Biology subjects

Yan, S.

Publications and source records attributed to Yan, S..

At least 73 records · Page 4Linked to original sources

bioRxiv2022

The multi-BRCT domain protein DDRM2 is required for homologous recombination in plants

DNA double-strand breaks (DSBs) are the most toxic DNA damage for cells. Homologous recombination (HR) is a precise DSB repair mechanism as well as a basis for gene targeting using genome-editing techniques. Despite the importance of HR, the HR mechanism in plants is poorly understood. In a genetic screen for DNA Damage Response Mutants (DDRMs), we find that the Arabidopsis ddrm2 mutant is hypersensitive to DSB-inducing reagents. DDRM2 encodes a protein with four BRCA1 C-terminal (BRCT) domains and is highly conserved in plants including the earliest land plant linage, bryophytes. The plant-specific transcription factor SOG1 binds to the promoter of DDRM2 and activates its expression, suggesting that DDRM2 is a direct target of SOG1. In consistence, the expression of DDRM2 is induced by DSBs in a SOG1-dependent manner. Epistasis analysis indicates that DDRM2 functions downstream of SOG1. Similar to the sog1 mutant, the ddrm2 mutant shows dramatically reduced HR efficiency. Our study suggests that the SOG1-DDRM2 module is required for HR, providing new insights into the HR mechanisms in plants and a potential target for improving the efficiency of gene targeting. One Sentence SummaryA genetic screen in Arabidopsis reveals that the multi-BRCT domain protein DDRM2 is required for homologous recombination and is targeted by the master DNA damage response regulator SOG1.

plant biology↗

bioRxiv2022

An evolutionarily conserved mechanism for control the translation of long proteins

Plants have evolved sophisticated mechanisms to regulate gene expression to activate immune responses against pathogen infections. However, how the translation system contributes to plant immunity is largely unknown. The evolutionarily conserved thiolation modification of tRNA ensures efficient decoding during translation. Here we show that tRNA thiolation is required for plant immunity in Arabidopsis. We identify a cgb Arabidopsis mutant, which is hyper-susceptible to the pathogen Pseudomonas syringae. CGB encodes ROL5, a homolog of yeast NCS6 required for tRNA thiolation. ROL5 physically interacts with CTU2, a homolog of yeast NCS2. Mutations in either ROL5 or CTU2 result in loss of tRNA thiolation. Further analyses reveal that both transcriptional reprogramming and translational reprogramming during immune responses are compromised in cgb. Notably, the translation of the salicylic acid receptor NPR1 is reduced in cgb, resulting in reduced salicylic acid signaling. Our study not only reveals a new regulatory mechanism for plant immunity but also uncovers a new biological function of tRNA thiolation.

biochemistry↗

bioRxiv2022

A transcytotic actin shift polarizes vesicle trajectories and partitions apicobasal epithelial membrane domains

AbstractIn prevailing epithelial polarity models, membrane-based polarity cues such as the partitioning-defective PARs specify the positions and identities of apicobasal membrane domains. Recent findings suggest, however, that vesicle-associated polarity cues specify membrane polarity by positioning the apical domain, upstream of membrane-based polarity cues. These findings raised the question how vesicles acquire apicobasal directionality independent of polarized target membrane domains. Here, we show that the apical directionality of vesicle trajectories depends on intracellular actin dynamics during the establishment of membrane polarity in the C. elegans intestine. We find that actin, powered by branched-chain actin dynamics, determines the position of apical membrane components, PARs, and itself on expanding membranes. Using photomodulation, we demonstrate that F-actin travels through the cytoplasm and along the cortex towards the future apical domain. Our findings suggest an alternative polarity model where actin-dependent directional trafficking inserts the nascent apical domain into the growing membrane to partition its apicobasal domains.

cell biology↗

bioRxiv2022

Graphics processing unit-accelerated Monte Carlo simulation of polarized light in complex three-dimensional media

SignificanceMonte Carlo (MC) methods have been applied for studying interactions between polarized light and biological tissues, but most existing MC codes supporting polarization modeling can only simulate homogeneous or multi-layered domains, resulting in approximations when handling realistic tissue structures. AimOver the past decade, the speed of MC simulations has seen dramatic improvement with massively-parallel computing techniques. Developing hardware-accelerated MC simulation algorithms that can accurately model polarized light inside 3-D heterogeneous tissues can greatly expand the utility of polarization in biophotonics applications. ApproachHere we report a highly efficient polarized MC algorithm capable of modeling arbitrarily complex media defined over a voxelated domain. Each voxel of the domain can be associated with spherical scatters of various radii and densities. The Stokes vector of each simulated photon packet is updated through photon propagation, creating spatially resolved polarization measurements over the detectors or domain surface. ResultsWe have implemented this algorithm in our widely disseminated MC simulator, Monte Carlo eXtreme (MCX). It is validated by comparing with a reference CPU-based simulator in both homogeneous and layered domains, showing excellent agreement and a 931-fold speedup. ConclusionThe polarization-enabled MCX (pMCX) offers biophotonics community an efficient tool to explore polarized light in bio-tissues, and is freely available at http://mcx.space/.

biophysics↗

bioRxiv2022

Differential Requirement of DICER1 Activity during Development of Mitral and Tricuspid Valves

Mitral and tricuspid valves are essential for unidirectional blood flow in the heart. They are derived from similar cell sources, and yet congenital dysplasia affecting both valves is clinically rare, suggesting the presence of differential regulatory mechanisms underlying their development. We specifically inactivated Dicer1 in the endocardium during cardiogenesis, and unexpectedly found that Dicer1-deletion caused congenital mitral valve stenosis and regurgitation, while it had no impact on other valves. We showed that hyperplastic mitral valves were caused by abnormal condensation and extracellular matrix (ECM) remodeling. Our single-cell RNA Sequencing analysis revealed impaired maturation of mesenchymal cells and abnormal expression of ECM genes in mutant mitral valves. Furthermore, expression of a set of miRNAs that target ECM genes was significantly lower in tricuspid valves compared to mitral valves, consistent with the idea that the miRNAs are differentially required for mitral and tricuspid valve development. Our study thus reveals miRNA-mediated gene regulation as a novel molecular mechanism that differentially regulates mitral and tricuspid valve development, thereby enhancing our understanding of the non-association of inborn mitral and tricuspid dysplasia observed clinically. Summary statementAlthough mitral and tricuspid heart valves are both derived from same cell sources in the atrioventricular region through similar initiation and remodeling processes, congenital dysplasia simultaneously affecting both valves is clinically uncommon. We show that DICER1 activity is only essential for mitral valve development whereas it is dispensable for other valves. Our study thus reveals miRNA-mediated gene regulation as a novel molecular mechanism that is differentially required to regulate mitral and tricuspid valve development, thereby enhancing our understanding of the non-association of inborn mitral and tricuspid dysplasia observed clinically.

developmental biology↗

bioRxiv2021

Ubiquitin Ligase SmDDA1b of Eggplant (Solanum melongena) Enhances Bacterial Wilt Resistance via SmNAC Degradation

Bacterial wilt (BW) is a soil-borne disease that severely impacts plant growth and productivity globally. Ubiquitination plays a crucial role in disease resistance. Our previous research indicated that NAC transcription factor SmNAC negatively regulates BW resistance in eggplant (Solanum melongena). However, whether the ubiquitin/26S proteasome system (UPS) participates in this regulation is unknown. This study used SmNAC as a bait to screen eggplant cDNA library and obtained SmDDA1b, an E3 ubiquitin ligase. Subcellular location and bimolecular fluorescence complementation assays revealed that SmDDA1b could interact with SmNAC in the nucleus. The in vivo and in vitro ubiquitination experiments indicated that SmDDA1b can degrade SmNAC through UPS. However, the discovery of negative regulation of SmDDA1b expression by SmNAC showed that there was a negative feedback loop between SmNAC and SmDDA1b in eggplant. The SmDDA1b-overexpressed lines showed a higher BW resistance associated with high expression levels of salicylic acid (SA)-related genes and SA content than the wild-type lines. However, SmDDA1b-silencing lines showed the opposite results, indicating that SmDDA1b is a positive regulatory gene for BW resistance. This study provides a candidate gene that can enhance BW resistance in eggplants. In addition, it provides insight into a mechanism that promotes plant disease resistance via the SmDDA1b-SmNAC-SA pathway.

molecular biology↗

bioRxiv2021

Obesity influences composition of salivary and fecal microbiota and impacts the interactions between bacterial taxa

Obesity is an increasing global health concern and is associated with a broad range of morbidities. The gut microbiota are increasingly recognized as important contributors to obesity and cardiometabolic health. This study aimed to characterize oral and gut microbial communities, and evaluate host:microbiota interactions between clinical obesity classifications. We performed 16S rDNA sequencing on fecal and salivary samples, global metabolomics profiling on plasma and stool samples, and dietary profiling in 135 healthy individuals. We grouped individuals by obesity status, based on body mass index (BMI), including lean (BMI 18-24.9), overweight (BMI 25-29.9), or obese (BMI [≥]30). We analyzed differences in microbiome composition, community inter-relationships, and predicted microbial function by obesity status. We found that salivary bacterial communities of lean and obese individuals were compositionally and phylogenetically distinct. An increase in obesity status was positively associated with strong correlations between bacterial taxa, particularly with bacterial groups implicated in metabolic disorders including Fretibacterium, and Tannerella. Consumption of sweeteners, especially xylitol, significantly influenced compositional and phylogenetic diversities of salivary and fecal bacterial communities. In addition, obesity groups exhibited differences in predicted bacterial metabolic activity, which was correlated with hosts metabolite concentrations. Overall, obesity was associated with distinct changes in bacterial community dynamics, particularly in saliva. Consideration of microbiome community structure, and inclusion of salivary samples may improve our ability to understand pathways linking microbiota to obesity and cardiometabolic disease. IMPORTANCEObesity is a worldwide epidemic that is associated with a wide range of health issues. Microbiota were shown to influence metabolism and obesity development. Our study aimed to evaluate the interactions between obesity, salivary and fecal microbiota, and metabolite concentrations in healthy individuals. The oral bacterial community was more impacted by the obesity status of the host than fecal microbiota. Consistently for oral and fecal microbiota, the number of strong interactions between bacteria increased with the increase in the obesity status. Several predicted microbial metabolic pathways that were shown to be associated with metabolic health were uniquely enriched between obesity groups. In addition, these metabolic pathways were correlated with plasma and stool metabolites. Our results suggest that oral microbiota might better reflect the obesity status of the host than fecal microbiota, and that correlations between microbial taxa are altered during obesity.

microbiology↗

bioRxiv2021

Mapping brain-wide excitatory projectome of primate prefrontal cortex at submicron resolution: relevance to diffusion tractography

Resolving trajectories of axonal pathways in the primate prefrontal cortex remains crucial to gain insights into higher-order processes of cognition and emotion, which requires a comprehensive map of axonal projections linking demarcated subdivisions of prefrontal cortex and the rest of brain. Here we report a mesoscale excitatory projectome issued from the ventrolateral prefrontal cortex (vlPFC) to the entire macaque brain by using viral-based genetic axonal tracing in tandem with high-throughput serial two-photon tomography, which demonstrated prominent monosynaptic projections to other prefrontal areas, temporal, limbic and subcortical areas, relatively weak projections to parietal and insular cortices but no projections directly to the occipital lobe. In a common 3D space, we quantitatively validated an atlas of diffusion tractography-derived vlPFC connections with correlative enhanced green fluorescent protein-labelled axonal tracing, and observed generally good agreement except a major difference in the posterior projections of inferior fronto-occipital fasciculus. These findings raise an intriguing question as to how neural information passes along long-range association fiber bundles in macaque brains, and call for the caution of using diffusion tractography to map the wiring diagram of brain circuits.

neuroscience↗

bioRxiv2021

Dry heat sterilization as a method to recycle N95 respirator masks: the importance of fit

In times of crisis, including the current COVID-19 pandemic, the supply chain of filtering facepiece respirators, such as N95 respirators, are disrupted. To combat shortages of N95 respirators, many institutions were forced to decontaminate and reuse respirators. While several reports have evaluated the impact on filtration as a measurement of preservation of respirator function after decontamination, the equally important fact of maintaining proper fit to the users face has been understudied. In the current study, we demonstrate the complete inactivation of SARS-CoV-2 and preservation of fit test performance of N95 respirators following treatment with dry heat. We apply scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM/EDS), X-ray diffraction (XRD) measurements, Raman spectroscopy, and contact angle measurements to analyze filter material changes as a consequence of different decontamination treatments. We further compared the integrity of the respirator after autoclaving versus dry heat treatment via quantitative fit testing and found that autoclaving, but not dry heat, causes the fit of the respirator onto the users face to fail, thereby rendering the decontaminated respirator unusable. Our findings highlight the importance to account for both efficacy of disinfection and mask fit when reprocessing respirators to for clinical redeployment.

scientific communication and education↗

bioRxiv2021

MCX Cloud - a modern, scalable, high-performance and in-browser Monte Carlo simulation platform with cloud computing

SignificanceDespite the ample progress made towards faster and more accurate Monte Carlo (MC) simulation tools over the past decade, the limited usability and accessibility of these advanced modeling tools remain key barriers towards widespread use among the broad user community. AimAn open-source, high-performance, web-based MC simulator that builds upon modern cloud computing architectures is highly desirable to deliver state-of-the-art MC simulations and hardware acceleration to general users without the need for special hardware installation and optimization. ApproachWe have developed a configuration-free, in-browser 3-D MC simulation platform - MCX Cloud - built upon an array of robust and modern technologies, including a Docker Swarm-based cloud-computing backend and a web-based graphical user interface (GUI) that supports in-browser 3-D visualization, asynchronous data communication, and automatic data validation via JavaScript Object Notation (JSON) schemas. ResultsThe front-end of the MCX Cloud platform offers an intuitive simulation design, fast 3-D data rendering, and convenient simulation sharing. The Docker Swarm container orchestration backend is highly scalable and can support high-demand GPU MC simulations using Monte Carlo eXtreme (MCX) over a dynamically expandable virtual cluster. ConclusionMCX Cloud makes fast, scalable, and feature-rich MC simulations readily available to all biophotonics researchers without overhead. It is fully open-source and can be freely accessed at http://mcx.space/cloud.

biophysics↗

bioRxiv2021

Breaching the cell-envelope barriers of gram-positive and fungal microbes by a type VI secretion system in Acidovorax citrulli

The type VI secretion system (T6SS) is a double-tubular toxin-injection nanomachine widely found in gram-negative human and plant pathogens. The current model depicts that the T6SS spear-like Hcp tube is powered by the contraction of an outer sheath to drill through the envelope of a neighboring cell, achieving cytosol to cytosol delivery. However, gram-positive bacteria seem to be impenetrable to such T6SS action. Here we report that a plant pathogen Acidovorax citrulli (AC) deploys a highly potent T6SS to kill a range of bacteria including Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, and Mycobacterium smegmatis as well as fungal species including Candida albicans and Pichia pastoris. Using bioinformatic and biochemical assays, we identified a group of T6SS effectors and characterized one effector RhsB that is critical for interspecies interaction. We report that RhsB contains a conserved YD-repeat domain and a C-terminal nuclease domain. Toxicity of RhsB was neutralized by its downstream immunity proteins through direct interaction. RhsB was cleaved at the C-terminal end and a catalytic mutation within the internal aspartic protease abolished such cleavage. Collectively, the T6SS of AC displays potent activities to penetrate the cell envelope barriers of gram-positive and fungal species, highlighting the greatly expanded capabilities of T6SS in modulating microbiome compositions in complex environments.

microbiology↗

bioRxiv2021

Improved methods and optimized design for CRISPR Cas9 and Cas12a homology-directed repair

CRISPR-Cas proteins are used to introduce double-stranded breaks (DSBs) at targeted genomic loci. DSBs are repaired by endogenous cellular pathways such as non-homologous end joining (NHEJ) and homology-directed repair (HDR). Providing a DNA template during repair allows for precise introduction of a desired mutation via the HDR pathway. However, rates of repair by HDR are often slow compared to the more rapid but less accurate NHEJ-mediated repair. Here, we describe comprehensive design considerations and optimized methods for highly efficient HDR using single-stranded oligodeoxynucleotide (ssODN) donor templates for several CRISPR-Cas systems including S.p. Cas9, S.p. Cas9 D10A nickase, and A.s. Cas12a delivered as ribonucleoprotein complexes with synthetic guide RNAs. Features relating to guide RNA selection, donor strand preference, and incorporation of blocking mutations in the donor template to prevent re-cleavage were investigated and were implemented in a novel online tool for HDR donor template design. Additionally, we employ chemically modified HDR donor templates in combination with a small molecule to boost HDR efficiency up to 10-fold. These findings allow for high frequencies of precise repair utilizing HDR in multiple mammalian cell lines. Tool availability: www.idtdna.com/HDR

molecular biology↗

bioRxiv2021

To knot and not: Multiple conformations of the SARS-CoV-2 frameshifting RNA element

The SARS-CoV-2 frameshifting RNA element (FSE) is an excellent target for therapeutic intervention against Covid-19. This small gene element employs a shifting mechanism to pause and backtrack the ribosome during translation between Open Reading Frames 1a and 1b, which code for viral polyproteins. Any interference with this process has profound effect on viral replication and propagation. Pinpointing the structures adapted by the FSE and associated structural transformations involved in frameshifting has been a challenge. Using our graph-theory-based modeling tools for representing RNA secondary structures, "RAG" (RNA-As-Graphs), and chemical structure probing experiments, we show that the 3-stem H-type pseudoknot (3_6 dual graph), long assumed to be the dominant structure has a viable alternative, an HL-type 3-stem pseudoknot (3_3) for longer constructs. In addition, an unknotted 3-way junction RNA (3_5) emerges as a minor conformation. These three conformations share Stems 1 and 3, while the different Stem 2 may be involved in a conformational switch and possibly associations with the ribo-some during translation. For full-length genomes, a stem-loop motif (2_2) may compete with these forms. These structural and mechanistic insights advance our understanding of the SARS-CoV-2 frameshifting process and concomitant virus life cycle, and point to three avenues of therapeutic intervention.

biochemistry↗

bioRxiv2021

Mitochondrial Fission Regulates Transcription of Ribosomal Protein Genes in Embryonic Hearts

Mitochondrial dysfunction causes severe congenital heart diseases and prenatal/neonatal lethality. The lack of sufficient knowledge regarding how mitochondrial abnormalities affect cardiogenesis poses a major barrier for the development of clinical applications that target inborn heart defects due to mitochondrial deficiency. Mitochondrial morphology, which is regulated by fission and fusion, plays key roles in determining mitochondrial activity. Drp1 encodes a dynamin-related GTPase required for mitochondrial fission. To investigate the role of mitochondrial fission on cardiogenesis during the embryonic metabolic shift period, we specifically inactivated Drp1 in second heart field derived structures. Deletion of Drp1 in embryonic cardiomyocytes led to severe defects in mitochondrial morphology, ultrastructure, and activity. These defects caused increased cell death, decreased cell survival, disorganized cardiomyocytes, and embryonic lethality. Through characterizing this model, we reveal a novel AMPK-SIRT7-GABPB axis that relays the mitochondrial fission anomaly to reduced transcription of ribosomal protein genes in mutant cardiomyocytes. We therefore provide the first mouse genetic evidence to show that mitochondrial fission is essential for embryonic heart development. Furthermore, we uncovered a novel signaling cascade that mediates the crosstalk between mitochondrial dysfunction and protein synthesis. Our research provides further mechanistic insight regarding how mitochondrial dysfunction causes pathological molecular and cellular alterations during cardiogenesis.

developmental biology↗

bioRxiv2021

Modeling of histone modifications reveals formation mechanism and function of bivalent chromatin

Bivalent chromatin is characterized by occupation of both activating histone modifications and repressive histone modifications. While bivalent chromatin is known to link with many biological processes, the mechanisms responsible for its multiple functions remain unclear. Here, we develop a mathematical model that involves antagonistic histone modifications H3K4me3 and H3K27me3 to capture the key features of bivalent chromatin. Three necessary conditions for the emergence of bivalent chromatin are identified, including advantageous methylating activity over demethylating activity, frequent noise conversions of modifications, and sufficient nonlinearity. The first condition is further confirmed by analyzing the experimental data from a recent study. Investigation of the composition of bivalent chromatin reveals that bivalent nucleosomes carrying both H3K4me3 and H3K27me3 account for no more than half of nucleosomes at the bivalent chromatin domain. We identify that bivalent chromatin not only allows transitions to multiple states but also serves as a stepping stone to facilitate a step-wise transition between repressive chromatin state and activating chromatin state, and thus elucidate crucial roles of bivalent chromatin in mediating phenotypical plasticity during cell fate determination.

systems biology↗

bioRxiv2020

Neural network aided approximation and parameterinference of stochastic models of gene expression

Non-Markov models of stochastic biochemical kinetics often incorporate explicit time delays to effectively model large numbers of intermediate biochemical processes. Analysis and simulation of these models, as well as the inference of their parameters from data, are fraught with difficulties because the dynamics depends on the systems history. Here we use an artificial neural network to approximate the time-dependent distributions of non-Markov models by the solutions of much simpler time-inhomogeneous Markov models; the approximation does not increase the dimensionality of the model and simultaneously leads to inference of the kinetic parameters. The training of the neural network uses a relatively small set of noisy measurements generated by experimental data or stochastic simulations of the non-Markov model. We show using a variety of models, where the delays stem from transcriptional processes and feedback control, that the Markov models learnt by the neural network accurately reflect the stochastic dynamics across parameter space.

systems biology↗

bioRxiv2020

Light transport modeling in highly complex tissues using implicit mesh-based Monte Carlo algorithm

The mesh-based Monte Carlo (MMC) technique has grown tremendously since its initial publication nearly a decade ago. It is now recognized as one of the most accurate Monte Carlo (MC) methods, providing accurate reference solutions for the development of novel biophotonics techniques. In this work, we aim to further advance MMC to address a major challenge in biophotonics modeling, i.e. light transport within highly complex tissues, such as dense microvascular networks, porous media and multi-scale tissue structures. Although the current MMC framework is capable of simulating light propagation in such media given its generality, the run-time and memory usage grow rapidly with increasing media complexity and size. This greatly limits our capability to explore complex and multi-scale tissue structures. Here, we propose a highly efficient implicit mesh-based Monte Carlo (iMMC) method that incorporates both mesh- and shape-based tissue representations to create highly complex yet memory efficient light transport simulations. We demonstrate that iMMC is capable of providing accurate solutions for dense vessel networks and porous tissues while reducing memory usage by greater than a hundred- or even thousand-fold. In a sample network of microvasculature, the reduced shape complexity results in nearly 3x speed acceleration. The proposed algorithm is now available in our open-source MMC software at http://mcx.space/#mmc.

biophysics↗

bioRxiv2020

A hybrid mesh and voxel based Monte Carlo algorithm for accurate and efficient photon transport modeling in complex bio-tissues

Over the past decade, an increasing body of evidence has suggested that threedimensional (3-D) Monte Carlo (MC) light transport simulations are affected by the inherent limitations and errors of voxel-based domain boundaries. In this work, we specifically address this challenge using a hybrid MC algorithm, namely split-voxel MC or SVMC, that combines both mesh and voxel domain information to greatly improve MC simulation accuracy while remaining highly flexible and efficient in parallel hardware, such as graphics processing units (GPU). We achieve this by applying a marching-cubes algorithm to a pre-segmented domain to extract and encode sub-voxel information of curved surfaces, which is then used to inform ray-tracing computation within boundary voxels. This preservation of curved boundaries in a voxel data structure demonstrates significantly improved accuracy in several benchmarks, including a human brain atlas. The accuracy of the SVMC algorithm is comparable to that of mesh-based MC (MMC), but runs 2x-6x faster and requires only a lightweight preprocessing step. The proposed algorithm has been implemented in our open-source software and is freely available at http://mcx.space.

biophysics↗