Although coagulase-negative Staphylococcus(CNS),along with technological activities,plays a key role in fermented sausage flavour and nutrient production,the molecular mechanism of these activities remains elusive.In ...Although coagulase-negative Staphylococcus(CNS),along with technological activities,plays a key role in fermented sausage flavour and nutrient production,the molecular mechanism of these activities remains elusive.In this study,18 CNS strains with high proteolytic activity were isolated from Chinese Dong fermented pork(Nanx Wudl),and their technological and transcriptomic properties were investigated.After biochemical identification and genetic analysis,their technological properties,including nitrate reductase,catalase,antioxidant,and lipolytic activities and their growth under varying temperatures,salt concentrations,and p H levels were evaluated.Their aroma-producing potential was also determined in a model medium resembling fermented sausages.Transcriptomic analysis was performed using the most promising isolates.Biochemical identification and 16S rDNA sequencing revealed that the 18 Staphylococcus strains belonged to Staphylococcus xylosus,Staphylococcus saprophyticus,Staphylococcus carnosus,Staphylococcus sciuri,and Staphylococcus equorum.In terms of technological properties,16 strains showed a nitrate-reducing ability,while 11 strains had a lipolytic activity.All strains exhibited superoxide dismutase(SOD)and catalase activities;four strains displayed an SOD activity of>50%.They also tolerated 10%NaCl and 150 mg/kg of nitrite.They showed significant differences in ketone and acid production.The transcriptomic analysis of S.xylosus strains Sx3 and Sx6,which were selected because of their excellent enzymatic activities and aroma-producing ability,revealed the remarkable effect of genes related to pyruvate catabolism and amino acid metabolism on aroma generation.Therefore,this study provided valuable insights into the metabolic mechanisms underlying the technological properties of CNS and identified promising candidates as starter cultures in fermented sausage manufacturing.展开更多
Andrias davidianus(Chinese giant salamander,CGS)is the largest and oldest extant amphibian species in the world and is a source of prospective functional food in China.However,the progress of functional peptides minin...Andrias davidianus(Chinese giant salamander,CGS)is the largest and oldest extant amphibian species in the world and is a source of prospective functional food in China.However,the progress of functional peptides mining was slow due to lack of reference genome and protein sequence data.In this study,we illustrated full-length transcriptome sequencing to interpret the proteome of CGS meat and obtain 10703 coding DNA sequences.By functional annotation and amino acid composition analysis,we have discovered various genes related to signal transduction,and 16 genes related to longevity.We have also found vast variety of functional peptides through protein coding sequence(CDS)analysis by comparing the data obtained with the functional peptide database.Val-Pro-Ile predicted by the CDS analysis was released from the CGS meat through enzymatic hydrolysis,suggesting that our approach is reliable.This study suggested that transcriptomic analysis can be used as a reference to guide polypeptide mining in CGS meat,thereby providing a powerful mining strategy for the bioresources with unknown genomic and proteomic sequences.展开更多
Foxtail millet(Setaria italica)is an important C4 model crop;however,due to its high-density planting and high stature,lodging at the filling stage resulted in a serious reduction in yield and quality.Therefore,it is ...Foxtail millet(Setaria italica)is an important C4 model crop;however,due to its high-density planting and high stature,lodging at the filling stage resulted in a serious reduction in yield and quality.Therefore,it is imperative to identify and deploy the genes controlling foxtail millet plant height.In this study,we used a semi-dwarf line 263A and an elite high-stalk breeding variety,Chuang 29 to construct an F2 population to identify dwarf genes.We performed transcriptome analysis(RNA-seq)using internode tissues sampled at three jointing stages of 263A and Chuang 29,as well as bulk segregant analysis(BSA)on their F2 population.A total of 8918 differentially expressed genes(DEGs)were obtained from RNA-seq analysis,and GO analysis showed that DEGs were enriched in functions such as‘‘gibberellin metabolic process”and‘‘oxidoreductase activity”,which have previously been shown to be associated with plant height.A total 593 mutated genes were screened by BSA-seq method.One hundred and seventy-six out of the 593 mutated genes showed differential expression levels between the two parental lines,and seven genes not only showed differential expression in two or three internode tissues but also showed high genomic variation in coding regions,which indicated they play a crucial role in plant height determination.Among them,we found a gibberellin biosynthesis related GA20 oxidase gene(Seita.5G404900),which had a single-base at the third exon,leading to the frameshift mutation at 263A.Cleaved amplified polymorphic sequence assay and association analysis proved the single-base in Seita.5G404900 co-segregated with dwarf phenotype in two independent F2 populations planted in entirely different environments.Taken together,the candidate genes identified in this study will help to elucidate the genetic basis of foxtail millet plant height,and the molecular marker will be useful for marker-assisted dwarf breeding.展开更多
Tomato(Solanum lycopersicum)is a perishable fruit because of its fast water loss and susceptibility to pathogens in the post-harvest stage,which leads to huge economic losses every year.In this study,firstly from 19 t...Tomato(Solanum lycopersicum)is a perishable fruit because of its fast water loss and susceptibility to pathogens in the post-harvest stage,which leads to huge economic losses every year.In this study,firstly from 19 tomato cultivars,we screened out two cultivars,Riogrand and SalarF1,having long and short shelf-life spans,respectively.Secondly,shelf-life analysis was carried out for both cultivars at room temperature.Results exhibited that Riogrand showed higher firmness and less weight loss than SalarF1.The ethylene production was higher in SalarF1,compared with Riogrand during post-harvest storages.We performed transcriptomic analysis of both cultivars in different storage stages.We discovered 2913,2188,and 11,119 differentially expressed genes(DEGs)for three post-harvest stages(0,20,and 40 Days Post-Harvest(DPH)),respectively.These genes are enriched in ethylene biosynthesis and response,as well as cell wall-related genes.Ethylene response factor(ERF)ERF2 and ERF4 were highly expressed in SalarF1 with a short shelf life in 40 DPH,and the ethylene biosynthetic genes ACO1,ACO4,ACS6,and ACS2 were significantly upregulated in SalarF1.Regarding cell wall loosening and cell wall-related genes XTH3,XTH7,XTH23,1,3;1,4-β-D-Gluc-like,pGlcT1,Cellulase,PGH1,PL5,PL-like 1,PL-like 2 exhibited the highest levels of significance,being notably upregulated in the last stage of SalarF1.The quantitative real-time polymerase chain reaction(qRT-PCR)analysis validated these gene expressions,which is in line with the transcriptome analysis.The findings suggested that the extension of tomato fruit shelf life is mostly dependent on ethylene biosynthesis,signaling pathway genes,cell wall loosening,and cell wall-associated genes.展开更多
Rui Chena,b,Tangbing Cui a,b,∗a School of Biology and Biological Engineering,South China University of Technology,Guangzhou 510006,China b Guangdong Key Laboratory of Fermentation and Enzyme Engineering,South China Un...Rui Chena,b,Tangbing Cui a,b,∗a School of Biology and Biological Engineering,South China University of Technology,Guangzhou 510006,China b Guangdong Key Laboratory of Fermentation and Enzyme Engineering,South China University of Technology,Guangzhou 510006,China The authors regret that the published version of this article contained several errors and omissions,which are described and corrected below.1.Figs.3 and 4(figure order and legends).In the published article,Figs.3 and 4 were inadvertently published in reversed order.The figures should be swapped so that the figure content matches its caption.The correct figures and their legends are provided on the following page.2.Title correction.The compound name in the published title was incorrectly typeset as“benzo[a]pyrene”The correct spelling is“benzo[a]pyrene.”3.Text corrections in Section 2.4.Several typographical errors occurred in Section 2.4(“Up-regulation of acetoin,lactate,and kanosamine biosynthesis under sodium gluconate treatment”).展开更多
Conventional random mutation breeding remains the simplest and most cost-effective approach in enhancing strains in fermentation industry.Nonetheless,extensive research on compound mutagenesis are limited to screening...Conventional random mutation breeding remains the simplest and most cost-effective approach in enhancing strains in fermentation industry.Nonetheless,extensive research on compound mutagenesis are limited to screening target strains,and few studies on the interaction mechanism of compound mutagenesis factors.Herein,transcriptomic was employed to elucidate the molecular mechanism behind helium-neon(He-Ne)laser and ultraviolet(UV)compound mutagenesis in Bacillus subtilis.Transcriptomic sequencing analysis was conducted on five sample groups(control/CK,UV,laser/LA,UV-laser/UL,and laser-UV/LU),facilitating the statistical com-parison of differentially expressed genes(DEGs)across 4 sample relationships(CK-vs-UV,CK-vs-LA,CK-vs-LU,and CK-vs-UL).The DEGs revealed that UV irradiation improved the biosynthesis of pyrimidine nucleotides by upregulating the activity of key enzymes(pyrimidine nucleotides synthetase,pyruvate dehydrogenase,phos-photransferase system(PTS)fructose-specific enzyme),while laser irradiation stimulated metabolism through the regulation of transmembrane transporter activity.Further KEGG enrichment analysis of 1891 DEGs in UV-vs-LU sample relationship unveiled 89 genes significantly enriched in the two-component system,which potentially linked to phytochrome.Moreover,analysis of 784 DEGs in UV-vs-UL sample relationship indicated up-regulation of genes associated with translation,replication,and genetic repair pathways,affirming the laser’s induction of UV damage repair mechanisms.Subsequently,9 pivotal genes(liaS,yvfT,yxdK,cheA,ykoW,uvrC,pcrA,recA,and ruvB)were selected for quantitative reverse transcriptional PCR(qRT-PCR)validation,demonstrating consistent trends with transcriptomic data.Conclusively,our findings unveiled interplay mechanism between UV and laser compound mutagenesis at molecular level,offered valuable insights for mutagenesis mode selection and further elucidation of mutagenesis mechanisms.展开更多
To better understand the bitterness effect and molecule mechanism of myosin-derived peptides activating bitter receptors,the interaction between myosin-derived peptides of dry-cured ham and bitter receptors was invest...To better understand the bitterness effect and molecule mechanism of myosin-derived peptides activating bitter receptors,the interaction between myosin-derived peptides of dry-cured ham and bitter receptors was investigated by molecular docking and molecular dynamics simulation;the signal transduction mechanism of myosinderived peptides was explored by HEK-293T cells using calcium imaging and transcriptomics analysis.Lower CDOCKER energy was observed during the interaction between myosin-derived peptides and hT2R1 by molecular docking compared with hT2R4,hT2R5,hT2R8,hT2R14 and hT2R16.Hydrogen bonds and hydrophobic interaction were the most important interaction forces which stabilized the interaction of hT2R1 and myosinderived peptides.Compared with LEKEKSELK and TEELEEAKK,the RMSF values and EC50 values of HVLATLGEK were lower,indicating that hT2R1 was more sensitive to HVLATLGEK stimulation.Transcriptomics and KEGG analyses showed that 767 differentially expressed genes were found and mainly involved in cAMP signaling pathway,neuroactive ligand-receptor interaction,calcium signaling pathway and MAPK signaling pathway after stimulating of HVLATLGEK.Protein-protein interaction network further demonstrated that DDIT3,FOS,FOSB,MYC,EGR1 and CCN2 were the key genes to connect the six functional clusters including ligandreceptor interaction and signal transduction.展开更多
The WSC proteins produced by Penicillium expansum play a crucial role in causing blue mold on pears.To analyze the role of the WSC1 gene in the pathogenic process of this fungal pathogen,we conducted transcriptomic an...The WSC proteins produced by Penicillium expansum play a crucial role in causing blue mold on pears.To analyze the role of the WSC1 gene in the pathogenic process of this fungal pathogen,we conducted transcriptomic analysis of a WSC1 knockout(ΔWSC1)strain.The knockout of WSC1 significantly altered the gene expression profile in P.expansum,particularly for genes involved in cell wall integrity,signaling,stress response,and toxin production.The differential expression of these genes might make theΔWSC1 strain more vulnerable to environmental stress,while reducing the toxin production capacity,ultimately leading to a decrease in the pathogenicity.The transcriptomic analysis revealed that the expression of genes related to stress response signals,defense mechanisms and oxidative stress management changed when pear fruits were infected with theΔWSC1 strain.These changes may trigger a cascade of responses in pear fruits.In addition,compared with those infected with the wild-type strain,pear fruits infected with theΔWSC1 strain exhibited up-regulated expression of genes related to defense and oxidative stress.This study clarifies how the WSC1 gene influences P.expansum’s ability to infect pear fruits and how pear fruits respond to the infection.展开更多
The loss of a pregnancy,including ectopic pregnancy(EP)and early pregnancy loss(EPL),significantly impacts women’s quality of life.Unfortunately,definitive causes can be identified in less than half of EP and EPL cas...The loss of a pregnancy,including ectopic pregnancy(EP)and early pregnancy loss(EPL),significantly impacts women’s quality of life.Unfortunately,definitive causes can be identified in less than half of EP and EPL cases,presenting a substantial challenge for clinical treatment.Previous studies have revealed a significant relationship between the history of EPL and the increased risk of EP.1 Nevertheless,the interplay between EPL and EP remains unclear,highlighting the need to discover novel biomarkers to guide personalized treatment and clinical management.展开更多
To the Editor:Ovarian cancer(OC)is the third cause of death among women globally.[1]Approximately 90%of OC cases are derived from epithelial cells,and these tumors have distinct epidemiological,molecular,and clinical ...To the Editor:Ovarian cancer(OC)is the third cause of death among women globally.[1]Approximately 90%of OC cases are derived from epithelial cells,and these tumors have distinct epidemiological,molecular,and clinical characteristics.[2]High-grade serous ovarian cancer(HGSOC)is the most common subtype of epithelial ovarian cancer(EOC)and has been widely investigated.[3]Ovarian carcinosarcoma(OCS),also known as malignant mixed mesodermal tumor,is a rare and aggressive tumor that typically develops in the female genital tract.[4]Histologically,OCS is considered a high-grade lesion that harbors both carcinomatous and sarcomatous components.[5]Although OCS accounts for only 1–4%of EOC cases,it presents the worst prognosis among all EOC subtypes,[6,7]with a median survival time(MST)of less than 18 months.[5]Due to its rarity,ovarian OCS is challenging to study through prospective trials,resulting in a limited understanding of the disease.Despite this,no targeted treatment strategies are specifically developed for OCS.展开更多
Salinity is a critical environmental factor in aquaculture,and Clostridium autoethanogenum protein(CAP)shows potential as a new feed protein source.This 8-week study compared two diets(fish meal[FM]and CAP)for juvenil...Salinity is a critical environmental factor in aquaculture,and Clostridium autoethanogenum protein(CAP)shows potential as a new feed protein source.This 8-week study compared two diets(fish meal[FM]and CAP)for juvenile Pacific white shrimp(Litopenaeus vannamei)at salinity levels of 15‰,30‰,and 45‰.A total of 720 L.vannamei with an initial average body weight of 0.38±0.01 g were randomly assigned to six experimental groups,each with three biological replicates of 40 shrimp per replicate.The study examined CAP's impact on shrimp growth,immune response,and transcriptome,using two-way ANOVA to analyze the results.The results indicated that compared to the FM group,the shrimp in the CAP group exhibited a significantly higher weight gain rate and specific growth rate at the same salinity(P<0.05).However,at 45‰ salinity,the shrimp in the CAP group had a higher feed conversion ratio and feed intake compared to the FM group(P<0.05).After infection with white spot syndrome virus,the CAP group exhibited a significantly higher survival rate at 15‰ and 45‰ salinity compared to the FM group(P<0.05).As salinity increased,most immune enzyme activities and gene expression levels in the FM group initially increased and then decreased(P<0.05).Under the same salinity,except for phenoloxidase activity which showed no significant difference at 45‰ salinity,all other immune-related indicators and gene expressions in the CAP group were significantly higher than those in the FM group(P<0.05).Transcriptome analysis revealed that the differentially expressed genes(DEGs)between FM and CAP groups at various salinity levels were primarily associated with immune and metabolic pathways.Additionally,by combining the analysis of these DEGs with immune-related indicators,it was observed that under different salinity conditions,CAP was associated with the co-expression of immune and metabolism-related genes as well as changes in enzyme activity.In summary,CAP as the main protein source boosts growth,disease resistance,and nonspecific immunity in L.vannamei,while also regulating immune enzyme activity and gene expression to improve adaptability to salinity changes.展开更多
The predominant causal agent of poplar leaf blight is the pathogenic fungus Alternaria alternata (Fr.) Keissl., which exhibits host specificity toward Populus species. To elucidate the molecular response mechanisms of...The predominant causal agent of poplar leaf blight is the pathogenic fungus Alternaria alternata (Fr.) Keissl., which exhibits host specificity toward Populus species. To elucidate the molecular response mechanisms of A. alternata under fludioxonil fungicide stress, the fungus was cultured at the half-maximal effective concentration (EC₅₀) of fludioxonil. Transcriptomic and metabolomic profiles were analyzed using mycelia harvested under these conditions. Comparative analysis revealed 1,001 differentially expressed genes (DEGs) in the resistant strain (RS) relative to the wild-type strain (WT), comprising 628 upregulated and 373 downregulated genes. Concurrently, 524 differentially accumulated metabolites (DAMs) were identified, with 336 upregulated and 188 downregulated metabolites. KEGG pathway enrichment demonstrated pronounced upregulation in glycerophospholipid metabolism, α-linolenic acid metabolism, nucleic acid biosynthesis, and glycosylation processes. Conversely, arachidonic acid and galactose metabolism pathways were suppressed. Significant downregulation was observed in phosphatidylinositol signaling, aflatoxin biosynthesis, and cutin/suberin/wax biosynthesis pathways. Transcriptomic profiling further indicated that upregulated DEGs were predominantly associated with amino sugar/nucleotide sugar metabolism, ABC transporters, aflatoxin biosynthesis, and purine metabolism, while downregulated DEGs were enriched in N-glycan biosynthesis, endoplasmic reticulum protein processing, steroid biosynthesis, and riboflavin metabolism. Fludioxonil exerted substantial inhibitory effects on fungal growth, pathogenicity, and metabolic activity. Mechanistically, A. alternata counteracted fungicide-induced stress through modulation of its antioxidant defense system. This integrative multi-omics study delineates the dynamic gene expression and metabolic reprogramming in A. alternata under fludioxonil exposure, providing novel insights into potential molecular targets and informing the development of next-generation fungicidal strategies for phytopathogen control.展开更多
Mounting evidence suggests that circadian rhythm disruption may be linked to the onset and progression of Alzheimer’s disease.However,whether this disruption occurs before the appearance of cognitive symptoms and whe...Mounting evidence suggests that circadian rhythm disruption may be linked to the onset and progression of Alzheimer’s disease.However,whether this disruption occurs before the appearance of cognitive symptoms and whether it drives disease development remain unclear.Understanding the temporal relationship between circadian rhythm dysregulation and early Alzheimer’s disease pathological changes may open up new avenues for disease prevention and intervention.To determine if circadian rhythm disruption precedes cognitive decline,we conducted high-resolution transcriptome analyses of the hippocampus in a 5-month-old mouse model of Alzheimer’s disease and age-matched wild-type control mice at multiple time points over a 24-hour period.While the mouse model of Alzheimer’s disease did not exhibit obvious cognitive symptoms at this stage,the expression of circadian-related genes in the hippocampus exhibited extensive abnormalities.In the control group,2109 genes exhibited rhythmic expression characteristics.In the mouse model of Alzheimer’s disease,a marked proportion of these genes lost their rhythmicity,some genes newly developed rhythmicity,and some maintained rhythmicity but with altered expression patterns.Genes related to neuronal function,including those involved in protein homeostasis regulation,neuroinflammation,and ion homeostasis,showed significant changes in circadian rhythm amplitude and phase,and some completely lost their rhythmicity.These findings point to the following critical early events in Alzheimer’s disease:hippocampal circadian gene disruption occurs before cognitive symptoms emerge,genes related to neuronal function are uniquely susceptible to this early dysregulation,and circadian dysfunction may even precede the pathological changes of Alzheimer’s disease and influence disease onset.This work advances Alzheimer’s disease research by clarifying that circadian disruption is an early pre-symptomatic event,reinforcing the potential of circadian rhythm regulation as a strategy for early intervention of Alzheimer’s disease,and identifying neuronal pathways that may serve as intervention targets.展开更多
Red-fleshed fruits are valued for their vibrant color and high anthocyanin content.Pre-harvest fruit bagging enhances fruit peel pigmentation,but its effect on flesh coloration remains poorly characterized.This study ...Red-fleshed fruits are valued for their vibrant color and high anthocyanin content.Pre-harvest fruit bagging enhances fruit peel pigmentation,but its effect on flesh coloration remains poorly characterized.This study revealed that removing bags from‘Gengcunyangtao’red-fleshed peach fruits triggers the rapid and uniform accumulation of anthocyanins in the flesh,resulting in anthocyanin levels that exceed those in unbagged fruits.The exposure to light after bag removal triggered significant increases in anthocyanin levels within 24 h.This was accompanied by the rapid upregulation of light-responsive and flavonoid biosynthetic gene expression levels within 6 h.A metabolomic analysis indicated that anthocyanin precursors,especially p-coumaric acid,accumulated before bag removal,thereby increasing substrate availability for rapid anthocyanin synthesis.On the basis of a weighted gene co-expression network analysis,MYB transcription factors,anthocyanin transporters,glutathione S-transferase,and multidrug and toxic compound extrusion(MATE)were identified as key regulators that coordinate precursor storage along with light-induced transcriptional activation.Notably,PpMYB4 binds to the promoter of PpGSTF14 and activates its expression,thereby promoting anthocyanin accumulation.The study findings elucidated the temporal coordination of metabolic priming and light-responsive transcriptional regulation driving rapid anthocyanin biosynthesis,with possible implications for improving peach fruit flesh coloration.展开更多
For red pear,the anthocyanin content is a crucial factor determining the fruit skin color,which affects consumer preferences.Low overnight temperatures promote anthocyanin accumulation,but the molecular mechanism resp...For red pear,the anthocyanin content is a crucial factor determining the fruit skin color,which affects consumer preferences.Low overnight temperatures promote anthocyanin accumulation,but the molecular mechanism responsible is unclear.In this study,‘Hongzaosu’pear(Pyrus pyrifolia×Pyrus communis)fruit were treated with a low nighttime temperature(LNT,16℃)or a warm nighttime temperature(WNT,26℃),with sampling conducted within two diurnal cycles.The results showed that LNT promoted anthocyanin accumulation in the fruit skin.The structural anthocyanin biosynthetic genes PpCHS,PpF3H,and PpUFGT exhibited a rhythmic increase in expression at night under LNT.To examine the underlying mechanism,RNA sequencing was conducted using pear calli exposed to LNT and WNT for different durations(24,48,72,or 96 h).Transcriptome analysis revealed 285 differentially expressed genes(DEGs)common to all pairwise comparisons of LNT-and WNT-treated calli of‘Clapp's Favorite’(P.communis)at the sampling time points.KEGG pathway and gene ontology enrichment analyses indicated that the common DEGs were enriched in secondary metabolic processes and phenylpropanoid metabolic processes,which are associated with anthocyanin biosynthesis.The transcription factor PpCDF5,which was responsive to LNT,was selected for further study.Dual-luciferase assays showed that PpCDF5 activated the transcription of anthocyanin biosynthetic genes PpMYB10,PpCHS,PpF3H,PpDFR,PpANS,and PpUFGT.The yeast one-hybrid and EMSA assays demonstrated that PpCDF5 directly binds to the PpF3H promoter,which contains an AAAG motif.Overexpression of PpCDF5 in pear calli and transient overexpression in pear fruit both increased anthocyanin accumulation.The results indicate that PpCDF5 is involved in LNT-induced anthocyanin biosynthesis in pear fruit and provide insights into the molecular regulation of commercial fruit coloration.展开更多
Lepidopteran insects produce cocoons with unique properties.The cocoons are made of silk produced in the larval tissue silk gland and our understanding of the silk genes is still very limited.Here,we investigated silk...Lepidopteran insects produce cocoons with unique properties.The cocoons are made of silk produced in the larval tissue silk gland and our understanding of the silk genes is still very limited.Here,we investigated silk genes in the bagworm moth Eumeta variegata,a species that has recently been found to produce extraordinarily strong and tough silk.Using short-read transcriptomic analysis,we identified a partial sequence of the fibroin heavy chain gene and its product was found to have a C-terminal structure that is conserved within nonsaturniid species.This is in accordance with the presence of fibroin light chain/fibrohexamerin genes and it is suggested that the bagworm moth is producing silk composed of fibroin ternary complex.This indicates that the fibroin structure has been evolutionarily conserved longer than previously thought.Other than fibroins we identified candidates for sericin genes,expressed strongly in the middle region of the silk gland and encoding serine-rich proteins,and other silk genes,that are structurally conserved with other lepidopteran homologues.The bagworm moth is thus considered to be producing conventional lepidopteran type of silk.We further found a number of genes expressed in a specific region of the silk gland and some genes showed conserved expression with Bombyx mori counterparts.This is the first study allowing comprehensive silk gene identification and expression analysis in the lepidopteran Psychidae family and should contribute to the understanding of silk gene evolution as well as to the development of novel types of silk.展开更多
Background： Chronic intermittent hypoxia is the most remarkable feature of obstructive sleep apnea/hypopnea syndrome and it can induce the change of hypoxia-inducible factor-1α （H IF-1α） expression and contractil...Background： Chronic intermittent hypoxia is the most remarkable feature of obstructive sleep apnea/hypopnea syndrome and it can induce the change of hypoxia-inducible factor-1α （H IF-1α） expression and contractile properties in the genioglossus. To clarify the role of HIF-lot in contractile properties of the genioglossus, this study generated and compared high-throughput RNA-sequencing data from genioglossus between HIF-1α conditional knockout （KO） mice and littermate wild-type （WT） mice. Methods： KO mice were generated with cre-loxP strategy. Gene expression profile analysis was performed using gene enrichment analysis. Gene ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway analyses of differently expressed messenger RNAs were performed to identify the related pathways and biological lhnctions. Six differentially expressed genes （DEGs） were validated by qualitative reverse transcription polymerase chain reaction. Results： A total of 142 （77 upregulated and 65 downregulated） transcripts were found to exhibit statistically significant difference between the HIF-la-KO and WT mice. GO and KEGG analyses indicated that DEGs included genes involved in ＂skeletal muscle cell differentiation,＂ ＂muscle organ development,＂ ＂glucose metabolic process,＂ ＂glycogen biosynthetic and metabolic process,＂ etc. Conclusion： This study might provide evidence that H IF-lot affects the expression of multiple genes involved in the myogenesis, muscle developrnent, and carbohydrate metabolism through transcriptome analysis in conditional HIE-1α-KO mice.展开更多
Methicillin-resistant Staphylococcus aureus(MRSA)has become a rising clinical problem as its occurrence has increased due to the overuse and misuse of antibiotics.In this work,upconversion nanoparticles@AgBiS2 core–s...Methicillin-resistant Staphylococcus aureus(MRSA)has become a rising clinical problem as its occurrence has increased due to the overuse and misuse of antibiotics.In this work,upconversion nanoparticles@AgBiS2 core–shell were produced with enhanced photothermal transformation efficiency and ability to produce reactive oxygen species for synergistic photodynamic photothermal and photodynamic antibacterial performance.The nanoparticles exhibit good antibacterial effects in vitro and satisfactory therapeutic performance on healing MRSA-infected wounds in vivo experiments.RNA-sequencing technique has been used to investigate and reveal that photothermal–photodynamic therapy using the nanoparticles can interfere with metabolic processes such as galactose metabolism in MRSA bacteria,destroy the transport system on the surface of MRSA,and affect quorum sensing to hinder the formation of biofilms to achieve effective antibacterial efficacy.It was demonstrated that this work presents an alternative near-infrared photoactive multimodal nanostructure for antibacterial applications.展开更多
Fish skin acts as the first immune barrier against pathogens from external environments.Recently,fish skin immunity research has gradually become a hot topic in aquaculture disease control.Interestingly,the skin can d...Fish skin acts as the first immune barrier against pathogens from external environments.Recently,fish skin immunity research has gradually become a hot topic in aquaculture disease control.Interestingly,the skin can do air-breathing in some bimodal respiration fish.However,there is no comprehensive understanding of these two functions.In this study,the skin regeneration of loach(Paramisgurnus dabryanus)was investigated through morphological and histological observations.Then,original skins(OS)and the regenerated skins(RS)when their capillaries were the most abundant during healing,were collected for transcriptomic analysis.285,899,386 clean reads with a total length of 42.34 Gb were obtained.A total of 1282 differentially expressed genes(DEGs)were detected,including 1030 DEGs up-regulated and 252 DEGs down-regulated in the comparison of RS vs.OS.Fc gamma R-mediated phagocytosis(containing gelsolin(Gsn)),chemokine signaling pathway(containing C-C motif chemokine ligand 28(Ccl28)),and B cell receptor signaling pathway(containing CD80 molecule(Cd81))were closely related to skin immune response of the loach.PI3K-Akt signaling pathway[containing fibronectin 1(Fn1)and lysyl oxidase-like 2b(Loxl2b)],TGF-beta signaling pathway[containing thrombospondin 1(Thbs1)],ECM-receptor interaction[containing integrin alpha 7(Itga7),Itgb8,Itgb10 and Itgb5],and dilated cardiomyopathy[containing laminin subunit alpha1(Lama1)]were closely associated with skin air-breathing of the loach.This study is conducive to explore the molecular mechanisms of skin immune response during its regeneration and air-breathing of bimodal respiration fish.This study will benefit for the aquaculture of P.dabryanus and its related species.展开更多
Background and aims:Polygonum cuspidatum Sieb.et Zucc.(P.cuspidatum)and its active components have been clinically proven to have anti-hepatocellular carcinoma effects.However,the potential targets of P.cuspidatum for...Background and aims:Polygonum cuspidatum Sieb.et Zucc.(P.cuspidatum)and its active components have been clinically proven to have anti-hepatocellular carcinoma effects.However,the potential targets of P.cuspidatum for these effects have not yet been revealed.Methods:We used network pharmacology and single-cell transcriptomic analysis with molecular docking to elucidate the active components and targets of P.cuspidatum for hepatocellular carcinoma.Results:CDK1,ESR1,HSP90A11,and MAPK1 were shown to be the key targets of P.cuspidatum for hepatocellular carcinoma.P.cuspidatum was found to be likely correlated with the improved abnormal expression of CDK1 and ESR1 and the poor prognosis of HSP90AA1 and MAPK1.CDK1 was identified as the most potential antihepatocellular carcinoma target of P.cuspidatum.Among the active components of P.cuspidatum,physcion diglucoside was found to have the most potential to treat hepatocellular carcinoma by targeting CDK1.Conclusion:Our study provides novel insights into the anti-hepatocellular carcinoma pharmacological effects of P.cuspidatum,which could serve as a scientific basis for its development as a medicinal resource and the targeting of CDK1 for hepatocellular carcinoma treatment.展开更多
基金the financial support of the National Natural Science Foundation of China(32102016)the Taishan Industrial Experts Program。
文摘Although coagulase-negative Staphylococcus(CNS),along with technological activities,plays a key role in fermented sausage flavour and nutrient production,the molecular mechanism of these activities remains elusive.In this study,18 CNS strains with high proteolytic activity were isolated from Chinese Dong fermented pork(Nanx Wudl),and their technological and transcriptomic properties were investigated.After biochemical identification and genetic analysis,their technological properties,including nitrate reductase,catalase,antioxidant,and lipolytic activities and their growth under varying temperatures,salt concentrations,and p H levels were evaluated.Their aroma-producing potential was also determined in a model medium resembling fermented sausages.Transcriptomic analysis was performed using the most promising isolates.Biochemical identification and 16S rDNA sequencing revealed that the 18 Staphylococcus strains belonged to Staphylococcus xylosus,Staphylococcus saprophyticus,Staphylococcus carnosus,Staphylococcus sciuri,and Staphylococcus equorum.In terms of technological properties,16 strains showed a nitrate-reducing ability,while 11 strains had a lipolytic activity.All strains exhibited superoxide dismutase(SOD)and catalase activities;four strains displayed an SOD activity of>50%.They also tolerated 10%NaCl and 150 mg/kg of nitrite.They showed significant differences in ketone and acid production.The transcriptomic analysis of S.xylosus strains Sx3 and Sx6,which were selected because of their excellent enzymatic activities and aroma-producing ability,revealed the remarkable effect of genes related to pyruvate catabolism and amino acid metabolism on aroma generation.Therefore,this study provided valuable insights into the metabolic mechanisms underlying the technological properties of CNS and identified promising candidates as starter cultures in fermented sausage manufacturing.
基金funded by Shenzhen Science and Technology Innovation Commission(KCXFZ20201221173207022)。
文摘Andrias davidianus(Chinese giant salamander,CGS)is the largest and oldest extant amphibian species in the world and is a source of prospective functional food in China.However,the progress of functional peptides mining was slow due to lack of reference genome and protein sequence data.In this study,we illustrated full-length transcriptome sequencing to interpret the proteome of CGS meat and obtain 10703 coding DNA sequences.By functional annotation and amino acid composition analysis,we have discovered various genes related to signal transduction,and 16 genes related to longevity.We have also found vast variety of functional peptides through protein coding sequence(CDS)analysis by comparing the data obtained with the functional peptide database.Val-Pro-Ile predicted by the CDS analysis was released from the CGS meat through enzymatic hydrolysis,suggesting that our approach is reliable.This study suggested that transcriptomic analysis can be used as a reference to guide polypeptide mining in CGS meat,thereby providing a powerful mining strategy for the bioresources with unknown genomic and proteomic sequences.
基金supported by the National Key Research and Development Program of China (2018YFD1000702/ 2018YFD1000700)the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural SciencesOperating Expenses for Basic Scientific Research of Institute of Crop Science, Chinese Academy of Agricultural Sciences
文摘Foxtail millet(Setaria italica)is an important C4 model crop;however,due to its high-density planting and high stature,lodging at the filling stage resulted in a serious reduction in yield and quality.Therefore,it is imperative to identify and deploy the genes controlling foxtail millet plant height.In this study,we used a semi-dwarf line 263A and an elite high-stalk breeding variety,Chuang 29 to construct an F2 population to identify dwarf genes.We performed transcriptome analysis(RNA-seq)using internode tissues sampled at three jointing stages of 263A and Chuang 29,as well as bulk segregant analysis(BSA)on their F2 population.A total of 8918 differentially expressed genes(DEGs)were obtained from RNA-seq analysis,and GO analysis showed that DEGs were enriched in functions such as‘‘gibberellin metabolic process”and‘‘oxidoreductase activity”,which have previously been shown to be associated with plant height.A total 593 mutated genes were screened by BSA-seq method.One hundred and seventy-six out of the 593 mutated genes showed differential expression levels between the two parental lines,and seven genes not only showed differential expression in two or three internode tissues but also showed high genomic variation in coding regions,which indicated they play a crucial role in plant height determination.Among them,we found a gibberellin biosynthesis related GA20 oxidase gene(Seita.5G404900),which had a single-base at the third exon,leading to the frameshift mutation at 263A.Cleaved amplified polymorphic sequence assay and association analysis proved the single-base in Seita.5G404900 co-segregated with dwarf phenotype in two independent F2 populations planted in entirely different environments.Taken together,the candidate genes identified in this study will help to elucidate the genetic basis of foxtail millet plant height,and the molecular marker will be useful for marker-assisted dwarf breeding.
基金supported by the National Natural Science Foundation of China(Grant No.U23A20204)the“Wanjiang Scholar Program(Anhui Province)”.
文摘Tomato(Solanum lycopersicum)is a perishable fruit because of its fast water loss and susceptibility to pathogens in the post-harvest stage,which leads to huge economic losses every year.In this study,firstly from 19 tomato cultivars,we screened out two cultivars,Riogrand and SalarF1,having long and short shelf-life spans,respectively.Secondly,shelf-life analysis was carried out for both cultivars at room temperature.Results exhibited that Riogrand showed higher firmness and less weight loss than SalarF1.The ethylene production was higher in SalarF1,compared with Riogrand during post-harvest storages.We performed transcriptomic analysis of both cultivars in different storage stages.We discovered 2913,2188,and 11,119 differentially expressed genes(DEGs)for three post-harvest stages(0,20,and 40 Days Post-Harvest(DPH)),respectively.These genes are enriched in ethylene biosynthesis and response,as well as cell wall-related genes.Ethylene response factor(ERF)ERF2 and ERF4 were highly expressed in SalarF1 with a short shelf life in 40 DPH,and the ethylene biosynthetic genes ACO1,ACO4,ACS6,and ACS2 were significantly upregulated in SalarF1.Regarding cell wall loosening and cell wall-related genes XTH3,XTH7,XTH23,1,3;1,4-β-D-Gluc-like,pGlcT1,Cellulase,PGH1,PL5,PL-like 1,PL-like 2 exhibited the highest levels of significance,being notably upregulated in the last stage of SalarF1.The quantitative real-time polymerase chain reaction(qRT-PCR)analysis validated these gene expressions,which is in line with the transcriptome analysis.The findings suggested that the extension of tomato fruit shelf life is mostly dependent on ethylene biosynthesis,signaling pathway genes,cell wall loosening,and cell wall-associated genes.
文摘Rui Chena,b,Tangbing Cui a,b,∗a School of Biology and Biological Engineering,South China University of Technology,Guangzhou 510006,China b Guangdong Key Laboratory of Fermentation and Enzyme Engineering,South China University of Technology,Guangzhou 510006,China The authors regret that the published version of this article contained several errors and omissions,which are described and corrected below.1.Figs.3 and 4(figure order and legends).In the published article,Figs.3 and 4 were inadvertently published in reversed order.The figures should be swapped so that the figure content matches its caption.The correct figures and their legends are provided on the following page.2.Title correction.The compound name in the published title was incorrectly typeset as“benzo[a]pyrene”The correct spelling is“benzo[a]pyrene.”3.Text corrections in Section 2.4.Several typographical errors occurred in Section 2.4(“Up-regulation of acetoin,lactate,and kanosamine biosynthesis under sodium gluconate treatment”).
基金supported by the National Key Research and Devel-opment Program of China[Grant No.2021YFC2104200,2022YFF0710101]Jiangsu Provincial Key Research and Development Program[Grant No.BE2018368]Zhenjiang Key Research and Development Plan[Grant No.NY2023001].
文摘Conventional random mutation breeding remains the simplest and most cost-effective approach in enhancing strains in fermentation industry.Nonetheless,extensive research on compound mutagenesis are limited to screening target strains,and few studies on the interaction mechanism of compound mutagenesis factors.Herein,transcriptomic was employed to elucidate the molecular mechanism behind helium-neon(He-Ne)laser and ultraviolet(UV)compound mutagenesis in Bacillus subtilis.Transcriptomic sequencing analysis was conducted on five sample groups(control/CK,UV,laser/LA,UV-laser/UL,and laser-UV/LU),facilitating the statistical com-parison of differentially expressed genes(DEGs)across 4 sample relationships(CK-vs-UV,CK-vs-LA,CK-vs-LU,and CK-vs-UL).The DEGs revealed that UV irradiation improved the biosynthesis of pyrimidine nucleotides by upregulating the activity of key enzymes(pyrimidine nucleotides synthetase,pyruvate dehydrogenase,phos-photransferase system(PTS)fructose-specific enzyme),while laser irradiation stimulated metabolism through the regulation of transmembrane transporter activity.Further KEGG enrichment analysis of 1891 DEGs in UV-vs-LU sample relationship unveiled 89 genes significantly enriched in the two-component system,which potentially linked to phytochrome.Moreover,analysis of 784 DEGs in UV-vs-UL sample relationship indicated up-regulation of genes associated with translation,replication,and genetic repair pathways,affirming the laser’s induction of UV damage repair mechanisms.Subsequently,9 pivotal genes(liaS,yvfT,yxdK,cheA,ykoW,uvrC,pcrA,recA,and ruvB)were selected for quantitative reverse transcriptional PCR(qRT-PCR)validation,demonstrating consistent trends with transcriptomic data.Conclusively,our findings unveiled interplay mechanism between UV and laser compound mutagenesis at molecular level,offered valuable insights for mutagenesis mode selection and further elucidation of mutagenesis mechanisms.
基金supported by National Natural Science Foundation of China(32101975)National Key Research and Development Program of China(2021YFD2100104)+4 种基金Modern Agricultural Technical Foundation of China(CARS-42-25)Zhejiang Province Natural Science Foundation(LQ22C200017)Open Project of China Food Flavor and Nutrition Health Innovation Center(CFC2023A-001)Young leading Talents program of Ningbo(2023QL034)Natural Science Foundation of Ningbo(2022J086).
文摘To better understand the bitterness effect and molecule mechanism of myosin-derived peptides activating bitter receptors,the interaction between myosin-derived peptides of dry-cured ham and bitter receptors was investigated by molecular docking and molecular dynamics simulation;the signal transduction mechanism of myosinderived peptides was explored by HEK-293T cells using calcium imaging and transcriptomics analysis.Lower CDOCKER energy was observed during the interaction between myosin-derived peptides and hT2R1 by molecular docking compared with hT2R4,hT2R5,hT2R8,hT2R14 and hT2R16.Hydrogen bonds and hydrophobic interaction were the most important interaction forces which stabilized the interaction of hT2R1 and myosinderived peptides.Compared with LEKEKSELK and TEELEEAKK,the RMSF values and EC50 values of HVLATLGEK were lower,indicating that hT2R1 was more sensitive to HVLATLGEK stimulation.Transcriptomics and KEGG analyses showed that 767 differentially expressed genes were found and mainly involved in cAMP signaling pathway,neuroactive ligand-receptor interaction,calcium signaling pathway and MAPK signaling pathway after stimulating of HVLATLGEK.Protein-protein interaction network further demonstrated that DDIT3,FOS,FOSB,MYC,EGR1 and CCN2 were the key genes to connect the six functional clusters including ligandreceptor interaction and signal transduction.
文摘The WSC proteins produced by Penicillium expansum play a crucial role in causing blue mold on pears.To analyze the role of the WSC1 gene in the pathogenic process of this fungal pathogen,we conducted transcriptomic analysis of a WSC1 knockout(ΔWSC1)strain.The knockout of WSC1 significantly altered the gene expression profile in P.expansum,particularly for genes involved in cell wall integrity,signaling,stress response,and toxin production.The differential expression of these genes might make theΔWSC1 strain more vulnerable to environmental stress,while reducing the toxin production capacity,ultimately leading to a decrease in the pathogenicity.The transcriptomic analysis revealed that the expression of genes related to stress response signals,defense mechanisms and oxidative stress management changed when pear fruits were infected with theΔWSC1 strain.These changes may trigger a cascade of responses in pear fruits.In addition,compared with those infected with the wild-type strain,pear fruits infected with theΔWSC1 strain exhibited up-regulated expression of genes related to defense and oxidative stress.This study clarifies how the WSC1 gene influences P.expansum’s ability to infect pear fruits and how pear fruits respond to the infection.
基金supported by the Hangzhou Joint Fund of the Zhejiang Provincial Natural Science Foundation of China(No.LHZSD24H290001).
文摘The loss of a pregnancy,including ectopic pregnancy(EP)and early pregnancy loss(EPL),significantly impacts women’s quality of life.Unfortunately,definitive causes can be identified in less than half of EP and EPL cases,presenting a substantial challenge for clinical treatment.Previous studies have revealed a significant relationship between the history of EPL and the increased risk of EP.1 Nevertheless,the interplay between EPL and EP remains unclear,highlighting the need to discover novel biomarkers to guide personalized treatment and clinical management.
基金supported by grants from the National Natural Science Foundation of China(No.81702569)the Natural Science Foundation of Jiangsu Province(No.BK20221183)+3 种基金the Science Fund for Distinguished Young Scholars of Jiangsu Province(No.BK20211533)the Jiangsu Maternal and Child Health Research Association(No.FYX202344)the Postgraduate Research&Practice Innovation Program of Jiangsu Province(No.KYCX23_1969)the Nanjing Medical Science and Technique Development Foundation(No.YKK23156).
文摘To the Editor:Ovarian cancer(OC)is the third cause of death among women globally.[1]Approximately 90%of OC cases are derived from epithelial cells,and these tumors have distinct epidemiological,molecular,and clinical characteristics.[2]High-grade serous ovarian cancer(HGSOC)is the most common subtype of epithelial ovarian cancer(EOC)and has been widely investigated.[3]Ovarian carcinosarcoma(OCS),also known as malignant mixed mesodermal tumor,is a rare and aggressive tumor that typically develops in the female genital tract.[4]Histologically,OCS is considered a high-grade lesion that harbors both carcinomatous and sarcomatous components.[5]Although OCS accounts for only 1–4%of EOC cases,it presents the worst prognosis among all EOC subtypes,[6,7]with a median survival time(MST)of less than 18 months.[5]Due to its rarity,ovarian OCS is challenging to study through prospective trials,resulting in a limited understanding of the disease.Despite this,no targeted treatment strategies are specifically developed for OCS.
基金supported by the Special Projects in Key Fields of Ordinary University in Guangdong Province(2023ZDZX4010)Central Public-interest Scientific Institution Basal Research Fund(Grant No.1630012025808)the Chinese Academy of Tropical Agricultural Sciences for Science and Technology Innovation Team of National Tropical Agricultural Science Center(CATASCXTD2024016).
文摘Salinity is a critical environmental factor in aquaculture,and Clostridium autoethanogenum protein(CAP)shows potential as a new feed protein source.This 8-week study compared two diets(fish meal[FM]and CAP)for juvenile Pacific white shrimp(Litopenaeus vannamei)at salinity levels of 15‰,30‰,and 45‰.A total of 720 L.vannamei with an initial average body weight of 0.38±0.01 g were randomly assigned to six experimental groups,each with three biological replicates of 40 shrimp per replicate.The study examined CAP's impact on shrimp growth,immune response,and transcriptome,using two-way ANOVA to analyze the results.The results indicated that compared to the FM group,the shrimp in the CAP group exhibited a significantly higher weight gain rate and specific growth rate at the same salinity(P<0.05).However,at 45‰ salinity,the shrimp in the CAP group had a higher feed conversion ratio and feed intake compared to the FM group(P<0.05).After infection with white spot syndrome virus,the CAP group exhibited a significantly higher survival rate at 15‰ and 45‰ salinity compared to the FM group(P<0.05).As salinity increased,most immune enzyme activities and gene expression levels in the FM group initially increased and then decreased(P<0.05).Under the same salinity,except for phenoloxidase activity which showed no significant difference at 45‰ salinity,all other immune-related indicators and gene expressions in the CAP group were significantly higher than those in the FM group(P<0.05).Transcriptome analysis revealed that the differentially expressed genes(DEGs)between FM and CAP groups at various salinity levels were primarily associated with immune and metabolic pathways.Additionally,by combining the analysis of these DEGs with immune-related indicators,it was observed that under different salinity conditions,CAP was associated with the co-expression of immune and metabolism-related genes as well as changes in enzyme activity.In summary,CAP as the main protein source boosts growth,disease resistance,and nonspecific immunity in L.vannamei,while also regulating immune enzyme activity and gene expression to improve adaptability to salinity changes.
基金supported by the Northeast Asia Biodiversity Research Center(grant number 411147021003).
文摘The predominant causal agent of poplar leaf blight is the pathogenic fungus Alternaria alternata (Fr.) Keissl., which exhibits host specificity toward Populus species. To elucidate the molecular response mechanisms of A. alternata under fludioxonil fungicide stress, the fungus was cultured at the half-maximal effective concentration (EC₅₀) of fludioxonil. Transcriptomic and metabolomic profiles were analyzed using mycelia harvested under these conditions. Comparative analysis revealed 1,001 differentially expressed genes (DEGs) in the resistant strain (RS) relative to the wild-type strain (WT), comprising 628 upregulated and 373 downregulated genes. Concurrently, 524 differentially accumulated metabolites (DAMs) were identified, with 336 upregulated and 188 downregulated metabolites. KEGG pathway enrichment demonstrated pronounced upregulation in glycerophospholipid metabolism, α-linolenic acid metabolism, nucleic acid biosynthesis, and glycosylation processes. Conversely, arachidonic acid and galactose metabolism pathways were suppressed. Significant downregulation was observed in phosphatidylinositol signaling, aflatoxin biosynthesis, and cutin/suberin/wax biosynthesis pathways. Transcriptomic profiling further indicated that upregulated DEGs were predominantly associated with amino sugar/nucleotide sugar metabolism, ABC transporters, aflatoxin biosynthesis, and purine metabolism, while downregulated DEGs were enriched in N-glycan biosynthesis, endoplasmic reticulum protein processing, steroid biosynthesis, and riboflavin metabolism. Fludioxonil exerted substantial inhibitory effects on fungal growth, pathogenicity, and metabolic activity. Mechanistically, A. alternata counteracted fungicide-induced stress through modulation of its antioxidant defense system. This integrative multi-omics study delineates the dynamic gene expression and metabolic reprogramming in A. alternata under fludioxonil exposure, providing novel insights into potential molecular targets and informing the development of next-generation fungicidal strategies for phytopathogen control.
基金Shenzhen Science Technology and Innovation Commission,No.JCYJ20220531100811026Shenzhen Clinical Research Center for Trauma Treatment,No.LCYSSQ20220823091405012(both to YZ)Shenzhen Science and Technology Program,No.KQTD20240729102249044.
文摘Mounting evidence suggests that circadian rhythm disruption may be linked to the onset and progression of Alzheimer’s disease.However,whether this disruption occurs before the appearance of cognitive symptoms and whether it drives disease development remain unclear.Understanding the temporal relationship between circadian rhythm dysregulation and early Alzheimer’s disease pathological changes may open up new avenues for disease prevention and intervention.To determine if circadian rhythm disruption precedes cognitive decline,we conducted high-resolution transcriptome analyses of the hippocampus in a 5-month-old mouse model of Alzheimer’s disease and age-matched wild-type control mice at multiple time points over a 24-hour period.While the mouse model of Alzheimer’s disease did not exhibit obvious cognitive symptoms at this stage,the expression of circadian-related genes in the hippocampus exhibited extensive abnormalities.In the control group,2109 genes exhibited rhythmic expression characteristics.In the mouse model of Alzheimer’s disease,a marked proportion of these genes lost their rhythmicity,some genes newly developed rhythmicity,and some maintained rhythmicity but with altered expression patterns.Genes related to neuronal function,including those involved in protein homeostasis regulation,neuroinflammation,and ion homeostasis,showed significant changes in circadian rhythm amplitude and phase,and some completely lost their rhythmicity.These findings point to the following critical early events in Alzheimer’s disease:hippocampal circadian gene disruption occurs before cognitive symptoms emerge,genes related to neuronal function are uniquely susceptible to this early dysregulation,and circadian dysfunction may even precede the pathological changes of Alzheimer’s disease and influence disease onset.This work advances Alzheimer’s disease research by clarifying that circadian disruption is an early pre-symptomatic event,reinforcing the potential of circadian rhythm regulation as a strategy for early intervention of Alzheimer’s disease,and identifying neuronal pathways that may serve as intervention targets.
基金supported by the Key Scientific and Technological Grant of Zhejiang for Breeding New Agricultural Varieties(Grant No.2021C12066-4)Huzhou Agricultural Science and Technology Innovation Team Project(Grant No.2022HN01).
文摘Red-fleshed fruits are valued for their vibrant color and high anthocyanin content.Pre-harvest fruit bagging enhances fruit peel pigmentation,but its effect on flesh coloration remains poorly characterized.This study revealed that removing bags from‘Gengcunyangtao’red-fleshed peach fruits triggers the rapid and uniform accumulation of anthocyanins in the flesh,resulting in anthocyanin levels that exceed those in unbagged fruits.The exposure to light after bag removal triggered significant increases in anthocyanin levels within 24 h.This was accompanied by the rapid upregulation of light-responsive and flavonoid biosynthetic gene expression levels within 6 h.A metabolomic analysis indicated that anthocyanin precursors,especially p-coumaric acid,accumulated before bag removal,thereby increasing substrate availability for rapid anthocyanin synthesis.On the basis of a weighted gene co-expression network analysis,MYB transcription factors,anthocyanin transporters,glutathione S-transferase,and multidrug and toxic compound extrusion(MATE)were identified as key regulators that coordinate precursor storage along with light-induced transcriptional activation.Notably,PpMYB4 binds to the promoter of PpGSTF14 and activates its expression,thereby promoting anthocyanin accumulation.The study findings elucidated the temporal coordination of metabolic priming and light-responsive transcriptional regulation driving rapid anthocyanin biosynthesis,with possible implications for improving peach fruit flesh coloration.
基金supported by the National Natural Science Foundation of China(Grant Nos.32072545,32272639 and 32260745)Zhejiang Provincial Natural Science Foundation of China(Grant Nos.LTGN23C150009 and LY22C150003)Zhejiang University Experimental Technology Research Project(Grant No.SYBJS202217).
文摘For red pear,the anthocyanin content is a crucial factor determining the fruit skin color,which affects consumer preferences.Low overnight temperatures promote anthocyanin accumulation,but the molecular mechanism responsible is unclear.In this study,‘Hongzaosu’pear(Pyrus pyrifolia×Pyrus communis)fruit were treated with a low nighttime temperature(LNT,16℃)or a warm nighttime temperature(WNT,26℃),with sampling conducted within two diurnal cycles.The results showed that LNT promoted anthocyanin accumulation in the fruit skin.The structural anthocyanin biosynthetic genes PpCHS,PpF3H,and PpUFGT exhibited a rhythmic increase in expression at night under LNT.To examine the underlying mechanism,RNA sequencing was conducted using pear calli exposed to LNT and WNT for different durations(24,48,72,or 96 h).Transcriptome analysis revealed 285 differentially expressed genes(DEGs)common to all pairwise comparisons of LNT-and WNT-treated calli of‘Clapp's Favorite’(P.communis)at the sampling time points.KEGG pathway and gene ontology enrichment analyses indicated that the common DEGs were enriched in secondary metabolic processes and phenylpropanoid metabolic processes,which are associated with anthocyanin biosynthesis.The transcription factor PpCDF5,which was responsive to LNT,was selected for further study.Dual-luciferase assays showed that PpCDF5 activated the transcription of anthocyanin biosynthetic genes PpMYB10,PpCHS,PpF3H,PpDFR,PpANS,and PpUFGT.The yeast one-hybrid and EMSA assays demonstrated that PpCDF5 directly binds to the PpF3H promoter,which contains an AAAG motif.Overexpression of PpCDF5 in pear calli and transient overexpression in pear fruit both increased anthocyanin accumulation.The results indicate that PpCDF5 is involved in LNT-induced anthocyanin biosynthesis in pear fruit and provide insights into the molecular regulation of commercial fruit coloration.
基金This work was supported by grants-in-aid from the JST/JICA,SATREPS(Science and Technology Research Partnership for Sustainable Devel Devel opment)and Ministry of Agriculture,Forestry,and Fisheries,Japan.
文摘Lepidopteran insects produce cocoons with unique properties.The cocoons are made of silk produced in the larval tissue silk gland and our understanding of the silk genes is still very limited.Here,we investigated silk genes in the bagworm moth Eumeta variegata,a species that has recently been found to produce extraordinarily strong and tough silk.Using short-read transcriptomic analysis,we identified a partial sequence of the fibroin heavy chain gene and its product was found to have a C-terminal structure that is conserved within nonsaturniid species.This is in accordance with the presence of fibroin light chain/fibrohexamerin genes and it is suggested that the bagworm moth is producing silk composed of fibroin ternary complex.This indicates that the fibroin structure has been evolutionarily conserved longer than previously thought.Other than fibroins we identified candidates for sericin genes,expressed strongly in the middle region of the silk gland and encoding serine-rich proteins,and other silk genes,that are structurally conserved with other lepidopteran homologues.The bagworm moth is thus considered to be producing conventional lepidopteran type of silk.We further found a number of genes expressed in a specific region of the silk gland and some genes showed conserved expression with Bombyx mori counterparts.This is the first study allowing comprehensive silk gene identification and expression analysis in the lepidopteran Psychidae family and should contribute to the understanding of silk gene evolution as well as to the development of novel types of silk.
基金This study was supported by grants from the National Natural Science Foundation of China （No. 81271192 and No. 81600897）, and the Shanghai Science and Technology Committee of China （No. 15140903500）.
文摘Background： Chronic intermittent hypoxia is the most remarkable feature of obstructive sleep apnea/hypopnea syndrome and it can induce the change of hypoxia-inducible factor-1α （H IF-1α） expression and contractile properties in the genioglossus. To clarify the role of HIF-lot in contractile properties of the genioglossus, this study generated and compared high-throughput RNA-sequencing data from genioglossus between HIF-1α conditional knockout （KO） mice and littermate wild-type （WT） mice. Methods： KO mice were generated with cre-loxP strategy. Gene expression profile analysis was performed using gene enrichment analysis. Gene ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway analyses of differently expressed messenger RNAs were performed to identify the related pathways and biological lhnctions. Six differentially expressed genes （DEGs） were validated by qualitative reverse transcription polymerase chain reaction. Results： A total of 142 （77 upregulated and 65 downregulated） transcripts were found to exhibit statistically significant difference between the HIF-la-KO and WT mice. GO and KEGG analyses indicated that DEGs included genes involved in ＂skeletal muscle cell differentiation,＂ ＂muscle organ development,＂ ＂glucose metabolic process,＂ ＂glycogen biosynthetic and metabolic process,＂ etc. Conclusion： This study might provide evidence that H IF-lot affects the expression of multiple genes involved in the myogenesis, muscle developrnent, and carbohydrate metabolism through transcriptome analysis in conditional HIE-1α-KO mice.
基金supported by the National Natural Science Foundation of China(No.52172276).
文摘Methicillin-resistant Staphylococcus aureus(MRSA)has become a rising clinical problem as its occurrence has increased due to the overuse and misuse of antibiotics.In this work,upconversion nanoparticles@AgBiS2 core–shell were produced with enhanced photothermal transformation efficiency and ability to produce reactive oxygen species for synergistic photodynamic photothermal and photodynamic antibacterial performance.The nanoparticles exhibit good antibacterial effects in vitro and satisfactory therapeutic performance on healing MRSA-infected wounds in vivo experiments.RNA-sequencing technique has been used to investigate and reveal that photothermal–photodynamic therapy using the nanoparticles can interfere with metabolic processes such as galactose metabolism in MRSA bacteria,destroy the transport system on the surface of MRSA,and affect quorum sensing to hinder the formation of biofilms to achieve effective antibacterial efficacy.It was demonstrated that this work presents an alternative near-infrared photoactive multimodal nanostructure for antibacterial applications.
基金supported by the National Natural Science Foundation of China (32172962 and 31872579)the Fundamental Research Funds for the Central Universities of China (Project Number:2662020SCPY002).
文摘Fish skin acts as the first immune barrier against pathogens from external environments.Recently,fish skin immunity research has gradually become a hot topic in aquaculture disease control.Interestingly,the skin can do air-breathing in some bimodal respiration fish.However,there is no comprehensive understanding of these two functions.In this study,the skin regeneration of loach(Paramisgurnus dabryanus)was investigated through morphological and histological observations.Then,original skins(OS)and the regenerated skins(RS)when their capillaries were the most abundant during healing,were collected for transcriptomic analysis.285,899,386 clean reads with a total length of 42.34 Gb were obtained.A total of 1282 differentially expressed genes(DEGs)were detected,including 1030 DEGs up-regulated and 252 DEGs down-regulated in the comparison of RS vs.OS.Fc gamma R-mediated phagocytosis(containing gelsolin(Gsn)),chemokine signaling pathway(containing C-C motif chemokine ligand 28(Ccl28)),and B cell receptor signaling pathway(containing CD80 molecule(Cd81))were closely related to skin immune response of the loach.PI3K-Akt signaling pathway[containing fibronectin 1(Fn1)and lysyl oxidase-like 2b(Loxl2b)],TGF-beta signaling pathway[containing thrombospondin 1(Thbs1)],ECM-receptor interaction[containing integrin alpha 7(Itga7),Itgb8,Itgb10 and Itgb5],and dilated cardiomyopathy[containing laminin subunit alpha1(Lama1)]were closely associated with skin air-breathing of the loach.This study is conducive to explore the molecular mechanisms of skin immune response during its regeneration and air-breathing of bimodal respiration fish.This study will benefit for the aquaculture of P.dabryanus and its related species.
基金Supported by National Training Program of Innovation and Entrepreneurship for Undergraduates(202410145118).
文摘Background and aims:Polygonum cuspidatum Sieb.et Zucc.(P.cuspidatum)and its active components have been clinically proven to have anti-hepatocellular carcinoma effects.However,the potential targets of P.cuspidatum for these effects have not yet been revealed.Methods:We used network pharmacology and single-cell transcriptomic analysis with molecular docking to elucidate the active components and targets of P.cuspidatum for hepatocellular carcinoma.Results:CDK1,ESR1,HSP90A11,and MAPK1 were shown to be the key targets of P.cuspidatum for hepatocellular carcinoma.P.cuspidatum was found to be likely correlated with the improved abnormal expression of CDK1 and ESR1 and the poor prognosis of HSP90AA1 and MAPK1.CDK1 was identified as the most potential antihepatocellular carcinoma target of P.cuspidatum.Among the active components of P.cuspidatum,physcion diglucoside was found to have the most potential to treat hepatocellular carcinoma by targeting CDK1.Conclusion:Our study provides novel insights into the anti-hepatocellular carcinoma pharmacological effects of P.cuspidatum,which could serve as a scientific basis for its development as a medicinal resource and the targeting of CDK1 for hepatocellular carcinoma treatment.
