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Ma, Y.

Publications and source records attributed to Ma, Y..

At least 199 records · Page 11Linked to original sources

Experimental capture of genomic islands defines a widespread class of genetic element capable of non-autonomous transfer

Bacteria acquire new genes by horizontal gene transfer (HGT), typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages and certain integrative and conjugative elements (ICEs) are well characterized, the broader diversity of MGEs remains poorly understood. Here, we propagated the bacterium Pseudomonas fluorescens SBW25 in the presence of filtrate obtained from garden compost communities. Genome sequencing of derived colonies revealed acquisition of three different mobile elements, each integrated immediately downstream of tmRNA, flanked by direct repeats, and encoding a tyrosine integrase (intY) and putative phage defense systems. Absent are genes with recognized roles in autonomous transfer. Interrogation of DNA sequence databases showed that similar elements are widespread in the genus Pseudomonas and beyond, with Vibrio Pathogenicity Island-1 (VPI-1) from V. cholerae as a notable example. Bioinformatic analyses demonstrate frequent horizontal transfer among diverse hosts. Detailed analysis of a single element, I55, showed that it is transferred between cells by a jumbo phage, and confers a fitness benefit via a type II restriction-modification system. Significance StatementThe impact of horizontal gene transfer on the evolution of bacteria outpaces that driven by spontaneous mutation, but knowledge of the range of mediators, the genes mobilized, and the mechanisms of movement have largely depended on inferences stemming from bioinformatics. Here we describe a real-time evolution experiment in which a single focal strain propagated with filtrate from a complex microbial community captured genetic elements carrying a diverse cargo of genes whose mobility was previously uncharacterized. The elements represent a widespread class of mobile DNA dependent only on a tyrosine integrase targeting a highly conserved genomic site. Genetic analysis of one element shows that it confers a significant fitness advantage via defense against bacteriophages, and hijacks a jumbo bacteriophage for intercellular transfer. Our findings reveal new insights into the hidden diversity and dynamics of MGEs in natural environments. ClassificationBiological Sciences / Microbiology

microbiology↗

Differential encoding of mammalian proprioception by voltage-gated sodium channels

Animals that require purposeful movement for survival are endowed with mechanosensory neurons called proprioceptors that provide essential sensory feedback from muscles and joints to spinal cord circuits, which modulates motor output. Despite the essential nature of proprioceptive signaling in daily life, the mechanisms governing proprioceptor activity are poorly understood. Here, we have identified distinct and nonredundant roles for two voltage-gated sodium channels (NaVs), NaV1.1 and NaV1.6, in mammalian proprioception. Deletion of NaV1.6 in somatosensory neurons (NaV1.6cKO mice) causes severe motor deficits accompanied by complete loss of proprioceptive transmission, which contrasts with our previous findings using similar mouse models to target NaV1.1 (NaV1.1cKO). In NaV1.6cKO animals, loss of proprioceptive feedback caused non-cell- autonomous impairments in proprioceptor end-organs and skeletal muscle that were absent in NaV1.1cKO mice. We attribute the differential contribution of NaV1.1 and NaV1.6 in proprioceptor function to distinct cellular localization patterns. Collectively, these data provide the first evidence that NaV subtypes uniquely shape neurotransmission within a somatosensory modality. TeaserVoltage gated sodium channels differentially encode mammalian proprioception via distinct cellular localization patterns.

neuroscience↗

Restraint of melanoma progression by cells in the local skin environment

Keratinocytes, the dominant cell type in the melanoma microenvironment during tumor initiation, exhibit diverse effects on melanoma progression. Using a zebrafish model of melanoma and human cell co-cultures, we observed that keratinocytes undergo an EMT-like transformation in the presence of melanoma, reminiscent of their behavior during wound healing. Surprisingly, overexpression of the EMT transcription factor Twist in keratinocytes led to improved overall survival in zebrafish melanoma models, despite no change in tumor initiation rates. This survival benefit was attributed to reduced melanoma invasion, as confirmed by human cell co-culture assays. Single-cell RNA-sequencing revealed a unique melanoma cell cluster in the Twist-overexpressing condition, exhibiting a more differentiated, less invasive phenotype. Further analysis nominated homotypic jam3b-jam3b and pgrn-sort1a interactions between Twist-overexpressing keratinocytes and melanoma cells as potential mediators of the invasive restraint. Our findings suggest that EMT in the tumor microenvironment may paradoxically limit melanoma invasion through altered cell-cell interactions.

cancer biology↗

Systemic identification of functionally conserved lncRNA metabolic regulators in human and mouse livers

BACKGROUND & AIMSUnlike protein-coding genes, the majority of human long non-coding RNAs (lncRNAs) lack conservation based on their sequences, posing a challenge for investigating their role in a pathophysiological context for clinical translation. This study explores the hypothesis that non-conserved lncRNAs in human and mouse livers may share similar metabolic functions, giving rise to functionally conserved lncRNA metabolic regulators (fcLMRs). METHODSWe developed a sequence-independent strategy to select putative fcLMRs, and performed extensive analysis to determine the functional similarities of putative human and mouse LMR pairs (h/mLMRs). RESULTSWe found that several pairs of putative fcLMRs share similar functions in regulating gene expression. We further demonstrated that a pair of fcLMRs, h/mLMR1, robustly regulated triglyceride levels by modulating the expression of a similar set of lipogenic genes. Mechanistically, h/mLMR1 binds to PABPC1, a regulator of protein translation, via short motifs on either lncRNA with divergent sequences but similar structures. This interaction inhibits protein translation, activating an amino acid-mTOR-SREBP1 axis to regulate lipogenic gene expression. Intriguingly, PABPC1-binding motifs on each lncRNA fully rescued the functions of their corresponding LMRs in the opposite species. Given the elevated expression of h/mLMR1 in humans and mice with hepatic steatosis, the PABPC1-binding motif on hLMR1 emerges as a potential non-conserved human drug target whose functions can be fully validated in a physiologically relevant setting before clinical studies. CONCLUSIONSOur study supports that fcLMRs represent a novel and prevalent biological phenomenon, and deep phenotyping of genetic mLMR mouse models constitutes a powerful approach to understand the pathophysiological role of lncRNAs in the human liver.

physiology↗

Computing hematopoiesis plasticity in response to genetic mutations and environmental stimulations

Cell plasticity (CP), describing a dynamic cell state, plays a crucial role in maintaining homeostasis during organ morphogenesis, regeneration and damage-to-repair biological process. Single-cell-omics datasets provide unprecedented resource to empowers analysis on CP. Hematopoiesis offers fertile opportunities to develop quantitative methods for understanding CP with rich supports from experimental ground-truths. In this study we generated high-quality lineage-negative (Lin-) single-cell RNA-sequencing datasets under various conditions and introduced a working pipeline named Snapdragon to interrogate naive and disturbed plasticity of hematopoietic stem and progenitor cells (HSPCs) with mutational or environmental challenges. Utilizing embedding methods UMAP or FA, a continuum of hematopoietic development is visually observed in wildtype where the pipeline confirms a very low Proportion of hybrid-cells (Phc, with bias range: 0.4-0.6) on a transition trajectory. Upon Tet2 mutation, a driver of leukemia, or treatment of DSS, an inducer of colitis, Phc is increased and plasticity of HSPCs was enhanced. Quantitative analysis indicates that Tet2 mutation enhances HSC self-renewal capability while DSS treatment results in an enhanced myeloid-skewing trajectory, suggesting their similar but different consequences. We prioritized several transcription factors (i.e the EGR family) and signaling pathways (i.e. receptors IL1R1 and ADRB, inflammation and sympathy-sensing respectively) which are responsible for Phc alterations. CellOracle-based simulation suggests that knocking-out EGR regulons or pathways of IL1R1 and ADRB partially reverses Phc promoted by Tet2 mutation and inflammation. In conclusion, the study provides high-quality datasets with single-cell transcriptomic matrices for diversified hematopoietic simulations and a computational pipeline Snapdragon for quantifying disturbed Phc and CP. (247 words) HighlightsO_LITo guide CP analysis, we introduce a quantizable parameter Phc and a pipeline Snapdragon, which discriminate naive and disturbed hematopoiesis; C_LIO_LIThe Snapdragon pipeline analysis on Tet2+/-Lin- cells demonstrates many novel insights, including enhanced HSC plasticity and increased PHC; similar trends are observed in inflammatory Lin- cells; C_LIO_LIRegulon analysis suggests that transcriptional factor EGR1 is significantly activated to elevated the HSC plasticity and change hematopoietic trajectory; C_LIO_LIStress-response-related signaling pathways mediated by receptors IL1R1 or ADRB were obviously activated in the challenged hematopoiesis; C_LIO_LICellOracle-based simulation suggests that knocking-out EGR regulons or pathways of IL1R1 and ADRB partially reverses Phc promoted by Tet2 mutation and inflammation. C_LI

developmental biology↗

MLCK/MLCP regulates mammalian axon regeneration via the redistribution of the growth cone F-actin

Axon regrowth is a key determinant of the restoration of the biological function of the nervous system after trauma. However, mature mammalian neurons have limited capacity for axon regeneration. We have previously demonstrated that neuronal axon growth both in the central and the peripheral nervous systems is markedly enhanced when non-muscle myosin II (NMII) is inhibited with blebbistatin. The activity of NMII is primarily regulated by MLCK and MLCP via the phosphorylation and dephosphorylation of its light chain, respectively; however, the functional roles of MLCK and MLCP in mammalian axonal regeneration remain unknown. In the present study, we provide strong evidence that the inhibition of MLCK activity significantly blocks axon regeneration in mice. Conversely, the inhibition of MLCP promotes axon regrowth of both the peripheral and central nervous system. Our findings further indicate that the MLCK/MLCP regulates axon regeneration and redistributes the growth cone F-actin, and this result suggests that direct regulation of the growth cone machinery is a potential strategy to promote axon regeneration.

physiology↗

Conformational dynamics and asymmetry in multimodal inhibition of membrane-bound pyrophosphatases

Membrane-bound pyrophosphatases (mPPases) are homodimeric proteins that hydrolyse pyrophosphate and pump H+/Na+ across membranes. They are crucial for the virulence of protist pathogens, making them attractive drug targets. In this study, we investigate the inhibitory effects of seven distinct bisphosphonates against Thermotoga maritima mPPase to explore their mode of action and assist in future small molecule inhibitor development. We solved two structures of mPPase bound to the inhibitors in the enzyme active sites and probed the conformational dynamics of mPPase under multiple inhibitors and functionally relevant conditions by double electron-electron resonance (DEER) spectroscopy. We found that mPPase adopts distinct conformational equilibria in solution in the presence of different inhibitors, including states consistent with asymmetric binding in the active site (closed-open), but a symmetric apo-like conformation on the periplasmic side (open-open). Combined with solid-supported membrane-based electrophysiology recordings, this revealed that during catalysis, one monomer of the dimer remains open, and Na+ can only be pumped in a closed state. These results further support symmetry-breaking across the membrane, consistent with half-of-the-sites-reactivity.

biochemistry↗

The m6A Reader ECT1 Mediates Seed Germination via the DAG2-ECT1-PHYB Regulatory Cascade in Arabidopsis

The N6-methyladenosine (m6A) RNA modification, a significant epitranscriptomic mark, is integral to plant growth and development. m6A reader proteins are capable of recognizing m6A modifications to impact RNA metabolic and biological processes. Here, we discovered ECT1 as an m6A reader protein that directly binds to the m6A site and plays a role in positively regulating seed germination in the context of gibberellins (GAs). ECT1 undergoes m6A modification to ensure its own stability and engages in self-interaction to enhance its protein stability. Moreover, ECT1 establishes a regulatory circuit with DAG2, which has been reported to play a positive regulatory role in GA-mediated seed germination. We found that DAG2 directly binds to the ECT1 promoter to control its transcription. ECT1 modulates the mRNA stability of DAG2. Furthermore, we identified PHYB, which encodes a key photoreceptor controlling GA-regulated seed germination, as a common downstream target of DAG2 and ECT1. DAG2 and ECT1 regulate the expression of PHYB at the transcriptional and post-transcriptional levels, respectively. ECT1 binds directly to PHYB, thereby influencing its stability. While DAG2 binds to the PHYB promoter to regulate its transcription. Together, these results unveil that ECT1 participates in the m6A signaling pathway through complex and multifaceted molecular mechanisms, broadening the spectrum of m6A reader functions and deepening our insight into the m6A signaling network in Arabidopsis.

plant biology↗

Controlled and orthogonal partitioning of large particles into biomolecular condensates

Biomolecular condensates arising from liquid-liquid phase separation contribute to diverse cellular processes, such as gene expression. Partitioning of client molecules into condensates is critical to regulating the composition and function of condensates. Previous studies suggest that client size limits partitioning, with dextrans >5 nm excluded from condensates. Here, we asked whether larger particles, such as macromolecular complexes, can partition into condensates based on particle-condensate interactions. We sought to discover the biophysical principles that govern particle inclusion in or exclusion from condensates using polymer nanoparticles with tailored surface chemistries as models of macromolecular complexes. Particles coated with polyethylene glycol (PEG) did not partition into condensates. We next leveraged the PEGylated particles as an inert platform to which we conjugated specific adhesive moieties. Particles functionalized with biotin partitioned into condensates containing streptavidin, driven by high-affinity biotin-streptavidin binding. Oligonucleotide-decorated particles exhibited varying degrees of partitioning into condensates, depending on condensate composition. Partitioning of oligonucleotide-coated particles was tuned by altering salt concentration, oligonucleotide length, and oligonucleotide surface density. Remarkably, beads with distinct surface chemistries partitioned orthogonally into immiscible condensates. Based on our experiments, we conclude that arbitrarily large particles can controllably partition into biomolecular condensates given sufficiently strong condensate-particle interactions, a conclusion also supported by our coarse-grained molecular dynamics simulations and theory. These findings may provide insights into how various cellular processes are achieved based on partitioning of large clients into biomolecular condensates, as well as offer design principles for the development of drug delivery systems that selectively target disease-related biomolecular condensates. Significance StatementBiomolecular condensates are subcellular compartments that selectively recruit or exclude client molecules, even though condensates lack an enclosing membrane. Many biochemical reconstitution experiments have investigated mechanisms by which membraneless organelles control partitioning, modeling how cells spatiotemporally recruit components into condensates to regulate cellular functions. One outstanding question is whether partitioning is strictly limited by client size. In this work, we engineered nanoparticles with various sizes and surface functionalities and measured how these variables determine partitioning. We observed controlled and orthogonal partitioning of large particles into several condensate types, driven by strong particle-condensate interactions. Molecular simulations recapitulated key results. Our work advances understanding of how condensate composition is regulated, and our nanoparticle toolbox may also inspire a platform for drug delivery.

biophysics↗

Biomolecular condensates can function as inherent catalysts

We report the discovery that chemical reactions can be catalyzed by condensates formed by intrinsically disordered proteins (IDPs). The proteins themselves lack any catalytic activities. Catalytic functions of condensates emerge as a consequence of sequence-dependent mesoscale electrochemical microenvironments created by phase separation. Stimulated Raman spectroscopy suggests that the catalytic behaviors of condensates are attributable to the spatial variations of water activities across condensate interiors and interfaces. We show that condensates are capable of catalyzing diverse cellularly relevant hydrolysis reactions. Through sequence design, the electrochemical properties of condensates can be programmed to exert control over catalytic behaviors. Incorporation of synthetic condensates into live cells alters transcription profiles and enables the activation of gene circuits that depend on products of hydrolysis reactions catalyzed by condensates. Our discovery of suggests that condensates, depending on their composition-dependent electrochemical properties, can be "Condenzymes", which contribute unexpected emergent chemical functions in cells.

biophysics↗

Activity-dependent synthesis of Emerin gates neuronal plasticity by regulating proteostasis

Neurons dynamically regulate their proteome in response to sensory input, a key process underlying experience-dependent plasticity. We characterized the visual experience-dependent nascent proteome within a brief, defined time window after stimulation using an optimized metabolic labeling approach. Visual experience induced cell type-specific and age-dependent alterations in the nascent proteome, including proteostasis-related processes. We identified Emerin as the top activity-induced candidate plasticity protein and demonstrated that its rapid activity-induced synthesis is transcription-independent. In contrast to its nuclear localization and function in myocytes, activity-induced neuronal Emerin is abundant in the endoplasmic reticulum and broadly inhibits protein synthesis, including translation regulators and synaptic proteins. Downregulating Emerin shifted the dendritic spine population from predominantly mushroom morphology to filopodia and decreased network connectivity. In mice, decreased Emerin reduced visual response magnitude and impaired visual information processing. Our findings support an experience-dependent feed-forward role for Emerin in temporally gating neuronal plasticity by negatively regulating translation.

neuroscience↗

Mechanotransduction and inflammation: an updated comprehensive representation

Mechanotransduction is the process that enables the conversion of mechanical cues into biochemical signaling. While all our cells are well known to be sensitive to such stimuli, the details of the systemic interaction between mechanical input and inflammation are not always well integrated. Often, they are considered and studied in relatively compartmentalized areas, and we therefore argue here that to understand the relationship of mechanical stimuli with inflammation - with high translational potential - it is crucial to offer and analyze a unified view of mechanotransduction. We therefore offer here a pathway representation, recollected with the standard systems biology markup language (SBML) and explored with network biology approaches. We present RAC1 as an exemplar and emerging molecule with potential for medical translation.

bioinformatics↗

Electrochemically controlled switching of dyes for enhanced super-resolution optical fluctuation imaging (SOFI)

In super-resolution optical fluctuation imaging (SOFI), the locations of molecules spaced closer than the diffraction limit of light can be identified through spatial and temporal correlation analysis of the fluorescence intensity fluctuation. Using organic dyes as fluorophore probes, the fast but stochastic switching of the individual dyes is favourable for improving SOFI imaging resolution and speed, especially in the case of high-order cumulant analysis. While in practice, fluorophore switching can be non-uniform, with some fluorophores remaining in ON or OFF state for extended periods. Furthermore, in some cases the overall rate of switching of the fluorophores can be too slow, presenting practical limitations for high-resolution and fast SOFI imaging. In this work, we demonstrate how to overcome these challenges using electrochemical controlled fluorophore switching. The oscillating electrochemical potential setting with high frequency increases the switching rate and reduces the switching heterogeneity of fluorophores. The dye Alexa Fluor 647, applied here as an example, exhibits over 3-fold decrease in average ON time and over 2-fold decrease in switching variance, resulting in significantly improved SOFI image resolution with fewer frames. We demonstrated that this new electrochemically controlled SOFI imaging modality can achieve a SOFI image with [~]130 nm resolution in 2 seconds of acquisition time, and 80 nm resolution in 6 seconds. This advancement enables fast, large area tile-scan super-resolution imaging, which opens the full potential of SOFI imaging.

biophysics↗

Amygdala engages non-emotional multi-item working memory maintenance through amygdala-hippocampus interaction

Retaining information in working memory (WM) is an active process that requires neural activity within and between regions. The human amygdala (AMY) and hippocampus (HPC) are known to play crucial roles in WM processing. Although electrophysiological studies have revealed that the HPC supports multi-item maintenance in a load-dependent manner, the characteristics of the AMY and the circuit-level mechanisms underlying AMY-HPC interactions remain largely unexplored. To address this knowledge gap, intracranial EEG recordings from the AMY and HPC in nine epileptic patients were employed to evaluate intraregional neural representations and interregional communications during maintenance under different non-emotional WM loads. High load enhanced low-frequency power and intraregional theta-gamma phase-amplitude coupling (PAC) in the AMY and HPC. At the network level, a high load elicited an increase in the strength of the HPC theta phase modulation, which entrains the AMY gamma amplitude. Furthermore, a high load increased AMY-anterior HPC (aHPC) theta phase synchrony and directional connectivity strength from the aHPC to the AMY. Conversely, posterior HPC (pHPC)-AMY synchrony was not affected by load variations. Overall, these findings highlight the importance of the AMY in non-emotional WM tasks and provide new insights into the neurophysiological basis of AMY-HPC interactions during WM maintenance.

neuroscience↗

AptaGPT: Advancing aptamer design with a generative pre-trained language model

Aptamers, synthetic oligonucleotide ligands, have shown significant promise for therapeutic and diagnostic applications owing to their high specificity and affinity for target molecules. However, the conventional Systematic Evolution of Ligands by Exponential Enrichment (SELEX) for aptamer selection is time-consuming and often yields limited candidates. To address these limitations, we introduce AptaGPT, a novel computational strategy that leverages a Generative Pre-trained Transformer (GPT) model to design and optimize aptamers. By training on SELEX data from early rounds, AptaGPT generated a diverse array of aptamer sequences, which were then computationally screened for binding using molecular docking. The results of this study demonstrated that AptaGPT is an effective tool for generating potential high-affinity aptamer sequences, significantly accelerating the discovery process and expanding the potential for aptamer research. This study showcases the application of generative language models in bioengineering and provides a new avenue for rapid aptamer development.

bioinformatics↗

Ccrk-Mak/Ick kinase signaling axis is a ciliary transport regulator essential for retinal photoreceptor maintenance

Primary cilia are microtubule-based sensory organelles whose dysfunction leads to ciliopathies in humans. The formation, function, and maintenance of primary cilia depend crucially on intraflagellar transport (IFT); however, the regulatory mechanisms of IFT and their physiological roles are poorly understood. In the current study, we screened and identified that the ciliopathy kinase Mak is a ciliary tip-localized IFT regulator that cooperatively acts with the ciliopathy kinase Ick, an IFT regulator. Simultaneous disruption of Mak and Ick resulted in loss of photoreceptor ciliary axonemes and severe degeneration in the mouse retina. Mak overexpression restored ciliary defects caused by Ick deficiency in cultured cells. Gene delivery of Ick and pharmacological inhibition of FGF receptors, negative regulators of Ick, ameliorated retinal degeneration in Mak-/-mice. In addition, we identified that Ccrk kinase is an upstream activator of Mak and Ick in retinal photoreceptor cells. Furthermore, overexpression of Mak, Ick, and Ccrk and pharmacological inhibition of FGF receptors suppressed ciliopathy-related phenotypes caused by cytoplasmic dynein inhibition in cultured cells. Collectively, our results show that the Ccrk-Mak/Ick axis is an essential IFT regulator crucial for retinal photoreceptor maintenance. This study sheds light on pathological mechanisms underlying retinitis pigmentosa caused by mutations in the human MAK gene and presents activation of Ick as a potential therapeutic approach for this retinal degenerative disease.

developmental biology↗

A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma

Multiple Myeloma (MM) remains incurable despite advances in treatment options. Although tumor subtypes and specific DNA abnormalities are linked to worse prognosis, the impact of immune dysfunction on disease emergence and/or treatment sensitivity remains unclear. We established a harmonized consortium to generate an Immune Atlas of MM aimed at informing disease etiology, risk stratification, and potential therapeutic strategies. We generated a transcriptome profile of 1,149,344 single cells from the bone marrow of 263 newly diagnosed patients enrolled in the CoMMpass study and characterized immune and hematopoietic cell populations. Associating cell abundances and gene expression with disease progression revealed the presence of a proinflammatory immune senescence-associated secretory phenotype in rapidly progressing patients. Furthermore, signaling analyses suggested active intercellular communication involving APRIL-BCMA, potentially promoting tumor growth and survival. Finally, we demonstrate that integrating immune cell levels with genetic information can significantly improve patient stratification.

genomics↗

Brain-wide functional connectome analysis of 40,000 individuals reveals brain networks that show aging effects in older adults

The functional connectome changes with aging. We systematically evaluated aging related alterations in the functional connectome using a whole-brain connectome network analysis in 39,675 participants in UK Biobank project. We used adaptive dense network discovery tools to identify networks directly associated with aging from resting-state fMRI data. We replicated our findings in 499 participants from the Lifespan Human Connectome Project in Aging study. The results consistently revealed two motor-related subnetworks (both permutation test p-values <0.001) that showed a decline in resting-state functional connectivity (rsFC) with increasing age. The first network primarily comprises sensorimotor and dorsal/ventral attention regions from precentral gyrus, postcentral gyrus, superior temporal gyrus, and insular gyrus, while the second network is exclusively composed of basal ganglia regions, namely the caudate, putamen, and globus pallidus. Path analysis indicates that white matter fractional anisotropy mediates 19.6% (p<0.001, 95% CI [7.6% 36.0%]) and 11.5% (p<0.001, 95% CI [6.3% 17.0%]) of the age-related decrease in both networks, respectively. The total volume of white matter hyperintensity mediates 32.1% (p<0.001, 95% CI [16.8% 53.0%]) of the aging-related effect on rsFC in the first subnetwork.

neuroscience↗