Biology subjects

Tan, S.

Publications and source records attributed to Tan, S..

At least 109 records · Page 6Linked to original sources

bioRxiv2022

CLE42 Delays Leaf Senescence by Antagonizing Ethylene Pathway in Arabidopsis

Leaf senescence is the final stage of leaf development and is influenced by numerous internal and environmental factors. CLE family peptides are plant-specific peptide hormones that regulate various developmental processes. However, the role of CLE in regulating leaf senescence remains unclear. Here, we found that CLE42 is a negative regulator of leaf senescence by using a CRISPR/Cas9-produced CLE mutant collection. The cle42 mutant displayed earlier senescence phenotypes, while overexpression of CLE42 delayed age-dependent and dark-induced leaf senescence. Moreover, application of the synthesized 12-aa peptide (CLE42p) also delayed leaf senescence under natural and dark conditions. CLE42 and CLE41/44 displayed functional redundancy in leaf senescence, and the cle41 cle42 cle44 triple mutant displayed more pronounced earlier senescence phenotypes than any single mutant. Analysis of differentially expressed genes obtained by RNA-Seq methodology revealed that ethylene pathway was suppressed by overexpressing CLE42. Moreover, CLE42 suppressed ethylene biosynthesis and thus promoted the protein accumulation of EBF, which in turn decreased the function of EIN3. Accordingly, mutation of EIN3/EIL1 or overexpression of EBF1 suppressed the earlier senescence phenotypes of the cle42 mutant. Together, our results reveal that the CLE peptide hormone regulates leaf senescence by communicating with ethylene pathway.

plant biology↗

bioRxiv2022

Low vision impairs implicit sensorimotor adaptation in response to small errors, but not large errors

Successful goal-directed actions require constant fine-tuning of the motor system. This fine-tuning is thought to rely on an implicit adaptation process that is driven by sensory prediction errors (i.e., where you see your hand after reaching versus where you expected it to be). Individuals with low vision experience challenges with visuomotor control, but whether they also experience challenges with implicit adaptation is unknown. To explore this question, we assessed individuals with low vision and matched controls with normal vision on a visuomotor task designed to isolate implicit adaptation. We found that low vision was associated with attenuated implicit adaptation only for small visual errors, but not large visual errors. This result not only underscores an unappreciated motor learning impairment associated with low vision, but also highlights an important constraint on how low-fidelity visual information is processed by the nervous system to enable successful implicit adaptation. New and NoteworthyWhether implicit adaptation is also impacted by visual uncertainty intrinsic to the nervous system remains unknown. To test this, we examined 20 people who live with visual uncertainty in daily life due to low vision on a visuomotor task that isolates implicit adaptation. We found that low vision attenuates adaptation in response to small errors only, paving the way for new developments in rehabilitation and assistive devices for individuals with sensory impairments.

neuroscience↗

bioRxiv2021

Improved immunoassay sensitivity and specificity using single-molecule colocalization

Enzyme-linked immunosorbent assays (ELISAs) are a cornerstone of modern molecular detection, but the technique still suffers some notable challenges. One of the biggest problems is discriminating true signal generated by target molecules versus non-specific background arising from the interaction of detection antibodies with the assay substrate or interferents in the sample matrix. Single-Molecule Colocalization Assay (SiMCA) overcomes this problem by employing total internal reflection fluorescence (TIRF) microscopy to quantify target proteins based on the colocalization of fluorescent signal from orthogonally labeled capture and detection antibodies. By specifically counting colocalized fluorescent signals, we can essentially eliminate the confounding effects of background produced by non-specific binding of detection antibodies. We further employed a normalization strategy to account for the heterogeneous distribution of the capture antibodies, greatly improving the reproducibility of our measurements. In a series of experiments with TNF-, we show that SiMCA can achieve a three-fold lower limit of detection compared to conventional single-color assays using the same antibodies and exhibits consistent performance for assays performed in complex specimens such as chicken serum and human blood. Our results help define the pernicious effects of non-specific background in immunoassays and demonstrate the diagnostic gains that can be achieved by eliminating those effects.

biophysics↗

bioRxiv2021

Non-rapid eye movement sleep and wake neurophysiology in schizophrenia

Motivated by the potential of objective neurophysiological markers to index thalamocortical function in patients with severe psychiatric illnesses, we comprehensively characterized key NREM sleep parameters across multiple domains, their interdependencies, and their relationship to waking event-related potentials and symptom severity. In 130 schizophrenia (SCZ) patients and controls, we confirmed a marked reduction in sleep spindle density in SCZ and extended these findings to show that only slow spindles predicted symptom severity, and that fast and slow spindle properties were largely uncorrelated. We also describe a novel measure of slow oscillation and spindle interaction that was attenuated in SCZ. The main sleep findings were replicated in a demographically distinct sample, and a joint model, based on multiple NREM components, predicted disease status in the replication cohort. Although also altered in patients, auditory event-related potentials elicited during wake were unrelated to NREM metrics. Consistent with a growing literature implicating thalamocortical dysfunction in SCZ, our characterization identifies independent NREM and wake EEG biomarkers that may index distinct aspects of SCZ pathophysiology and point to multiple neural mechanisms underlying disease heterogeneity. This study lays the groundwork for evaluating these neurophysiological markers, individually or in combination, to guide efforts at treatment and prevention as well as identifying individuals most likely to benefit from specific interventions.

neuroscience↗

bioRxiv2021

Serum Amyloid A promotes Acetaminophen-induced liverinjury by damaging sinusoidal endothelial cell and exacerbating platelet aggregation in liver

BackgroundAcetaminophen (APAP) is the most commonly used non-prescription antipyretic and analgesic drugs. Overuse of APAP can cause hepatotoxicity. Liver sinusoidal endothelial cells (LSECs) damage is an important early event in APAP-induced liver injury. Serum amyloid A (SAA) is an acute phase protein that mainly produced by hepatocytes, and promotes endothelial dysfunction via a pro-inflammatory and pro-thrombotic effect in atherosclerosis and renal disease. However, the role of SAA in APAP-induced liver injury remains unclear. MethodsIn this study, we used neutralizing antibody (anti-SAA) or antagonistic small peptide derived from sequence of human SAA1/2 (SAA-pep) to block the functional activity of Saa1/2 in mouse serum. Immunohistochemistry staining, Evans blue and platelet adhesion assays were performed to examine the liver damage, the integrity of sinusoidal endothelium and platelets accumulation in APAP-induce liver injury. ResultsOur study showed that in the early stage of APAP-induced acute liver injury in mice, the intrahepatic and serum Saa1/2 levels were significantly increased within 24 hours, and then gradually reduced to normal level from 3 days. Neutralization of Saa1/2 by antibodies or peptides effectively prevented the destruction of hepatic sinusoids, reduced the intrahepatic hemorrhage and platelet accumulation in liver, as well as increased the survival rate of mice treated with lethal dose of APAP. In vitro experiments showed that Saa1/2 aggravated LSECs death induced by APAP. Moreover, Saa1/2 promoted platelets adhesion on LSECs via Tlr2/Vcam-1 axis. ConclusionOur findings suggest that Saa1/2 promotes APAP-induced liver injury by damaged LSECs and exacerbated platelets aggregation. This study provides a potential target for intervention of acute liver injury/failure caused by hepatotoxic drugs such as APAP.

pharmacology and toxicology↗

bioRxiv2021

Spatial relationships of intra-lesion heterogeneity in Mycobacterium tuberculosis microenvironment, replication status, and drug efficacy

A hallmark of Mycobacterium tuberculosis (Mtb) infection with critical impact on disease development and outcome is the marked heterogeneity that exists, spanning differences in lesion types to changes in microenvironment as the infection progresses1-7. A mechanistic understanding of how this heterogeneity affects Mtb growth and treatment efficacy necessitates single bacterium-level studies in the context of intact host tissue architecture; however, such an evaluation has been technically challenging. Here, we exploit fluorescent reporter Mtb strains and the C3HeB/FeJ murine model in an integrated imaging approach to study microenvironment heterogeneity within a single lesion in situ, and analyze how these differences relate to non-uniformity in Mtb replication state, activity, and drug efficacy. We show that the pH and chloride environments differ spatially in a caseous necrotic lesion, with increased acidity and chloride levels in the lesion cuff versus the necrotic core. Conversely, a higher percentage of Mtb in the necrotic core versus the lesion cuff were in an actively replicating state, and correspondingly active in transcription and translation. Finally, examination of three first-line anti-tubercular drugs showed that efficacy of isoniazid was strikingly poor against bacteria in the lesion cuff. Our study reveals spatial relationships of intra-lesion heterogeneity, sheds light on important considerations in the development of anti-tubercular treatment strategies, and establishes a foundational framework for Mtb infection heterogeneity analysis at the single cell level in situ.

microbiology↗

bioRxiv2021

eIF6 rebinding dynamically couples ribosome maturation and translation

Protein synthesis is a cyclical process consisting of translation initiation, elongation, termination and ribosome recycling. The release factors SBDS and EFL1 (both mutated in the leukaemia predisposition disorder Shwachman-Diamond syndrome) license entry of nascent 60S ribosomal subunits into active translation by evicting the anti-association factor eIF6 from the 60S intersubunit face. Here, we show that in mammalian cells, eIF6 holds all free cytoplasmic 60S subunits in a translationally inactive state and that SBDS and EFL1 are the minimal components required to recycle these 60S subunits back into additional rounds of translation by evicting eIF6. Increasing the dose of eIF6 in mice in vivo impairs terminal erythropoiesis by sequestering post-termination 60S subunits in the cytoplasm, disrupting subunit joining and attenuating global protein synthesis. Our data reveal that ribosome maturation and recycling are dynamically coupled by a mechanism that is disrupted in an inherited leukaemia predisposition disorder.

cell biology↗

bioRxiv2021

Yersinia pseudotuberculosis YopE prevents uptake by M cells and instigates M cell extrusion in human ileal enteroid-derived monolayers.

Many pathogens use M cells to access the underlying Peyers patches and spread to systemic sites via the lymph as demonstrated by ligated loop murine intestinal models. However, the study of interactions between M cells and microbial pathogens has stalled due to the lack of cell culture systems. To overcome this obstacle, we use human ileal enteroid-derived monolayers containing five intestinal cell types including M cells to study the interactions between the enteric pathogen, Yersinia pseudotuberculosis (Yptb) and M cells. The Yptb type three secretion system (T3SS) effector Yops inhibit host defenses including phagocytosis and are critical for colonization of the intestine and Peyers patches. Therefore, it is not understood how Yptb traverses through M cells to breach the epithelium. By growing Yptb under two physiological conditions that mimic the early infectious stage (low T3SS-expression) or host-adapted stage (high T3SS-expression), we found that large numbers of Yptb specifically associated with M cells, recapitulating murine studies. Transcytosis through M cells was significantly higher by Yptb expressing low levels of T3SS, because YopE and YopH prevented Yptb uptake. YopE also caused M cells to extrude from the epithelium without inducing cell-death or disrupting monolayer integrity. Sequential infection with early infectious stage Yptb reduced host-adapted Yptb association with M cells. These data underscore the strength of enteroids as a model by discovering that Yops impede M cell function, indicating that early infectious stage Yptb more effectively penetrates M cells while the host may defend against M cell penetration of host-adapted Yptb.

microbiology↗

bioRxiv2021

Development of Functional Connectome Gradients during Childhood and Adolescence

Connectome mapping studies have documented a principal primary-to-transmodal gradient in the adult brain network, capturing a functional spectrum which ranges from perception and action to abstract cognition. However, how this gradient pattern develops and whether its development is linked to cognitive growth, topological reorganization, and gene expression profiles remain largely unknown. Using longitudinal resting-state functional magnetic resonance imaging data from 305 children (ages 6-14), we describe substantial changes in the primary-to-transmodal gradient between childhood and adolescence, including emergence as the principal gradient, expansion of global topography, and focal tuning in primary and default-mode regions. These gradient changes are mediated by developmental changes in network integration and segregation, and are associated with abstract processing functions such as working memory and expression levels of calcium ion regulated exocytosis, synaptic transmission, and axon and synapse part related genes. Our findings have implications for understanding connectome maturation principles in normal development and developmental disorders. TeaserOur study reported the maturation of the core connectome gradient and its association with cognitions and genes expression.

neuroscience↗

bioRxiv2021

Oxidative phosphorylation safeguards pluripotency via UDP-N-acetylglucosamine

The roles of mitochondrial respiration in pluripotency remain largely unknown. We show here that mouse ESC mitochondria possess superior respiration capacity compared to somatic cell mitochondria, and oxidative phosphorylation (OXPHOS) generates the majority of cellular ATP in ESCs. Inhibition of OXPHOS results in extensive pluripotency and metabolic gene expression reprogram, leading to disruption of self-renewal and pluripotency. Metabolomics profiling identifies UDP-N-acetylglucosamine (UDP-GlcNAc) as one of the most significantly decreased metabolites in response to OXPHOS inhibition. The loss of ESC identity induced by OXPHOS inhibition can be ameliorated by directly adding GlcNAc both in vitro and in vivo. This work demonstrates that mitochondrial respiration, but not glycolysis, produces the majority of ATP in ESCs, and uncovers a novel mechanism whereby mitochondrial respiration is coupled with the hexosamine biosynthesis pathway to generate UDP-GlcNAc for ESC identity maintenance. SIGNIFICANCEOxidative phosphorylation (OXPHOS) and glycolysis are the two major pathways for generating ATP in mammalian cells. It is widely assumed that somatic cells utilize OXPHOS, whereas embryonic stem cells (ESCs) utilize glycolysis with low mitochondrial respiration rates even under aerobic conditions. However, the relative contribution of OXPHOS and glycolysis to ATP generation in ESCs, and the role of mitochondrial respiration in regulating ESC identity, have remained unclear. In this study, Cao et al demonstrate that mouse ESC mitochondria have a significantly higher respiration capacity than somatic cell mitochondria. Oxidative phosphorylation produces the majority of cellular ATP in mESCs and is coupled with the hexosamine biosynthesis pathway to generate UDP-GlcNAc for pluripotency maintenance. These findings define the function and mechanism of OXPHOS in regulating pluripotency, and challenge the traditional concept that mESCs rely on glycolysis over OXPHOS for their major supply of energy. HIGHLIGHTSO_LIESC mitochondria have a significantly higher respiration capability than somatic cell mitochondria C_LIO_LIOXPHOS, but not glycolysis, produces the majority of cellular ATP in ESCs C_LIO_LIOXPHOS inhibition induces a decrease in O-GlcNAcylation and the expression of pluripotency genes in blastocysts that can be partially rescued by adding GlcNAc C_LIO_LIOXPHOS is coupled with the hexosamine biosynthesis pathway for UDP-GlcNAc biosynthesis to maintain ESC identity C_LI

cell biology↗

bioRxiv2021

FishExp: a comprehensive database and analysis platform for gene expression and alternative splicing of fish species

The publicly archived RNA-seq data has grown exponentially, but its valuable information has not yet been fully discovered and utilized, especially for alternative splicing. This is true for fish species, which play important roles in ecology, research, and the food industry. To mitigate this, we present FishExp, a web-based data platform covering gene expression and alternative splicing in 26,081 RNA-seq experiments from 44 fishes. In addition to searching by gene identifiers and symbols, FishExp allows users to query the data using various functional terms and BLAST alignment. Notably, the user can customize experiments and tools to perform differential/specific expression and alternative splicing analysis, provided with functional enrichments. The results of retrieval and analysis can be visualized on the gene-, transcript- and splicing event-level webpage in a highly interactive and intuitive manner. The manually curated sample information, uniform data processing and visualization tools make it efficient for users to gain new insights from these large datasets. All data in FishExp can be downloaded for more in-depth analysis. FishExp is freely accessible at https://bioinfo.njau.edu.cn/fishExp.

bioinformatics↗

bioRxiv2021

Land-surface evapotranspiration derived from a first-principles primary production model

We propose an application of eco-evolutionary optimality theory in the context of monitoring and modelling physical land-surface processes. Evapotranspiration (ET) links the water and carbon cycles in the atmosphere, hydrosphere, and biosphere. We develop an ET modelling framework based on the hypothesis that canopy conductance acclimates to plant growth conditions so that the total costs of maintaining carboxylation and transpiration capacities are minimized. This is combined with the principle of co-ordination between the light- and Rubisco-limited rates of photosynthesis to predict gross primary production (GPP). Transpiration (T) is predicted from GPP via canopy conductance. No plant type- or biome-specific parameters are required. ET is estimated from T by calibrating a site-specific (but time-invariant) ratio of modelled average T to observed average ET. Predicted seasonal cycles of GPP were well supported by (weekly) GPP data at 20 widely distributed eddy-covariance flux sites (228 site-years), with correlation coefficients (r) = 0.81 and root-mean-square error (RMSE) = 18.7 gC/week and Nash-Sutcliffe efficiency coefficient (NSE) = 0.61. Seasonal cycles of ET were also well supported, with r = 0.85, RMSE = 5.5 mm week-1 and NSE = 0.66. Estimated T/ET ratios (0.52-0.92) showed significant positive relationships to radiation, precipitation and green vegetation cover and negative relationships to temperature and modelled T (r = 0.84). Although there are still uncertainties to be improved in the current framework, particularly in estimating T/ET, we see the application of eco-evolutionary principles as a promising direction for water resources research. HighlightsO_LIBuilding an evapotranspiration estimation framework based on a priori primary productivity model (the P model). C_LIO_LIAssessing the contribution of environmental indicators to the ratio of transpiration to evapotranspiration. C_LIO_LIProving the reliability of this approach to estimate evapotranspiration. C_LI

ecology↗

bioRxiv2021

Development of Large-Scale Brain Network Dynamics in Children

Functional brain networks require dynamic reconfiguration to support flexible cognitive function. However, the developmental principles shaping brain network dynamics remain poorly understood. Here, we report the longitudinal development of large-scale brain network dynamics during childhood and adolescence, and its connection with gene expression profiles. Using a multilayer network model, we show the temporally varying modular architecture of child brain networks, with higher network switching primarily in the association cortex and lower switching in the primary regions. This topographical profile exhibits progressive maturation, which manifests as reduced modular dynamics, particularly in the transmodal (e.g., default-mode and frontoparietal) and sensorimotor regions. These developmental refinements mediate age-related enhancements of global network segregation and are linked with the expression profiles of genes associated with the enrichment of ion transport and nucleobase-containing compound transport. These results highlight a progressive stabilization of brain dynamics, which expand our understanding of the neural mechanisms that underlie cognitive development.

neuroscience↗

bioRxiv2021

The PELOTA-HBS1 Complex Orchestrates mRNA Translation Surveillance and PDK1-mediated Plant Growth and Development

The quality control system for messenger RNA is fundamental for cellular activities in eukaryotes. To elucidate the molecular mechanism of 3-Phosphoinositide-Dependent Protein Kinase1 (PDK1), an essential regulator throughout growth and development of eukaryotes, a forward genetic approach was employed to screen for suppressors of the loss-of-function T-DNA insertional pdk1.1 pdk1.2 double mutant in Arabidopsis. Notably, the severe growth attenuation of pdk1.1 pdk1.2 is rescued by sop21 (suppressor of pdk1.1 pdk1.2) that harbours a loss-of-function mutation in PELOTA1 (PEL1). PEL1 is a homologue of mammalian PELOTA and yeast DOM34, which form a heterodimeric complex with the GTPase HBS1, responsible for ribosome rescue to assure the quality and fidelity of mRNA molecules. Genetic analysis further reveals that the dysfunction of PEL1-HBS complex fails to degrade the T-DNA-disrupted, truncated but functional PDK1 transcripts, thus rescuing pdk1.1 pdk1.2. Our studies demonstrate the functionality and identify the essential functions of a homologous PELOTA-HBS1 complex in higher plant, and provide novel insights into the mRNA quality control mechanism.

plant biology↗

bioRxiv2021

Efficient prediction of microplastic counts from mass measurements

Microplastics must be characterized and quantified to assess their impact. Current quantification procedures are time-consuming and prone to human error. This study evaluates the use of machine learning to estimate the number of microplastic particles based on aggregate particle weight measurements. Synthetic datasets are used to test the performance of linear regression, kernel ridge regression and decision trees. Kernel ridge regression achieves the strongest performance, and it is also tested with experimental datasets. The numerical results show that the algorithm is better at predicting the counts of larger and more homogeneous samples, and that contamination by organics does not significantly increase error. In mixed samples, prediction error is lower for heavier particles, with an error rate comparable to or better than that of manual counting. Overall, the proposed method is faster and easier than current approaches.

ecology↗

bioRxiv2020

mTOR S-nitrosylation inhibits autophagy and lysosomal proteolysis

Mammalian Target of Rapamycin (mTOR) is a master regulator of autophagy and lysosomes, and its downstream kinase-dependent pathways have been extensively characterized. Here, we report an unexpected kinase-independent regulation of autophagy and lysosomes by S-nitrosylation at Cys423 position of mTOR that resulted in suppression of VPS34 and PIKfyve-dependent phosphoinositide synthesis. Physiologically, S-nitrosylation of mTOR reduced basal lysosomal proteolysis via nitric oxide synthase (NOS)-mediated synthesis of NO from lysosomal arginine precursor, a marker of cellular nutrition status. Significantly, we found increased lysosomal NOS-mTOR complexes in APP-PS1 Alzheimers disease (AD) murine model, and increased mTOR S-nitrosylation in AD patient-derived fibroblasts. Lastly, we demonstrated that pharmacological inhibition of NOS or overexpression of mTORCys423Ala mutant reversed lysosomal and autophagic dysfunction in AD patient-derived fibroblasts, suggesting novel therapeutic strategies for autophagosome-lysosomal activation.

cell biology↗

bioRxiv2020

SARS-CoV-2 Quasispecies provides insight into its genetic dynamics during infection

A novel coronavirus disease (COVID-19) caused by SARS-CoV-2 has been pandemic worldwide. The genetic dynamics of quasispecies afford RNA viruses a great fitness on cell tropism and host range. However, no quasispecies data of SARS-CoV-2 have been reported yet. To explore quasispecies haplotypes and its transmission characteristics, we carried out single-molecule real-time (SMRT) sequencing of the full-length of SARS-CoV-2 spike gene within 14 RNA samples from 2 infection clusters, covering first-to third-generation infected-patients. We observed a special quasispecies structure of SARS-CoV-2 (modeled as One-King): one dominant haplotype (mean abundance ~70.15%) followed by numerous minor haplotypes (mean abundance < 0.10%). We not only discovered a novel dominant haplotype of F1040 but also realized that minor quasispecies were also worthy of attention. Notably, some minor haplotypes (like F1040 and currently pandemic one G614) could potentially reveal adaptive and converse into the dominant one. However, minor haplotypes exhibited a high transmission bottleneck (~6% could be stably transmitted), and the new adaptive/dominant haplotypes were likely originated from genetic variations within a host rather than transmission. The evolutionary rate was estimated as 2.68-3.86 x 10-3 per site per year, which was larger than the estimation at consensus genome level. The One-King model and conversion event expanded our understanding of the genetic dynamics of SARS-CoV-2, and explained the incomprehensible phenomenon at the consensus genome level, such as limited cumulative mutations and low evolutionary rate. Moreover, our findings suggested the epidemic strains may be multi-host origin and future traceability would face huge difficulties.

pathology↗

bioRxiv2020

Molluscan dorsal-ventral patterning relying on BMP2/4 and Chordin provides insights into spiralian development and bilaterian body plan evolution

Although a conserved mechanism relying on bmp2/4 and chordin is suggested in animal dorsal-ventral (DV) patterning, this mechanism has not been reported in spiralians, one of the three major clades of bilaterians. Studies on limited spiralian representatives have suggested markedly diverse DV patterning mechanisms, a considerable amount of which no longer deploy BMP signaling. Here, we showed that bmp2/4 and chordin regulated DV patterning in the mollusk Lottia goshimai, which was predicted in spiralians but not reported before. In the context of the diverse reports in spiralians, it conversely represents a relatively unusual case. We then showed that bmp2/4 and chordin coordinated to mediate signaling from the D-quadrant organizer to induce the DV axis, among which chordin transferred breakdown-of-symmetry information. Further investigations on the L. goshimai embryos with influenced DV patterning suggested roles of BMP signaling in regulating the localization of the blastopore and the organization of the nervous system, indicating a cooption of DV patterning and the transition of these key characteristics at the origin of bilaterians. These findings provide insights into the evolution of animal DV patterning, the unique development mode of spiralians driven by the D-quadrant organizer, and the evolution of bilaterian body plans.

developmental biology↗