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Xu, J.

Publications and source records attributed to Xu, J..

At least 415 records · Page 23Linked to original sources

Crystallographic, kinetic, and calorimetric investigation of PKA interactions with L-type calcium channels and Rad GTPase

{beta}-adrenergic signalling leads to activation of cAMP-dependent protein kinase (PKA), which can regulate the activity of L-type voltage-gated calcium channels (CaVs) in multiple tissues. In CaV1.2, various sites have been proposed to be involved, including Ser1981 in the C-terminal tail. Its phosphorylation is linked to diabetes progression, synaptic plasticity, and the augmentation of Ca2+ currents in smooth muscle. Its role in augmenting cardiac Ca2+ currents has been heavily scrutinized, with alternative models including the sites Ser1718 and Ser1535. Recently, the GTPase Rad has been identified as a critical PKA target that mediates the augmentation of cardiac CaV1.2 currents upon its phosphorylation. However, it is unclear which of the four potential sites (Ser25, Ser38, Ser272, and Ser300) are favored by PKA. Using quantitative binding experiments and enzyme kinetics, we show that there are two Tiers of target sites, with CaV1.2 residue Ser1981 and Rad residues Ser25 and Ser272 forming Tier 1 substrates for PKA. The other sites form a second Tier, with PKA only showing minimal detectable activity. The Tier 1 substrates share a common feature with two arginine residues that anchor the peptide into the active site of PKA. We report crystal structures of the PKA catalytic subunit (PKAc) with and without a CaV1.2 substrate that represent different successive conformations prior to product turnover. Different target sites utilize different anchoring residues, highlighting the plasticity of PKAc to recognize substrates. SummaryStress signals can alter the electrical properties of excitable cells. cAMP-dependent protein kinase A (PKA) is a key enzyme that is activated upon {beta}-adrenergic stimulation and can alter the function of L-type voltage-gated calcium channels (CaVs) in various tissues. There is a lot of controversy surrounding the exact recognition and specificity of PKA towards CaV1.2, a key calcium channel located in neuronal, cardiac, and smooth muscle tissue, among others. Using a quantitative and unbiased approach, we determined the substrate specificities of PKA towards various sites in CaV1.2 and Rad, an inhibitory protein. Our work highlights two Tiers of substrates, suggesting a potential graded response. Using X-ray crystallography, we determined a high-resolution structure of PKA bound to its strongest target site in CaV1.2, showing how PKA undergoes multiple structural transitions towards binding and how it makes use of a unique anchoring residue.

biochemistry↗

High-throughput single-cell sorting by stimulated Raman-activated cell ejection

Single-cell sorting is essential to explore cellular heterogeneity in biology and medicine. Recently developed Raman-activated cell sorting (RACS) circumvents the limitations of fluorescence-activated cell sorting, such as the cytotoxicity of labels. However, the sorting throughputs of all forms of RACS are limited by the intrinsically small cross-section of spontaneous Raman scattering. Here, we report a stimulated Raman-activated cell ejection (S-RACE) platform that enables high-throughput single-cell sorting based on high-resolution multi-channel stimulated Raman chemical imaging, in situ image decomposition, and laser-induced cell ejection. The performance of this platform was illustrated by sorting a mixture of 1 m polymer beads, where 95% yield, 98% purity, and 14 events per second throughput were achieved. Notably, our platform allows live cell ejection, allowing for the growth of single colonies of bacteria and fungi after sorting. To further illustrate the chemical selectivity, lipid-rich Rhodotorula glutinis cells were successfully sorted from a mixture with Saccharomyces cerevisiae, confirmed by downstream quantitative PCR. Furthermore, by integrating a closed-loop feedback control circuit into the system, we realized real-time single-cell imaging and sorting, and applied this method to precisely eject regions of interest from a rat brain tissue section. The reported S-RACE platform opens exciting opportunities for a wide range of single-cell applications in biology and medicine. Significance statementImage-guided single-cell sorting is a potent tool in diverse biological applications. Current microfluidic cell sorting methods encounter challenges in handling smaller cells and are not applicable to tissue sections. To address these challenges, we have developed a stimulated Raman-activated cell ejection (S-RACE) platform, which is the first demonstration of single-cell ejection coupled with coherent Raman scattering. S-RACE allows label-free chemical imaging guided cell sorting through multispectral stimulated Raman scattering (SRS) imaging, on-the-fly image analysis, and laser-induced cell ejection. Versatile applications of S-RACE to a wide range of samples, such as polymer particles, single-live bacteria, single-live fungus, and tissue sections, are demonstrated.

bioengineering↗

Cell-autonomous targeting of arabinogalactan by host immune factors inhibits mycobacterial growth

Deeper understanding of the crosstalk between host cells and Mycobacterium tuberculosis (Mtb) provides crucial guidelines for the rational design of novel intervention strategies against tuberculosis (TB). Mycobacteria possess a unique complex cell wall with arabinogalactan (AG) as critical component. AG has been identified as a virulence factor of Mtb which is recognized by host galectin-9. Here we demonstrate that galectin-9 directly inhibited mycobacterial growth through AG-binding property of carbohydrate-recognition domain 2. Furthermore, IgG antibodies with AG specificity were detected in serum of TB patients. Based on the interaction between galectin-9 and AG, we developed monoclonal antibody (mAb) screening assay and identified AG-specific mAbs which profoundly inhibit Mtb growth. Mechanistically, proteomic profiling and morphological characterizations revealed that AG-specific mAbs regulate AG biosynthesis, thereby inducing cell wall swelling. Thus, direct AG-binding by galectin-9 or antibodies contributes to protection against TB. Our findings pave the way for the rational design of novel immunotherapeutic strategies for TB control.

immunology↗

Regional specialization, polyploidy, and seminal fluid transcripts in the Drosophila female reproductive tract

Internal fertilization requires the choreographed interaction of female cells and molecules with seminal fluid and sperm. In many animals, including insects, the female reproductive tract is physically subdivided into sections that carry out specialized functions. For example, females of many species have specialized organs for sperm storage. Drosophila melanogaster is a premier model system for investigating many aspects of animal reproduction. Nevertheless, in contrast to males, much of the basic biology of the D. melanogaster female reproductive tract remains poorly understood or completely unknown. Here we use single-cell RNA-seq data and in situ hybridization to reveal a rich and previously unknown female reproductive tract cell diversity, including widespread variation in ploidy levels. We find that many so-called seminal fluid protein genes appear to be transcribed in specialized cells of the female reproductive tract, motivating a re-evaluation of the functional and evolutionary biology of this major class of proteins.

cell biology↗

Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates -- MosAIC (Mosquito-Associated Isolate Collection)

Mosquitoes transmit medically important human pathogens, including viruses like dengue virus and parasites such as Plasmodium spp., the causative agent of malaria. Mosquito microbiomes are critically important for the ability of mosquitoes to transmit disease-causing agents. However, while large collections of bacterial isolates and genomic data exist for vertebrate microbiomes, the vast majority of work in mosquitoes to date is based on 16S rRNA gene amplicon data that provides limited taxonomic resolution and no functional information. To address this gap and facilitate future studies using experimental microbiome manipulations, we generated a bacterial Mosquito-Associated Isolate Collection (MosAIC) consisting of 392 bacterial isolates with extensive metadata and high-quality draft genome assemblies that are publicly available for use by the scientific community. MosAIC encompasses 142 species spanning 29 bacterial families, with members of the Enterobacteriaceae comprising 40% of the collection. Phylogenomic analysis of three genera, Enterobacter, Serratia, and Elizabethkingia, reveal lineages of mosquito-associated bacteria isolated from different mosquito species in multiple laboratories. Investigation into species pangenomes further reveals clusters of genes specific to these lineages, which are of interest for future work to identify functions underlying mosquito host association. Altogether, we describe the generation of a physical collection of mosquito-associated bacterial isolates, their genomic data, and analyses of selected groups in context of genome data from closely related isolates, providing a unique, highly valuable resource to investigate factors for bacterial colonisation and adaptation within mosquito hosts. Future efforts will expand the collection to include broader geographic and host species representation, especially from individuals collected from field populations, as well as other mosquito-associated microbes, including fungi, archaea, and protozoa.

microbiology↗

A resource for probing influences of perinatal factors on neurodevelopment in 3-10-years-old Chinese children

Adverse perinatal factors can disrupt the normal development of the brain, with potential long-term impacts on childrens overall development. Currently, the neuropathological mechanisms by which these factors lead to various neurodevelopmental disorders (NDDs) remain largely unknown. An open resource that integrate perinatal factors with brain and mental health development is essential for investigating NDD-related aetiology. In this Data Descriptor, we introduce a multicentre database containing information on perinatal factors that influence childrens brain-mind development, namely, periCBD, that combines neuroimaging and behavioural phenotypes with perinatal factors associated with a high incidence of NDDs at county/region/central district hospitals. PeriCBD was designed to establish a platform for the investigation of individual differences in brain-mind development among children aged 3-10 years are associated with perinatal factors. Ultimately, our goal was to develop an early prediction and screening model for NDDs that leverages normative data to facilitate NDD aetiology research. Herein, we provide a systematic overview of the data acquisition/cleaning/quality control/sharing, processes of periCBD and present preliminary brain-mind associations.

neuroscience↗

Comparative single-cell regulome reveals evolutionary innovations in neural progenitor cells during primate corticogenesis

The cellular and genetic mechanism underlying the human-specific features of cortex development remains unclear. We generated a cell-type resolved atlas of transcriptome and regulome of the developing macaque and mouse prefrontal cortex, and conducted evolutionary analyses with the published complementary human data. We discovered a primate-specific expansion of two neural progenitor subclasses, glia-committed radial glia (RG) and truncated RG. Specifically, the human neural progenitors show extensive transcriptional rewiring in the growth factor and extracellular matrix pathways. Expression of the human-specific progenitor marker ITGA2 in the cortex of fetal mouse promotes progenitor proliferation and an increased upper-layer neuron proportion. We demonstrate that these transcriptional divergences are primarily driven by the activity changes of the distal regulatory elements in the genome. Markedly, the chromatin regions with human-gained accessibility enrich the human-fixed sequence changes, as well as sequence polymorphisms associated with intelligence and neuropsychiatric disorders. Our results uncover evolutionary innovations in neural progenitors and gene regulatory mechanism during primate cortex evolution.

evolutionary biology↗

Diversity and distribution of viruses inhabiting the oil reservoirs

Oil reservoirs, being one of the most significant subsurface repositories of energy and carbon, have long hosted diverse microorganisms affecting energy production and carbon emissions. Viruses play crucial roles in the ecology of microbiomes, however, their distribution and ecological significance in oil reservoirs remain undetermined. Here, we assembled an extensive catalogue encompassing viral and prokaryotic genomes sourced from oil reservoirs. The catalogue comprises 7,229 prokaryotic genomes and 6,218 viral genomes from 182 oil reservoir metagenomes, respectively. Based on sequence clustering we identified 3,886 Operational Taxonomic Units (vOTUs) approximately at species level, 94.80% of which were not found in any other environments. The results showed that viruses were widely distributed in oil reservoirs, and oil reservoirs contain a significant number of unique and unexplored viruses. We also constructed a catalogue of 322,060 viral gene clusters including 105 virus-encoded putative auxiliary metabolic genes (AMGs) that participate in host metabolism and adaptation to the environment. Furthermore, our investigation has yielded a total of 7,197 putative virus-host pairs based on CRISPR and tRNA profiles. Viruses within oil reservoirs profoundly infected bacterial Actinobacteriota, Desulfobacterota, as well as archaeal Halobacteriota and Methanobacteriota. Combined microcosm enrichment experiments and bioinformatics analysis, we validated the ecological roles of viruses in regulating the community structure of sulfate reduction microorganisms, primarily through the predation of virulent viruses. Collectively, these findings have unveiled a rich diversity of novel viruses and their ecological functions within oil reservoirs. This study provides a comprehensive understanding of the role of viral communities in the biogeochemical cycle of the deep biosphere. It also facilitates microbial applications aimed at addressing challenges related to fossil-fuel production and carbon emissions in the petroleum industry.

microbiology↗

Replay-triggered Brain-wide Activation in Humans

The consolidation of discrete experiences into a coherent narrative shape our cognitive map, providing a structured mental representation of our experiences. Neural replay, by fostering crucial hippocampal-cortical dialogue, is thought to be pivotal in this process. However, the brain-wide engagement coinciding with replay bursts remains largely unexplored. In this study, by employing simultaneous EEG-fMRI, we capture both the spatial and temporal dynamics of replay. We find that during mental simulation, the strength of on-task replay, as detected via EEG, correlates with heightened fMRI activity in the hippocampus and medial prefrontal cortex. Intriguingly, increased replay strength also enhances the functional connectivity between the hippocampus and the default mode network, a set of brain regions key to representing cognitive map. Furthermore, during the post-learning resting state, we observed a positive association between increased task-related reactivation, hippocampal activity, and augmented connectivity to the entorhinal cortex. Our findings elucidate the neural mechanism of human replay in both time and space, providing novel insights into dynamics of replay and associated brain-wide activation.

neuroscience↗

Elf1 promotes Rad26 interaction with lesion-arrested Pol II for transcription-coupled repair

Transcription-coupled nucleotide excision repair (TC-NER) is a highly conserved DNA repair pathway that removes bulky lesions in the transcribed genome. Cockayne syndrome B protein (CSB), or its yeast ortholog Rad26, has been known for decades to play important roles in the lesion-recognition steps of TC-NER. Another conserved protein ELOF1, or its yeast ortholog Elf1, was recently identified as a core transcription-coupled repair factor. How Rad26 distinguishes between RNA polymerase II (Pol II) stalled at a DNA lesion or other obstacles and what role Elf1 plays in this process remains unknown. Here, we present cryo-EM structures of Pol II-Rad26 complexes stalled at different obstacles that show that Rad26 uses a universal mechanism to recognize a stalled Pol II but interacts more strongly with a lesion-arrested Pol II. A cryo-EM structure of lesion-arrested Pol II-Rad26 bound to Elf1 revealed that Elf1 induces new interactions between Rad26 and Pol II when the complex is stalled at a lesion. Biochemical and genetic data support the importance of the interplay between Elf1 and Rad26 in TC-NER initiation.

biophysics↗

Antibody Humanization via Protein Language Model and Neighbor Retrieval

Antibody (Ab), also known as immunoglobulin (Ig), is an essential macromolecule involved in human immune response and plays an increasingly vital role in drug discovery. However, the development of antibody drugs heavily relies on humanization of murine antibodies, which often necessitates multiple rounds of sequence optimizations through laborious experimental processes. In recent years, the remarkable capabilities of machine learning have revolutionized the field of natural sciences and have also demonstrated promising applications in the field of antibody humanization. Here, we present Protein-LAnguage-model-knN (PLAN), a machine learning model leveraging protein language model and information retrieval for improving humanization of antibodies. Further, we propose DE, a computed value shows a positive correlation with antigen-binding affinity. Our in silico experimental results demonstrate that 1) the PLAN-humanized sequences average humanness score reaches 0.592, improving over the best existing method by 44.7%; 2) a 63% overlap between the PLAN-proposed mutations and the mutations validated through wet lab experiments, which is 16.7% higher than the best existing result; 3) comparable antigen-binding affinity after DE guided back mutation.

bioinformatics↗

Causal Genetic Loci for a Motivated Behavior Spectrum Harbor Psychiatric Risk Genes

Behavioral diversity is critical for population fitness. Individual differences in risk-taking are observed across species, but underlying genetic mechanisms and conservation are largely unknown. We examined dark avoidance in larval zebrafish, a motivated behavior reflecting an approach-avoidance conflict. Brain-wide calcium imaging revealed significant neural activity differences between approach-inclined versus avoidance-inclined individuals. We used a population of [~]6,000 to perform the first genome-wide association study (GWAS) in zebrafish, which identified 34 genomic regions harboring many genes that are involved in synaptic transmission and human psychiatric diseases. We used CRISPR to study several causal genes: serotonin receptor-1b (htr1b), nitric oxide synthase-1 (nos1), and stress-induced phosphoprotein-1 (stip1). We further identified 52 conserved elements containing 66 GWAS significant variants. One encoded an exonic regulatory element that influenced tissue-specific nos1 expression. Together, these findings reveal new genetic loci and establish a powerful, scalable animal system to probe mechanisms underlying motivation, a critical dimension of psychiatric diseases.

neuroscience↗

Prosocial Decision-Making and Human Brain: A Graph Theory Analysis on Resting-State Functional Magnetic Resonance Image

Prosocial behavior is the cornerstone of a harmonious society. However, the functional organization of the brain underlying prosocial decision-making needs to be further explored. Here, we used graph theory analysis to investigate the brain functional connectivity derived from functional magnetic resonance imaging (fMRI) scans during rest in 55 female Chinese university students. The behavioral responses were collected in another fMRI scan during which participants completed an economic exchange game task by making multiple choices between a prosocial and a selfish option against either human counterparts (i.e., social environment) or robot counterparts (i.e., non-social environment). We found that making more prosocial decisions is accompanied by a longer path length in the right anterior superior temporal gyrus (aSTG), higher degree centrality in the posterior cingulate cortex (PCC), and higher betweenness centrality in the left aSTG. Our results suggest that human prosocial decisions are associated with greater inter-regional collaborations that are dominated by a few core nodes within the brain network of Theory of Mind (ToM). Moreover, an individuals preference for making prosocial decisions could be uncovered by graph theory analysis of the functional brain network even without explicit task requirements.

neuroscience↗

The Impact of the Local Mechanical Environment on Cell Shape and Chondrogenesis of Mesenchymal Stromal Cells in 3D Biomimetic Composite Materials

Efforts to model and repair connective tissue through engineered tissue constructs have generated great interest in culturing cells in 3d polymer network environments. It has been shown that the polymer environment is influential in determining cellular responses such as differentiation, migration and morphology. Hydrogels are used to mimic the cellular microenvironment, but in most cases hydrogels consisting of one polymeric component are used whereas tissues are composites of different polymers. A clear understanding of how different extracellular components and their mechanical characteristics influence cell behaviour is lacking. Here we developed and characterised composite hydrogels of hyaluronan and fibrin and evaluated their use for cartilage tissue engineering. We demonstrate that these cartilage-mimicking composites have a higher stiffness relative to the individual constituents. Next, we cultured human mesenchymal stromal cells in these 3D hydrogels with chondrogenic media and revealed marked differences in cell morphology, gene expression and cartilage-like matrix deposition depending on the specific extracellular composition. We found that, despite evidence for strong adhesion of the cells to fibrin networks in 2D systems, in 3D systems the primary determinant of cellular morphology is the significantly denser hyaluronan network. Dense hyaluronan hydrogels cause local cell confinement evidenced by rounder cell morphologies, independent of the presence of fibrin. While the composite fibrin-hyaluronan hydrogels led to lower expression of chondrogenic genes than hyaluronan alone, the larger linear modulus and resistance to cell-mediated contraction due to the composite nature of the matrix provides a strong advantage in terms of macroscopic mechanical stability. These findings highlight the potential of multi-component hydrogels for controlling cellular behaviour and bulk mechanical properties of cell-hydrogel constructs independently, therefore opening avenues for better understanding the complex interplay between cells and their extracellular environment and thus improve the biofabrication of connective tissues for disease modelling and tissue regeneration. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/555478v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@151962org.highwire.dtl.DTLVardef@1358890org.highwire.dtl.DTLVardef@198dcedorg.highwire.dtl.DTLVardef@d04f80_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

SIDERITE: Unveiling Hidden Siderophore Diversity in the Chemical Space Through Digital Exploration

Siderophores, a highly diverse family of secondary metabolites, play a crucial role in facilitating the acquisition of the essential iron. However, the current discovery of siderophore relies largely on manual approaches. In this work, we introduced SIDERTE, a digitized siderophore information database containing 872 siderophore records with 649 unique structures. Leveraging this digitalized dataset, we gained a systematic overview of siderophores by their clustering patterns in the chemical space. Building upon this, we developed a functional group-based method for predicting new iron-binding molecules. Applying this method to 4,314 natural product molecules from TargetMols Natural Product Library for high throughput screening, we experimentally confirmed that 40 out of the 48 molecules predicted as siderophore candidates possessed iron-binding abilities. Expanding our approach to the COCONUT natural product database, we predicted a staggering 3,199 siderophore candidates, showcasing remarkable structure diversity that are largely unexplored. Our study provides a valuable resource for accelerating the discovery of novel iron-binding molecules and advancing our understanding towards siderophores.

biochemistry↗

Loss of finger control complexity and intrusion of flexor biases are dissociable in finger individuation impairment after stroke

The ability to control each finger independently is an essential component of human hand dexterity. A common observation of hand function impairment after stroke is the loss of this finger individuation ability, often referred to as enslavement, i.e., the unwanted coactivation of non-intended fingers in individuated finger movements. In the previous literature, this impairment has been attributed to several factors, such as the loss of corticospinal drive, an intrusion of flexor synergy due to upregulations of the subcortical pathways, and/or biomechanical constraints. These factors may or may not be mutually exclusive and are often difficult to tease apart. It has also been suggested, based on a prevailing impression, that the intrusion of flexor synergy appears to be an exaggerated pattern of the involuntary coactivations of task-irrelevant fingers seen in a healthy hand, often referred to as a flexor bias. Most previous studies, however, were based on assessments of enslavement in a single dimension (i.e., finger flexion/extension) that coincide with the flexor bias, making it difficult to tease apart the other aforementioned factors. Here, we set out to closely examine the nature of individuated finger control and finger coactivation patterns in all dimensions. Using a novel measurement device and a 3D finger-individuation paradigm, we aim to tease apart the contributions of lower biomechanical, subcortical constraints, and top-down cortical control to these patterns in both healthy and stroke hands. For the first time, we assessed all five fingers full capacity for individuation. Our results show that these patterns in the healthy and paretic hands present distinctly different shapes and magnitudes that are not influenced by biomechanical constraints. Those in the healthy hand presented larger angular distances that were dependent on top-down task goals, whereas those in the paretic hand presented larger Euclidean distances that arise from two dissociable factors: a loss of complexity in finger control and the dominance of an intrusion of flexor bias. These results suggest that finger individuation impairment after stroke is due to two dissociable factors: the loss of finger control complexity present in the healthy hand reflecting a top-down neural control strategy and an intrusion of flexor bias likely due to an upregulation of subcortical pathways. Our device and paradigm are demonstrated to be a promising tool to assess all aspects of the dexterous capacity of the hand.

neuroscience↗

Step-wise activation of a Family C GPCR

Metabotropic glutamate receptors belong to a family of G protein-coupled receptors that are obligate dimers and possess a large extracellular ligand-binding domain (ECD) that is linked via a cysteine-rich domain (CRDs) to their 7-transmembrane (TM) domain. Upon activation, these receptors undergo a large conformational change to transmit the ligand binding signal from the ECD to the G protein-coupling TM. In this manuscript, we propose a model for a sequential, multistep activation mechanism of metabotropic glutamate receptor subtype 5. We present a series of structures in lipid nanodiscs, from inactive to fully active, including agonist-bound intermediate states. Further, using bulk and single-molecule fluorescence imaging we reveal distinct receptor conformations upon allosteric modulator and G protein binding.

biophysics↗

In situ structural insights into the excitation contraction coupling mechanism of skeletal muscle

Excitation-contraction coupling (ECC) is a fundamental mechanism in control of skeletal muscle contraction and occurs at triad junctions, where dihydropyridine receptors (DHPRs) on transverse tubules sense excitation signals and then cause calcium release from the sarcoplasmic reticulum via coupling to type 1 ryanodine receptors (RyR1s), inducing the subsequent contraction of muscle filaments. However, the molecular mechanism remains unclear due to the lack of structural details. Here, we explored the nanometre-resolution architecture of triad junction by cryo-electron tomography, solved the in situ structure of RyR1 in complex with FKBP12 and calmodulin, and discovered the intact RyR1-DHPR supercomplex. RyR1s arrange into two rows on the terminal cisternae membrane by forming right-hand corner-to-corner contacts, and tetrads of DHPRs bind to RyR1s in an alternating manner, forming another two rows on the transverse tubule membrane. Such unique arrangement is important for synergistic calcium release and provides direct evidence of physical coupling in ECC.

biophysics↗