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Biology subjects

Shi, X.

Publications and source records attributed to Shi, X..

At least 73 records · Page 4Linked to original sources

Optimization of Extraction Process by Response Surface Methodology of Total Flavonoids from Ziziphus Jujube Flesh and its Sedative-Hypnotic Effects

Background & aimsThis study optimizes the extraction process of total flavonoids from Ziziphus jujube flesh (TFZJF) by response surface methodology and investigating its sedative-hypnotic effects and mechanisms in a para-chlorophenylalanine (PCPA)-induced insomnia mouse model. It provides theoretical support for the further comprehensive utilization of Ziziphus jujube fruit and flesh. MethodsSingle-factor experiment and Box-Behnken response surface design were used to study the ethanol reflux extraction process of TFZJF, with flavonoid extraction rate as the indicator, to obtain the optimal extraction process of TFZJF. An insomnia model in mice was induced via an intraperitoneal injection of PCPA, and the effects of TFZJF on this model, along with its underlying mechanisms, were assessed using various approaches, including sodium pentobarbital-induced sleep potentiation, HE staining of tissue sections, ELISA, RT-PCR, WB, and serum metabolomics. ResultsThe results showed that the optimized extraction conditions for TFZJF included a solid-liquid ratio (SLR) of 1:25 g{middle dot}mL-1, ethanol concentration of 60%, and extraction time of 60 min, yielding an extraction efficiency of 1.98%. Data from the experimental groups indicated dose-dependent sleep improvement in the insomnia model, with the high-dose TFZJF (TFZJF-H) group exhibiting the most significant effect, followed by the medium-dose (TFZJF-M) and low-dose (TFZJF-L) groups. Metabolomic analysis revealed that TFZJF administration positively impacted the metabolic profile of PCPA-induced insomnia, particularly affecting pathways related to phenylalanine, tyrosine, cytochrome P450, and alanine metabolism on non-targeted metabolomics. ConclusionsThe extraction process is stable and reliable, which can be used for the extraction of TFZJF; meanwhile, TFZJF demonstrated significant sleep-enhancing effects in the PCPA-induced insomnia mouse model, supporting its potential for resource development and the utilization of non-medicinal parts of Ziziphus jujube.

biochemistry↗

Hydrogen-bonded organic framework nanotransducers enabled sono-optogenetics for Parkinsonian rats

Cell-type-specific activation of parvalbumin (PV)-expressing neurons in the external globus pallidus (GPe) through optogenetics has shown promise in facilitating long-lasting movement dysfunction recovery in mice with Parkinsons disease. However, its translational potential is hindered by adverse effects stemming from the invasive implantation of optical fibers into the brain. In this study, we have developed a non-invasive optogenetics approach, utilizing focused ultrasound-triggered mechanoluminescent nanotransducers to enable remote photon delivery deep in the brain for genetically targeted neuromodulation. These mechanoluminescent nanotransducers consist of sonosensitized hydrogen-bonded frameworks and chemiluminescent L012, serving as a nanoscale light source through ultrasound-induced cascade reactions. This system offers high ultrasound-triggered brightness and long-lasting light emission, facilitating repeatable deep brain stimulation. Our sono-optogenetics technology demonstrated effective modulation in the mouse motor cortex for limb motion control and activation of PV-GPe neurons for rescuing movement dysfunction over time in dopamine-depleted Parkinsons disease rats. This approach demonstrates the pathway for achieving genetically targeted and non-invasive neuromodulation for long-lasting treatment of Parkinsons disease, towards non-human primate models and clinical applications.

bioengineering↗

Roles of spoVF operon subunits A and B in regulating cell morphology and biofilm formation in the biocontrol agent Bacillus subtilis

Enhanced expression of spoVF operon (sporulation initiation factor; dipicolinic acid (DPA) synthase) in Bacillus subtilis vegetative cells has been reported to increase host attachment and biocontrol ability. However, how the spoVF operon regulates these essential biocontrol factors remains unknown. In this study, it was found that the knockout of the spoVFA or spoVFB subunits, individually ({Delta}A and{Delta} B), or together ({Delta}A{Delta}B), decreased DPA biosynthesis, host attachment, nutrient competition ability, and biocontrol efficacy in B. subtilis. Moreover, the cell shape of the knockout strains changed from short rod to spherical. qRT-PCR analysis indicated that the spoVF operon regulates TCA cycle expression and biofilm formation by balancing the amounts of various transcriptional factors, such as spo0A, SinR, and AbrB, and the cofactor NADPH. The regulatory mechanism of the spoVF operon in B. subtilis biofilm-related genes was proposed for the first time. IMPORTANCEBacillus subtilis SpoVF operon contains the spoVFA or spoVFB subunits, which are responsible for the dipicolinic acid synthase activity. Dipicolinic acid is an important component of B. subtilis spores. In this study, the roles of spoVFA or spoVFB subunits in the biocontrol ability B. subtilis were examined, indicating that the spoVFA subunit plays a key role in B. subtilis biofilm formation, cell morphology, growth, and nutrient competition ability. Additionally, the regulatory network connecting the spoVF operon with biofilm formation-related genes of B. subtilis was proposed. The results obtained in this study help to understand key genes involved in the biocontrol ability of B. subtilis.

microbiology↗

The dominance of non-native plants over native plants increases with the number of global change factors

Global environmental change and plant invasion are both recognized as key indicators of the Anthropocene, with the former potentially accelerating the latter. Still, whether multiple co-acting global change factors (GCFs) influence plant invasions even stronger remains untested despite the fact that in nature GCFs usually act together rather than alone. Here, four non-native and four native species were cultivated jointly as communities in mesocosm pots, and we tested their responses to increasing GCF numbers (0, 1, 2, 3, 4, 5). We found that GCF number had no influence on community productivity but increased the biomass proportion of non-native plants. GCF number increased biomass but had no influence on height for non-native plants, whereas both biomass and height of native plants decreased with increasing GCF number. Consequently, our findings indicate that dominance may increases when habitats experience multiple global change factors, and thus that invasion risk of non-native plants could potentially be underestimated from studies on single GCFs. Open Research statementThe data supporting the results will be made available upon acceptance.

ecology↗

SUMO E1 covalent allosteric inhibitors modulate polyamine synthesis via the MAT2A-AdoMetDC axis

Upregulation of protein SUMOylation is associated with various diseases, and SUMOylation inhibitors are promising drug candidates. We performed the first virtual screening of SUMO E1 covalent allosteric inhibitors (CAIs) and identified two SUMO E1 CAIs with new scaffolds and covalent warheads. We further demonstrated that these new CAIs perturbed the SUMOylation pathway and protein SUMOylation. Specifically, these CAIs affected the SUMOylation of the methionine adenosyltransferases MAT2A. The inhibition of MAT2A SUMOylation unexpectedly stimulated polyamine synthesis. Lastly, we showed that the combination of SUMO E1 CAIs with a polyamine synthesis inhibitor had synergistic effects in inhibiting T47D cells. Our work demonstrated the first cost-effective virtual screening of SUMO E1 CAIs, found that the downregulation of MAT2A SUMOylation increases polyamine synthesis, and SUMO E1 CAIs can synergize with polyamine synthesis inhibitors. This work would be of great value to the study of SUMOylation, covalent/allosteric drugs, and the polyamine metabolism network.

pharmacology and toxicology↗

Two distinct structural variants involving EDN3 cause hyperpigmentation in chicken

Phenotypic diversity and its genetic basis are central questions in biology, with domesticated animals offering valuable insights due to their rapid evolution the last 10,000 years. In chickens, fibromelanosis (FM) is a striking pigmentation phenotype characterized by hyperpigmentation. A previous study identified a complex structural variant causing upregulated expression of the Endothelin 3 (EDN3) gene. However, the detailed structural arrangement and functional consequences of the variant remained unclear. In this study, we conducted a comprehensive genomic survey of 692 FM chickens representing 55 breeds and uncovered two distinct structural variants causing the FM phenotype: FM*A, the previously reported complex rearrangement involving the EDN3 locus1, and FM*B, a tandem duplication of a 16 kb region upstream of EDN3. We demonstrate that both structural variants (SVs) significantly upregulate EDN3 expression, with FM*B associated with even higher expression than FM*A. A luciferase reporter assays showed that the 16 kb region in FM*B contains powerful enhancers and the copy number expansion of this element is a likely explanation for EDN3 upregulation and hyperpigmentation. Furthermore, our analysis of linkage disequilibrium patterns allowed us to resolve the complex arrangement of duplications and inversion on the FM*A haplotype.

genomics↗

Distinct Binding Modes of Inter-Spike Cross-Linking Suggest a Supplementary Mechanism for SARS-CoV-2 Antibody Neutralization

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its Omicron subvariants drastically amplifies transmissibility, infectivity, and immune escape, mainly due to their resistance to most neutralizing antibodies. Thus, exploring the mechanisms underlying antibody evasion is crucial. Although the full-length native form of antibody, immunoglobulin G (IgG), offers valuable insights into the neutralization, structural investigations primarily focus on the fragment of antigen-binding (Fab). Here, we employ single-particle cryo-electron microscopy (cryo-EM) to characterize a W328-6H2 antibody, in its native IgG form complexed with severe acute respiratory syndrome (SARS), severe acute respiratory syndrome coronavirus 2 wild-type (WT) and Omicron variant BA.1 spike protein (S). Three high-resolution structures reveal that the full-length IgG forms a centered head-to-head dimer of trimer when bound fully stoichiometrically with both SARS and WT S, while adopting a distinct offset configuration with Omicron BA.1 S. Combined with functional assays, our results suggest that, beyond the binding affinity between the RBD epitope and Fab, the higher-order architectures of S trimer and full-length IgG play an additional role in neutralization, elucidate a potential molecular basis of Omicron immune escape, and expand our understanding on antibody evasion mechanisms.

immunology↗

Positive impact of Type-A and -C response regulator genes on growth and panicle architecture in rice

Cytokinin signal transduction occurs through a "two-component system." Type-A and -C response regulators (RRs) are groups of proteins of similar structures constituting significant components of cytokinin signal transduction. In rice, 13 (Type-A) and two (Type-C) RRs have been identified to date; however, their functions remain partially known. In this study, we examined the expression patterns of Type-A and Type-C RRs in rice using RNA-Seq and confirmed their functions by constructing mutants of the 15 genes with CRISPR/Cas9. Almost all Type-A RRs played positive roles in the development of secondary branches and secondary spikelets, particularly RR2 and RR4. Notably, rr1 rr2 and rr8 rr12 rr13 higher-order mutants displayed small panicle sizes and decreased plant height. Additionally, both Type-C RRs played positive roles in regulating heading date. RNA-seq revealed several genes with significantly altered expression in the rr2 and rr4 mutants, with almost half of the differentially expressed genes (DEGs) overlapping between the two mutants. Many of the DEGs were associated with the cytokinin and abscisic acid pathways. Our findings provide new insights into the functions of Type-A and -C RRs in rice growth and may serve as a foundation for future studies focusing on cytokinin signaling.

plant biology↗

Mechanical stretch induced collective cell alignment

Cell alignment is a fundamental process in tissue morphogenesis. While density-dependent collective cell alignment has been widely observed, its underlying mechanisms remain poorly understood. Here, using C2C12 myoblasts, we demonstrate that static uniaxial mechanical stretch induces collective cell alignment in a density-dependent manner: densely populated cultures align robustly, whereas sparse populations do not. We reveal a biphasic alignment process, comprising an initial passive phase and a subsequent active phase. The passive phase, driven by substrate deformation, transiently biases cell orientation along the stretch axis regardless of density. In the active phase, initial alignment progressively dissipates in low-density cultures, but is sustained and reinforced in high-density cultures. Supported by coarse-grained agent-based simulations, we propose that self-generated cellular forces facilitate kinetic transitions between orientations, enabling cells to explore orientational states, whereas cell-cell interactions provide a thermodynamic bias that stabilizes the locally aligned state. In dense cultures, strong intercellular interactions promote this stabilization, enabling persistent alignment. In contrast, sparse cultures lack sufficient cell-cell interaction, leading to alignment dissipation. Within this C2C12 system, our findings highlight the cooperative roles of cellular forces and intercellular interactions in orchestrating multicellular ordering, offering new insights into mechanobiology of tissue morphogenesis.

bioengineering↗

Fusobacterium necrophorum and Fusobacterium varium are commensal members of the bovine reproductive microbiota and may colonize calf prenatally

Fusobacterium necrophorum is an important pathogen associated with several infectious diseases in cattle. However, recent sequencing-based studies have indicated that F. necrophorum is positively associated with pregnancy in beef cows and that Fusobacterium is the most abundant genus in the bull seminal microbiota, suggesting the potential role of Fusobacterium in reproductive health and fertility. Here, we performed a comprehensive screening to 1) determine whether Fusobacterium necrophorum (subspecies necrophorum [FNN] and funduliforme [FNF]), and Fusobacterium varium (FV) are part of the commensal members of the reproductive microbiota in cattle; 2) to explore whether these Fusobacterium spp. are colonized in calf prenatally. For this, we screened 11 different sample types including bovine and ram semen, bovine vaginal and uterine swabs, and bull fecal samples, as well as samples from 180- and 260-days old calf fetuses and their respective dams using both quantitative PCR (514 samples) and targeted culturing (499 samples). By qPCR, all the targeted Fusobacterium spp. were detected across all sample types, with FNF being the highly prevalent in the bull semen (66.7%) and maternal ruminal fluids (87.1%), which was confirmed by culturing. All the targeted Fusobacterium were identified in vaginal and uterine (3.1%-9.4%) as well as placental caruncles, and fetal fluids, ruminal and meconium samples (2.7% - 26.3%) by qPCR and were not isolated by culture method. Overall, our results suggest that F. necrophorum is a commensal member of healthy male reproductive microbiota, and that FNF, FNN and FV are present in bovine vagino-uterine microbiota, and calf intestine prenatally.

microbiology↗

Curative levels of endogenous gene replacement achieved in non-human primate liver using programmable genomic integration

The ability to efficiently place a large piece of DNA in a specific genomic location has been a goal for the gene therapy field since its inception; however, despite significant advances in gene editing technology, this had yet to be achieved. Here we describe two methods of programmable genomic integration (PGI) that overcome some of the limitations of current approaches. Using a combination of clinically validated delivery technologies (LNP, AAV), we demonstrate the ability to specifically integrate large (>2 kb) DNA sequences into endogenous introns in the liver of non-human primates (NHP). PGI was effective across multiple genomic locations and transgenes, and insertion led to expression from the endogenous promoter. PGI was highly efficient, achieving expression in >50% of liver cells after a single course of treatment, which would be curative for most monogenic recessive liver diseases. This is the first report of clinically curative level of gene insertion at endogenous loci in NHP.

bioengineering↗

Deciphering gene regulatory programs in mouse embryonic skin through single-cell multiomics analysis

BackgroundCell type-specific transcriptional heterogeneity in embryonic mouse skin is well-documented, but few studies have investigated the regulatory mechanisms. ResultsHere, we present high throughput single-cell chromatin accessibility and transcriptome sequencing (HT-scCAT-seq), a method that simultaneously profiles transcriptome and chromatin accessibility. We utilized HT-scCAT-seq to dissect the gene regulatory mechanism governing epidermal stratification, periderm terminal differentiation, and fibroblast specification. ConclusionsBy linking chromatin accessibility to gene expression, we identified candidate cis-regulatory elements (cCREs) and target genes crucial for dermal and epidermal development. We described cells with similar gene expression profiles that exhibit distinct chromatin accessibility statuses during periderm terminal differentiation. Finally, we characterized the underlying lineage-determining transcription factors (TFs), and demonstrated that ALX4 and RUNX2 were candidate TF regulators of the dermal papilla lineage development through in silico perturbation analysis.

developmental biology↗

The dynamics of wild Vitis species in response to climate change facilitate the breeding of grapevine and its rootstocks with climate resilience

Climate change poses significant challenges to agricultural suitability and food security due to the limited adaptability of domesticated crops, however, our understanding of their climate adaptability is still limited. In this study, we compare the potential distributional dynamics in response to future climate change between grapevine and its wild relatives (Vitis L.) based on ecological niche models (ENMs). We reveal that the annual mean temperature is the primary factor influencing the potential distribution of cultivated grapes (V. vinifera L.). By 2080, under RCP 8.5, suitable areas for wine and table grapes from V. vinifera are predicted to reduced by 15.04x105 km{superscript 2} and 13.26x105 km{superscript 2}, respectively. The results suggest that grape cultivation, particularly for table grapes, will face serious threats from future climate change. In contrast, seventy percent of wild grapes are well able to withstand future climate conditions. For example, under RCP 8.5, North American wild grapes like V. rotundifolia and V. labrusca, as well as East Asian wild grapes such as V. heyneana and V. davidii, are projected to demonstrate significant adaptability. These wild grapes have the potential to provide rootstocks that could enhance the adaptability of cultivated grapes and serve as invaluable resources for breeding programs aimed at developing new cultivars better suited to withstand the environmental pressures of climate change. Our results not only predict potential suitable distribution areas of wild grapes in the future, but also emphasize the essential impact of these wild genetic resources on grape breeding for promoting adaptation to future climate change.

plant biology↗

Skeletal Metastasis of Prostate Cancer Is Augmented by Activation of EphA2 Noncanonical Signaling and Ligand-Deficient Bone Microenvironment

EphA2, a member of Eph family receptor tyrosine kinases (RTKs), is overexpressed in multiple types of solid human tumors, particularly at the late stages. However, whether and how it drives specific malignant processes remain elusive. We report that EphA2 is elevated during prostate cancer (PCa) progression in multiple syngeneic murine models. Interestingly, human metastatic PCa specimens from two Rapid Autopsy Programs showed selective overexpression of EphA2 in metastasis to the bone, but not to the lymph nodes or viscera. Serine 897 phosphorylation that mediates the pro-oncogenic, noncanonical signaling by EphA2 was also upregulated in bone metastasis. Analysis of human datasets shows EphA2 overexpression is associated with skeletal but not visceral metastases. Ephrin-A1, a major cognate ligand for EphA2, is lost in PCa bone metastasis, which is correlated with poor prognosis. Further, the bone microenvironment is unique in expressing little of the five EFNA genes, providing permissive microenvironment for bone colonization. S897A mutation that ablates EphA2 noncanonical signaling, suppressed PCa development. Restoration of ephrin-A1 expression in PC-3, a model cell line for double negative prostate cancer derived from bone metastasis and devoid of ephrin-As, profoundly changed global tyrosine phosphorylation profiles, inhibited basal ERK and Src activities in vitro, and suppressed tumor development in the bone. Together these results demonstrate EphA2 overexpression and concomitant loss of ligands in PCa lead to activation of noncanonical signaling that is sustained in ephrin-A1-deficient skeletal milieu to promote bone metastasis.

cancer biology↗

Molecular basis of the urate transporter URAT1 inhibition by gout drugs

Hyperuricemia is a condition when uric acid, a waste product of purine metabolism, accumulates in the blood1. Untreated hyperuricemia can lead to crystal formation of monosodium urate in the joints, causing a painful inflammatory disease known as gout. These conditions are associated with many other diseases and affect a significant and increasing proportion of the population2-4. The human urate transporter 1 (URAT1) is responsible for the reabsorption of [~]90% of uric acid in the kidneys back into the blood, making it a primary target for treating hyperuricemia and gout5. Despite decades of research and development, clinically available URAT1 inhibitors have limitations because the molecular basis of URAT1 inhibition by gout drugs remains unknown5. Here we present cryo-electron microscopy structures of URAT1 alone and in complex with three clinically relevant inhibitors: benzbromarone, lesinurad, and the novel compound TD-3. Together with functional experiments and molecular dynamics simulations, we reveal that these inhibitors bind selectively to URAT1 in inward-open states. Furthermore, we discover differences in the inhibitor dependent URAT1 conformations as well as interaction networks, which contribute to drug specificity. Our findings illuminate a general theme for URAT1 inhibition, paving the way for the design of next-generation URAT1 inhibitors in the treatment of gout and hyperuricemia.

biophysics↗

A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes

BackgroundThe agamid dragon lizard Pogona vitticeps is one of the most popular domesticated reptiles to be kept as pets worldwide. The capacity of breeding in captivity also makes it emerging as a model species for a range of scientific research, especially for the studies of sex chromosome origin and sex determination mechanisms. ResultsBy leveraging the CycloneSEQ and DNBSEQ sequencing technologies, we conducted whole genome and long-range sequencing for a captive-bred ZZ male to construct a chromosome-scale reference genome for P. vitticeps. The new reference genome is [~]1.8 Gb in length, with a contig N50 of 202.5 Mb and all contigs anchored onto 16 chromosomes. Genome annotation assisted by long-read RNA sequencing greatly expanded the P. vitticeps lncRNA catalog. With the chromosome-scale genome, we were able to characterize the whole Z sex chromosome for the first time. We found that over 80% of the Z chromosome remains as pseudo-autosomal region (PAR) where recombination is not suppressed. The sexually differentiated region (SDR) is small and occupied mostly by transposons, yet it aggregates genes involved in male development, such as AMH, AMHR2 and BMPR1A. Finally, by tracking the evolutionary origin and developmental expression of the SDR genes, we proposed a model for the origin of P. vitticeps sex chromosomes which considered the Z-linked AMH as the master sex-determining gene. ConclusionsOur study provides novel insights into the sex chromosome origin and sex determination of this model lizard. The near-complete P. vitticeps reference genome will also benefit future study of amniote evolution and may facilitate genome-assisted breeding.

genomics↗

Large Serine Integrase Off-target Discovery and Validation for Therapeutic Genome Editing

While numerous technologies for the characterization of potential off-target editing by CRISPR/Cas9 have been described, the development of new technologies and analytical methods for off-target recombination by Large Serine Integrases (LSIs) are required to advance the application of LSIs for therapeutic gene integration. Here we describe a suite of off-target recombination discovery technologies and a hybrid capture validation approach as a comprehensive framework for off-target characterization of LSIs. HIDE- Seq (High-throughput Integrase-mediated DNA Event Sequencing) is a PCR-free unbiased genome-wide biochemical assay capable of discovering sites with LSI- mediated free DNA ends (FDEs) and off-target recombination events. Cryptic-Seq is a PCR-based unbiased genome-wide biochemical or cellular-based assay that is more sensitive than HIDE-Seq but is limited to the discovery of sites with off-target recombination. HIDE-Seq and Cryptic-Seq discovered 38 and 44,311 potential off-target sites respectively. 2,455 sites were prioritized for validation by hybrid capture NGS in LSI- edited K562 cells and off-target integration was detected at 52 of the sites. We benchmarked the sensitivity of our LSI off-target characterization framework against unbiased whole genome sequencing (WGS) on LSI-edited samples, and off-target integration was detected at 5 sites with an average genome coverage of 40x. This reflects a greater than 10-fold increase in sensitivity for off-target detection compared to WGS, however only 4 of the 5 sites detected by WGS were also validated by hybrid capture NGS. The dissemination of these technologies will help advance the application of LSIs in therapeutic genome editing by establishing methods and benchmarks for the sensitivity of off-target detection.

genomics↗

A single-molecule nanopore sequencing platform

Nanopore sequencing, a third-generation sequencing technology, has revolutionized the gene sequencing industry with its advantages of long reads, fast speed, real-time sequencing and analysis, and potential in detecting base modifications. This technology allows researchers to sequence longer DNA fragments in a single read, providing more comprehensive genomic information compared to previous methods. Nanopore sequencing operates on electrical signals generated by a nanopore embedded in a membrane separating two electrolyte-filled chambers. When single-stranded DNA (ssDNA) passes through the nanopore, it creates variations in the current that correspond to different DNA bases. By analyzing these current fluctuations with machine learning algorithms, the DNA sequence can be determined. In this study, we introduced several improvements to nanopore sequencing, including nanopore local chemistry sequencing, novel motor and pore proteins, chip design, and basecalling algorithms. Our new nanopore sequencing platform, CycloneSEQ, demonstrated long-duration sequencing (107 hours) on a single chip with high yield (>50 Gb). In human genomic DNA sequencing, CycloneSEQ was able to produce long reads with N50 33.6 kb and modal identity 97.0%. Preliminary findings on human whole-genome de novo assembly, variant calling, metagenomics sequencing, and single-cell RNA sequencing have further highlighted CycloneSEQs potential across different areas of genomics.

genomics↗