPase cycling to coordinate late endosome maturation by a process involving proton signaling.

cell biology↗

bioRxiv2024

A negative binomial latent factor model for paired microbiome sequencing data

MotivationMicrobiome compositional data are often collected from several body sites and exhibit dependency among them. Analyzing microbial compositions from different sites jointly allows for effective borrowing of information by exploiting the underlying cross-site correlation, which can lead to more effective statistical analysis, especially when the sample size at one or both sites is limited. To this end, we introduce a joint model for microbiome compositions at two (or more) sites within the same subjects. Our model incorporates (i) latent factors shared across two body sites to explain the common subject effects and to serve as the source of correlation between the two sites; and (ii) mixtures of latent factors to allow heterogeneity among the samples in their level of cross-site association. The model is illustrated with synthetic data and we apply it in a case study involving samples of the urinary and vaginal microbiome collected from women. ResultsSimulation studies show how common subject effects influence regression analysis results; a stronger association between two sites in the data causes a greater degree of bias in the analysis. The model with latent factors mitigates the bias present in the model without latent factors, whereas the two models perform comparably for the data set without paired associations. In a case study involving samples collected from a study on the female urogenital microbiome with aging (e.g., the UMICRO study), our model leads to the detection of covariate associations of the vaginal and urinary microbiome composition that are otherwise not statistically significant under a similar regression model applied to the two sites separately. Our model also enables prediction of the microbial abundance at one site based on observations from another site. We also consider a model extension that allows the clustering of subjects (samples) and cluster-specific levels of paired association. Under the extended modeling framework, the clusters can be classified according to their association strengths.

bioinformatics↗

bioRxiv2024

Single amino acid mutations in histone H3.3 illuminate the functional significance of H3K4 methylation in plants

Although numerous data have revealed correlations between histone modifications and chromatin activities such as transcription, proofs of their causal importance in gene expression regulation remain limited. Sequence variants within each histone family expand chromatin diversity and may carry specific modifications, further raising the question of how histone modifications coordinate with different variants. Here, we investigate the regulatory role of lysine 4 (K4) of Arabidopsis histone H3 by point mutating K4 in two major H3 variants, H3.1 and H3.3. K4 is essential for the function of H3.3 but not H3.1 in plant development. H3K4 methylation levels decrease drastically upon K4 mutation in H3.3, and the associated transcriptome changes are similar to those observed in a mutant lacking SDG2, a major enzyme responsible for depositing H3K4 trimethylation (H3K4me3). Moreover, H3.3K4 and SDG2 are required for de novo gene activation and RNA Pol II elongation. H3K4 methylation is preferentially accumulated on H3.3 compared to H3.1, likely due to the close association of the H3.3 deposition and H3K4 methylation machineries. Furthermore, we reveal the diverse impacts of K4 nearby residue mutations on H3K4 methylation and H3.3 function. Collectively, these findings suggest that H3.3 serves as a critical substrate for H3K4 methylation, which is important for gene expression regulation. In addition, our work highlights the potential of using plants as a platform to directly investigate the importance of histone amino acids and their modifications.

plant biology↗

bioRxiv2024

In situ Membrane Protein Expression by Efficient Recruitment of mRNA to the Membranes of Synthetic Cells

The synthesis of artificial cells is crucial for understanding the origins of life. In synthetic cells, however, the absence of membrane-bound organelles and auxiliary proteins severely limits the efficient expression and precise localization of membrane proteins using cell-free expression systems. Here we introduce a robust method that significantly enhances membrane protein synthesis by recruiting mRNA to phospholipid membranes. This is achieved through the use of cholesterol-modified, single-stranded DNA that anchors to the membrane and pairs with the mRNAs untranslated region. This strategic placement facilitates the assembly of protein expression machinery, promoting direct co-translational folding at the membrane. Our approach not only ensures correct protein topology and functionality but also demonstrates broad applicability for the in situ expression of various membrane proteins. It effectively addresses the challenges of membrane protein localization and assembly in synthetic cells, showcasing its versatility for synthesizing a wide array of membrane proteins.

synthetic biology↗

bioRxiv2024

Spontaneous Brain Dynamics Associated With Acceleration Of Longterm Functional Connectome In Postnatal Development

The first six postnatal months are a critical period for brain development, marked by rapid changes in functional neural circuits. However, long-term changes in neonatal functional connectome lacks an interpretive imaging indicator for the future development due to the non-linearity characteristics. In this study, we introduce an approach to extract intrinsic brain states from short-term brain dynamics to study the long-term (longitudinal) development. We found a high association (r=0.460) between the co-activated pattern of specific brain state and the acceleration pattern of non-linear development of static functional connectome. The fractional occupancy, self-sustaining probability of this short-term state share the similar age tendency with the long-term change rate within the majority of the function connectome. These findings suggest that short-term brain dynamics could serve as potential biomarkers for predicting the long-term development of functional connectome.

neuroscience↗

bioRxiv2024

Targeted pre-conditioning and cell transplantation in the murine lower respiratory tract

Transplantation of airway basal stem cells could achieve a durable cure for genetic diseases of the airway, such as cystic fibrosis and primary ciliary dyskinesia. Recent work demonstrated the potential of primary- and pluripotent stem cell (PSC)-derived basal cells to efficiently engrai into the mouse trachea aier injury. However, there are many hurdles to overcome in translating these approaches to humans including developing safe and efficient methods for delivery in larger animal models. We propose a model which targets preconditioning and cell-delivery to the intrapulmonary airways utilizing a micro- bronchoscope for delivery. The detergent polidocanol was adapted for distal lung pre-conditioning, inducing intrapulmonary airway epithelial denudation by 5 and 24-hours post-delivery. While initial re- epithelialization of airways occurred later than tracheas, complete repair was observed within 7-days. Both PSC-derived and primary basal cells delivered via micro-bronchoscope post-polidocanol injury engraied in tracheas and intrapulmonary airways, respectively. Transplanted cells differentiated into ciliated and secretory lineages while maintaining a population of basal cells. These findings demonstrate the utility of bronchoscopically targeted pre-conditioning and cell delivery to the conducting intra- pulmonary airways, providing an important framework for pre-clinical translation of approaches for engineered airway epithelial regeneration.

cell biology↗

bioRxiv2024

Enhanced lentiviral gene delivery to mammalian cells via paired cell surface and viral envelope engineering

Lentiviral vectors that facilitate gene delivery to desired cell types have been widely used in routine laboratory research and therapeutic cell engineering. However, the lack of proper entry receptors on many cell types often results in poor gene delivery. Here, we present a simple paired virus-cell engineering approach that promotes lentiviral gene delivery into mammalian cells. Lentiviruses are dual-pseudotyped with VSV-G and a chimeric envelope protein specifically recognizing a small molecule fluorescein (FITC-Env), and target cells are transiently labelled with FITC to create surrogate receptors for lentivirus attachment. The synthetic interaction between FITC-labeled cells and FITC-binding LVs enables efficient LV docking, viral entry and stable transgene expression in a range of mammalian cell lines and primary T cells. We showed that this approach enabled efficient delivery of a CD19-targeted chimeric antigen receptor (CAR) into naive human T cells that are naturally refractory to conventional VSV-G LVs, which upon activation rapidly eradicated CD19+ leukemic cells. This paired cell surface and virus envelope engineering approach may serve as a universal method for engineering synthetic virus-cell interactions to improve lentiviral gene delivery to mammalian cells.

bioengineering↗

bioRxiv2024

Sociality shapes the adaptive response of breeders to harsh thermal environments? An experiment in a burying beetle

O_LIThe rapid pace of environmental change seems to outstrip the evolutionary response rates of many species. Physiological, morphological, and behavioral plasticity alone may also not suffice to cope with environments drastic changes, potentially hindering individuals ability to adapt. Therefore, it has been proposed that social flexibility may be a powerful mechanism for fast adaptation, but empirical evidence is lacking. C_LIO_LIWe investigated the combined effects of manipulated social conditions and ambient temperature during the reproductive phase on parental care, reproductive success, and offspring performance of the burying beetle (Nicrophorus vespilloides), a facultative social breeding insect. C_LIO_LIWe conducted a mixed factorial design experiment, establishing four categories of social conditions during breeding (no-care, unifemale-care, biparenta-care, and multiple-care) alongside two thermal conditions (benign: 20{degrees}C and harsh: 23{degrees}C). Additionally, dispersed larvae produced from each of these breeding conditions were allocated to climate rooms maintained at either 20{degrees}C or 23{degrees}C for pupation. Data on brood size, brood mass, dispersed larval weight, larval development duration, body size and lifespan of newly eclosed beetles, and parental care were collected C_LIO_LIOur results showed that (1) harsh temperature and the without-care condition (i.e., no-care compared to the other three social conditions) reduced brood size, brood mass, body size of newly eclosed beetles; (2) social and ambient thermal conditions had interactive effects on dispersed larval weight, larval development duration, and newly eclosed beetles lifespan; and (3) harsh temperature reduced both individual and total parental care, whereas sociality had opposing effects: individual care decreased, but total care increased from unifemale-care to biparental-care and multiple-care conditions. C_LIO_LIOur findings shed light on the critical role of sociality in modulating the adaptive response of individuals to harsh thermal environments, one of the ecological problems exacerbated by ongoing global warming. C_LI

evolutionary biology↗

bioRxiv2024

Improved split prime editors enable efficient in vivo genome editing

Prime editor (PE) is a precise genome-editing tool that enables all 12 possible base-to-base conversions, as well as insertions and deletions, that does not require DSBs or donor DNA. The efficient delivery of prime editors in vivo is critical for realizing the full potential of prime editing in disease modeling and therapeutic correction. Although PE has been divided into two halves and delivered using dual adeno-associated viruses (AAVs), editing efficiency at different gene loci varies among split sites, and efficient split sites within Cas9 nickase are limited. In this study, by screening multiple split sites, we demonstrated that 1115 (Asn) is an efficient split site when delivering PE by dual-AAV. Besides, we utilized a feature reported by others recently that RNase could be detached from the Cas9n and designed split sites in the first half of Cas9n. We found that split-PE-367 enabled high prime editing efficiency with Rma intein. To test the editing efficiency in vivo, dual-AAV split-ePE3-367 was packaged in AAV9 and delivered by tail vein injection in mice, achieving 24.4% precise genome editing 4 weeks after injection. Our findings establish an alternative split-PE architecture that could achieve robust gene editing efficiency, facilitating the potential utility both in model organisms and as a therapeutic modality.

genomics↗

bioRxiv2024

Spatiotemporal transcriptomic analyses reveal molecular gradient patterning during development and the tonotopic organization along cochlear axis

While cochlear tonotopic organization is essential for sound frequency discrimination, the spatiotemporal molecular programs shaping this architecture remain unresolved. Here, we integrate spatiotemporal transcriptomics (E17.5-P8-adult) with single-cell RNA-seq to construct a single-cell-resolution atlas of mouse cochlear development. As marked by differential gradient expression genes, distinct spatially and molecularly defined hair cell (HC) subtypes along the apical-basal axis were identified: such as the apical Myo7a+++/Calb1+++ outer hair cell (OHC) subtype, the basal Myo7a+/Calb1{square} OHC subtype, the apical vGlut3+++/Calb2+ inner hair cell (IHC) subtype, and the basal vGlut3+/Calb2+++ IHC subtype. In addition, the spatial data also demonstrate the developmental reversal of Myo7a/Calb2Nefh gradient patterns in HCs and spiral ganglion neurons (SGNs), revealing dynamic plasticity and complexity in frequency coding during development. Spatial analyses further demonstrate regional heterogeneity in cell communication intensity between HCs and SGNs, and also reveal core signaling hubs coordinating tonotopic organization, such as Fgf10-Fgfr2 pathway in the basal region and Ptn-Sdc pathway in the apical region HC or SGNs at P8 stage. Our study provides an open-access spatial database and reveals the morphological and molecular foundations underlying cochlear tonotopic organization, linking molecular and developmental mechanisms to auditory pathophysiology.

developmental biology↗

bioRxiv2024

Connectomic Organization of the Suprachiasmatic Nucleus

The suprachiasmatic nucleus (SCN), the mammalian master clock, is a special structure dedicated to the time computation. However, a connectomic understanding of the nucleus as a whole is lacking. Using serial section electron microscopy, we reconstructed multiscale and multimodal SCN communication networks. Intra-SCN synaptic network consists of 9,566 morphologically similar neurons and 4.3 million synapses, organized into multiscale circuitries that interact with SCN-traversing axon fascicles. Strikingly, SCN neurons engage in unique soma-soma ephaptic interaction, forming 2,038 electrotonic integrative units with the largest overlapping the light-responsive area (LRA). SCNs paracrine modality contains 47,396 m3 dense core vesicles, with notable scarcity in the LRA, suggesting cross-modal coordination and functional integration. These distinct network features provide comprehensive insights into the system architecture of the mammalian circadian clock.

neuroscience↗

bioRxiv2024

Ecological and social factors lead to variation in parental care between sexes in a burying beetle

Sexual conflict over parental care represents a divergence in the evolutionary interests between males and females, consequently leading to distinct sex roles in parental care and reproductive strategies. However, whether and how various ecological and social environments influence such sex differences remains largely unclear. In the present study, using the burying beetles Nicrophorus vespilloides, we experimentally investigated the impacts of resource availability and inter- and intra-specific competition pressure on individual parental care and reproduction in males and females. We manipulated the resource availability for the breeding pairs by providing them with either large or small mouse carcasses, and constructed the presence of intra- and inter-specific competition, by introducing an additional, small pair of beetles and blowfly maggots Calliphora, respectively. We expected that males would decrease their parental care, while females would increase theirs, in response to smaller carcass. We also expected that the presence of intra- and inter-specific competition differentially affected the cares of males and females. We found that, compared to males and females breeding on large carcasses, males did not change their care, whereas females increased their care, when breeding on small carcasses. In the presence of another pair of adults, both males and females increased their parental care, whereas in the presence of blowfly maggots they both decreased their parental care. Our results showed that males and females adjust their parental care based on resource availability and competition pressure, with sex-specific differences driven by ecological and social factors. Our study sheds light on the importance of sex-specific parental care in response to various external drivers which contributes to a better understanding of the evolution of sex conflict over parental care.

animal behavior and cognition↗

bioRxiv2024

Endogenous Huntingtin aggregates are a huge organized scaffold and mold for Golgi apparatus impaired by mutant Huntingtin protein

Abstract Huntingtin (HTT) is a naturally aggregating protein that causes Huntington's disease (HD) when its polyglutamine (polyQ) tract exceeds 38 repeats. Despite its importance, the biology of HTT aggregates remains poorly defined. Here, using high resolution imaging of cells derived from HD families, we redefine polyQ assemblies, traditionally regarded as pathogenic aggregates, as dynamic and structurally organized intracellular compartments resembling knitted-fabric patches. These assemblies closely associate with and encircle the Golgi apparatus, integrating Golgi ribbons and stacks to form a previously unrecognized polyQ assembly-Golgi complex. Mechanistically, fragmentation of polyQ assemblies is dynamically coupled with mitotic Golgi fragmentation, whereas inhibition of ADP-ribosylation factor (ARF) function by Brefeldin A disrupts and fragments the complex, revealing an intimate structural and functional coupling between polyQ assemblies and Golgi architecture. The presence of mutant HTT (mHTT) destabilizes these assemblies and complexes, altering their response to nutrient deprivation and autophagy enhancers but not to antisense oligonucleotide (ASO) therapy. Functionally, polyQ assemblies in HD cells compromise the scaffolding capacity of the Golgi apparatus, clathrin-coated vesicles, and ARF1, impair Golgi glycosylation, and promote aberrant neuronal firing activity. Collectively, these findings establish polyQ assemblies as dynamic structural regulators of Golgi organization and function and demonstrate that mHTT disrupts the homeostatic dynamics of the polyQ assembly-Golgi complex, leading to Golgipathy.

pathology↗

bioRxiv2024

Rfx3 controls outer hair cell differentiation, maintenance, and hair bundle formation by regulating the expression of Insm1, Ikzf2, and Triobp genes

The RFX family of transcription factors plays crucial roles in the regulation of ciliogenesis and organ development. Mutations of RFX transcription factors lead to various genetic diseases, including ciliopathies and hearing loss, although the underlying mechanisms remain unclear. This study comprehensively analyzed the expression patterns of RFX family members during different inner ear developmental stages. Rfx3 and Rfx7 were identified as the dominantly expressed members in cochlear hair cells, exhibiting alternative splicing variants and dynamic subcellular localization at different stages. Integration of single-cell transcriptomics, ChIP-seq, and ATAC-seq data indicates that Rfx3 functions as either a transcriptional activator or repressor, binding to numerous genes related to ciliogenesis, hair bundle structures, and planar cell polarity. Rfx3 regulates the spatiotemporal expression of hair bundle gene Triobp in hair cells by binding to and modulating its intronic enhancer. Additionally, Rfx3 binds to hair cell differentiation and fate determination genes Tbx2, Insm1, and Ikzf2. The results demonstrate that Rfx3 and Rfx7 are dominantly expressed in outer hair cells, with their subcellular localization shifting to cytoplasm at later developmental stages. This suggests a previously unknown function of Rfx3 and Rfx7 beyond transcriptional regulation, highlighting their complex roles in hair cell differentiation and maintenance.

developmental biology↗