Biology subjects

li, y.

Publications and source records attributed to li, y..

18 recordsLinked to original sources

bioRxiv2026

Cell-Lens: Advancing LLM Reasoning at Single-Cell Resolution

Recent work applies large language models (LLMs) to single-cell data, but the cell usually reaches the model as a short ranked list of genes. This list drops much of what defines a cell, so the model reasons from a partial view. Yet the information is not lost in the measurement, only in the text. Here, we introduce Cell-Lens, a training-free structured representation of the measured cell. It writes the cell as typed blocks, from paired measurements to marker-supported programs. On CellVerse, SOAR, CellPuzzles, and SC-Arena, across five model families, Cell-Lens improves performance by up to 27.1 points. It also narrows the model gap and reduces API-reported reasoning-token usage. The largest gains occur when a defining RNA marker falls out of the ranked list. In these cases, the paired protein data still capture the corresponding signal. Shuffling the added blocks removes the gain. The gain persists after selected label-associated proteins are removed. These controls link the improvement to cell-matched biological content. We also build and release CellSpectrum, a broader benchmark spanning eight sources and seven tasks with paired modalities. The gains hold there across tasks, tissues, and modalities. These results show that a better cell representation can improve single-cell reasoning without retraining the model. Code and CellSpectrum are publicly available at https://github.com/LiZaiyuan0619/Cell-Lens.

bioinformatics↗

bioRxiv2026

A cis-regulatory variant in ASIP causes gray coat color in the donkey

BackgroundGray is one of the relatively rare coat colors in donkeys. The Hetian Gray donkey is a distinctive indigenous breed from the Xinjiang Uygur Autonomous Region of Northwestern China, characterized by progressive hair depigmentation with aging while retaining dark skin pigmentation. However, the genetic basis underlying this unique gray coat color phenotype remains unclear. ResultsTo elucidate the genetic basis, we conducted whole-genome resequencing of Gray and non-Gray donkeys. Genome-wide selection signature analyses identified a candidate region on chromosome 15. Subsequent fine-mapping using mass spectrometry-based genotyping of 42 loci refined the candidate interval and revealed a SNP within intron 2 of the ASIP gene, located in a genomic fragment with highly similar sequences, showing complete association with the gray coat color. Association analysis in an expanded population further confirmed a strong correlation between this variant and the gray phenotype. Gene expression analyses also supported the role of ASIP in regulating pigmentation in donkeys. ConclusionsThese findings identify a genetic determinant of gray coat color in donkeys and provide new insights into the molecular mechanisms underlying age-related depigmentation in domestic animals.

genomics↗

bioRxiv2025

Association between KCNC1 gene polymorphism and blood lipid levels in determining the efficacy of high-intensity interval training

ObjectiveThe potassium voltage-gated channel subfamily C member 1 (KCNC1) gene plays a crucial role in both neural excitability and lipid metabolism. However, the impact of its genetic polymorphisms on individual blood lipid levels and the efficacy of exercise interventions remains unclear. This study aimed to investigate the association between KCNC1 single nucleotide polymorphisms (SNPs) and baseline blood lipid levels in young Han Chinese individuals, as well as the relationship between lipid profiles and sensitivity to high-intensity interval training (HIIT). This research provides theoretical support for developing personalised exercise prescriptions based on genetic background to improve lipid health. MethodsThis study recruited 245 healthy Han Chinese university students (114 males, 131 females) without regular exercise habits. Participants underwent a standardised 12-week HIIT intervention programme, conducted three times weekly. Total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) levels were measured before and after the intervention. Genotyping of the KCNC1 gene SNP was performed using the Infinium CGA chip. PLINK software was employed to construct linear regression models (with age, sex, BMI, and baseline lipid levels as covariates) to analyse the association between genetic polymorphisms and changes ({Delta}) in lipid parameters. ResultsFollowing 12 weeks of HIIT, all participants demonstrated significant improvements in TC, HDL-C, LDL-C, and TG levels (P<0.01). Association analysis revealed: 1) At baseline, the rs757511 locus was significantly correlated with HDL-C levels in males ({beta} = -0.112, P = 0.0445), with individuals carrying the A allele exhibiting higher baseline HDL-C; 2) Regarding HIIT responsiveness, three loci exhibited significant sex-specific associations: the C allele at rs6083540 was significantly associated with improved TG levels in females ({beta} = 0.1564, P = 0.025); the A allele at rs61882396 was significantly associated with improved TG levels in females ({beta} = -0.129, P = 0.032); the C allele at rs12574348 was significantly associated with improved LDL-C levels in males ({beta} = 0.1608, P = 0.048). ConclusionThis study first demonstrates an association between KCNC1 gene polymorphisms (rs6083540, rs12574348, rs61882396) and lipid sensitivity to HIIT in young Han Chinese populations, with this association exhibiting significant sex specificity. The findings suggest that the KCNC1 gene may serve as a key genetic mediator in exercise-regulated lipid metabolism. Future development of tailored HIIT programmes should account for individual genotypic and gender variations.

physiology↗

bioRxiv2025

Analysis of Nutritional Components in Brown Sugar and Its Effects on Anti-fatigue, Alleviation of Qi Deficiency and Blood Stasis, and Antioxidant Effects

Brown sugar (BS), Red granulated sugar (RGS) and White sugar(WS) are three key sweeteners and food additives in China. Notably, BS possesses significant nutritional value and has been widely used in Chinese medicine for its supportive therapeutic properties.This study evaluated the anti-fatigue, the amelioration of qi deficiency and blood stasis, as well as the antioxidant activities of these sugars using a zebrafish model. BS and RGS demonstrated significantly greater efficacy than WS in terms of both anti-fatigue effects and amelioration of qi Deficiency and blood stasis in the zebrafish model. Antioxidant assays revealed that BS, RGS, and WS (500 g/mL) significantly enhanced superoxide dismutase (SOD) activity in zebrafish embryos compared with the control group. Furthermore, the mineral composition of sugar were determined. Nine mineral elements--potassium (K), calcium (Ca), sodium (Na), magnesium (Mg), iron (Fe), zinc (Zn), copper (Cu), phosphorus (P), and selenium (Se)--were analyzed. BS exhibited markedly higher concentrations of P, Ca, Fe, and Mg than RGS and WS, while selenium (detected at 50 mg/kg) was exclusively detected in BS. Intriguingly, RGS contained four-fold higher potassium levels than BS. Total polyphenol content, quantified by Folin-Ciocalteu assay, was 4.35 g/kg in BS and 1.53 g/kg in RGS, with no detectable polyphenols in WS.

biochemistry↗

bioRxiv2025

Telomere-to-telomere gap-free genome assembly of a male donkey and the identification of novel SVs associated with functional genes

Previous assemblies of the donkey genome remain with gaps and structural errors, and a complete donkey genome will greatly facilitate genetic research related to donkeys. In the present study, a 2.78-Gb telomere-to-telomere gap-free donkey genome (CAU_T2T_donkey) was assembled, including a 29.78-Mb Y chromosome, aided by ONT and trio-binning approach. CAU_T2T_donkey corrected the structural errors of previous assemblies and added a total of 153.8-Mb previously unresolved regions and 354 genes to the reference genome EquAss-T2T_v2. We identified a 1.9-Mb PAR on CAU_T2T_donkey-chromosome Y, and added 17.1Mb regions and 75 new genes to the chromosome Y of the previous reference genome ASM1607732v2. Multi-copy genes, such as TSPY, L1RE, ETY, HSFY, and ETSTY were also identified in CAU_T2T_donkey-chromosome Y. Totally 6 types of repetitive sequences in centromeric regions were identified, and the features of the centromeric regions were revealed, and satellite-free centromeres were identified. We aligned HiFi long-read sequences of donkeys from six breeds against CAU_T2T_donkey and identified SVs in previously unresolved regions, and some of the novel SVs were located in functional genes, such as AOX1 (Chr4:DEL61), ASIC2 (Chr13:INS954), and Twist2 (Chr19:DEL98).

genomics↗

bioRxiv2025

Lactobacillus acidophilus Attenuates Polyethylene Glycol-Induced Susceptibility to Citrobacter rodentium Infection via Microbiota Modulation

ObjectivePolyethylene glycol (PEG), a globally prevalent laxative, is extensively utilized for bowel preparation prior to colonoscopy or abdominal surgery owing to its exceptional safety profile. Nevertheless, emerging evidence suggests that PEG administration may induce significant alterations in colonic microbiota composition, with dysbiotic effects persisting for over two weeks. The potential implications of such microbiota perturbations on the colonization and invasion of opportunistic pathogens remain underexplored. Methods and AnalysisTo investigate this, we employed a murine model infected with Citrobacter rodentium (C.R.), a surrogate for Enteropathogenic Escherichia coli (EPEC) and Enterohemorrhagic Escherichia coli (EHEC), following PEG-induced bowel preparation. ResultsThe severity of infectious enteritis was assessed, and the prophylactic efficacy of Lactobacillus acidophilus (LAC) supplementation was evaluated. Our findings indicate that PEG administration significantly elevated C.R. load, enhanced virulence gene expression, and exacerbated intestinal inflammation post-infection, with the infection window extending approximately 14 days. Through fecal metagenomic analysis and co-housing experiments, we demonstrated that PEG-associated enteritis is critically mediated by gut microbiota dysbiosis. Furthermore, supplementation with LAC was shown to mitigate susceptibility to C.R. infection. ConclusionsThese results suggest that PEG increases intestinal susceptibility to infection in a microbiota-dependent manner, highlighting the therapeutic potential of LAC in restoring microbial homeostasis.

microbiology↗

bioRxiv2025

Peritoneal cavity-derived GATA6+ macrophages inhibit fibrosis through IL33 in endometrium

Macrophages exhibit a high degree of plasticity and play pivotal roles both in the normal physiological cycle of the endometrium and in its regeneration following injury. Although some new subsets of endometrial macrophages have been identified, their origins and functions remain to be further explored. In this study, we employed single-cell sequencing to analyze the endometrium of patients with normal endometrium and intrauterine adhesion (IUA) caused by injury. We identified a unique subset of macrophages distinguished by the expression of GATA6, a marker indicative of cavity macrophages. We verified that these GATA6+ macrophages were large peritoneal macrophages (LPMs) that migrated from the peritoneal cavity to the injured endometrium. Upon activation by injured endometrium, these LPMs demonstrated increased expression of Interleukin-33 (IL33), mediated by the Lars-Fos signaling axis, which interacts with the IL33 enhancer. Moreover, our studies revealed that IL33 derived from LPMs inhibited the differentiation of endometrial stromal cells (ESCs) into myofibroblasts, a critical step in the development of endometrial fibrosis. Furthermore, we confirmed the inhibitory effect occurred through the binding of IL33 to the ST2 receptor on ESCs, leading to the upregulation of JMJD3 and subsequent suppression of myofibroblast differentiation. Our findings highlight the essential role of LPMs in promoting endometrial repair and inhibiting fibrosis in IUA. Significance StatementThis study reveals the presence of a unique population of macrophages within the endometrium, originating from large peritoneal macrophages (LPMs), that are pivotal in endometrial repair. This finding offers new insights into the plasticity of macrophages and their potential therapeutic applications in treating endometrial fibrotic disorders.

immunology↗

bioRxiv2024

Ligand-independent c-Met activation by HHLA2 drives hepatocellular carcinoma and predicts c-MET inhibitor efficacy

The HGF/c-Met signaling pathway facilitates the initiation, progression, and metastasis of hepatocellular carcinoma (HCC). c-Met activation, however, is complex and not solely dependent on HGF, hindering targeted therapy development. This study identifies a critical oncogenic role for HHLA2, a B7 family member, in HCC and highlights its potential as a therapeutic target. We demonstrate that HHLA2 directly interacts with and activates c-Met through N-glycosylation, triggering sustained signaling and promoting aggressive HCC features. Mechanistically, we identified the pro-tumorigenic role of HHLA2 required downstream upregulation of MMP9 and VEGFA, both implicated in tumor progression. In multiple mouse models, HHLA2 overexpression accelerated tumor progression, metastasis, and reduced liver NK cell infiltration, all of which were reversed by c-Met inhibition. In a cohort of 176 HCC patients, HHLA2 expression strongly correlated with c-Met phosphorylation, advanced tumor stage, and poor prognosis. Importantly, HHLA2 expression predicted sensitivity to c-Met inhibitors in cell lines and patient-derived organoids and could be detected in patient serum, suggesting its potential as a prognostic biomarker. Collectively, our findings reveal an HHLA2-mediated mechanism of c-Met activation and provide a strong rationale for targeting the HHLA2-c-Met axis as a novel therapeutic strategy, with HHLA2 serving as a potential prognostic biomarker. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=173 SRC="FIGDIR/small/622557v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@8b10dforg.highwire.dtl.DTLVardef@b43dorg.highwire.dtl.DTLVardef@394c4aorg.highwire.dtl.DTLVardef@1bfbc8c_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Integrative multi-omics data elucidating the biosynthesis and regulatory mechanisms of furanocoumarins in Angelica dahurica

Furocoumarins (FCs) are crucial natural products playing a dual role as plant defense molecules and pharmacologically active substances. Angelica dahurica is a renowned herb with diverse and abundant FCs. However, the accumulation pattern over developmental stages, biosynthesis pathway and regulatory mechanisms of FCs in A. dahurica remain elusive, hindering the production of FCs via synthetic biology approaches. Here, we constructed a chromosome-level reference genome for A. dahurica and quantified the content dynamics of 17 coumarins across six developmental stages of its medicinal organ, root. It showed a gradual decrease in FC concentration with root enlargement. The combined analyses of transcriptomic and metabolomic data, together with in vivo enzymatic assay, confirmed that CYP71AZ18 was involved in the biosynthesis of bergaptol, whereas CYP71AZ19 and CYP83F95 contributed to the biosynthesis of xanthotoxol. Notably, CYP71AZ19 originated from a proximal duplication event of CYP71AZ18, specific to A. dahurica, subsequently undergoing neofunctionalization. Accessible chromatin regions (ACRs), especially proximal ACRs, are correlated with higher gene expression levels, including the three validated genes involved in FC biosynthesis, showing potential to regulate metabolite biosynthesis. Our findings provide new insights into the biosynthetic pathway of FCs and the epigenetic regulation of metabolite biosynthesis.

synthetic biology↗

bioRxiv2023

Spatiotemporal Dynamics of Vcam1 Regulates Cholangiocarcinoma Mass Expansion and Tumor Dissemination under Growth-suppressive Peritumoral Myofibroblasts

Intrahepatic cholangiocarcinoma (iCCA) is characterized by its highly desmoplastic stroma. Myofibroblasts (MFs) are present both within the tumor mass (intratumoral MFs, iMFs) and at the tumor border (peritumoral MFs, pMFs). Using a spheroid-based coculture system, we show that the initial iCCA-pMF contact is growth suppressive to the tumor cells. However, prolonged iCCA-pMF interaction elicits significant tumor cell invasion and dissemination. We find that vascular cell adhesion molecule-1 (Vcam1) level is elevated in tumor cells in contact with pMFs but low in disseminated tumor cells both in vitro and in vivo. A gene regulatory network analysis of mouse and patient iCCA tumors and Vcam1 knockout (Vcam1KO) demonstrate a heavy involvement of Vcam1 in epithelial-to-mesenchymal transition. While Vcam1KO has only a limited impact on tumor cell growth in their monoculture, Vcam1KO spheroids exhibit instant dissemination and a severe growth defect when cocultured with pMFs. When transplanted into the liver, Vcam1KO iCCA cells show a similar increase in dissemination but a significant defect in establishing primary and metastatic tumors. Incomplete blocking of Vcam1 in vivo reduces the size but increase the number of metastatic lesions. Overall, our study shows a spatiotemporal regulation of iCCA growth and dissemination by pMFs in a Vcam1-dependent manner.

cancer biology↗

bioRxiv2021

M-CSF-stimulated myeloid cells can convert into epithelial cells to participate in re-epithelialization and hair follicle regeneration during skin wound healing

Skin wound healing is a complex process which requires the interaction of many cell types and mediators in a highly sophisticated temporal sequence. Myeloid cells compose a significant proportion of the inflammatory cells recruited to a wound site and play important roles in clearance of damaged tissue and microorganisms. Myeloid cells have also been suggested to convert into fibro-blast-like cells and endothelial cells in participation of wound healing process. However, whether myeloid cells in wound skin can convert into epithelial cells and contribute to re-epithelialization and skin appendage regeneration is still unclear. In this study, we performed double immunofluorescent staining with antibodies for hematopoietic cells and keratinocytes as well as cell tracing technique to investigate hematopoietic cell conversion. The result show that during the healing process, some of the CD45-positive hematopoietic cells are overlapped with keratin 14, the markers of keratinocytes. Further, CD11b-positive myeloid cells seem the origin of converted epithelial cells. To confirm these results, we culture CD11b-posiitve myeloid cells from mouse splenocytes in a medium containing macrophage colony-stimulating factor (M-CSF) and dermal injection of these cells into the healthy skin when punch biopsy is created in mouse skin. Tracing injected labeled splenocyte-derived myeloid cells in skin, we confirm that myeloid cells able to convert into keratinocytes in repaired skin. Furthermore, our results from in vivo experiments provide new information on contribution of myeloid cells in hair follicle regeneration. In conclusion, this work highlights the myeloid cell contributions in wound repair and hair follicle regeneration in mice through conversion of M-CSF-stimulated CD11b+ myeloid cells into epithelial cells.

cell biology↗

bioRxiv2020

Rigorous anterograde trans-monosynaptic tracing of genetic defined neurons with retargeted HSV1 H129

Neuroanatomical tracing technology is fundamental for unraveling the complex network of brain connectome. Tracing tools that could spread between neurons are urgently needed, especially the rigorous trans-monosynaptic anterograde tracer is still lacking. HSV1 strain H129 was proved to be an anterograde tracer and has been used to trace neuronal networks in several reports. However, H129 has a serious defect that it was demonstrated to infect neurons via axon terminals. Thus, when using H129 to dissect output neural circuit, its terminal take up capacity should be carefully considered. Here, we report a recombinant H129 that carrying the anti-Her2 scFv in glycoprotein D to target genetically defined neurons. With the usage of helper virus complementarily expressing Her2 and gD, we can realize the elucidation of direct projection regions of either a given brain nucleus or a specific neuron type. The retargeted H129 system complements the current neural circuit tracer arsenal, which provides a rigorous and practical anterograde trans-monosynaptic tool.

neuroscience↗

bioRxiv2020

A potent antibiofilm agent inhibits and eradicates mono- and multi-species biofilms

Biofilms are surface-attached multicellular communities that create many problems in human health and various industries. Given the prominence of biofilms in biofouling and infectious diseases, antibiofilm control approaches are highly sought after. In the present study, we identified elasnin as a potent antibiofilm agent through a bioassay-guided approach. Elasnin specifically inhibited the biofilm formation of bacterial mono-species and eradicated the mature biofilm of Gram-positive bacteria at concentrations below 2.5 g/mL with a low toxic effect on cells and a low resistance risk. Confocal observations illustrated that elasnin decreased cell aggregations and destroyed the biofilm matrix. Furthermore, elasnin-based antibiofilm coatings were prepared and inhibited the formation of multi-species biofilms and the attachment of large biofouling organisms in the field test. These findings suggest that elasnin is a promising antibiofilm agent for future applications in biofilm control. ImportanceDue to the increased diversity of biofilm-associated infections and the failure of conventional antimicrobial treatment, new and effective biofilm-specific pharmacologic strategies are urgently needed. Elasnin is a new antibiofilm natural product produced by Streptomyces with high efficiency and low toxicity. Elasnin effectively destroyed the biofilm matrix of Gram-positive bacteria, thus making them more susceptible to antibiotics. Unlike currently deployed antibiotic vancomycin, which exclusively targets essential life processes and kills the pathogen, elasnin did not exhibit bactericidal effect and thus held great potential in delaying resistance. With high yield, elasnin-based coatings were easily prepared with low expenditures and exhibited favorable performance in field test. Collectively, the antibiofilm properties of elasnin, combined with the low cost of supply and the low risk of resistance, could provide the basis for the development of a novel antibiofilm agent that could help fight to antibiotics resistance.

microbiology↗

bioRxiv2019

A reversible KO model reveals therapeutic 1 potentials of defective Tregs

Tregs must be activated to suppress immune responses, but the transcriptional program controlling Treg activation remains incompletely understood. We previously found that Treg-specific deletion of the chromatin remodeling factor Brg1 impairs Treg activation and causes fatal autoimmunity in mice. Here, using a method that allows gene KO to be reversed in a Tamoxifen-dependent manner, we addressed whether reinstating Brg1 expression in the defective Tregs in the sick mice could restore Treg function, and if so, whether such Tregs could stop and resolve the fatal inflammation. We found that reexpressing Brg1 unexpectedly converted the defective Tregs into highly potent \"SuperTregs\", which effectively rescued the dying mice. Remarkably, Brg1 reexpression in as little as 8% of the Tregs sufficed for the rescue in some cases. Brg1-deleted Tregs in the inflamed mice experienced excessive cytokine stimulation, became hyperactivated upon Brg1 reexpression and then deactivated as the inflammation subsided, suggesting that BRG1 acted in conjunction with inflammation to induce and maintain the SuperTreg phenotype. These data illustrate the power of reversible KO models in uncovering gene functions, and suggest a novel therapeutic strategy for IPEX(-related) disorders that exploits the defective Tregs and the inflammatory environment preexisting within the patients.

immunology↗

bioRxiv2019

INeo-Epp: T-cell HLA class I immunogenic or neoantigenic epitope prediction via random forest algorithm based on sequence related amino acid features

In silico T-cell epitope prediction plays an important role in immunization experimental design and vaccine preparation. Currently, most epitope prediction research focuses on peptide processing and presentation, e.g. proteasomal cleavage, transporter associated with antigen processing (TAP) and major histocompatibility complex (MHC) combination. To date, however, the mechanism for immunogenicity of epitopes remains unclear. It is generally agreed upon that T-cell immunogenicity may be influenced by the foreignness, accessibility, molecular weight, molecular structure, molecular conformation, chemical properties and physical properties of target peptides to different degrees. In this work, we tried to combine these factors. Firstly, we collected significant experimental HLA-I T-cell immunogenic peptide data, as well as the potential immunogenic amino acid properties. Several characteristics were extracted, including amino acid physicochemical property of epitope sequence, peptide entropy, eluted ligand likelihood percentile rank (EL rank(%)) score and frequency score for immunogenic peptide. Subsequently, a random forest classifier for T cell immunogenic HLA-I presenting antigen epitopes and neoantigens was constructed. The classification results for the antigen epitopes outperformed the previous research (the optimal AUC=0.81, external validation data set AUC=0.77). As mutational epitopes generated by the coding region contain only the alterations of one or two amino acids, we assume that these characteristics might also be applied to the classification of the endogenic mutational neoepitopes also called neoantigens. Based on mutation information and sequence related amino acid characteristics, a prediction model of neoantigen was established as well (the optimal AUC=0.78). Further, an easy-to-use web-based tool INeo-Epp was developed (available at http://www.biostatistics.online/INeo-Epp/neoantigen.php)for the prediction of human immunogenic antigen epitopes and neoantigen epitopes.

immunology↗

bioRxiv2019

Selective labelling of arginine residues engaged in binding sulfatedglycosaminoglycans

IThe activities of hundreds of proteins in the extracellular space are regulated by binding to the glycosaminoglycan heparan sulfate (HS). These interactions are driven by ionic bonds between sulfate and carboxylate groups on the polysaccharide and the side chains of basic residues in the protein. Here we develop a method to selectively label the guanidino side chains of arginine residues in proteins that engage the anionic groups in the sugar. The protein is bound to heparin (a common experimental proxy for HS) on an affinity column. Arginine side chains that are exposed to solvent, and thus involved in binding, are protected by reaction with the dicarbonyl phenylgyoxal (PGO). Elution of the bound proteins then exposes arginine side chains that had directly engaged with anionic groups on the polysaccharide. These are reacted with hydroxyl-phenylglyoxal (HPG). PGO was found to generate three products: a 1:1 product, the 1:1 water condensed product and a 2:1 PGO:arginine product. These three reaction products and that of HPG had distinct masses. Scripts were written to analyse the mass spectra and so identify HPG labelled arginine residues. Proof of principle was acquired on model peptides. The method was then applied to the identification of heparin binding arginine residues in fibroblast growth factors (FGF) 1 and 2. The data demonstrate that four out of eleven arginine residues on FGF2 and five out of six arginine residues of FGF1 engage heparin. Our approach provides a rapid and reliable means to identify arginines involved in functional complexes such as those of proteins with heparin

biochemistry↗

bioRxiv2019

Genetic diversity analysis of an isolate of microsporidia infesting Athetis lepigone

In this study, PCR amplification, cloning and sequencing analysis were adopted to explore genetic diversity of microsporidia (LEP9557) infecting Athetis lepigone. The small subunit ribosomal DNA (SSU rDNA), internal transcribed spacer (ITS) and intergenic spacers (IGS) of ribosomal RNA (rRNA) were cloned from the strain and sequenced. By means of multiple sequence alignment, we found that the three gene regions had different levels of polymorphism. There was greater polymorphism in ITS (74 variable sites) and IGS (55.59%) regions than in the SSU rDNA (17 variable sites). Phylogenetic analysis was performed using Kimura 2-parameter with neighbor joining and the results showed that LEP9557 had a close relationship with Nosema bombycis. Sequences of each clone were submitted to Genbank (Accession number: MF150254-MF150258). All of the results indicated the presence of genetic diversity in LEP9557, which established the foundation for identifying the phylogeny and relationships with other microsporidian strains, and had significant biological meaning for maintaining the survival and population continuity of the strain.

microbiology↗

bioRxiv2018

Single-cell level transcriptome of the maize pathogenic fungi cochliobolus heterostrophus race O in infection reveal the virulence related genes, and potential circRNA effector

Cochliobolus heterostrophus is a crucial pathogenic fungus that causes southern corn leaf blight (SCLB) in maize worldwide, however, the virulence mechanism of the dominant race O remains unclear. In this report, the single-cell level of pathogen tissue at three infection stages were collected from the host interaction-situ, and were performed next-generation sequencing from the perspectives of mRNA, circular RNA(circRNA) and long noncoding RNA(lncRNA). In the mRNA section, signal transduction, kinase, oxidoreductase, and hydrolase, et al. were significantly related in both differential expression and co-expression between virulence differential race O strains. The expression pattern of the traditional virulence factors nonribosomal peptide synthetases (NPSs), polyketide synthases (PKSs) and small secreted proteins (SSPs) were multifarious. In the noncoding RNA section, a total of 2279 circRNAs and 169 lncRNAs were acquired. Noncoding RNAs exhibited differential expression at three stages. The high virulence strain DY transcribed 450 more circRNAs than low virulence strain WF. Informatics analysis revealed numbers of circRNAs which positively correlate with race O virulence, and a cross-kingdom interaction between the pathogenic circRNA and host miRNA was predicted. An important exon-intron circRNA Che-cirC2410 combines informatics characteristics above, and highly expressed in the DY strain. Che-cirC2410 initiate from the pseudogene chhtt, which doesnt translate genetic code into protein. In-situ hybridization tells the sub-cellular localization of Che-cirC2410 include pathogen`s mycelium, periplasm, and the diseased host tissues. The target of Che-cirC2410 was predicted to be zma-miR399e-5P, and the interaction between noncoding RNAs was proved. More, the expression of zma-miR399e-5P exhibited a negative correlation to Che-cirC2410 in vivo. The deficiency of Che-circ2410 decreased the race O virulence. The host resistance to SCLB was weakened when zma-miR399e-5P was silenced. Thus, a novel circRNA-type effector and its resistance related miRNA target are proposed cautiously in this report. These findings enriched the pathogen-host dialogue by using noncoding RNAs as language, and revealed a new perspective for understanding the virulence of race O, which may provide valuable strategy of maize breeding for disease resistance.\n\nAuthor SummaryThe southern corn leaf blight (caused by Cochliobolus heterostrophus) is not optimistic in Asia, however we have limit knowledge about the infection mechanism of the dominant C.heterostrophus race O. We take full advantage of the ideal C.heterostrophus genome database, laser capture microdissection and single-cell level RNA sequencing. Hence, we could avert the artificial influence such as medium, and profile the real gene mobilization strategy in the infection. The results of coding RNA section were accessible, virulence related genes (such as the signal transduction, PKS, SSP) were detected in RNA-seq,which accord with previous reports. However, the results of noncoding RNA was astonished, 2279 circular RNAs (circRNA) and 169 long noncoding RNAs (lncRNA) were revealed in our results. Generally, the function of noncoding RNA was hypothesized in single species, but we boldly guess that the function of circRNA is rather complicated in the pathogen-host interaction. Finally, the circRNA in-situ hybridization (ISH) demonstrate the secretion of pathogen circRNA into the host tissue. By bioinformatic prediction, we found a sole microRNA target, and proved the interaction between circRNA and microRNA. These findings are likely to reveal a novel pathogen effector type: secreted circRNA.

microbiology↗