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Shen, W.

Publications and source records attributed to Shen, W..

At least 55 records · Page 3Linked to original sources

Thiolation-Based Protein-Protein Hydrogels for Improved Wound Healing

The limitations of protein-based hydrogels, including their insufficient mechanical properties and restricted biological functions, arise from the highly specific functions of proteins as natural building blocks. A potential solution to overcome these shortcomings is the development of protein-protein hydrogels, which integrate structural and functional proteins. In this study, we introduce a protein-protein hydrogel formed by crosslinking bovine serum albumin (BSA) and a genetically engineered intrinsically disordered collagen-like protein (CLP) through Ag-S bonding. Our approach involves thiolating lysine residues of BSA and crosslinking CLP with Ag+ ions, utilizing thiolation of BSA and the free-cysteines of CLP. The resulting protein-protein hydrogels exhibit exceptional properties, including notable plasticity, inherent self-healing capabilities, and gel-sol transition in response to redox conditions. Furthermore, in comparison to standalone BSA hydrogels, these protein-protein hydrogels demonstrate remarkable antibacterial properties, enhanced cellular viability, and improved cellular migration. In vivo experiments provide conclusive evidence of accelerated wound healing, observed not only in murine models with streptozotocin (Step)-induced diabetes but also in zebrafish models subjected to UV-burn injuries. Detailed mechanistic insights, combined with assessments of pro-inflammatory cytokines and the expression of epidermal differentiation-related proteins, robustly validate the protein-protein hydrogels effectiveness in promoting wound repair. This pioneering approach advances the development of protein-protein hydrogels and serves as a reference for the creation of multifunctional protein-based hydrogels.

bioengineering↗

Designing efficient randstrobes for sequence similarity analyses

Substrings of length k, commonly referred to as k-mers, play a vital role in sequence analysis, reducing the search space by providing anchors between queries and references. However, k-mers are limited to exact matches between sequences. This has led to alternative constructs, such as spaced k-mers, that can match across substitutions. We recently introduced a class of new constructs, strobemers, that can match across substitutions and smaller insertions and deletions. Randstrobes, the most sensitive strobemer proposed in [18], has been incorporated into several bioinformatics applications such as read classification, short read mapping, and read overlap detection. Randstrobes are constructed by linking together k-mers in a pseudo-random fashion and depend on a hash function, a link function, and a comparator for their construction. Recently, we showed that the more random this linking appears (measured in entropy), the more efficient the seeds for sequence similarity analysis. The level of pseudo-randomness will depend on the hashing, linking, and comparison operators. However, no study has investigated the efficacy of the underlying operators to produce randstrobes. In this study, we propose several new construction methods. One of our proposed methods is based on a Binary Search Tree (BST), which lowers the time complexity and practical runtime to other methods for some parametrizations. To our knowledge, we are also the first to describe and study the types of biases that occur during construction. We designed three metrics to measure the bias. Using these new evaluation metrics, we uncovered biases and limitations in previous methods and showed that our proposed methods have favorable speed and sampling uniformity to previously proposed methods. Lastly, guided by our results, we change the seed construction in strobealign, a short-read mapper, and find that the results change substantially. Also, we suggest combining the two versions to improve accuracy for the shortest reads in our evaluated datasets. Our evaluation highlights sampling biases that can occur and provides guidance on which operators to use when implementing randstrobes.

bioinformatics↗

A redundant chloroplast protein is co-opted by potyvirids as the scaffold protein to mediate viral intercellular movement complex assembly

For viruses in the family Potyviridae (potyvirids), three virus-encoded proteins (P3N-PIPO, CI and CP) and several host components are known to coordinately regulate viral cell-to-cell movement. Here, we found that HCPro2 encoded by areca palm necrotic ring spot virus is involved in the intercellular movement, which could be functionally complemented by its counterpart HCPro from a potyvirus. The affinity purification and mass spectrum analysis identified several viral factors (including CI and CP) and a variety of host proteins that physically associate with HCPro2. We demonstrated that HCPro2 interacts with either CI or CP in planta, and the three form plasmodesmata (PD)-localized interactive complex in viral infection. Further, we screened HCPro2-associating host proteins, and identified a common host protein RbCS that mediates the interactions of HCPro2-CI, HCPro2-CP and CI-CP among the complex. Knockdown of NbRbCS simultaneously impairs the interactions of HCPro2-CI, HCPro2-CP and CI-CP, and significantly attenuates the intercellular movement and systemic infection for ANRSV and other three tested potyvirids. This study highlights that a nucleus-encoded chloroplast-targeted protein is hijacked by potyvirids as the scaffold protein to mediate the assembly of viral intercellular movement complex to promote viral infection.

microbiology↗

Bio-inspired mineralization collagen induce fibrocartilage regeneration after tendon-bone injury by activating Gli1+Dkk3+ progenitor cells

A fibrocartilaginous connection between the tendon and bone, plays a critical role in transferring force from muscle to bone to enable joint movement. However, due to the high mechanical stress it experiences, the enthesis is vulnerable to injury and incapable of regenerating. The spatial relationship and functional basis of the principal components of the fibrocartilage - mineral and collagen - have not been clearly elucidated, which is a significant remaining gap in reconstructing complex architectures for promoting interface tissue regeneration. Here, using three-dimensional electron tomography imaging and high-resolution two-dimensional electron microscopy, we discover that mineral particles form a continuous cross-fibrillar phase within the fibrocartilage region. By developing a "floating mineralization" system, we fabricate a three-layer hydrogel that mimics the hierarchical nano- to micro-scale structure of tendon-bone interface (TBI). The middle layer is noteworthy for its resemblance to the nanostructure of fibrocartilage and its superior ability to induce mineralized fibrochondrogenesis in vitro. Based on motor function analysis, imaging diagnosis, histological staining, immunofluorescence staining, and biomechanics performance, we demonstrate that in situ transplantation of the gradient hydrogel achieved tendon-fibrocartilage-bone synchronous regeneration and result in 68% maximum mechanical recovery at 8-week postoperation. Single-cell RNA sequencing analysis reveals that a unique atlas of in situ stem/progenitor cells is generated during the TBI healing in vivo. Notably, the bio-inspired hydrogel microenvironment drived endogenous Gli1+Dkk3+ progenitor cells, playing a key role in TBI regeneration. Therefore, we have successfully decoded and reconstructed the nanostructure of fibrocartilage, which has great potential in TBI regeneration.

bioengineering↗

Astrocytes gate long-term potentiation in hippocampal interneurons

Long-term potentiation is involved in physiological processes such as learning and memory, motor learning and sensory processing, and pathological conditions such as addiction. In contrast to the extensive studies on the mechanism of long-term potentiation on excitatory glutamatergic synapses onto excitatory neurons (LTPE[->]E), the mechanism of LTP on excitatory glutamatergic synapses onto inhibitory neurons (LTPE[->]I) remains largely unknown. In the central nervous system, astrocytes play an important role in regulating synaptic activity and participate in the process of LTPE[->]E, but their functions in LTPE[->]I remain incompletely defined., We studied the role of astrocytes in regulating LTPE[->]I in the hippocampal CA1 region and their impact on cognitive function using electrophysiological, pharmacological, confocal calcium imaging, chemogenetics and behavior tests. We showed that LTPE[->]I in the stratum oriens of hippocampal CA1 is astrocyte independent. However, in the stratum radiatum, synaptically released endocannabinoids increase astrocyte Ca2+ via type-1 cannabinoid receptors, stimulate D-serine release, and potentiate excitatory synaptic transmission on inhibitory neurons through the activation of (N-methyl-D-aspartate) NMDA receptors. We also revealed that chemogenetic activation of astrocytes is sufficient for inducing NMDA-dependent de novo LTPE[->]I in the stratum radiatum of the hippocampus. Furthermore, we found that disrupting LTPE[->]I by knocking down {gamma}CaMKII in interneurons of the stratum radiatum resulted in dramatic memory impairment. Our findings suggest that astrocytes release D-serine, which activates NMDA receptors to regulate LTPE[->]I, and that cognitive function is intricately linked with the proper functioning of this LTPE[->]I pathway.

neuroscience↗

A peptide that regulates metalation of the Arabidopsis ethylene receptor.

Ethylene signalling represents one of the classic hormonal pathways in plants, with diverse roles in development and stress responses. The dimeric ethylene receptor localizes to the endoplasmic reticulum (ER) and contains Cu(I) ions essential for ethylene binding and signal transduction. We previously discovered that mutants in the Arabidopsis gene POLARIS (PLS), encoding a 36 amino acid peptide, exhibit enhanced ethylene signalling responses, suggestive of reduced receptor activity, but the role and activity of the peptide in this signalling cascade has not been defined. Here we report PLS binds copper as a 1:2 thiol-dependent Cu(I):PLS2 complex, with an affinity of 3.79 ({+/-}1.5) x1019 M-2, via two cysteine residues also found in the related species Camelina sativa. These residues are also essential for biological function. This affinity precludes PLS as a cytosolic Cu chaperone. We demonstrate that PLS localizes to endomembranes and interacts with the transmembrane domain of receptor protein ETR1. PLS-ETR1 binding is increased in the presence of copper, and this interaction provides a Cu-dependent mechanism for mediating a repression of ethylene responses. PLS transcription is up-regulated by auxin and down-regulated by ethylene, and so PLS-ETR1 interactions also provide a mechanism to modulate ethylene responses in high auxin tissues.

plant biology↗

Cotyledon Peeling Method for Passion Fruit Protoplasts: a versatile cell system for transient gene expression in passion fruit (Passiflora edulis)

Passion fruit (Passiflora edulis) is a perennial evergreen vine that grows mainly in tropical and subtropical regions due to its nutritional, medicinal and ornamental values. However, the molecular biology study of passion fruit is extremely hindered by the lack of an easy and efficient method for transformation. The protoplast transformation system plays a vital role in plant regeneration, gene function analysis and genome editing. Here, we present a new method ( Cotyledon Peeling Method) for simple and efficient passion fruit protoplast isolation using cotyledon as the source tissue. A high yield (2.3 x 107 protoplasts per gram of fresh tissues) and viability (76%) of protoplasts were obtained upon incubation in the enzyme solution [1% (w/v) cellulase R10, 0.25% (w/v) macerozyme R10, 0.4 M mannitol, 10 mM CaCl2, 20 mM KCl, 20 mM MES and 0.1% (w/v) BSA, pH 5.7] for 2 hours. In addition, we achieved high transfection efficiency of 83% via the polyethylene glycol (PEG)-mediated transformation with a green fluorescent protein (GFP)-tagged plasmid upon optimization. The crucial factors affecting transformation efficiency were optimized as follows: 3 g of plasmid DNA, 5 min transfection time, PEG concentration at 40% and protoplast density of 100 x 104 cells/ml. Furthermore, the established protoplast system was successfully applied for subcellular localization analysis of multiple fluorescent organelle markers and protein-protein interaction study. Taken together, we report a simple and efficient passion fruit protoplast isolation and transformation system, and demonstrate its usage in transient gene expression for the first time in passion fruit. The protoplast system would provide essential support for various passion fruit biology studies, including genome editing, gene function analysis and whole plant regeneration.

plant biology↗

Multi-omics of the gut microbial ecosystem in the immunotherapy resistance in microsatellite instability-high gastrointestinal cancer patients

Despite the encouraging efficacy of anti-PD-1/PD-L1 immunotherapy in microsatellite instability-high/deficient mismatch repair (MSI-H/dMMR) advanced gastrointestinal cancer, many patients exhibit primary or acquired resistance. Using multi-omics approaches, we interrogated gut microbiome, blood metabolome and cytokines/chemokines of MSI-H/dMMR advanced gastrointestinal cancer patients (N=77) and identified a number of microbes (e.g. Alistipes putredinis) and metabolites (e.g. arginine and SCFA) highly associated with primary resistance. Fecal microbiota transplantation of patients stool replicated the clinical responsiveness as well as certain molecular signatures. Based on the clinical microbiome data, we developed a predictive machine learning model for primary resistance and achieved accuracy at 0.83 on an external validation set. Furthermore, several microbes were pinpointed which gradually changed during the process of acquired resistance. In summary, our study demonstrated the essential role of gut microbiome in drug resistance, and this could be utilized as a preventative diagnosis tool as well as therapeutic targets in the future.

cancer biology↗

KDM2B regulates hippocampal morphogenesis by transcriptionally silencing Wnt signaling in neural progenitors

The hippocampus plays major roles in learning and memory. Similar to other parts of the brain, the development of hippocampus requires precise coordination of patterning, cell proliferation, differentiation, and migration, with both cell-intrinsic and extrinsic mechanisms involved. Here we genetically removed the chromatin-association capability of KDM2B - a key component of the variant Polycomb repressive complex 1 (PRC1) - in the progenitors of developing dorsal telencephalon (Kdm2b{Delta}CxxC) to surprisingly discover that the size of Kdm2b{Delta}CxxC hippocampus, particularly the dentate gyrus, became drastically smaller with disorganized cellular components and structure. Kdm2b{Delta}CxxC mice displayed prominent defects in spatial memory, motor learning and fear conditioning. The differentiation trajectory of the developing Kdm2b{Delta}CxxC hippocampus was greatly delayed, with a significant amount of TBR2-expressing intermediate progenitors stuck along the migratory/differentiation path. Transcriptome and chromatin immunoprecipitation studies of neonatal hippocampi and their progenitors indicated that genes implicated in stemness maintenance, especially components of canonical Wnt signaling, could not be properly silenced by PRC1 and PRC2. Activating the Wnt signaling disturbed hippocampal neurogenesis, recapitulating the effect of KDM2B loss. Together, we unveiled a previously unappreciated gene repressive program mediated by KDM2B that controls progressive fate specifications and cell migration, hence morphogenesis of hippocampus during development. Graphic AbstractLoss of KDM2B-CxxC reduces repressive histone modifications - H2AK119ub and H3K27me3 - on key Wnt signal genes, hence leading to the block of their attenuation over time. Hampered differentiation and migration of hippocampal progenitors leads to hippocampal agenesis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/525636v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@18fbbdborg.highwire.dtl.DTLVardef@17633f9org.highwire.dtl.DTLVardef@14e36b9org.highwire.dtl.DTLVardef@1eadb8a_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

Changes of platelet morphology, ultrastructure and function in patients with acute ischemic stroke based on super-resolution microscopy.

Platelets are important in acute ischemic stroke (AIS) thrombosis. The observation and evaluation of platelet ultrastructure and efficacy of antiplatelet drug in AIS patients is difficult due to microscopic limitations and sensitivity of platelet. The new super-resolution microscope (SIM) can accurately, quickly analyze the platelet ultrastructure and antiplatelet drug in AIS patients. We applied SIM to observe the morphology and ultrastructure of platelets with AIS patients in different state. SIM images were analyzed to specify the dense granules and granules change of platelets in AIS patients. Testing platelet factor 4 (PF4) to reflect platelet releasing function. We observed that platelet activation in AIS patients was greater after stimulation, with granule showing a pattern of parenchymatous masses. SIM images analyzing showed diameter of platelets, average size of granules, area% of granules per field and mean area of granules per platelet in AIS patient were lower than healthy people. Platelet releasing function was suppressed at rest stage and more efficacy release after stimulation. 2MeSamp inhibited parenchymatous masses of granules and reduced PF4 release of platelets after stimulation. According to the results, the structure and function of platelets in AIS patients are indeed altered. Additionally, SIM could be used as a new method to indicates the onset of AIS and assess antiplatelet drugs.

cell biology↗

MSdb: an integrated expression atlas of human musculoskeletal system

We introduce MSdb (https://www.msdb.org.cn), a database for visualization and integrated analysis of next-generation sequencing data from human musculoskeletal system, along with manually curated patient phenotype data. Systematic categorizing, standardized processing and freely accessible knowledge enables the reuse of public data. MSdb provides various types of analysis, including sample-level browsing of metadata information, gene/miRNA expression, and single-cell RNA-seq dataset. In addition, MSdb also allows integrated analysis for cross-samples and cross-omics analysis, including customized differentially-expressed gene/microRNA analysis, microRNA-gene network, scRNA-seq cross-sample/disease integration, and gene regulatory network analysis.

bioinformatics↗

MERISTEM-DEFECTIVE/DEFECTIVELY ORGANIZED TRIBUTARIES2 regulates the balance between stemness and differentiation in the root meristem through RNA splicing control.

Plants respond to environmental stresses through controlled stem cell maintenance and meristem activity. One level of transcriptional control is RNA alternative splicing. However the mechanistic link between stress, meristem function and RNA splicing is poorly understood. The MERISTEM-DEFECTIVE (MDF)/DEFECTIVELY ORGANIZED TRIBUTARIES (DOT2) gene of Arabidopsis encodes a SR-related family protein, required for meristem function and leaf vascularization, and is the likely orthologue of the human SART1 and yeast snu66 splicing factors. MDF is required for the correct splicing and expression of key transcripts associated with root meristem function. We identified RSZ33 and ACC1, both known to regulate cell patterning, as splicing targets required for MDF function in the meristem. MDF expression is modulated by osmotic and cold stress, associated with differential splicing and specific isoform accumulation and shuttling between nucleus and cytosol, and acts in part via a splicing target SR34. We propose a model in which MDF controls splicing in the root meristem to promote stemness and repress stress response and cell differentiation pathways. Summary statementThe protein MERISTEM-DEFECTIVE regulates Arabidopsis meristem function through its role as a splicing factor, mediated through splicing targets RSZ33, ACC1 and SR34.

plant biology↗

A bi-functional PARP-HDAC inhibitor with activity in Ewing sarcoma

HDAC inhibition has been shown to induce pharmacological BRCAness in cancer cells with proficient DNA repair activity. This provides a rationale for exploring combination treatments with HDAC and PARP inhibition in cancer types that are insensitive to single-agent PARP inhibitors. Here, we report the concept and characterization of a novel bifunctional PARP inhibitor (kt-3283) with dual activity towards PARP1/2 and HDAC enzymes in Ewing sarcoma cells. Compared to the FDA-approved PARP (olaparib) and HDAC (vorinostat) inhibitors, kt-3283 displayed enhanced cytotoxicity in Ewing sarcoma models. The kt-3283-induced cytotoxicity was associated with a strong S and G2/M cell cycle arrest in the nanomolar concentration range and elevated DNA damage as assessed by {gamma}H2AX tracking and comet assays. In three-dimensional spheroid models of Ewing sarcoma, kt-3283 showed efficacy in lower concentrations than olaparib and vorinostat and kt-3283 inhibited colonization of Ewing sarcoma cells in an ex vivo lung metastasis model. In summary, our data demonstrates the preclinical justification for studying the benefit of dual PARP and HDAC inhibition in the treatment of Ewing sarcoma in a clinical trial and provides proof-of-concept for a bi-functional single-molecule therapeutic strategy.

cancer biology↗

Crystal structure of monkeypox H1 phosphatase, an Antiviral Drug Target

The current monkeypox outbreak has caused over 64,000 global cases, but the effective treatments are very limited. The dual specific phosphatase (H1) from monkeypox antagonizes the immune response and is crucial for viral replication, making it an attractive antiviral target. Here we determined a 1.8-[A] crystal structure of H1, which forms a domain swapped dimer resembling a butterfly. Each active site, which consists of a Cys-Arg-Asp triad, captures a phosphate ion. The observed conformation mimics the final step of catalysis prior to product release. The crystal structure provides a strong foundation for the discovery of new antivirals against this emerging worldwide pathogen.

microbiology↗

Copresent microbiome and short-chain fatty acids profiles of plant biomass utilization in rumen simulation technique system

Rumen contents have considerable utility in converting plant biomass to short- chain fatty acids (SCFAs) when used as inoculum for in vitro fermentation. To better understand the microbial communities and their functions when in vitro ruminal fermentation, the microbiome and SCFAs production were investigated using rumen simulation technique (RUSITEC) system which was inoculated/co- inoculated with rumen contents from goat and cow. This study reconstructed 1677 microbial metagenome-assembled genomes (MAGs) from metagenomic sequencing. The copresent microbiome containing 298 MAGs were found in metagenomic data of these contents and previous ruminal representative samples. These copresent MAGs were overrepresented in decomposing various substrates, especially pectin and xylan. Additionally, the SCFAs productions in RUSITEC were linked with copresent MAGs. Copresent MAGs obtained from this study shows promise to point out the direction for further research on in vitro ruminal fermentation, and enables a better understanding of rumen microbiotal structures and functions under in vitro condition. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/497131v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@310c66org.highwire.dtl.DTLVardef@251334org.highwire.dtl.DTLVardef@fdfecorg.highwire.dtl.DTLVardef@363d8f_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

Evolution of nasal and olfactory infection characteristics of SARS-CoV-2 variants

SARS-CoV-2 infection of the upper airway and the subsequent immune response are early, critical factors in COVID-19 pathogenesis. By studying infection of human biopsies in vitro and in a hamster model in vivo, we demonstrated a transition in tropism from olfactory to respiratory epithelium as the virus evolved. Analyzing each variants revealed that SARS-CoV-2 WA1 or Delta infects a proportion of olfactory neurons in addition to the primary target sustentacular cells. The Delta variant possesses broader cellular invasion capacity into the submucosa, while Omicron displays longer retention in the sinonasal epithelium. The olfactory neuronal infection by WA1 and the subsequent olfactory bulb transport via axon is more pronounced in younger hosts. In addition, the observed viral clearance delay and phagocytic dysfunction in aged olfactory mucosa is accompanied by a decline of phagocytosis related genes. Furthermore, robust basal stem cell activation contributes to neuroepithelial regeneration and restores ACE2 expression post-infection. Together, our study characterized the nasal tropism of SARS-CoV-2 strains, immune clearance, and regeneration post infection. The shifting characteristics of viral infection at the airway portal provides insight into the variability of COVID-19 clinical features and may suggest differing strategies for early local intervention.

pathology↗

KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping

MotivationThe growing number of microbial reference genomes enables the improvement of metagenomic profiling accuracy but also imposes greater requirements on the indexing efficiency, database size, and runtime of taxonomic profilers. Additionally, most profilers focus mainly on bacterial, archaeal, and fungal populations, while less attention is paid to viral communities. ResultsWe present KMCP, a novel k-mer-based metagenomic profiling tool that utilizes genome coverage information by splitting the reference genomes into chunks and then stores k-mers in a modified and optimized COBS index for fast alignment-free sequence searching. KMCP combines k-mer similarity and genome coverage information to reduce the false positive rate of k-mer-based taxonomic classification and profiling methods. Benchmarking results based on simulated and real data demonstrate that KMCP, despite a longer running time than all other methods, not only allows the accurate taxonomic profiling of prokaryotic and viral populations but also provides confident pathogen detection in clinical samples of low depth. Availability and ImplementationThe software is open-source under the MIT license and available at https://github.com/shenwei356/kmcp.

bioinformatics↗

dbGSRV: a manually curated database of genetic susceptibility to respiratory virus

Human genetics has been proposed to play an essential role in inter-individual differences in respiratory virus infection occurrence and outcomes. To systematically understand human genetic contributions to respiratory virus infection, we developed the database dbGSRV, a manually curated database that integrated the host genetic susceptibility and severity studies of respiratory viruses scattered over literatures in PubMed. At present, dbGSRV contains 1932 records of genetic association studies relating 1010 unique variants and seven respiratory viruses, manually curated from 168 published articles. Users can access the records by quick searching, batch searching, advanced searching and browsing. Reference information, infection status, population information, mutation information and disease relationship are provided for each record, as well as hyper links to public databases in convenient of users accessing more information. In addition, a visual overview of the topological network relationship between respiratory viruses and associated genes is provided. Therefore, dbGSRV offers a promising avenue to facilitate researchers to dissect human factors in respiratory virus infection, define novel drug targets, conduct risk stratification of population and develop personalized medicine approaches. Database URL: http://www.ehbio.com/dbGSRV/front/

bioinformatics↗