Biology subjects

Liu, X.

Publications and source records attributed to Liu, X..

At least 685 records · Page 38Linked to original sources

bioRxiv2024

Genome-wide CRISPRi-seq identified ferredoxin-NADP reductase FprB as a synergistic target for gallium therapy in Pseudomonas aeruginosa

With the rise of antibiotic-resistant bacteria, non-antibiotic therapies like gallium are increasingly gaining attention. Gallium ions exhibit potent activity against multidrug-resistant bacteria and intravenous gallium nitrite is under phase 2 clinical trials to treat chronic Pseudomonas aeruginosa infections in cystic fibrosis patients. However, its clinical efficacy is constrained by the achievable peak concentration in human tissue. To address this limitation, we applied a genome-wide CRISPR interference approach (CRISPRi-seq), to identify potential synergistic targets with gallium. Through the systemic screening, we classified the essential genes by response time and growth reduction, pinpointing the most vulnerable therapeutic targets in this species. In addition, we identified a highly conserved gene fprB, encoding a ferredoxin-NADP+ reductase, the downregulation of which dramatically sensitized the cells to gallium. Using a null mutant, we confirmed the loss of fprB lowers the minimum inhibitory concentration of gallium from 320 {micro}M to 10 {micro}M and shifted galliums mode of action from bacteriostatic to bactericidal. Further investigation revealed that FprB plays a critical role in modulating oxidative stress induced by gallium, via control of the iron homeostasis and reactive oxygen species accumulation. Deleting fprB also enhanced galliums efficacy against biofilms formation and improved outcomes in murine lung infection model of P. aeruginosa, suggesting FprB as a promising drug target in combination with gallium. Overall, our data showed CRISPRi-seq as a powerful tool for systematic genetic analysis of P. aeruginosa, advancing identification of novel therapeutic targets.

microbiology↗

bioRxiv2024

Enhancing Photosynthesis under Salt Stress via Directed Evolution in Cyanobacteria

A key aspect of enhancing photosynthesis is improving its recycling kinetics, enabling swift resumption of photochemical quenching following environmental disruptions or stress. Salt stress exacerbates high light stress in cyanobacteria and leads to severe yield losses in crop plants. Genetic traits that confer salt tolerance without compromising photosynthetic performance are essential for improving photosynthesis under these conditions. Here we applied accelerated evolution in Synechococcus elongatus PCC 7942 by conditionally suppressing its methyl-directed mismatch repair system to obtain beneficial genetic traits for enhanced photosynthesis under salt stress. Screening over 10,000 mutants, we isolated eight strains with increased biomass or sucrose productivity under salt stress. Genome sequencing revealed an average of 8-20 single nucleotide polymorphisms (SNPs) or indels per genome. Notably, mutations in the photosystem II (PSII) reaction center D1 gene, resulting in the amino acid changes L353F, I358N, and H359N at the carboxyl terminus of the pre-D1 (pD1) protein, improve photosynthesis under salt and combined salt and light stress by potentially accelerating D1 maturation during PSII repair. Phylogenetic analysis of pD1 across cyanobacteria and red algae highlights the broad significance of these adaptive genetic traits, underscoring the importance of leveraging evolutionary insights to improve photosynthesis under stress or fluctuating environments.

plant biology↗

bioRxiv2024

High-throughput Image-based Clustering of CAR-T/Tumor Cocultures for Rapid and Facile Hit Identification

AO_SCPLOWBSTRACTC_SCPLOWChimeric antigen receptor T cell is important because of its potential to treat various diseases. As deep learning continues to advance, using unsupervised methods to classify medical images has become a significant focus because collecting high-quality labeled data for medical images is labor-intensive and time-consuming. Beyond the need for accurate labeling, there is a desire to explore the underlying characteristics of the data, even when labels may be ambiguous or uncertain. To address these challenges, we present a novel approach that combines image clustering with an insightful explanation of how these clusters are formed. Our method employs a U-net combined with a clustering algorithm to segment the dataset into different groups. After clustering, we use various techniques to interpret and elucidate the results. Moreover, our paper introduces a unique dataset focused on cell data, specifically highlighting the developmental patterns of cancer cells and T cells under various experimental conditions. This dataset offers a rich source of information and presents a complex challenge for image classification due to the diversity of conditions and cell behaviors involved. Our study thoroughly compares different architectural models on this new dataset, demonstrating the superior performance of our proposed architecture. Through experimental analysis and ablation studies, we provide substantial evidence of the benefits offered by our architecture, not only in terms of accuracy but also in its ability to reveal deeper insights into the data. This work advances the field of image classification and opens new possibilities for understanding complex biological processes through computer vision.

cell biology↗

bioRxiv2024

Photoperiodicity in Glucose Metabolism in the Human Brain

Photoperiodicity in the human brain function, which is a critical factor for social well-being, has been widely debated. In this study, 432 healthy males underwent fasting-state brain [18F]fluorodeoxyglucose positron emission tomography (PET) scanning twice: first at the baseline and then at the 5-year follow-up. We analyzed the effect of day length on brain glucose uptake separately for the baseline and follow-up studies and examined changes in glucose consumption as a function of the day length deviation for each participant between the repeated PET scans. Glucose uptake in the cuneus was consistently predicted by the day length on the day of scanning and by within-participant day length deviations. This longitudinal large-scale PET study provides a landmark evidence for photoperiodicity in glucose metabolism in the human brain. The cuneus may be an essential part of the visual cortex, translating environmental photoperiodic changes into temporal cues that influence cognitive function and social behavior. Significance statementPhotoperiodicity in the human brain function has been widely debated. The current study provides a landmark evidence in this regard by demonstrating how the photoperiod shapes glucose metabolism in the brain of healthy males, highlighting the crucial role of the cuneus in processing visual information related to photoperiodic changes in the environment. Understanding photoperiodicity in the function of the human brain offers insights into how humans adapt to their environments for social well-being and underscores the potential health implications of changes in the exposure of natural light.

neuroscience↗

bioRxiv2024

Vibrio cholerae RbmB is an α-1,4-polysaccharide lyase with biofilm-dispersal activity against Vibrio Polysaccharide (VPS)

Many pathogenic bacteria form biofilms as a protective measure against environmental and host hazards. The underlying structure of the biofilm matrix consists of secreted macromolecules, usually including exopolysaccharides. To escape the biofilm, bacteria may produce a number of matrix-degrading enzymes, including glycosidic enzymes that digest exopolysaccharide scaffolds. The human pathogen Vibrio cholerae assembles and secretes an exopolysaccharide called VPS (Vibrio polysaccharide) which is essential in most cases for the formation of biofilms and consists of a repeating tetrasaccharide unit. Previous studies have indicated that a secreted glycosidase called RbmB is involved in Vibrio cholerae biofilm dispersal, although the mechanism by which this occurs is not understood. To approach the question of RbmB function, we recombinantly expressed and purified RbmB and tested its activity against purified VPS. Using a fluorescence-based biochemical assay, we show that RbmB specifically cleaves VPS in vitro under physiological conditions. Analysis of the cleavage products using mass spectrometry, solid-state NMR, and solution NMR indicates that RbmB cleaves VPS at a specific site (at the -1,4 linkage between D-galactose and a modified L-guluronic acid) into a mixture of tetramers and octamers. We demonstrate that the product of the cleavage contains a double bond in the modified-guluronic acid ring, strongly suggesting that RbmB is cleaving using a glycoside lyase mechanism. Finally, we show that recombinant RbmB from Vibrio cholerae and the related aquatic species Vibrio coralliilyticus are both able to disperse living Vibrio cholerae biofilms. Our results support the role of RbmB as a polysaccharide lyase involved in biofilm dispersal as well as an additional glycolytic enzyme to add to the toolbox of potential therapeutic antibacterial enzymes. Author summaryBiofilms are protective sheaths produced by many bacteria that play important roles in survival in the environment and in hosts during infection. Understanding how biofilms form and disperse is essential in the fight against harmful bacterial pathogens. Vibrio cholerae is a historically significant human pathogen that forms biofilms made of a polysaccharide called VPS and secreted accessory proteins. Within the V. cholerae biofilm gene cluster is a gene encoding a protein called RbmB, which is known to play a role in biofilm dispersal. Using a combination of biochemical and analytical tools, we show that RbmB indeed cleaves VPS into 4- and 8-monosaccharide fragments at a unique site and demonstrate that it falls into the family of polysaccharide lyase enzymes (as opposed to the more common hydrolases). Furthermore, recombinant RbmB disperses living V. cholerae biofilms further indicating that it may play a role in VPS processing or degradation.

biochemistry↗

bioRxiv2024

Loss of Insulin Signaling in Microglia Impairs Cellular Uptake of Aβ and Neuroinflammatory Response Exacerbating Alzheimer-like Neuropathology

Insulin receptors are present on cells throughout the body, including the brain. Dysregulation of insulin signaling in neurons and astrocytes has been implicated in altered mood, cognition, and the pathogenesis of Alzheimers disease (AD). To define the role of insulin signaling in microglia, the primary phagocytes in brain critical for maintenance and damage repair, we created mice with an inducible microglia-specific insulin receptor knockout (MG-IRKO). RiboTag profiling of microglial mRNAs revealed that loss of insulin signaling results in alterations of gene expression in pathways related to innate immunity and cellular metabolism. In vitro, loss of insulin signaling in microglia results in metabolic reprograming with an increase in glycolysis and impaired uptake of A{beta}. In vivo, MG-IRKO mice exhibit alterations in mood and social behavior, and when crossed with the 5xFAD mouse model of AD, the resultant mice exhibit increased levels of A{beta} plaque and elevated neuroinflammation. Thus, insulin signaling in microglia plays a key role in microglial cellular metabolism, neuroinflammation and the ability of the cells to take up A{beta}, such that reduced insulin signaling in microglia alters mood and social behavior and accelerates AD pathogenesis. Together these data indicate key roles of insulin action in microglia and the potential of targeting insulin signaling in microglia in treatment of AD.

neuroscience↗

bioRxiv2024

CH-related Mutant ASXL1 Promotes Atherosclerosis in Mice via Dysregulated Innate Immunity

Certain somatic mutations confer a fitness advantage in hematopoietic stem and progenitor cells (HSPCs) over normal HSPCs, resulting in the clonal expansion of mutant blood cells1, otherwise known as clonal haematopoiesis (CH). CH is frequently observed among healthy elderly people and is closely associated with the risk of cardiovascular diseases (CVDs). The most frequently mutated genes of CH include DNMT3A, TET2, and ASXL12. Among them, even though ASXL1 mutations are clinically associated with the highest risk for developing CVDs, little is known whether and how the mutations contribute to CVDs. Here we show accelerated development of atherosclerosis and increased inflammatory monocytes in mice transplanted with the bone marrow cells (BMCs) from the mice expressing mutant ASXL1 (ASXL1-MT) selectively in hematopoietic cells. RNA sequencing analysis of the plaque-macrophages derived from BMCs expressing ASXL1-MT showed more inflammatory signatures than those from control BMCs. Mechanistically, wild-type ASXL1 inhibited innate immune signalling through direct interactions with IRAK1/TRAF6/TAK1 in the cytoplasm, while ASXL1-MT, which only interacted with TAK1, lost this regulatory function, leading to NF-{kappa}B activation. This mechanism is unique and distinct from those of CH with Tet2 or Dnmt3a mutations, where overactivation of the IL-1{beta}/NLRP3 inflammasome plays critical roles3-5. Intriguingly, IRAK1/4 inhibition decreased the number of inflammatory monocytes and attenuated the development of atherosclerosis driven by ASXL1-MT. The present work connects the mutations of an epigenetic factor, ASXL1, with inflammation and CVDs and gives an indication for the prevention of CVDs in CH.

cell biology↗

bioRxiv2024

Cell size and selection for stress-induced binary cell fusion

In unicellular organisms, sexual reproduction typically begins with the fusion of two cells (plasmogamy) followed by the fusion of their two haploid nuclei (karyogamy) and finally meiosis. Most work on the evolution of sexual reproduction focuses on the benefits of the genetic recombination that takes place during meiosis. However, the selection pressures that may have driven the early evolution of binary cell fusion, which sets the stage for the evolution of karyogamy by bringing nuclei together in the same cell, have seen less attention. In this paper we develop a model for the coevolution of cell size and binary cell fusion rate. The model assumes that larger cells experience a survival advantage from their larger cytoplasmic volume. We find that under favourable environmental conditions, populations can evolve to produce larger cells that undergo obligate binary cell fission. However, under challenging environmental conditions, populations can evolve to subsequently produce smaller cells under binary cell fission that nevertheless retain a survival advantage by fusing with other cells. The model thus parsimoniously recaptures the empirical observation that sexual reproduction is typically triggered by adverse environmental conditions in many unicellular eukaryotes and draws conceptual links to the literature on the evolution of multicellularity. Author summarySexual reproduction is commonly observed, both in eukaryotic microorganisms and in higher multicellular organisms. Sex has evolved despite numerous apparent costs, including investment in finding a partner and the energetic requirements of sexual reproduction. Binary cell fusion is a process that sets the stage for sexual reproduction by bringing nuclei from different cells into contact. Here, we provide a mathematical explanation of the advantage conferred by binary cell fusion due to increased cell mass. We show that when unicellular organisms have the option to invest in either cell fusion or cell mass, they can evolve to fuse together as rapidly as possible in the face of adverse environments, instead of increasing their mass. These results are consistent with the empirical observation that sexual reproduction is often triggered by environmental stress in unicellular eukaryotes. Our results imply an advantage to cell fusion, which helps to shed light on the early evolution of sexual reproduction itself.

evolutionary biology↗

bioRxiv2024

SegFinder: an automated tool for identifying RNA virus genome segments through co-occurrence in multiple sequenced samples

Metagenomic sequencing has expanded the RNA virosphere, but many identified viral genomes remain incomplete, especially for segmented viruses. Traditional methods relying on sequence homology struggle to identify highly divergent segments and group them confidently within a single virus species. To address this, we developed a new bioinformatic tool - SegFinder - that identifies virus genome segments based on their common co-occurrence at similar abundance within segmented viruses. SegFinder successfully re-discovered all segments from a test data set of individual mosquito transcriptomes, which was also used to establish parameter thresholds for reliable segment identification. Using these optimal parameters, we applied SegFinder to 858 libraries from eight metagenomic sequencing projects, including vertebrates, invertebrates, plants, and environmental samples. Furthermore, we identified 108 (excluding RdRP) unique viral genome segments, of which 55 were novel and 32 showed no recognizable sequence homology to known sequences but which were verified by the presence of conserved sequences at the genome termini. SegFinder is also able to identify segmented genome structures in viruses previously considered to be predominantly unsegmented, and in doing so expanded the number of known families and orders of segmented RNA viruses, making it a valuable tool in an era of large-scale parallel sequencing.

bioinformatics↗

bioRxiv2024

Protein Arginine Methylation of the Translation Initiation Factor eIF1A Increases Usage of a Near-cognate Start Codon

Protein arginine methylation has emerged as a key post-translational modification responsible for many facets of eukaryotic gene expression. To better understand the extent of this modification in cellular pathways, we carried out bioorthogonal methylation profiling in Saccharomyces cerevisiae to comprehensively identify the in vivo substrates of the major yeast protein arginine methyltransferase Hmt1. Gene ontology analysis of candidate substrates revealed an enrichment of proteins involved in the process of translation. We verified one such factor, eIF1A, by in vitro methylation. Three sites on eIF1A were found to be responsible for its methylation: R13, R14, and R62, with varied capacity by which each site contributed to the overall methylation capacity in vitro. To determine the role of methylation in eIF1A function, we used a battery of arginine-to-alanine substitution mutants to evaluate translation fidelity in these mutants. Our data show that substitution mutants at R13 and R14 in the N-terminal tail improved the fidelity of start codon recognition in an initiation fidelity assay. Overall, our data suggest that Hmt1-mediated methylation of eIF1A fine-tunes the fidelity of start codon recognition for proper translation initiation.

molecular biology↗

bioRxiv2024

Placental and fetal microbiota in rhesus macaque: a case study using metagenomic sequencing

Recent evidence challenging the notion of a sterile intrauterine environment has sparked research into the origins and effects of fetal microbiota on immunity development during gestation. Rhesus macaques (RMs) serve as valuable non-human primate (NHP) models due to their similarities to humans in development, placental structure, and immune response. In this study, metagenomic analysis was applied to the placenta, umbilical cord, spleen, gastrointestinal (GI) tissues of an unborn RM fetus, and the maternal intestine, revealing the diversity and functionality of microbes in these tissues. We observed substantial microbial sharing between the mother and fetus, with the microbial composition of the placenta and umbilical cord more closely resembling that of the fetal organs than the maternal intestine. Notably, compared with other adult RMs, there was a clear convergence between maternal and fetal microbiota, alongside distinct differences between the microbiota of adults and the fetus, which underscores the unique microbial profiles in fetal environments. Furthermore, the fetal microbiota displayed a less developed carbohydrate metabolism capacity than adult RMs. It also shared antibiotic resistance genes (ARGs) with both maternal and adult RM microbiomes, indicating potential vertical transmission. Comparative analysis of the metagenomes between the RM fetus and a human fetus revealed significant differences in microbial composition and genes, yet also showed similarities in certain abundant microbiota. Collectively, our results contribute to a more comprehensive understanding of the intrauterine microbial environment in macaques.

microbiology↗

bioRxiv2024

Competition and Compromise between Exogenous Probiotics and Native Microbiota

Probiotic interventions are effective strategies to modulate the gut microbiome, but how exogenous probiotics compete with native gut microbiota remains elusive. Here, we use a mouse model and a well-documented probiotic Bifidobacterium animalis subsp. lactis V9 (BV9) to mechanistically investigate its competitive strategies. We perform metagenomic and whole genome sequencing of stool samples and isolated BV9, longitudinally collected from 24 mice orally administered with BV9 and different diets. Results show that a high-fiber diet most effectively supports the colonization of BV9, where BV9 selectively competes with Parabacteroides distasonis (P. distasonis), rather than extensively with other gut bacteria. By comparing the genomic structures of BV9 and P. distasonis isolated during the washout period, we infer their co-evolution mechanisms, highlighting their competition and compromise in utilizing inulin-derived glucose. Finally, our in vitro co-culture experiments validate such competitive dynamics. This study fills a critical gap in our understanding of niche competition in colonization.

microbiology↗

bioRxiv2024

Dual CRISPRi-Seq for genome-wide genetic interaction studies identifies key genes involved in the pneumococcal cell cycle

A major goal in biology is to uncover the relationship between genotype and phenotype. However, identifying gene function is often hampered by genetic redundancy. For example, under standard laboratory conditions, three-quarters of the genes in the human pathogen Streptococcus pneumoniae are non-essential. A powerful approach to unravel genetic redundancy is by identifying gene-gene interactions. To uncover genetic interactions (GIs) in S. pneumoniae on a genome-wide scale, a generally applicable dual CRISPRi-Seq method and associated analysis pipeline was developed. Specifically, we created a library of 869 dual sgRNAs targeting high-confidence operons that encode essential and non-essential genes, covering over 70% of the genetic elements in the pneumococcal genome. Testing these 378,015 unique combinations, 4,026 significant GIs were identified, including 1,935 negative and 2,091 positive interactions. Besides known GIs, we found and confirmed previously unknown interactions involving genes responsible for fundamental cellular processes such as cell division, cell shape maintenance, and chromosome segregation. The presented methods and bioinformatic approaches can serve as a roadmap for genome-wide gene interaction studies in other organisms. Lastly, all interactions are available for exploration via the Pneumococcal Genetic Interaction Network (PneumoGIN) at https://veeninglab.shinyapps.io/PneumoGIN, which can serve as a starting point for new biological discoveries and translational research.

microbiology↗

bioRxiv2024

A bone-derived protein primes rapid visual escape via GPR37 receptor in a subpopulation of VTA GABAergic neurons

Rapid escape against visual threats is critical for survival. Whether it requires a permissive mechanism is unknown. Here, we show that osteocalcin (OCN), a protein produced by bone and persisted in the brain, primes rapid visual escape response by increasing excitability of VTA GABAergic neuron subpopulation via OCN-GPR37-cAMP-THIK-1 (K2P13.1) pathway. Knock-out of OCN or its receptor GPR37, and conditional knock-out of GPR37 in VTA GABAergic or glutamatergic neurons caused delayed escape. Reconstituting OCN-GPR37 signaling specifically in VTA was sufficient to restore normal response. Single-cell transcriptomics combined with electrophysiology showed that OCN decreases potassium currents in a subpopulation of VTA GABAergic neurons via GPR37-induced cAMP reduction and subsequent THIK-1 suppression. This elevation of excitability in VTA neuron subpopulation can be recapitulated by HM4Di, an inhibitory chemogenetic GPCR commonly used to suppress neuronal activity. Our study demonstrated that visual behavior requires a bone-derived protein that tunes electrophysiology of central nervous system neurons. Graph AbstractO_ST_ABSIn briefC_ST_ABSThe bone-brain axis regulates visual escape behavior. Osteocalcin (OCN), a small protein secreted by bone, plays a permissive role in rapid visual escape. This is achieved through GPR37 receptor expressed in a subpopulation of VTA GABAergic neurons. OCN-GPR37 signaling increases neuronal excitability by decreasing K+ current via THIK-1 channel suppression. HighlightsO_LIThe bone-derived protein osteocalcin and its receptor GPR37 in VTA are required for rapid visual escape response. C_LIO_LIGPR37 is expressed in a subpopulation of VTA GABAergic neurons and primes rapid visual escape. C_LIO_LIOsteocalcin-GPR37 signaling increases neuronal excitability by suppressing THIK-1 (K2P13.1) channel via cAMP reduction. C_LIO_LIActivation of HM4Di increases excitability of subpopulation of VTA GABAergic neurons and enhances rapid visual escape. C_LI O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/607510v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@1b7ef5dorg.highwire.dtl.DTLVardef@c3eea2org.highwire.dtl.DTLVardef@167dd75org.highwire.dtl.DTLVardef@1fc5613_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

Upregulation of DEK Expression in Uterine Myomas and Cervical Cancer as a Potential Prognostic Factor

The aim of this pilot study is to investigate the role of the DEK protein as a potential prognostic marker in gynecological tumors, specifically focusing on uterine myomas and cervical cancer. The study cohort comprised Chinese female patients manifesting with menorrhagia and pelvisalgia, from whom neoplastic and adjacent non-neoplastic tissue specimens were procured during surgical intervention for either leiomyomas or cervical carcinoma. DEK protein and messenger RNA (mRNA) levels were measured across normal uterine tissue, uterine myomas, and cervical cancer tissues using Western blotting, immunohistochemistry, and quantitative real time polymerase chain reaction (qRT-PCR). Results revealed a marked increase in DEK protein expression in cervical cancer tissues, moderate expression in uterine myomas, and minimal levels in normal uterine tissues. Statistical analyses confirmed significant differences in DEK protein expression between tissue types, though mRNA expression differences did not reach statistical significance. These findings suggest DEKs involvement in tumor development and suppression, making it a promising biomarker for early detection in gynecological tumors. Further research is needed to elucidate DEKs mechanisms in gynecological tumorigenesis and its potential as an early biomarker, addressing critical need in womens health.

cancer biology↗

bioRxiv2024

TUG protein acts through a disordered region to organize the early secretory pathway

The endoplasmic reticulum (ER)-Golgi Intermediate Compartment (ERGIC) is a distinct compartment in mammalian cells, which forms in part by homotypic fusion of ER-derived vesicles and gives rise to the cis cisterna of the Golgi ribbon. How the ERGIC is regulated is not well understood. Here we show that the TUG protein is essential to maintain this compartment as a distinct organelle. TUG (UBXN9, Aspscr1) is known to regulate the cell type -specific trafficking of GLUT4 glucose transporters, but its role in more ubiquitous trafficking pathways has not been well characterized. TUG localized to the ERGIC and in fibroblasts its deletion enhanced anterograde flux and increased resorption of ERGIC markers into the cis-Golgi, perturbing membrane homeostasis in the early secretory pathway. TUG knockout cells had a compacted Golgi morphology, and ultrastructural studies revealed dilated cisterna with surrounding small vesicles. A central disordered region in TUG mediated its recruitment to ERGIC membranes, and an amino terminal domain was sufficient to induce oligomerization in cells. In TUG knockout cells, ERGIC-dependent processes such as autophagy are disrupted and model cargoes such as CFTR are missorted. Together, these results reveal a novel, TUG-dependent regulatory mechanism in the early secretory pathway, which modulates ERGIC organization and anterograde trafficking. This function is co-opted by GLUT4 and other proteins that employ an unconventional secretion pathway to the plasma membrane.

cell biology↗

bioRxiv2024

Extraction-free colorimetric RT-LAMP for SARS-CoV-2 RNA detection from saliva

AimTo develop a rapid and easy diagnostic assay for detection of SARS-CoV-2 RNA presented in saliva samples. MethodThe color-based RT-LAMP was used to detect nucleocapsid (N) gene of SARS-CoV-2 without RNA extraction from saliva. ResultsRNA spiked saliva can be used directly for cDNA synthesis after heat inactivation of the saliva and diluted 2-fold with either water or PBS. For both PCR and LAMP, 20% of saliva did not have obvious effect on the reaction. Saliva did not interfere with RT-LAMP when the volume of saliva was less than 20% of the total volume. The sensitivity of the RT-LAMP reached to 1.034x10-5 ng/{micro}l (475 copies/l). The RT-LAMP assay was validated by testing 20 RNA spiked saliva samples. The assay specificity was similar to that of data without saliva. ConclusionsThe RT-LAMP colorimetric assay can be used as a screening method with the advantages of being rapid, easy to use than the qRT-PCR.

microbiology↗

bioRxiv2024

Study on the phenotypic diversity and comprehensive evaluation analysis of 43 ornamental peonies of Sect. Paeonia.

The peony of Sect. Paeonia was a perennial herbaceous plant with numerous ornamental varieties and riched diversity in flower color and shape. It has ornamental, edible, and medicinal value and a long history of cultivation in China. The study of phenotypic diversity of plants is an important foundation for plants of Sect. Paeonia breeding. This study conducted phenotypic diversity analysis, principal component analysis, and cluster analysis on 43 varieties of Sect. Paeonia germplasm resources. Phenotypic traits included 30 qualitative traits and 7 quantitative traits. Through genetic diversity analysis, principal component analysis, comprehensive evaluation, and cluster analysis, we ultimately concluded that plant samples had relatively rich genetic phenotype traits. In principal component analysis, the first 12 principal components have covered the vast majority of information for phenotypic traits. The comprehensive evaluation results of phenotypic traits indicate that the F values of each variety in the germplasm sample were all positive number. The degree of stamen petals played a key role in determining the phenotypic diversity of plants, and the shape of the cotyledons and leaflets may determine the plants stress resistance performance, which provides a reference for breeding new varieties of peonies of Sect. Paeonia.

plant biology↗