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Biology subjects

Ye, J.

Publications and source records attributed to Ye, J..

At least 109 records · Page 6Linked to original sources

Biomaterial based implants caused remote liver fatty deposition through activated blood-derived Kupffer cells

Understanding the foreign-body response (FBR) of biomaterials is a prerequisite for the prediction of its clinical application, and the present assessments mainly rely on in vitro cell culture and in situ histopathology. However, remote organs responses after biomaterials implantation is unclear. Here, by leveraging body-wide-transcriptomics data, we performed in-depth systems analysis of biomaterials - remote organs crosstalk after abdominal implantation of polypropylene and silk fibroin using a rodent model, demonstrating local implantation caused remote organs responses dominated by acute-phase responses, immune system responses and lipid metabolism disorders. Of note, liver function was specially disturbed, defined as hepatic lipid deposition. Combining flow cytometry analyses and liver monocyte recruitment inhibition experiments, we proved that blood derived monocyte-derived Kupffer cells in the liver underlying the mechanism of abnormal lipid deposition induced by local biomaterials implantation. Moreover, from the perspective of temporality, the remote organs responses and liver lipid deposition of silk fibroin group faded away with biomaterial degradation and restored to normal at end, which highlighted its superiority of degradability. These findings were further indirectly evidenced by human blood biochemical examination from 141 clinical cases of hernia repair using silk fibroin mesh and polypropylene mesh. In conclusion, this study provided knowledge of biomaterials-body interactions. It is of great important for future development of biomaterial devices for clinical application. One Sentence SummaryAbdominal local biomaterials implantation induces remote organ fatty deposition through activated blood-derived Kupffer cells.

pharmacology and toxicology↗

SynEcoSys: a multifunctional platform of large-scale single-cell omics data analysis

Next generation sequencing technologies enable the analysis of the transcriptomes of individual cells, providing a higher resolution of gene expression and function at the single cell level. Various single-cell data are continuously generated every year, covering fields from scientific research to clinical development. The fast-growing public datasets are collected by distinctive platforms, which are designed to facilitate biological discoveries, disease diagnosis, and new treatments. However, these platforms are hard to meet the urgency of having a unified data integration pipeline to improve comparability between datasets. Here we present SynEcoSys, an online multifunctional platform for single-cell transcriptomic data analysis, visualization, and exploration. SynEcoSys by Singleron Biotechnologies currently provides a massive collection of publicly available single-cell sequencing dataset, involving 46,326,175 cells from 731 datasets across multiple platforms and species. All datasets are generated with a strict and uniform data analysis pipeline and cell marker-based manual annotation, thus facilitating more comprehensive and reliable data mining. SynEcoSys is available at: https://www.synecosys.com.

bioinformatics↗

Protein Sequence Design by Entropy-based Iterative Refinement

Inverse Protein Folding (IPF) is an important task of protein design, which aims to design sequences compatible with a given backbone structure. Despite the prosperous development of algorithms for this task, existing methods tend to leverage limited and noisy residue environment when generating sequences. In this paper, we develop an iterative sequence refinement pipeline, which can refine the sequence generated by existing sequence design models. It selects and retains reliable predictions based on the models confidence in predicted distributions, and decodes the residue type based on a partially visible environment. The proposed scheme can consistently improve the performance of a number of IPF models on several sequence design benchmarks, and increase sequence recovery of the SOTA model by up to 10%. We finally show that the proposed model can be applied to redesign Transposon-associated transposase B. 8 variants exhibit improved gene editing activity among the 20 variants we proposed. Our code and a demo of the refinement pipeline are provided in the online colab.

bioinformatics↗

DPHL v2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins.

A comprehensive pan-human spectral library is critical for biomarker discovery using mass spectrometry (MS)-based proteomics. DPHL v1, a previous pan-human library built from 1096 data-dependent acquisition (DDA) MS data of 16 human tissue types, allows quantifying 10,943 proteins. However, a major limitation of DPHL v1 is the lack of semi-tryptic peptides and protein isoforms, which are abundant in clinical specimens. Here, we generated DPHL v2 from 1608 DDA-MS data acquired using Orbitrap mass spectrometers. The data included 586 DDA-MS newly acquired from 17 tissue types, while 1022 files were derived from DPHL v1. DPHL v2 thus comprises data from 24 sample types, including several cancer types (lung, breast, kidney, and prostate cancer, among others). We generated four variants of DPHL v2 to include semi-tryptic peptides and protein isoforms. DPHL v2 was then applied to a publicly available colorectal cancer dataset with 286 DIA-MS files. The numbers of identified and significantly dysregulated proteins increased by at least 21.7% and 14.2%, respectively, compared with DPHL v1. Our findings show that the increased human proteome coverage of DPHL v2 provides larger pools of potential protein biomarkers.

bioinformatics↗

Multiple founding paternal lineages inferred from the newly-developed SNPSeqTyper 639 Y-SNP panel suggested the complex admixture and migration history of Chinese people

Non-recombining regions of the Y-chromosome are inherited male-specifically and recorded the evolutionary traces of male human populations. Recent whole Y-chromosome sequencing studies have identified previously unrecognized population divergence, expansion and admixture processes, which promotes a better understanding and application of the observed patterns of Y-chromosome genetic diversity. Here, we developed one highest-resolution Y-SNP panel for forensic pedigree search and paternal biogeographical ancestry inference, which included 639 phylogenetically informative SNPs (Y-SNPs). We genotyped these loci in 1033 Chinese male individuals from 33 ethnolinguistically diverse populations and identified 257 terminal Y-chromosomal lineages with frequency ranging from 0.010 (singleton) to 0.0687. We identified six dominant common founding lineages associated with different ethnolinguistic backgrounds, which included O2a2b1a1a1a1a1a1a1-M6539, O2a1b1a1a1a1a1a1-F17, O2a2b1a1a1a1a1b1a1b-MF15397, O2a2b2a1b1-A16609, O1b1a1a1a1b2a1a1-F2517 and O2a2b1a1a1a1a1a1-F155. The AMOVA and nucleotide diversity estimates revealed considerable differences and high genetic diversity among ethnolinguistically different populations. We constructed one representative phylogenetic tree among 33 studied populations based on the haplogroup frequency spectrum and sequence variations. Clustering patterns in principal component analysis and multidimensional scaling results showed a genetic differentiation between Tai-Kadai-speaking Li, Mongolic-speaking Mongolian and other Sinitic-speaking Han Chinese populations. Phylogenetic topology inferred from the BEAST and Network relationships reconstructed from the popART further showed the founding lineages from culturally/linguistically diverse populations, such as C2a/C2b was dominant in Mongolian people and O1a/O1b was dominant in island Li people. We also identified many lineages shared by more than two ethnolinguistically different populations with a high proportion, suggesting their extensive admixture and migration history. Our findings indicated that our developed high-resolution Y-SNP panel included major dominant Y-lineages of Chinese populations from different ethnic groups and geographical regions, which can be used as the primary and powerful tool for forensic practice. We should emphasize the necessity and importance of whole-sequencing of more ethnolinguistically different populations, which can help identify more unrecognized population-specific variations for the final promotion of Y-chromosome-based forensic applications.

genetics↗

Bovine blastocyst like structures derived from stem cell cultures

Understanding blastocyst formation and implantation is critical for improving farm animal reproduction but is hampered by a limited supply of embryos. We developed an efficient method to generate bovine blastocyst-like structures (termed blastoids) via the assembly of trophoblast stem cells and expanded potential stem cells. Bovine blastoids resemble blastocysts in morphology, cell composition, single-cell transcriptomes, and represent an accessible in vitro model for studying bovine embryogenesis.

developmental biology↗

Glucose modulates transcription factor dimerization to enable tissue differentiation

Glucose is a universal energy currency for living organisms, however, its non-energetic functions in processes such as differentiation are undefined. In epidermis, differentiating cells exhibit dynamic changes in gene expression1-4 driven by specific transcription factors (TFs)5-9. The interplay between such TFs and biomolecules that also change in this process is not understood. Metabolomic analyses revealed that increased intracellular glucose accompanies differentiation of epidermal keratinocytes. This elevation also occurred in differentiating cells from other tissues and was verified in epidermal tissue engineered with glucose sensors, which detected a glucose gradient that peaked in the outermost differentiated layers. Free glucose accumulation, unaccompanied by its increased metabolism, was essential for epidermal differentiation and required GLUT1, GLUT3, and SGLT1 transporters. Glucose affinity chromatography and azido-glucose click chemistry uncovered glucose binding to diverse regulatory proteins, including the IRF6 TF, whose epidermal knockout confirmed its requirement in glucose-dependent differentiation. Direct glucose binding enabled IRF6 dimerization, DNA binding, genomic localization, and induction of IRF6 target genes, including essential pro-differentiation TFs GRHL1, GRHL3, HOPX and PRDM1. The IRF6R84C mutant found in undifferentiated cancers was unable to bind glucose. These data identify a new role for glucose as a gradient morphogen that modulates protein multimerization in cellular differentiation.

molecular biology↗

Complex Intracellular Mechanisms of TBK1 Kinase Activation Revealed by a Specific Small Molecule Inhibitor

TANK-binding kinase 1 (TBK1), a dimeric serine/threonine protein kinase, plays a critical role in multiple signaling pathways including innate immunity, autophagy and cell death. TBK1 is activated by the phosphorylation of an essential serine residue 172 (S172) within the activation loop of the kinase domain, and this phosphorylation can occur by trans-autophosphorylation: one TBK1 dimer phosphorylates a second dimer at S172. Here we show that phosphorylation of TBK1 S172 in cultured human cells in response to multiple inducers is reduced, but not abolished by the highly specific and potent TBK1 small molecule inhibitor GSK8612. Thus, upstream kinase(s) must phosphorylate TBK1 in response to inducers in cultured cells. We show that distinct upstream kinases are recruited for the activation of TBK1 in response to different inducers. We also identify extensive crosstalk among TBK1, IKK{beta} and IKK{varepsilon} kinases in the cellular response to various inducers. In addition, we show that dsDNA and dsRNA trigger dynamic intracellular translocation of TBK1, leading to its localization and activation on the Golgi apparatus or mitochondria, respectively. GSK8612 does not block the intracellular localization of TBK1. We conclude that TBK1 is activated by both upstream kinase phosphorylation and by trans-autophosphorylation, and the signal-dependent spatial engagement of TBK1 with other signaling molecules is a fundamental mechanism for its specific activation by multiple inducers.

molecular biology↗

Trends in self-citation rates in neuroscience literature

Citation metrics influence academic reputation and career trajectories. Recent works have highlighted flaws in citation practices in the Neurosciences, such as the under-citation of women. However, self-citation rates--or how much authors cite themselves--have not yet been comprehensively investigated in the Neurosciences. This work characterizes self-citation rates in basic, translational, and clinical Neuroscience literature by collating 100,347 articles from 63 journals between the years 2000-2020. In analyzing over five million citations, we demonstrate four key findings: 1) increasing self-citation rates of Last Authors relative to First Authors, 2) lower self-citation rates in low- and middle-income countries, 3) gender differences in self-citation stemming from differences in the number of previously published papers, and 4) variations in self-citation rates by field. Our characterization of self-citation provides insight into citation practices that shape the perceived influence of authors in the Neurosciences, which in turn may impact what type of scientific research is done and who gets the opportunity to do it.

neuroscience↗

The Role of Students' Situational Interest in Classroom Learning: An Empirical Study based on both Laboratory and Naturalistic Paradigms

Interest has always been an important research object in the field of education. Moreover, understanding the role of interest in students classroom learning is conducive to teaching practices. By constructing a theoretical model of interest based on relevant theories and prior empirical evidence, this study examined the differences within research paradigms and explored the potential function of neurophysiological signals in representing students interest in learning. In both laboratory and naturalistic paradigms, self-report and neurophysiological data were collected from 10th graders of an urban secondary school in Beijing, China. Through the data-driven approach of machine learning, the neurophysiological data were employed to fit self-report situational interest, and relevant theoretical models were examined based on all data using structural equation modeling. The path coefficients in the models were subsequently compared to determine the similarities and differences between the two paradigms. Combined with the results of multiple linear regressions established via machine learning, this study demonstrates the ability of neurophysiological data to represent situational interest.

neuroscience↗

Improved Genome Editing by an Engineered CRISPR-Cas12a

CRISPR-Cas12a is an RNA-guided, programmable genome editing enzyme found within bacterial adaptive immune pathways. Unlike CRISPR-Cas9, Cas12a uses only a single catalytic site to both cleave target double-stranded DNA (dsDNA) (cis-activity) and indiscriminately degrade single-stranded DNA (ssDNA) (trans-activity). To investigate how the relative potency of cis- versus trans-DNase activity affects Cas12a-mediated genome editing, we first used structure-guided engineering to generate variants of Lachnospiraceae bacterium Cas12a (LbCas12a) that selectively disrupt trans-activity. The resulting engineered mutant with the biggest differential between cis- and trans-DNase activity in vitro showed minimal genome editing activity in human cells, motivating a second set of experiments using directed evolution to generate additional mutants with robust genome editing activity. Notably, these engineered and evolved mutants had enhanced ability to induce homology-directed repair (HDR) editing by 2-18-fold depending on the genomic locus. Finally, we found that a site-specific reversion mutation produced improved Cas12a (iCas12a) variants with superior genome editing efficiency at genomic sites that are difficult to edit using wild-type Cas12a. This strategy of coupled rational engineering and directed evolution establishes a pipeline for creating improved genome editing tools by combining structural insights with randomization and selection. The availability of experimental and predicted structures of other CRISPR-Cas enzymes will enable this strategy to be applied to improve the efficacy of other genome editing proteins.

biochemistry↗

Porous microneedle patch with sustained exosomes delivery repairs severe spinal cord injury

1.Mesenchymal stem cell-derived exosome (MSC-EXO) transplantation has been suggested as an efficacious treatment to suppress spinal cord injury (SCI)-triggered neuroinflammation. However, an ethically acceptable method to continuously deliver MSC-EXOs to acute spinal lesions, without damaging nearby tissues/axons, has never been achieved. In this study, we fabricated a device comprising a patch containing MSCs and a microneedle array (MN-MSC patch) to treat severe SCI. When topically applied to an acute spinal lesion beneath the spinal dura, the soft microneedle (MN) array with reasonable mechanical strength avoided damaging the nearby spinal tissues, and the porous microstructure of MNs facilitated highly efficient MSC-EXO delivery. With the capacity for sustained delivery of MSC-EXOs, the MN-MSC patch was evaluated in a contusive rat SCI model. The MSCs encapsulated in the patch could survive for at least 7 days, encompassing the optimal time window for downregulating SCI-triggered neuroinflammation. As a result, MN-MSC patch treatment led to reduced cavity and scar tissue formation, greater angiogenesis, and improved survival of nearby tissues/axons. Remarkably, rats treated by this method achieved superior muscle control and exhibited robust hindlimb locomotion functional recovery. Conclusively, the MN-MSC patch device proposed here overcomes the current dilemma between treatment efficacy and ethical issues in treating acute SCI.

bioengineering↗

Injectable hydrogel embedded with mesenchymal stem cells repairs severe spinal cord injury

Mesenchymal stem cell (MSC) transplantation was suggested as a promising approach to treat spinal cord injury (SCI). However, the heterogeneity of MSC and the lack of appropriate delivery methods impede its clinical application. To tackle these challenges, we first generated human MSCs derived from a single cell with a great homogeneity of batch quality and then developed a biocompatible injectable hydrogel to embed these cells to treat severe SCI. In a clinically relevant rat severe SCI model, we showed that the injection of MSCs with injectable hydrogel into the lesion site promoted robust functional recovery, while the intrathecal delivery of MSCs only resulted in limited therapeutic effects. Mechanistically, the hydrogel protected MSCs from the damage of harmful neuroinflammatory microenvironment in the spinal cord lesion. The hydrogel with the survived MSCs ameliorates the neuroinflammatory microenvironment of spinal cord lesion, preventing cavity formation and leads to the remnant of spared axons/tissues, which results in a better prognosis in the end.

bioengineering↗

SARS-CoV-2 S protein antagonizes type I interferon downstream signal pathway through interacting and attenuating phosphorylation of STAT1/STAT2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may keep patients in a clinically asymptomatic state by blocking cellular innate antiviral immunity, but the molecular mechanism remains unclear. Here, we screened the viral proteins of SARS-CoV-2 and found that the spike (S) protein inhibits the activation of interferon-stimulated genes (ISGs) and even reduces the expression of these genes to below background values. Mechanistically, the S protein interacted with STAT1, STAT2, and IRF9 and impedes the phosphorylation of STAT1/STAT2, thus preventing the formation of the interferon-stimulating gene factor 3 (ISGF3) complex and inhibiting the downstream production of Interferon-stimulated genes (ISGs). Remarkably, we also have found that the inhibitory mechanism of the S protein was conservative among SARS-CoV-2 variants and other human coronaviruses, including SARS-CoV, MERS-CoV, HCoV-229E, HCoV-NL63, and HCoV-HKU1. Truncation studies indicated that the most conserved S2 domain played a major inhibitory role. Altogether, our findings unveil a new mechanism by which SARS-CoV-2 S protein attenuated the hosts antiviral immune response and provide new insights into the pathogenic mechanism of coronavirus.

microbiology↗

Loss-of-function mutation in human Oxidation Resistance gene 1 disrupts the spatial-temporal regulation of histone arginine methylation in early brain development

We report a loss-of-function mutation in the TLDc domain of human Oxidation Resistance 1 (OXR1) gene, resulting in early-onset epilepsy, developmental delay, cognitive disabilities, and cerebellar atrophy. Patient lymphoblasts show impaired cell survival, proliferation, and hypersensitivity to oxidative stress. These phenotypes are rescued by TLDc domain replacement. We generated patient derived induced pluripotent stem cells (iPSCs) revealing impaired neural differentiation along with dysregulation of genes essential for neurodevelopment. We identified that OXR1 influences histone arginine methylation by activating protein arginine methyltransferases (PRMTs), suggesting OXR1 dependent mechanisms regulating gene expression during neurodevelopment. We modeled the function of OXR1 in early human brain development using patient derived brain organoids revealing that OXR1 contributes to the spatial-temporal regulation of histone arginine methylation in specific brain regions. Our work provides new insights into pathological features and molecular underpinnings associated with OXR1 deficiency, highlighting the therapeutic potential of OXR1 in numerous neurodegenerative and neurodevelopmental disorders.

pathology↗

FIB-SEM analysis on three-dimensional structures of growing organelles in wild Chlorella pyrenoidosa cells

To clarify dynamic changes of organelle microstructures in Chlorella pyrenoidosa cells during photosynthetic growth with CO2 fixation, three-dimensional organelle microstructures in three growth periods of meristem, elongation and maturity were quantitatively determined and comprehensively reconstructed with focused ion beam scanning electron microscopy (FIB-SEM). The single round-pancake mitochondria in each cell split into a dumbbell and then into a circular ring, while barycenter distance of mitochondria to chloroplast and nucleus was reduced to 45.5% and 88.3% to strengthen energy transfer, respectively. The single pyrenoid consisting of a large part and another small part in each chloroplast gradually developed to a mature state in which the two parts were nearly equal in size. The nucleolus progressively became larger with euchromatin replication. The number of starch grains gradually increased, but average grain volume remained nearly unchanged.

cell biology↗

Genomic analysis of population structure, antimicrobial resistance, and virulent factors of methicillin-resistant Macrococcus caseolyticus in global lineages

Macrococcus caseolyticus is an opportunistic pathogen frequently detected in dairy products as well as veterinary infections. The present study examined the population structure, antimicrobial resistance, and virulent factors of methicillin-resistant M. caseolyticus isolates in retail meat from Shanghai (n=10) and global isolates from GenBank (n=87). All strains were divided into five lineages that distributed in Europe (82.4%, n = 80), Asia (11.3%, n = 11), North America (4.1%, n = 4), Oceania (1%, n = 1) and Africa (1%, n = 1). MLST typing revealed novel alleles in Chinese M. caseolyticus strains. Furthermore, a total of 24 AMR genes associated with 10 classes of antimicrobial agents were identified in the isolates from global lineages, carried by dominant plasmids such as rep7a, rep22 and repUS56. Comparing to other lineages, genomes from the Chinese lineage carried significantly more AMR genes (p<0.005) and less virulent factors (p<0.001), which may be explained by the local evolution of M. caseolyticus in China. Finally, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were enrolled for morphology comparison between M. caseolyticus and S. aureus, showing that M. caseolyticus has a larger diameter and thicker cell wall. The present study showed geographical variation with regards to MLST profiles, antimicrobial resistance, and virulent factors in global M. caseolyticus lineages. This study suggests that such local evolution of foodborne or livestock origin M. caseolyticus may serve as vehicles for domestic transmission of methicillin resistance in retail meat in China. HighlightsO_LIGlobal M. caseolyticus strains were divided into five lineages from A to E. C_LIO_LIMLST typing revealed novel alleles in Chinese M. caseolyticus strains. C_LIO_LIChinese lineage carried significantly more AMR genes and less virulent factors. C_LIO_LIMacrococcus caseolyticus has a larger diameter and thicker cell wall compared with S.aureus. C_LIO_LIMacrococcus caseolyticus may enhance the domestic transmission of methicillin resistance in China. C_LI

microbiology↗

Improving functional recovery after severe spinal cord injury by a noninvasive dual functional approach of neuroprotection and neuromodulation

Despite tremendous unmet medical needs, there is no effective pharmacological treatment to promote functional recovery after spinal cord injury (SCI). Although multiple pathological events have been implicated in SCI, the development of a noninvasive pharmacological approach to simultaneously target the different mechanisms involved in SCI remains a formidable challenge. In this study, we report the development of a noninvasive nanodrug delivery system that consists of ROS-responsive amphiphilic copolymers and an encapsulated neurotransmitter-conjugated KCC2 agonist. We show that upon intravenous administration, the nanodrugs were able to enter the injured spinal cord due to blood spinal cord barrier disruption and ROS-responsive disassembly. Remarkably, once in the injured spinal cord, these nanodrugs exhibited dual functions: scavenging ROS accumulated in the lesion to protect spared connections and increasing neuronal excitability in the injured spinal cord through targeted delivery of the KCC2 agonist to inhibitory neurons. Thus, the noninvasive treatment led to significant functional recovery in the rats with contusive SCI. Together, these findings provide a much-needed translational pharmacological approach for treating severe SCI.

neuroscience↗