Biology subjects

Zhu, S.

Publications and source records attributed to Zhu, S..

At least 199 records · Page 11Linked to original sources

bioRxiv2020

A minimally disruptive method for measuring water potential in-planta using hydrogel nanoreporters

Leaf water potential is a critical indicator of plant water status, integrating soil moisture status, plant physiology, and environmental conditions. There are few tools for measuring plant water status (water potential) in situ, presenting a critical barrier for the development of appropriate phenotyping (measurement) methods for crop development and modeling efforts aimed at understanding water transport in plants. Here, we present the development of an in situ, minimally-disruptive hydrogel nanoreporter (AquaDust) for measuring leaf water potential. The gel matrix responds to changes in water potential in its local environment by swelling; the distance between covalently linked dyes changes with the reconfiguration of the polymer, leading to changes in the emission spectrum via Fluorescence Resonance Energy Transfer (FRET). Upon infiltration into leaves, the nanoparticles localize within the apoplastic space in the mesophyll; they do not enter the cytoplast or the xylem. We characterize the physical basis for AquaDusts response and demonstrate its function in intact maize (Zea mays L.) leaves as a reporter of leaf water potential. We use AquaDust to measure gradients of water potential along intact, actively transpiring leaves as a function of water status; the localized nature of the reporters allows us to define a hydraulic model that distinguishes resistances inside and outside the xylem. We also present field measurements with AquaDust through a full diurnal cycle to confirm the robustness of the technique and of our model. We conclude that AquaDust offers potential opportunities for high-throughput, field measurements and spatially resolved studies of water relations within plant tissues.

plant biology↗

bioRxiv2020

Wnt3 distribution in the zebrafish brain is determined by expression, diffusion and multiple molecular interactions

Wnt3 proteins are lipidated and glycosylated, secreted signaling molecules that play an important role in zebrafish neural patterning and brain development. However, the transport mechanism of lipid-modified Wnts through the hydrophilic extracellular environment for long-range action remains unresolved. Here, we determine how Wnt3 accomplishes long-range distribution in the zebrafish brain. First, we characterize the Wnt3-producing source and Wnt3-receiving target regions. Subsequently, we analyze Wnt3 mobility at different length scales by fluorescence correlation spectroscopy and fluorescence recovery after photo-bleaching. We demonstrate that Wnt3 spreads extracellularly and interacts with heparan sulfate proteoglycans (HSPG). We then determine the binding affinity of Wnt3 to its receptor, Frizzled1 (Fzd1), using fluorescence cross-correlation spectroscopy, and show that the co-receptor, low-density lipoprotein receptor-related protein 5 (Lrp5), is required for Wnt3-Fzd1 interaction. Our results are consistent with the extracellular distribution of Wnt3 by a diffusive mechanism that is modified by tissue morphology, interactions with HSPG and Lrp5-mediated receptor binding, to regulate zebrafish brain development.

developmental biology↗

bioRxiv2020

Endophilin A1 promotes Actin Polymerization in response to Ca2+/calmodulin to Initiate Structural Plasticity of Dendritic Spines

Dendritic spines of excitatory neurons undergo activity-dependent structural and functional plasticity, which are cellular correlates of learning and memory. However, mechanisms underlying the rapid morphological changes immediately after NMDAR-mediated Ca2+ influx into spines remain poorly understood. Here we report that endophilin A1, a neuronal N-BAR protein, orchestrates membrane dynamics with actin polymerization to initiate spine enlargement in the induction phase of long-term potentiation (LTP). Upon LTP induction, Ca2+/calmodulin enhances its binding to both membrane and p140Cap, a cytoskeleton regulator. As a result, endophilin A1 rapidly associates with the relaxed plasma membrane and promotes actin polymerization, leading to acute expansion of spine head. Moreover, not only the p140Cap-binding, but also calmodulin- and membrane-binding capacities of endophilin A1 are required for LTP and long-term memory. Thus, endophilin A1 functions as calmodulin effector to drive spine enlargement in response to Ca2+ influx in the initial phase of structural plasticity.

cell biology↗

bioRxiv2020

The flagellar motor of Vibrio alginolyticus undergoes major structural remodeling during rotational switching

The bacterial flagellar motor is an intricate nanomachine that switches rotational directions between counterclockwise (CCW) and clockwise (CW) to direct the migration of the cell. The cytoplasmic ring (C-ring) of the motor, which is composed of FliG, FliM, and FliN, is known for controlling the rotational sense of the flagellum. However, the mechanism underlying rotational switching remains elusive. Here, we deployed cryo-electron tomography to visualize the C-ring in two rotational biased mutants (CCW-biased fliG-G214S and CW-locked fliG-G215A) in Vibrio alginolyticus. Sub-tomogram averaging was utilized to resolve two distinct conformations of the C-ring. Comparison of the C-ring structures in two rotational senses provide direct evidence that the C-ring undergoes major structural remodeling during rotational switch. Specifically, FliG conformational changes elicit a large rearrangement of the C-ring that coincides with rotational switching, whereas FliM and FliN form a spiral-shaped base of the C-ring, likely stabilizing the C-ring during the conformational remodeling.

microbiology↗

bioRxiv2020

Effect of storage conditions on peripheral leukocytes transcriptome

IntroductionPeripheral blood leukocytes are essential components of the innate and adaptive immune responses. Their transcriptome reflects an individuals physiological and pathological state, consequently bulk and single-cell RNA sequencing have been used to assess health and disease. As RNA is dynamic and could be affected by ex vivo conditions before RNA stabilization, we have assessed the influence of temporary storage on the transcriptome. MethodsWe collected peripheral blood from six healthy donors and processed it immediately or stored it either at 4{square} or room temperature (RT, 18-22{square}) for 2h, 6h and 24h. Total cellular RNA was extracted from leukocytes after red blood cells lysis and the transcriptome analyzed using RNA sequencing. ResultsWe identified 152 up-regulated and 12 down-regulated coding genes in samples stored at 4{square} for 24h with most of the up-regulated genes related to nucleosome assembly. More coding genes changed expression at RT, with 1218 increased and 1480 decreased. The increased genes were particularly related to mRNA processing and apoptosis, while the decreased genes were associated with neutrophil activation and cytokine production, implying a reduced proportion of neutrophils, which was confirmed by leukocyte subsets analysis. Most house-keeping genes changed expression during storage, but genes such as TUBB and C1orf43 were relatively stable and could serve as reference genes. ConclusionTemporary storage conditions profoundly affect leukocyte gene expression profiles and change leukocyte subset proportions. Blood samples stored at 4{square} for 6h largely maintain their original transcriptome.

molecular biology↗

bioRxiv2020

Single-cell atlas of a non-human primate reveals new pathogenic mechanisms of COVID-19

Stopping COVID-19 is a priority worldwide. Understanding which cell types are targeted by SARS-CoV-2 virus, whether interspecies differences exist, and how variations in cell state influence viral entry is fundamental for accelerating therapeutic and preventative approaches. In this endeavor, we profiled the transcriptome of nine tissues from a Macaca fascicularis monkey at single-cell resolution. The distribution of SARS-CoV-2 facilitators, ACE2 and TMRPSS2, in different cell subtypes showed substantial heterogeneity across lung, kidney, and liver. Through co-expression analysis, we identified immunomodulatory proteins such as IDO2 and ANPEP as potential SARS-CoV-2 targets responsible for immune cell exhaustion. Furthermore, single-cell chromatin accessibility analysis of the kidney unveiled a plausible link between IL6-mediated innate immune responses aiming to protect tissue and enhanced ACE2 expression that could promote viral entry. Our work constitutes a unique resource for understanding the physiology and pathophysiology of two phylogenetically close species, which might guide in the development of therapeutic approaches in humans. Bullet pointsO_LIWe generated a single-cell transcriptome atlas of 9 monkey tissues to study COVID-19. C_LIO_LIACE2+TMPRSS2+ epithelial cells of lung, kidney and liver are targets for SARS-CoV-2. C_LIO_LIACE2 correlation analysis shows IDO2 and ANPEP as potential therapeutic opportunities. C_LIO_LIWe unveil a link between IL6, STAT transcription factors and boosted SARS-CoV-2 entry. C_LI

cell biology↗

bioRxiv2020

Insulin/IGF signaling and TOR promote vitellogenesis via inducing juvenile hormone biosynthesis

Vitellogenesis, including vitellogenin (Vg) production in the fat body and Vg uptake by maturing oocytes, is of great importance for the successful reproduction of adult females. The endocrinal and nutritional regulation of vitellogenesis differs distinctly in insects. Here, the complex crosstalk between juvenile hormone (JH) and the two nutrient sensors, insulin/IGF signaling (IIS) and target of rapamycin (TOR), was investigated to elucidate the molecular mechanisms regulating vitellogenesis in the American cockroach, Periplaneta americana. Our data showed that a block of JH biosynthesis or JH action arrested vitellogenesis, partially by inhibiting the expression of doublesex (Dsx), a key transcription factor gene involved in the sex determination cascade. Depletion of IIS and TOR blocked both JH biosynthesis and vitellogenesis. Importantly, the JH analog methoprene, but not bovine insulin (to restore IIS) and amino acids (to restore TOR activity), restored vitellogenesis in the neck-ligated (both nutrient- and JH-deficient) cockroaches. Combining classic physiology with modern molecular techniques, we have demonstrated that JH signaling alone is able to induce vitellogenesis and thus ovarian maturation. By contrast, IIS and TOR do not induce vitellogenesis independent of JH, the nutrient sensors promote vitellogenesis in an indirect manner via activating JH biosynthesis.

developmental biology↗

bioRxiv2020

Multiple approaches for massively parallel sequencing of HCoV-19 genomes directly from clinical samples

COVID-19 has caused a major epidemic worldwide, however, much is yet to be known about the epidemiology and evolution of the virus. One reason is that the challenges underneath sequencing HCoV-19 directly from clinical samples have not been completely tackled. Here we illustrate the application of amplicon and hybrid capture (capture)-based sequencing, as well as ultra-high-throughput metatranscriptomic (meta) sequencing in retrieving complete genomes, inter-individual and intra-individual variations of HCoV-19 from clinical samples covering a range of sample types and viral load. We also examine and compare the bias, sensitivity, accuracy, and other characteristics of these approaches in a comprehensive manner. This is, to date, the first work systematically implements amplicon and capture approaches in sequencing HCoV-19, as well as the first comparative study across methods. Our work offers practical solutions for genome sequencing and analyses of HCoV-19 and other emerging viruses.

genomics↗

bioRxiv2020

Macrophage scavenger receptor 1 controls Chikungunya virus infection through autophagy

Macrophage scavenger receptor 1 (MSR1) mediates the endocytosis of modified low-density lipoproteins and plays an important antiviral role. However, the molecular mechanism underlying MSR1 antiviral actions remains elusive. Herein, we report that MSR1 activates autophagy to restrict infection of Chikungunya virus (CHIKV), an arthritogenic alphavirus that causes acute and chronic crippling arthralgia. Msr1 expression was rapidly upregulated after CHIKV infection in mice. Msr1 knockout mice had elevated viral loads and increased susceptibility to CHIKV arthritis along with a normal type I IFN response. Induction of LC3 lipidation by CHIKV, a marker of autophagy, was reduced in Msr1-/- cells. Mechanistically, MSR1 interacted with ATG12 through its cytoplasmic tail and this interaction was enhanced by CHIKV nsP1 protein. MSR1 repressed CHIKV replication through ATG5-ATG12-ATG16L1 and this was dependent on the FIP200-and-WIPI2-binding domain, but not the WD40 domain of ATG16L1. Our results elucidate an antiviral role for MSR1 involving the autophagic function of ATG5-ATG12-ATG16L1.

microbiology↗

bioRxiv2020

Integrated profiling of single cell epigenomic and transcriptomic landscape of Parkinson's disease mouse brain

Parkinsons disease (PD) is a neurodegenerative disease leading to the impairment of execution of movement. PD pathogenesis has been largely investigated, but either restricted in bulk level or at certain cell types, which failed to capture cellular heterogeneity and intrinsic interplays among distinct cell types. To overcome this, we applied single-nucleus RNA-seq and single cell ATAC-seq on cerebellum, midbrain and striatum of PD mouse and matched control. With 74,493 cells in total, we comprehensively depicted the dysfunctions under PD pathology covering proteostasis, neuroinflammation, calcium homeostasis and extracellular neurotransmitter homeostasis. Besides, by multi-omics approach, we identified putative biomarkers for early stage of PD, based on the relationships between transcriptomic and epigenetic profiles. We located certain cell types that primarily contribute to PD early pathology, narrowing the gap between genotypes and phenotypes. Taken together, our study provides a valuable resource to dissect the molecular mechanism of PD pathogenesis at single cell level, which could facilitate the development of novel methods regarding diagnosis, monitoring and practical therapies against PD at early stage.

cell biology↗

bioRxiv2020

Intratumor Heterogeneity and Evolution of Colorectal Cancer

Intratumor heterogeneity (ITH) enable us to understand the evolution of cancer. ITH and evolution of colorectal cancer (CRC) has not been well studied. In this prospective study, we recruited different stages of 68 CRC patients with primary tumor at right-sided colon, left-sided colon and rectum. We performed high-depth whole exome sequencing of 206 multi-region tumor samples including primary tumors, lymph node metastasis (LN) and extranodal tumor deposits (ENTD). Our result showed extreme ITH with Darwinian pattern of CRC evolution, evolution pattern of left-sided CRC was more complex and divergent than right-sided CRC and both LN and ENTD were of polyclonal in origin. Extensive ITH was found in driver mutations in KRAS and PIK3CA genes, suggesting major limitations of single biopsies in clinical diagnosis for the CRC patients. In conclusion, our study showed the Darwinian pattern of CRC evolution with differences in evolution pattern between right-sided and left-sided CRC patients.

genetics↗

bioRxiv2020

Chamaeleo: a robust library for DNA storage coding schemes

Chamaeleo is currently the only collection library that focuses on adapting multiple well-established coding schemes for DNA storage. It provides a tool for researchers to study various coding schemes and apply them in practice. Chamaeleo adheres to the concept of high aggregation and low coupling for software design which will enhance the performance efficiency. Here, we describe the working pipeline of Chamaeleo, and demonstrate its advantages over the implementation of existing single coding schemes. The source code is available at https://github.com/ntpz870817/Chamaeleo, it can be also installed by the command of pip.exe, "pip install chamaeleo". Alternatively, the wheel file can be downloaded at https://pypi.org/project/Chamaeleo/. Detailed documentation is available at https://chamaeleo.readthedocs.io/en/latest/. Author SummaryDNA is now considered to be a promising candidate media for future digital information storage in order to tackle the global issue of data explosion. Transcoding between binary digital data and quanternary DNA information is one of the most important steps in the whole process of DNA digital storage. Although several coding schemes have been reported, researchers are still investigating better strategies. Moreover, the scripts of these coding schemes use different programming languages, software architectures and optimization contents. Therefore, we here introduce Chamaeleo, a library in which several classical coding schemes are collected, to reconstruct and optimize them. One of the key features of this tool is that we modulize the functions and make it feasible for more customized way of usage. Meanwhile, developers can also incorporate their new algorithms according to the framework expediently. Based on the benchmark tests we conducted, Chamaeleo shows better flexibility and expandability compared to original packages and we hope that it will help the further study and applications in DNA digital storage.

bioinformatics↗

bioRxiv2020

Single cell atlas of trisomy 21 cerebral cortex

Down syndrome (DS) is one of the most common human birth defects caused by trisomy 21 (T21), leading to a variety of cognitive impairments. The cellular composition of human brain has been explored using single cell RNA sequencing in both physiological and pathological conditions. However, the cellular heterogeneity of human brain with chromosome aneuploidy is largely unknown. Here, we profiled the transcriptome of 36046 cells in cerebral cortex of T21 human fetus, covering frontal lobe, parietal lobe, occipital lobe and temporal lobe. Intriguingly, we detected several genes positively associated with neurons maturation was dysregulated in T21 frontal cortex (HIC2, POU2F2, ZGLP1 and FOXK1). To share, explore and utilized the data resources of T21 cerebral cortex, we developed a comprehensive platform named T21atlas, composing of two functional modules (T21cluster and T21talk). Overall, our study provides, as far as we know, the first single cell atlas for T21 cerebral cortex, which could promote our understanding of the molecular mechanism of DS at an unprecedented resolution and could potentially facilitate the development of novel clinical therapeutics against T21.

neuroscience↗

bioRxiv2019

Single cell atlas of domestic pig brain illuminates the conservation and divergence of cell types at spatial and species levels

Domestic pig (Sus scrofa domesticus) has drawn much attention from researchers worldwide due to its implications in evolutionary biology, regenerative medicine and agriculture. The brain atlas of Homo sapiens (primate), Mus musculus (rodent), Danio rerio (fish) and Drosophila melanogaster (insect) have been constructed at single cell resolution, however, the cellular compositions of pig brain remain largely unexplored. In this study, we investigated the single-cell transcriptomic profiles of five distinct regions of domestic pig brain, from which we identified 21 clusters corresponding to six major cell types, characterized by unique spectrum of gene expression. By spatial comparison, we identified cell types enriched or depleted in certain brain regions. Inter-species comparison revealed cell-type similarities and divergences in hypothalamus between mouse and pig, providing invaluable resources for the evolutionary exploration of brain functions at single cell level. Besides, our study revealed cell types and molecular pathways closely associated with several diseases (obesity, anorexia, bulimia, epilepsy, intellectual disability, and autism spectrum disorder), bridging the gap between gene mutations and pathological phenotypes, which might be of great use to the development precise therapies against neural system disorders. Taken together, we reported, so far as we know, the first single cell brain atlas of Sus scrofa domesticus, followed by comprehensive comparisons across brain region and species, which could throw light upon future evo-devo, regenerative medicine, and agricultural studies.

bioinformatics↗

bioRxiv2019

Klf9 is a key feedforward regulator of the transcriptomic response to glucocorticoid receptor activity

The zebrafish has recently emerged as a model system for investigating the developmental roles of glucocorticoid signaling and the mechanisms underlying glucocorticoid-induced developmental programming. To assess the role of the Glucocorticoid Receptor (GR) in such programming, we used CRISPR-Cas9 to produce a new frameshift mutation, GR369-, which eliminates all potential in-frame initiation codons upstream of the DNA binding domain. Using RNA-seq to ask how this mutation affects the larval transcriptome under both normal conditions and with chronic cortisol treatment, we find that GR mediates most of the effects of the treatment, and paradoxically, that the transcriptome of cortisol-treated larvae is more like that of larvae lacking a GR than that of larvae with a GR, suggesting that the cortisol-treated larvae develop GR resistance. The one transcriptional regulator that was both underexpressed in GR369- larvae and consistently overexpressed in cortisol-treated larvae was klf9. We therefore used CRISPR-Cas9-mediated mutation of klf9 and RNA-seq to assess Klf9-dependent gene expression in both normal and cortisol-treated larvae. Our results indicate that Klf9 contributes significantly to the transcriptomic response to chronic cortisol exposure, mediating the upregulation of proinflammatory genes that we reported previously.

developmental biology↗

bioRxiv2019

Behavioral signatures of a developing neural code

During early life neural codes must develop to appropriately transform sensory inputs into behavioral outputs. Here we demonstrate a direct link between the maturity of neural coding in the visual brain and developmental changes in visually-guided behavior. In zebrafish larvae we show that visually-driven hunting behavior improves from 4 to 15 days post-fertilization, becoming faster and more accurate. During the same period population activity in the optic tectum refines, leading to improved decoding and information transmission of spatial position, particularly in the representation of the frontal visual field. Remarkably, individual differences in decoding can predict each fishs hunting success. Together these results show how the neural codes required to subserve a natural behavior emerge during development.

neuroscience↗

bioRxiv2019

Chronic cortisol exposure in early development leads to neuroendocrine dysregulation in adulthood

ObjectiveChronic early life stress can affect development of the neuroendocrine stress system, leading to its persistent dysregulation and consequently increased disease risk in adulthood. One contributing factor is thought to be epigenetic programming in response to chronic cortisol exposure during early development. We have previously shown that zebrafish embryos treated chronically with cortisol develop into adults with constitutively elevated whole body cortisol and aberrant immune gene expression. The objective of the experiments reported here was to further characterize the phenotype of those adults. ResultsWe find that adult zebrafish derived from cortisol-treated embryos have aberrant cortisol levels, tissue distribution, and dynamics, which correlate with differential activity of key glucocorticoid-responsive regulatory genes klf9 and fkbp5 in blood and brain.

developmental biology↗

bioRxiv2019

Development and validation of a deep learning framework for Alzheimers disease classification

Alzheimers disease (AD) is the primary cause of dementia worldwide (1), with an increasing morbidity burden that may outstrip diagnosis and management capacity as the population ages. Current methods integrate patient history, neuropsychological testing and magnetic resonance imaging (MRI) to identify likely cases, yet effective practices remain variably-applied and lacking in sensitivity and specificity (2). Here we report an explainable deep learning strategy that delineates unique AD signatures from multimodal inputs of MRI, age, gender, and mini-mental state examination (MMSE) score. Our framework linked a fully convolutional network (FCN) to a multilayer perceptron (MLP) to construct high resolution maps of disease probability from local brain structure. This enabled precise, intuitive visualization of individual AD risk en route to accurate diagnosis. The model was trained using clinically-diagnosed AD and cognitively normal (NC) subjects from the Alzheimers Disease Neuroimaging Initiative (ADNI) dataset (n=417) (3), and validated on three independent cohorts: the Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing (AIBL, n=382) (4), the Framingham Heart Study (FHS, n=102) (5), and the National Alzheimers Coordinating Center (NACC, n=582) (6). Model performance was consistent across datasets, with mean accuracy values of 0.966, 0.948, 0.815, and 0.916 for ADNI, AIBL, FHS and NACC, respectively. Moreover, our approach exceeded the diagnostic performance of a multi-institutional team of practicing neurologists (n=11), and high-risk cerebral regions predicted by the model closely tracked postmortem histopathological findings. This framework provides a clinically-adaptable strategy for using routinely available imaging techniques such as MRI to generate nuanced neuroimaging signatures for AD diagnosis, as well as a generalizable approach for linking deep learning to pathophysiological processes in human disease.

neuroscience↗