Biology subjects

Wu, J.

Publications and source records attributed to Wu, J..

At least 541 records · Page 30Linked to original sources

bioRxiv2022

Chromosome-level genome assembly of Torreya grandis provides insights into the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis

Species in genus Torreya are nut trees that produce dry fruits with a wide assortment of functions. Here, we report the 19-Gb chromosome-level genome assembly of T. grandis. The genome is shaped by an ancient whole genome duplication and recurrent LTR retrotransposon bursts. Comparative genomic analyses reveal key genes involved in reproductive organ development, cell wall biosynthesis and seed storage. Two genes encoding a C18 {Delta}9-elongase and a C20 {Delta}5-desaturase are identified in T. grandis to be responsible for sciadonic acid biosynthesis and both are present in diverse plant lineages except angiosperms. We demonstrate that the histidine-rich boxes of the {Delta}5-desaturase are crucial for its catalytic activity. Methylome analysis reveals that methylation valleys of the T. grandis seed genome harbor genes associated with important seed activities, including cell wall and lipid biosynthesis. Moreover, seed development is accompanied by DNA methylation changes that possibly fuel energy production. This study provides important genomic resource for gymnosperms and unravels key enzymes for biosynthesis of sciadonic acid as a hallmark metabolite of gymnosperms.

plant biology↗

bioRxiv2022

Capturing differences in the regulation of LRRK2 dynamics and conformational states by small molecule kinase inhibitors

Mutations in the human leucine rich repeat protein kinase-2 (LRRK2) create risk factors for Parkinsons Disease, and pathological functions of LRRK2 are often correlated with aberrant kinase activity. Past research has focused on developing selective LRRK2 kinase inhibitors. We showed previously that in addition to influencing intrinsic kinase activity, the global conformation of the LRRK2 protein plays a vital role in regulating LRRK2 signaling pathways. Deciphering the allosteric regulation in LRRK2 provides novel strategies for drug discovery. In this study, we combined enhanced sampling simulations with HDX-MS to analyze the inhibitor-induced dynamic changes and the allosteric communications in the C-terminal half of LRRK2, LRRK2RCKW. We find that a type I inhibitor (MLi-2) locks the kinase into a closed, active-like configuration, whereas a type II inhibitor (Rebastinib) shifts the kinase to an open, inactive configuration. While both type I and type II inhibitors reduce the kinase activity effectively, they have distinct effects on the LRRK2 conformational dynamics. Specifically, binding of MLi-2 stabilizes the kinase domain in a closed conformation and reduces the global dynamics of LRRK2RCKW, leading to a more compact LRRK2RCKW structure. In contrast, binding of Rebastinib stabilizes an open conformation where communication between the N- and C-lobe is severed, which promotes a more extended LRRK2RCKW structure. Rebastinib, based on HDX-MS, creates a more dynamic kinase domain especially at domain interfaces associated with the C-lobe. Our results also reveal the importance of the Dk-helix, which plays a crucial role in propagating communication between the kinase domain and the GTPase domain.

biochemistry↗

bioRxiv2022

Multi-omics of Circular RNAs and Their Responses to Hormones in Moso Bamboo (Phyllostachys edulis)

Circular RNAs are endogenous non-coding RNAs with covalently closed structures, which have important functions in plants. However, their biogenesis, degradation, and function upon treatment with gibberellins (GA) and auxins (NAA) remain unknown. Here, we systematically identified and characterized expression patterns, evolutionary conservation, genomic features, and internal structures of circRNAs using RNase R-treated libraries from moso bamboo (Phyllostachys edulis) seedlings. Moreover, we investigated the biogenesis of circRNAs dependent on both cis- and trans-regulation. We determined details regarding the function of circRNAs, including their roles in regulating microRNA-related genes and modulating the alternative splicing of their linear counterparts. Importantly, we developed a customized degradome sequencing approach to detect microRNA-mediated cleavage of circRNAs. Finally, we present a comprehensive view of the participation of circRNAs in the regulation of hormone metabolism upon treatment of bamboo seedlings with gibberellins (GA) and auxins (NAA). Collectively, our study uncovers important features of circRNAs including overall characteristics, biogenesis, function, and microRNA-mediated degradation of circRNAs in moso bamboo.

plant biology↗

bioRxiv2022

Development of an affinity-enhanced clinical candidate TCR targeting NY-ESO-1 with optimal potency and high specificity

The clinical success of T-cell receptor (TCR)-based immunotherapy depends on the efficacy and specificity of TCRs. Naturally occurring TCRs have limited anti-tumor potency due to their low affinity for tumor antigens. Affinity enhancement is a promising strategy to generate highly potent TCRs. However, it is concerned that affinity-enhanced TCRs are prone to lose specificity. We isolated low affinity TCRs specific for NY-ESO-1157-165/HLA-A*02:01 from peripheral blood mononuclear cells of healthy donors. An affinity-enhanced TCR candidate with optimal affinity and specificity was generated using phage display and an extensive set of in vitro and in vivo assays. Alanine scanning mutagenesis showed that the TCR candidate retained specificity by making extensive contacts to the side chains of NY-ESO-1157-165 peptide. Adoptive transfer of T cells engineered with this candidate (termed TAEST16001) significantly inhibited tumor growth in subcutaneous, metastatic, and patient-derived xenograft (PDX) mouse tumor models. This study demonstrates that sophisticated engineering and screening techniques can be utilized to generate a clinical candidate TCR with potent anti-tumor activity without losing specificity. TAEST16001 was approved by the Center for Drug Evaluation (CDE) as the first TCR-based immunotherapy clinical trial in China (ClinicalTrials.gov Identifier: NCT03159585).

immunology↗

bioRxiv2022

MAP4Ks inhibition promotes retinal neuron regeneration from Muumlller glia in adult mice

Mammalian Muller glia (MG) possess limited regenerative capacities. However, the intrinsic capacity of mammalian MG to transdifferentiate to generate mature neurons without transgenic manipulations remains speculative. Here we show that MAP4K4, MAP4K6 and MAP4K7, which are conserved Misshapen subfamily of ste20 kinases homologs, repress YAP activity in mammalian MG and therefore restrict their ability to be reprogrammed. However, by treating with a small molecule inhibitor of MAP4K4/6/7, mouse MG regain their ability to proliferate and enter into a retinal progenitor cell (RPC)-like state after NMDA-induced retinal damage; such plasticity was lost in YAP knockout MG. Moreover, spontaneous trans-differentiation of MG into retinal neurons expressing both amacrine and retinal ganglion cell (RGC) markers occurs after inhibitor withdrawal. Taken together, these findings suggest that MAP4Ks block the reprogramming capacity of MG in a YAP-dependent manner in adult mammals, which provides a novel avenue for the pharmaceutical induction of retinal regeneration in vivo.

neuroscience↗

bioRxiv2022

Gaq-PKD/PKCμ regulates the IkB transcription to limit the NF-kB mediated inflammatory response essential for early pregnancy

Decidualization, denoting the transformation of endometrial stromal cells into specialized decidual cells, is a prerequisite for normal embryo implantation and a successful pregnancy in human. Here we demonstrated that knockout of Gaq lead to an aberrantly enhanced inflammatory state during decidualization. Furthermore, we showed that deficiency of Gaq resulted in over-activation of nuclear factor (NF)-{kappa}B signaling, due to the decreased expression of NF{kappa}BIA, which encode the I{kappa}B protein and is the negative regulator for NF{kappa}B. Mechanistically, Gaq deficiency decreased the PKD/PKC phosphorylation levels, so leading to attenuated HDAC5 phosphorylation and thus its nuclear export. Aberrantly high level of nuclear HADC5 retarded histone acetylation to inhibit NF{kappa}BIA transcription during decidualization. Consistently, pharmacological activation of the PKD/PKC or inhibition of the HDAC5 signaling restored the inflammatory state and proper decidual response. Finally, we disclosed that over-active inflammatory state in Gaq deficient decidua deferred the blastocyst hatching and adhesion in vitro, and the decidual expression of Gq was significantly lower in women with recurrent pregnancy loss compared with normal pregnancy. In brief, we showed here that Gq as a key regulator of the inflammatory cytokines expression and decidual homeostasis in response to differentiation cues, which is required for successful implantation and early pregnancy.

cell biology↗

bioRxiv2022

A stem cell zoo uncovers intracellular scaling of developmental tempo across mammals

Differential speeds in biochemical reactions have been proposed to be responsible for the differences in developmental tempo between mice and humans. However, the underlying mechanism controlling the species-specific kinetics remains to be determined. Using in vitro differentiation of pluripotent stem cells, we recapitulated the segmentation clocks of diverse mammalian species varying in body weight and taxa: marmoset, rabbit, cattle and rhinoceros. Together with the mouse and human, the segmentation clock periods of the six species did not scale with the animal body weight, but were rather grouped according to phylogeny. The biochemical kinetics of the core clock gene HES7 displayed clear scaling with the species-specific segmentation clock period. However, the cellular metabolic rates did not show an evident correlation. Instead, genes involving biochemical reactions showed an expression pattern that scales with the segmentation clock period. Altogether, our stem cell zoo uncovered general scaling laws governing species-specific developmental tempo.*

developmental biology↗

bioRxiv2022

DeepCIP: a multimodal deep learning method for the prediction of internal ribosome entry sites of circRNAs

MotivationCircular RNAs (circRNAs) have been found to have the potential to code proteins. Internal ribosome entry sites (IRESs) are key RNA regulatory elements for the translation of proteins by circRNAs through a cap-independent mechanism. IRES can be identified by bicistronic assay, but the method is time-consuming and laborious. Therefore, it is important to develop computational methods for facilitating IRES identification, evaluation, and design in circRNAs. ResultsIn this study, we proposed DeepCIP, a multimodal deep learning approach for circRNA IRES prediction, by exploiting both sequence and structure information. As far as we know, DeepCIP is the first predictor for circRNA IRESs, which consists of an RNA processing module, an S-LSTM module, a GCN module, a feature fusion module, and an ensemble module. The comparative studies show that DeepCIP outperforms other comparative methods and justify the effectiveness of the sequence model and structure model of DeepCIP for extracting features. We found that the integration of structural information on the basis of sequence information effectively improves predictive performance. For the real circRNA IRES prediction, DeepCIP also outperforms other methods. DeepCIP may facilitate the study of the coding potential of circRNAs as well as the design of circRNA drugs. DeepCIP as a standalone program is freely available at https://github.org/zjupgx/DeepCIP.

bioinformatics↗

bioRxiv2022

Elephants have an adaptable prehensile grip

Elephants have long been observed to grip objects with their trunk, but little is known about how they adjust their strategy for different weights. In this study, we challenge a female African elephant at Zoo Atlanta to lift 20 to 60 kg barbell weights with only its trunk. We measure the trunks shape and wrinkle geometry from a frozen elephant trunk at the Smithsonian. We observe several strategies employed to accommodate heavier weights, including accelerating less, orienting the trunk more vertically, and wrapping the barbell with a greater trunk length. Mathematical models show that increasing barbell weights are associated with constant trunk tensile force and an increasing barbell-wrapping surface area due to the trunks wrinkles. Our findings may inspire the design of more adaptable soft robotic grippers that can improve grip using surface morphology such as wrinkles.

bioengineering↗

bioRxiv2022

Ribosome-rescuer PELO catalyzes the oligomeric assembly of NLR family proteins via activating their ATPase

NOD-like receptors (NLRs) are pattern recognition receptors for diverse innate immune responses. Self-oligomerization after engagement with a ligand was a generally accepted model for the activation of each NLR. We report here that a catalyzer is required for the self-oligomerization. Protein pelota homolog (PELO, Dom34 in yeast), a well-known surveillance factor in translational quality control/ribosome rescue, interacts with all cytosolic NLRs and activates their ATPase. In the case of flagellin-initiated NLRC4 inflammasome activation, flagellin-bound NAIP5 recruits the first NLRC4 and then PELO is required for correctly assembling the rest of NLRC4s into the NLRC4 complex one by one by activating the NLRC4 ATPase. Stoichiometric and functional data revealed that PELO cannot be a structural constituent of NLRC4 inflammasome but a powerful catalyzer for its assembly. The catalytic role of PELO in the activation of cytosolic NLRs is unexpected and may break new ground for future studies of NLR family members.

immunology↗

bioRxiv2022

A Hybrid Learning Method with High Specificity for Excluding Non-chromosome Objects Problem

BackgroundFor automated analysis of metaphase chromosome images, the chromosome objects on the images need to be segmented in advance. However, the segmentation results often contain a lot of non-chromosome objects in the images. Hence, elimination of non-chromosome objects is an essential process in automated chromosome image analysis. This study aims to exclude non-chromosome objects and preserve as many chromosomes as possible. In this paper, we propose a hybrid deep learning method to exclude non-chromosome objects from metaphase chromosome images. MethodThe proposed method consists of two phases. In the first phase, two classification results are obtained from feature-based and image-based convolutional neural networks (CNN) separately (the feature-based CNN uses the features of the images as input; the image-based CNN uses the images as input directly). In the second phase, the prediction results from the above two CNNs are combined and resent to another CNN to obtain final classification results. ResultsThe proposed method uses 18,757 non-chromosome objects and 43,398 chromosomes (including single and multiple overlapped chromosomes) from 1038 chromosome images to evaluate the performance. The experimental results show that the proposed method can detect and exclude 99.61% (18,683/18,757) of the non-chromosome objects and preserve 99.95% (43,375/43,398) of the chromosomes for further analysis. ConclusionsThe proposed method has a high effectiveness on excluding non-chromosome objects and could be used as a preprocessing procedure for chromosome image analysis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/511091v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1183f1forg.highwire.dtl.DTLVardef@d84d69org.highwire.dtl.DTLVardef@c23122org.highwire.dtl.DTLVardef@127e4e9_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphic AbstractC_FLOATNO C_FIG

bioinformatics↗

bioRxiv2022

Integrative dissection of gene regulatory elements at base resolution

Although vast numbers of putative gene regulatory elements have been cataloged, the sequence motifs and individual bases that underlie their functions remain largely unknown. Here we combine epigenetic perturbations, base editing, and deep learning models to dissect regulatory sequences within the exemplar immune locus encoding CD69. Focusing on a differentially accessible and acetylated upstream enhancer, we find that the complementary strategies converge on a [~]170 base interval as critical for CD69 induction in stimulated Jurkat T cells. We pinpoint individual cytosine to thymine base edits that markedly reduce element accessibility and acetylation, with corresponding reduction of CD69 expression. The most potent base edits may be explained by their effect on binding competition between the transcriptional activator GATA3 and the repressor BHLHE40. Systematic analysis of GATA and bHLH/Ebox motifs suggests that interplay between these factors plays a general role in rapid T cell transcriptional responses. Our study provides a framework for parsing gene regulatory elements in their endogenous chromatin contexts and identifying operative artificial variants. HighlightsO_LIBase editing screens and deep learning pinpoint sequences and single bases affecting immune gene expression C_LIO_LIAn artificial C-to-T variant in a regulatory element suppresses CD69 expression by altering the balance of transcription factor binding C_LIO_LICompetition between GATA3 and BHLHE40 regulates inducible immune genes and T cell states C_LI

molecular biology↗

bioRxiv2022

Transcriptomic remodeling of the retina in a Zebrafish model of Retinitis Pigmentosa

Inherited retinal degenerative diseases such as Retinitis Pigmentosa (RP) result in progressive loss of photoreceptors until an individual is completely blind. A hallmark of these diseases is progressive structural and functional remodeling of the remaining retinal neurons as rod photoreceptors are lost. While many studies focus on regenerative or bionic therapies to restore vision, extensive remodeling of retinal cell types throughout the course of retinal degenerative diseases stands as a barrier for successful implementation of these strategies. As a window onto the molecular basis of remodeling, we have performed a comparative analysis of single-cell transcriptome data from adult Zebrafish retina of wild-type and a P23H mutant rhodopsin model of RP. In addition to providing a benchmark atlas of retinal cell type transcriptomes in the wild-type adult Zebrafish retina, we find transcriptional changes in essentially all retinal cell types in the P23H model. Increased oxidative stress is evident not only in the rods but also in cones, retinal pigmented epithelium (RPE) and to a lesser extent in amacrine and bipolar cells. Metabolic changes increasing oxidative metabolism and glycolysis are found in rods and cones, while evidence of increased activity of the mitochondrial electron transport chain is found in retinal ganglion cells (RGCs). Evidence of synaptic remodeling is found throughout the retina, with changes to increase synaptic transmission in photoreceptors and bipolar cells, increased ionotropic glutamate receptors in amacrine and ganglion cells, and dendritic and axon remodeling throughout. Surprisingly, RPE, cones and bipolar cells in the P23H retinas also have increased expression of genes involved in circadian rhythm regulation. While this model system undergoes continuous regeneration, ongoing remodeling impacts the entire retina. This comprehensive transcriptomic analysis provides a molecular road map to understand how the retina remodels in the context of chronic retinal degeneration with ongoing regeneration.

neuroscience↗

bioRxiv2022

CURLYLEAF is a key modulator of apoplast water status in Arabidopsis leaf

The apoplast of plant leaf, the intercellular space between mesophyll cells, is normally largely filled with air with a minimal amount of water in it, which is essential for key physiological processes such as gas exchange to occur. Interestingly, phytopathogens exploit virulence factors to induce a water-rich environment, known as "water soaking", in the apoplast of the infected leaf tissue to promote disease. We propose that plants evolved a "water soaking" pathway, which normally keeps a "minimized and balanced" water level in the leaf apoplast for plant growth but is disturbed by microbial pathogens to facilitate infection. Investigation of the "water soaking" pathway and leaf water control mechanisms is a fundamental, yet previously-overlooked, aspect of plant physiology. To identify key components in the "water soaking" pathway, we performed a genetic screen to isolate Arabidopsis severe water soaking (sws) mutants that show leaf water over-accumulation under high air humidity, a condition required for visible water soaking. Here we report the sws1 mutant, which displays rapid water soaking upon high humidity treatment due to a loss-of-function mutation in CURLY LEAF (CLF), encoding a histone methyl-transferase in the POLYCOMB REPRESSIVE COMPLEX 2 (PRC2). We found that the sws1 (clf) mutant exhibits an enhanced abscisic acid (ABA) level and stomatal closure, which are indispensable for its water soaking phenotype and mediated by CLFs direct regulation of a group of ABA-associated NAC transcription factors, NAC019/055/072. Interestingly, the clf mutant showed a weakened immunity, which likely also contributes to the water soaking phenotype. In addition, the clf plant supports a significantly higher level of Pseudomonas syringae pathogen-induced water soaking and bacterial multiplication, in an ABA pathway and NAC019/055/072-dependent manner. Collectively, our study probes into a fundamental question in plant biology and demonstrates CLF as a key modulator of leaf water status via epigenetic regulation of ABA pathway and stomatal movement.

plant biology↗

bioRxiv2022

A SHR-IDD-PIN regulatory network mediates minor vein differentiation in rice

C3 and C4 grasses directly and indirectly provide the vast majority of calories to the human diet, yet our understanding of the molecular mechanisms driving photosynthetic productivity in grasses is largely unexplored. Here we define a genetic circuit comprised of SHR, IDD and PIN family members that specify vascular identify and ground cell proliferation in leaves of both C3 and C4 grasses. Ectopic expression and loss-of-function mutant studies of SHORT ROOT (SHR) paralogs in C3 Oryza sativa (rice) and C4 Setaria viridis (green millet) revealed a role in both minor vein formation and ground cell differentiation. Genetic and in vitro studies further suggest that SHR regulates this process through its interaction with Indeterminate Domain (IDD) IDD 12 and 13. We further show a direct interaction of these IDD proteins with a putative regulatory element within the auxin transporter PIN5c gene. Collectively, these studies indicated that a SHR-IDD regulatory circuit mediates auxin flow through the negative regulation of PIN protein expression to modulate minor vein patterning in the grasses.

plant biology↗

bioRxiv2022

A rapid protocol for ribosome profiling of low input samples

Ribosome profiling provides quantitative, comprehensive, and high-resolution snapshots of cellular translation by the high-throughput sequencing of short mRNA fragments that are protected from nucleolytic digestion by ribosomes. While the overall principle is simple, the workflow of ribosome profiling experiments is complex and challenging, and typically requires large amounts of sample, limiting its broad applicability. Here, we present a new protocol for ultra-rapid ribosome profiling from low-input samples. It features a robust strategy for sequencing library preparation within one day that employs solid phase purification of reaction intermediates, allowing to reduce the input to as little as 0.1 pmol of RNA. Hence, it is particularly suited for the analyses of small samples or targeted ribosome profiling. Its high sensitivity and its ease of implementation will foster the generation of higher quality data from small samples, which opens new opportunities in applying ribosome profiling.

systems biology↗

bioRxiv2022

Large scale production of human blastoids amenable to modeling blastocyst development and maternal-fetal crosstalk

Recent advances in human blastoids generated from naive pluripotent stem cells have opened a new avenue for modelling early human development and implantation. Despite the success, however, existing protocols have several limitations, e.g., the use of custom-built microwell arrays impedes wide adoption by the research community, and mass production of human blastoids is hampered by low-output or low-efficiency methods. To address these issues, here we developed an optimized protocol based on commercially available microwell plates, which enabled efficient generation of high-fidelity human blastoids at a large scale. Leveraging on the improved protocol, we identified MAPK. PI3K/AKT and mTOR signaling pathways were activated in both blastoids and blastocyst, and discovered endometrial stromal effects in promoting trophoblast cell survival, proliferation and syncytialization during extended co-culture with blastoids. Our optimized protocol will facilitate broader use of human blastoids as an accessible, perturbable, scalable, tractable, and ethical model for human blastocysts.

developmental biology↗

bioRxiv2022

Positive effects of tree diversity on tropical forest restoration in a field-scale experiment

Experiments under controlled conditions have established that ecosystem functioning is generally positively related to levels of biodiversity, but it is unclear how widespread these effects are in real-world settings and whether they can be harnessed for ecosystem restoration. We used a long-term, field-scale tropical restoration experiment to test how the diversity of planted trees affected recovery measured across a 500 ha area of selectively logged forest using multiple sources of satellite data. Replanting with species rich mixtures of tree seedlings that had higher phylogenetic and functional diversity accelerated restoration rates. Our results are consistent with a positive relationship between biodiversity and ecosystem functioning in the lowland dipterocarp rainforests of SE Asia and demonstrate that using diverse mixtures of species can enhance initial recovery after logging.

ecology↗