【Objective】This study aimed to clarify the key pathways and related genes of taro leaves in response to drought stress,analyze the gene expression patterns under drought conditions,and explore the molecular response...【Objective】This study aimed to clarify the key pathways and related genes of taro leaves in response to drought stress,analyze the gene expression patterns under drought conditions,and explore the molecular response mecha‐nisms.The findings would provide theoretical references for understanding the molecular mechanisms of taro’s drought regulation and for breeding different drought tolerant taro varieties in the future.【Method】Using Lipu taro as the experi‐mental material,leaf samples were collected after consecutive 7 d of drought treatment as the treatment group,while leaf samples from plants watered daily served as the control group.Transcriptome sequencing was performed to identify dif‐ferentially expressed genes,which were then subjected to GO functional annotation and KEGG pathway enrichment analysis.【Result】Under drought stress,there were 1613 differentially expressed genes(DEGs),including 1043 upregulated and 570 down-regulated genes.GO functional annotation analysis revealed that the DEGs were categorized into three major functional groups:molecular function,cellular component,and biological process.In the molecular function category,DEGs were annotated to binding and catalytic activity.In the cellular component category,DEGs were anno‐tated to cellular anatomical entities and protein-containing complexes.In the biological process category,DEGs were an‐notated to cellular processes and metabolic processes.KEGG signaling pathway enrichment analysis showed that 85.00%of the DEGs were enriched in metabolic pathway.Among these,the DEGs were primarily enriched in the glutathione me‐tabolism pathway and the starch and sucrose metabolism pathway,with 11 and 19 DEGs identified in each pathway re‐spectively.Under drought stress,a total of 112 differentially expressed transcription factors(TFs)were identified,mainly including members of the bHLH,ERF,WRKY and NAC families.Among all differentially expressed TFs,82.14%showed up-regulated transcription levels under drought conditions.Plant hormone signal transduction,carotenoid biosynthesis,and the MAPK signaling pathway-plant were identified as key abscisic acid-responsive pathways involved in drought response,influencing stomatal closure in taro leaves and seed dormancy to cope with drought stress.The reliability of the transcriptome data was confirmed by quantitative real-time PCR analysis.【Conclusion】Under drought stress,the gene expression in the glutathione metabolism pathway,the starch and sucrose metabolism pathway,and transcription factors in taro leaves is affected.Most TFs are positively involved in regulating taro plant’s drought response.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
Background： The conversion from non-embryogenic callus （NEC） to embryogenic callus （EC） is the key bottleneck step in regeneration of upland cotton （Gossypium hirsutum）, and hinders the transgenic breeding of u...Background： The conversion from non-embryogenic callus （NEC） to embryogenic callus （EC） is the key bottleneck step in regeneration of upland cotton （Gossypium hirsutum）, and hinders the transgenic breeding of upland cotton. To investigate molecular mechanisms underlying acquisition of embryogenic potential during this process, comparation analysis of transcriptome dynamics between two upland cotton cultivars with different somatic embryogenesis abilities was conducted. Results： Differentially expressed genes involved in the transformation from NEC to EC were detected in the two different cultivars. Principal component analysis based on DEGs showed that the NEC tissues of the two cultivars were highly heterogeneous, whereas the derived EC tissues were similar, which suggested the homogeneousness of EC between different lines. In the highly embryogenic cultivar CCRI 24, more of these genes were down-regulated, whereas, in the recalcitrant cultivar CCRI 12, more were up-regulated. Bioinformatics analysis on these DEGs showed that the vast majority of differentially expressed genes were enriched in metabolism and secondary metabolites biosynthesis pathways. Flavonoid biosynthesis and phenylpropanoid biosynthesis pathways were enriched in both cultivars, and the associated genes were down-regulated more in CCRI 24 than in CCRI 12. We deduced that vigorous secondary metabolism in CCRI 12 may hinder primary metabolism, resulting in tardiness of cell differentiation. Interestingly, genes involved in the plant hormone signal transduction pathway were enriched in the recalcitrant cultivar CCRI 12, but not in CCRI 24, suggesting more radical regulation of hormone signal transduction in the recalcitrant cultivar. Signal transduction rather than biosynthesis of plant hormones is more likely to be the determining factor triggering NEC to EC transition in recalcitrant cotton lines. Transcription factor encoding genes showed differential regulation between two cultivars. Conclusions： Our study provides valuable information about the molecular mechanism of conversion from NEC to EC in cotton and allows for identification of novel genes involved. By comparing transcriptome changes in transformation from NEC to EC between the two cultivars, we identified 46 transcripts that may contribute to initiating embryogenic shift.展开更多
Background:Soil salt stress seriously restricts the yield and quality of cotton worldwide.To investigate the molecular mechanism of cotton response to salt stress,a main cultivated variety Gossypium hirsutum L.acc.Xin...Background:Soil salt stress seriously restricts the yield and quality of cotton worldwide.To investigate the molecular mechanism of cotton response to salt stress,a main cultivated variety Gossypium hirsutum L.acc.Xinluzhong 54 was used to perform transcriptome and proteome integrated analysis.Results:Through transcriptome analysis in cotton leaves under salt stress for 0 h(T0),3 h(T3)and 12 h(T12),we identified 8436,11628 and 6311 differentially expressed genes(DEGs)in T3 vs.T0,T12 vs.T0 and T12 vs.T3,respectively.A total of 459 differentially expressed proteins(DEPs)were identified by proteomic analysis,of which 273,99 and 260 DEPs were identified in T3 vs.T0,T12 vs.T0 and T12 vs.T3,respectively.Metabolic pathways,biosynthesis of secondary metabolites,photosynthesis and plant hormone signal transduction were enriched among the identified DEGs or DEPs.Detail analysis of the DEGs or DEPs revealed that complex signaling pathways,such as abscisic acid(ABA)and jasmonic acid(JA)signaling,calcium signaling,mitogen-activated protein kinase(MAPK)signaling cascade,transcription factors,activation of antioxidant and ion transporters,were participated in regulating salt response in cotton.Conclusions:Our research not only contributed to understand the mechanism of cotton response to salt stress,but also identified nine candidate genes,which might be useful for molecular breeding to improve salt-toleranee in cotton.展开更多
OBJECTIVE To investigate the transcriptomic details on the biosynthetic pathways in different parts of the Panax notoginseng and the pharmacological activity of the saponins extracted from the flower(FS)on vascular in...OBJECTIVE To investigate the transcriptomic details on the biosynthetic pathways in different parts of the Panax notoginseng and the pharmacological activity of the saponins extracted from the flower(FS)on vascular insufficiency conditions.METHODS RNA sequencing of three different Panax notoginseng tissues was performed using next generation DNA sequencing and differential gene expression was validated by real-time PCR.In order to determine pro-angiogenic and therapeutic effects of FS on myocardial infraction(MI),FS was examined on the endothelial cell migration assay,vascular insufficiency model in zebrafish and MI model in rats.RESULTS After assembling the high quality sequencing reads into 107 340 unigenes,biochemical pathways were predicted and 9 908 unigenes were assigned to 135 KEGG pathways.Among them,270 unigenes were identified to be involved in triterpene saponin biosynthesis as well as 350 and 342unigenes were predicted to encode cytochrome P450 sand glycosyltransferases,respectively.One unigene was annotated as CYP716A53v2,probably participates in the formation of protopanaxatriol from protopanaxadiol and the differential expression of this gene was confirmed by real-time PCR.In addition,the pharmacological evaluation demonstrate that FS significantly promoted vascular endothelial growth factor(VEGF)induced the migration of human umbilical vein endothelial cells(HUVECs)and partially restored defective intersegmental vessels in a chemically induced vascular insufficiency model of zebrafish larva.Moreover,the two week posttreatment of the rat MI model with FS(25-50mg·kg-1·d-1)induced approximately 3-fold upregulation of VEGF mRNA expression,with a concomitant increase in blood vessel density in the peri-infarct area of the heart by 50.7%,compared to 41.4%in the MI group.Furthermore,TUNEL analysis indicates a reduction in the mean apoptotic nuclei per field in peri-infarct myocardium upon FS treatment.CONCLUSION We have established a global transcriptome dataset for Panax notoginseng and provided additional genetic information for further genome-wide research and analyses.Candidate genes involved in ginsenoside biosynthesis,including putative cytochrome P450 sand glycosyltransferases were obtained.The transcriptomes in different plant tissues also provide invaluable resources for future study of the differences in physiological processes and secondary metabolites in different parts of P.notoginseng.And the significant pro-angiogenic effect of FS in multiple experimental models renders the purified saponin preparation as potential preventive and therapeutic agent for cardiovascular diseases yet to be developed.展开更多
Cells actively modulate mechanobiological circuitry against external perturbations to stabilize whole cell/tissue physiology.The dynamic adaption of cells to mechanical force is critical for cells to perform vital bio...Cells actively modulate mechanobiological circuitry against external perturbations to stabilize whole cell/tissue physiology.The dynamic adaption of cells to mechanical force is critical for cells to perform vital biological functions,from single cell migration to embryonic development.Dysregulation of such dynamics has been associated with pathophysiological conditions in cardiovascular diseases,cancer,aging,and developmental disorders[1].Therefore,a direct understanding of cell’s biomechanical adaptive/maladaptive behaviors and the trigger factors causing the transformation of healthy adaption to maladaptation can help reveal the regulatory role of single cell mechanosensitive dynamics in the progression of various degenerative diseases and aging.However,current efforts for uncovering fundamental associations between disease and cell architecture have been focusing on'static'measurements of biophysical properties,which is limited by the requirement of large sample sizes to obtain statistically significant data.We therefore developed a single and highly integrated platform with mechanical stimulation and fine spatiotemporal sensing functions to probe the single cell mechanical dynamics at subcellular level to determine cell’s mechanophenotypes in healthy and disease conditions.We developed an integrated micromechanical system composed of an’ultrasound tweezer’stimulator[2]and a PDMS micropillar array [3] cellular force sensor to in situ noninvasively probe and monitor single cell mechanical dynamics.Vascular smooth muscle cells(VSMCs)from healthy mouse and mouse with induced abdominal aorta aneurysm(AAA)were used for cell mechanobiological study.An ultrasound transducer(V312-SM,Olympus)was used to generate ultrasound pulses to excite lipid-encapsulated microbubbles(Targeson)binding to cell membrane through an RGD-integrin linkage to apply a transient nanonewton force to VSMCs seeded on the PDMS micropillar array.PDMS micropillar array was fabricated and functionalized as previously described [3] and acts as the mechanical force sensor in our platform.Upon a 1 HZ and 10-second ultrasound stimulation,calcium influx was clearly detected in both healthy and AAA-VSMCs by using the fluo-4 calcium sensor,suggesting the microbubble-integrin-actin cytoskeleton(CSK)linkage can serve as a mechanosensory to sense the ultrasound stimulation.We then examined how healthy and AAA VSMCs would exhibit adaptions to mechanical stimulation at a global cellular scale.After the onset of a 10-second ultrasound stimulation,control and AAA-VSMCs displayed distinct dynamics of CSK tension within 30 mins,in which the CSK tension of healthy VSMCs increased within the reinforcement period(0-5 min)and restored to their ground state with the relaxation period(5-10 min);yet AAA-VSMCs displayed compromised dynamics of such CSK tension upon calcium influx.Quantitative analysis and theoretical modelling revealed the critical roles of myosin motor contraction,F-actin filament polymerization in regulating cell mechanosensitive dynamics in response to a transient mechanical perturbation.The distinct force and CSK dynamics in healthy and AAA conditions indicates that the force-dependent CSK molecular kinetics is a critical factor governing the distinct mechanosensitive dynamics of cells under pathologically dysfunctional conditions.Our results reveal that the mechanical adaptive process of cells to mechanical stimulus can measure the cellular mechanobiological phenotypes featured in both pathologically healthy and diseased context.We demonstrated that an altered mechanobiological phenotype,i.e.AAA-VSMCs with distinct actomyosin-CSK properties potentiates a mechanical maladaptation that reflects progressive accumulation of cellular damage and dysfunction.This may further reveal the pathogenic contexts and their physical mediators featuring biophysical dysregulation in cardiovascular diseases.展开更多
OBJECTIVE Palythoa caribaeorum(class Anthozoa) is a zoanthid that together jellyfishes,hydra,and sea anemones,which are venomous and predatory,belongs to the Phyllum Cnidaria.The distinguished feature in these marine ...OBJECTIVE Palythoa caribaeorum(class Anthozoa) is a zoanthid that together jellyfishes,hydra,and sea anemones,which are venomous and predatory,belongs to the Phyllum Cnidaria.The distinguished feature in these marine animals is the cnidocytes in the body tissues,responsible for toxin production and injection that are used majorly for prey capture and defense.With exception for other anthozoans,the toxin cocktails of zoanthids have been scarcely studied and are poorly known.METHODS Based on the analysis of P.caribaeorum transcriptome,numerous predicted venom-featured polypeptides were identified,including allergens,neuro-toxins,membrane-active and Kunitz-like peptides(PcKuz).The three predicted PcKuz isotoxins(1 to 3) were selected for functional studies.Through computational processing comprising structural phylogenetic analysis,molecular docking,and dynamics simulation,PcKuz3 was shown to be a potential voltage gated potassium-channel inhibitor.RESULTS PcKuz3 fitted well as new functional Kunitz-type toxins with strong anti-locomotor activity as in vivo assessed in zebrafish larvae,with weak inhibitory effect toward proteases,as evaluated in vitro.Notably,PcKuz3 can suppress,at low concentration,the 6-OHDA-induced neurotoxicity on the locomotive behavior of zebrafish,which indicated PcKuz3 may have a neuroprotective effect.CONCLUSION Taken together,PcK uz3 figures as a novel neurotoxin structure which differs from known homologous peptides expressed in sea anemone.Moreover,the novel PcKuz3 provides an insightful hint for bio-drug development for prospective neurodegenerative disease treatment.展开更多
In this project,we aim to elucidate the molecular mechanism controlling initiation and elongation of tetraploid Gossypium hirsutum fiber cells by setting up a high throughput custom-designed
Soybean mutants withα-nullβ-conglycinin are associated with high nutritional value and low allergenic risk.Although long noncoding RNAs(lncRNAs)are increasingly recognized as functional regulatory components affecti...Soybean mutants withα-nullβ-conglycinin are associated with high nutritional value and low allergenic risk.Although long noncoding RNAs(lncRNAs)are increasingly recognized as functional regulatory components affecting eukaryotic gene expression,little is known about lnc RNA profiles inα-null-type hypoallergenic soybeans.In this study,a genome-wide integrative analysis of lncRNAs,m RNAs and epigenomic data in the soybean cgy-2(confirmedα-null)near-isogenic line(NIL)and its recurrent parent Dongnong47(DN47)was conducted.Nineteen novel lncRNAs that were differentially expressed(DE)only in the NIL at 18 days after flowering(i.e.,α-null-associated DE lncRNAs)were delected.Sixteen putative soybean stress-responsive lncRNAs were identified,and observed to regulate 257 stress-related genes DE in the NIL.This result indicated that theα-null allele might represent an intrinsic defect stress that altered the expression of various stress-related genes inα-null-type hypoallergenic soybean.Additionally,25 epigenetic-related lncRNAs regulated 831 DE epigenetic-related genes and simultaneously initiated multiple epigenetic activities,including ubiquitination,methylation and acetylation.Kyoto encyclopedia of genes and genomes(KEGG)analysis indicated that the biosynthesis of amino acids pathway was enriched with 83 DE genes regulated by nine DE lncRNAs.Changes in the expression of these lncRNAs and genes might be the reason for the altered amino acid composition in the NIL.Among all detected DE lncRNAs,MSTRG.12518 was the most conspicuousα-null-specific cis/trans-lnc RNA that played an efficient,versatile and vital role in the NIL.The data indicated that the lnc RNA profile differed between the NIL and DN47.Variations in lncRNAs,gene expression levels and DNA methylation states likely contributed to the intrinsic defect stress response mechanism inα-null-type hypoallergenic soybeans.展开更多
Fiber cell initiation is a complex process involving many pathways,including phytohormones and components for transcriptional and posttranscriptional regulation.Here we report expression
OBJECTIVE o facilitate the basic acquaintance with the bioactive lycodine-type alkaloids biosynthetic pathways,we conducted the transcriptome analysis of L.casuarinoides by illumina sequencing.METHODS The plant of L.c...OBJECTIVE o facilitate the basic acquaintance with the bioactive lycodine-type alkaloids biosynthetic pathways,we conducted the transcriptome analysis of L.casuarinoides by illumina sequencing.METHODS The plant of L.casuarinoides was collected and was subjected to RNA isolation,cDNA library construction,and illumina sequencing before bioinformatics analysis.After sequencing,the clean reads were obtained for de novo assembly by using Trinity software,and then further processed with TGICL sequencing clustering software to generate unigenes,The unigenes are aligned by Blast X alignment to six public protein database.In addition,all unigenes are functionally annotated by GO,KEGG and characterized putative genes involved in lycopodium alkaloids biosynthesis.RESULTS In total,124,524 high-quality unigenes were obtained with an average sequence length of 601 bp.Among the L.casuarinoides transcripts,61,304 showed significant similarity(E-value<1 e-5) to the known proteins in the public database.Among the total 124 524 unigenes,47,538 open reading frame(ORFs) were predicted.Based on the bioinformatics analysis,all possible enzymes involved in the Lycodine-type alkaloids biosynthetic pathway of L.casuarinoides were identified,including primary amine oxidase(PAO),and Malonly-CoA decarboxylase.In addition,a total of 64 putative cytochrome P450(CYP450) and 827 transcription factors were selected as the candidates of Lycodine-type alka.loids modifiers.Furthermore,a total of 13 352 simple sequence repeats(SSRs) were identified from the 124,524 unigenes,of which dinucleotide motifs AG/CT(50.1%),were the most abundant.CONCLU.SION This transcriptome analysis of L.casuarinoides,provides many valuable candidate genes involv.ing in the biosynthesis of novel secondary metabolites but also lays the foundation for genetic diversity analysis via SSRs markers in L.casuarinoides.展开更多
Objective:Pelvic organ prolapse(POP)is a common condition in postmenopausal women,with an increasing prevalence due to aging.Some women experience POP recurrence after surgical treatment,significantly affecting their ...Objective:Pelvic organ prolapse(POP)is a common condition in postmenopausal women,with an increasing prevalence due to aging.Some women experience POP recurrence after surgical treatment,significantly affecting their physical and mental health.The uterosacral ligament is a critical pelvic support structure.This study aims to investigate the molecular pathological changes in the uterosacral ligament of postmenopausal women with recurrent POP using transcriptomic analysis.Methods:Transcriptomic data of uterosacral ligament tissues were obtained from the public dataset GSE28660,which includes samples from 4 postmenopausal women with recurrent POP,4 with primary POP,and 4 without POP.Differentially expressed genes(DEGs)were identified between recurrent POP and both primary and non-POP groups.Further analysis included intersection analysis of DEGs,gene ontology enrichment,protein protein interaction(PPI)network construction,gene set enrichment analysis(GSEA),single-sample GSEA,and xCell immune cell infiltration analysis to explore molecular pathological changes in recurrent POP.Additionally,histological and molecular differences in the uterosacral ligament were compared between simulated vaginal delivery(SVD)rat models with and without ovariectomy.Results:Compared with primary POP and non-POP groups,recurrent POP exhibited activation of adipogenesis and inflammation-related pathways,while pathways related to muscle proliferation and contraction were downregulated in the uterosacral ligament.Nine key DEGs(ADIPOQ,FABP4,IL-6,LIPE,LPL,PCK1,PLIN1,PPARG,and CD36)were identified,with most enriched in the peroxisome proliferator-activated receptor(PPAR)signaling pathway.These genes were significantly correlated with lipid accumulation,monocyte infiltration,and neutrophil infiltration in the uterosacral ligament.Urodynamic testing revealed that the bladder leak point pressure was significantly higher in ovariectomized SVD rats,both of which had higher values than the sham group.Masson staining showed pronounced adipogenesis in the uterosacral ligament of ovariectomized SVD rats,along with reduced collagen and muscle fibers compared to the sham and non ovariectomized SVD groups.Furthermore,real-time RT-PCR confirmed significantly elevated expression of key DEGs,including ADIPOQ,IL-6,PCK1,and PLIN1,in the uterosacral ligaments of ovariectomized SVD rats.Conclusion:Adipogenesis and inflammation in the uterosacral ligament may contribute to its reduced supportive function,potentially leading to recurrence POP in postmenopausal women.展开更多
为初步解析马尾松花粉对超低温保存的生理响应及相关代谢机制,该文以马尾松花粉为研究对象,在-196℃液氮进行超低温保存并分析冷存过程中[冻存前(CK)、液氮冻存后(LD)、化冻后(HD)]与活性氧(ROS)相关的生理指标及转录组数据。结果表明:...为初步解析马尾松花粉对超低温保存的生理响应及相关代谢机制,该文以马尾松花粉为研究对象,在-196℃液氮进行超低温保存并分析冷存过程中[冻存前(CK)、液氮冻存后(LD)、化冻后(HD)]与活性氧(ROS)相关的生理指标及转录组数据。结果表明:(1)马尾松花粉超低温保存的最适含水量为3.96%,该含水量下将花粉直接投入液氮保存至少48 h,冻存前后花粉存活率分别为78.54%和73.80%。(2)超氧化物歧化酶(SOD),抗坏血酸过氧化物酶(GSH),谷胱甘肽(APX),抑制羟自由基能力4个指标在冻存前后差异显著。(3)转录组测序共获得65.60 Gb过滤数据,有38505个基因比对到参考基因组(47.84%),CK vs LD、CK vs HD、LD vs HD的差异表达基因(DEGs数量分别为232个、268个、218个)。GO和KEGG分析表明,应激响应(response to stimulus)和抗氧化活性(antioxidant activity)等GO term显著富集;植物激素信号转导、MAPK信号途径、淀粉和蔗糖代谢、果糖和甘露醇代谢、过氧化物酶体等KEGG途径显著富集,从这些途径中进一步筛选到10个可能与冷冻保存过程中损伤和修复有关的基因。该研究结果为马尾松种质资源高效利用和安全保存提供了技术手段,也为进一步解析冷冻保存损伤的分子机制提供参考。展开更多
基金National Natural Science Foundation of China(32460756)Guangxi Key Research and Development Project(Guike AB20297041)+1 种基金Science and Technology Development Fund of Guangxi Academy of Agricultural Sciences(Gui‐nongke 2022JM58)Guangxi Lipu Taro Experimental Station Projec(tTS202113)。
文摘【Objective】This study aimed to clarify the key pathways and related genes of taro leaves in response to drought stress,analyze the gene expression patterns under drought conditions,and explore the molecular response mecha‐nisms.The findings would provide theoretical references for understanding the molecular mechanisms of taro’s drought regulation and for breeding different drought tolerant taro varieties in the future.【Method】Using Lipu taro as the experi‐mental material,leaf samples were collected after consecutive 7 d of drought treatment as the treatment group,while leaf samples from plants watered daily served as the control group.Transcriptome sequencing was performed to identify dif‐ferentially expressed genes,which were then subjected to GO functional annotation and KEGG pathway enrichment analysis.【Result】Under drought stress,there were 1613 differentially expressed genes(DEGs),including 1043 upregulated and 570 down-regulated genes.GO functional annotation analysis revealed that the DEGs were categorized into three major functional groups:molecular function,cellular component,and biological process.In the molecular function category,DEGs were annotated to binding and catalytic activity.In the cellular component category,DEGs were anno‐tated to cellular anatomical entities and protein-containing complexes.In the biological process category,DEGs were an‐notated to cellular processes and metabolic processes.KEGG signaling pathway enrichment analysis showed that 85.00%of the DEGs were enriched in metabolic pathway.Among these,the DEGs were primarily enriched in the glutathione me‐tabolism pathway and the starch and sucrose metabolism pathway,with 11 and 19 DEGs identified in each pathway re‐spectively.Under drought stress,a total of 112 differentially expressed transcription factors(TFs)were identified,mainly including members of the bHLH,ERF,WRKY and NAC families.Among all differentially expressed TFs,82.14%showed up-regulated transcription levels under drought conditions.Plant hormone signal transduction,carotenoid biosynthesis,and the MAPK signaling pathway-plant were identified as key abscisic acid-responsive pathways involved in drought response,influencing stomatal closure in taro leaves and seed dormancy to cope with drought stress.The reliability of the transcriptome data was confirmed by quantitative real-time PCR analysis.【Conclusion】Under drought stress,the gene expression in the glutathione metabolism pathway,the starch and sucrose metabolism pathway,and transcription factors in taro leaves is affected.Most TFs are positively involved in regulating taro plant’s drought response.
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 National Science and Technology Major Project(2016ZX08010004),China
文摘Background： The conversion from non-embryogenic callus （NEC） to embryogenic callus （EC） is the key bottleneck step in regeneration of upland cotton （Gossypium hirsutum）, and hinders the transgenic breeding of upland cotton. To investigate molecular mechanisms underlying acquisition of embryogenic potential during this process, comparation analysis of transcriptome dynamics between two upland cotton cultivars with different somatic embryogenesis abilities was conducted. Results： Differentially expressed genes involved in the transformation from NEC to EC were detected in the two different cultivars. Principal component analysis based on DEGs showed that the NEC tissues of the two cultivars were highly heterogeneous, whereas the derived EC tissues were similar, which suggested the homogeneousness of EC between different lines. In the highly embryogenic cultivar CCRI 24, more of these genes were down-regulated, whereas, in the recalcitrant cultivar CCRI 12, more were up-regulated. Bioinformatics analysis on these DEGs showed that the vast majority of differentially expressed genes were enriched in metabolism and secondary metabolites biosynthesis pathways. Flavonoid biosynthesis and phenylpropanoid biosynthesis pathways were enriched in both cultivars, and the associated genes were down-regulated more in CCRI 24 than in CCRI 12. We deduced that vigorous secondary metabolism in CCRI 12 may hinder primary metabolism, resulting in tardiness of cell differentiation. Interestingly, genes involved in the plant hormone signal transduction pathway were enriched in the recalcitrant cultivar CCRI 12, but not in CCRI 24, suggesting more radical regulation of hormone signal transduction in the recalcitrant cultivar. Signal transduction rather than biosynthesis of plant hormones is more likely to be the determining factor triggering NEC to EC transition in recalcitrant cotton lines. Transcription factor encoding genes showed differential regulation between two cultivars. Conclusions： Our study provides valuable information about the molecular mechanism of conversion from NEC to EC in cotton and allows for identification of novel genes involved. By comparing transcriptome changes in transformation from NEC to EC between the two cultivars, we identified 46 transcripts that may contribute to initiating embryogenic shift.
基金This work was supported by National R&D Project of Transgenic Crops of Ministry of Science and Technology of China(2016ZX08005–004-002).
文摘Background:Soil salt stress seriously restricts the yield and quality of cotton worldwide.To investigate the molecular mechanism of cotton response to salt stress,a main cultivated variety Gossypium hirsutum L.acc.Xinluzhong 54 was used to perform transcriptome and proteome integrated analysis.Results:Through transcriptome analysis in cotton leaves under salt stress for 0 h(T0),3 h(T3)and 12 h(T12),we identified 8436,11628 and 6311 differentially expressed genes(DEGs)in T3 vs.T0,T12 vs.T0 and T12 vs.T3,respectively.A total of 459 differentially expressed proteins(DEPs)were identified by proteomic analysis,of which 273,99 and 260 DEPs were identified in T3 vs.T0,T12 vs.T0 and T12 vs.T3,respectively.Metabolic pathways,biosynthesis of secondary metabolites,photosynthesis and plant hormone signal transduction were enriched among the identified DEGs or DEPs.Detail analysis of the DEGs or DEPs revealed that complex signaling pathways,such as abscisic acid(ABA)and jasmonic acid(JA)signaling,calcium signaling,mitogen-activated protein kinase(MAPK)signaling cascade,transcription factors,activation of antioxidant and ion transporters,were participated in regulating salt response in cotton.Conclusions:Our research not only contributed to understand the mechanism of cotton response to salt stress,but also identified nine candidate genes,which might be useful for molecular breeding to improve salt-toleranee in cotton.
基金The project supported by the Scheme B funding of the project′Establishment of the Centre for Microbial Genomics and Proteomics′and the Scheme D funding of the project′Enhancing the capabilities and strengthening the research personnel of CUHK in Bioinformatics′of the Focused Investment Scheme of The Chinese University of Hong Kongthe Overseas and Hong Kong,Macao Young Scholars Collaborative Research Fund by the Natural National Science Foundation of China(81328025)+1 种基金Science and Technology Development Fund of Macao SAR(058/2009and 078/2011/A3)Research Committee,University of Macao
文摘OBJECTIVE To investigate the transcriptomic details on the biosynthetic pathways in different parts of the Panax notoginseng and the pharmacological activity of the saponins extracted from the flower(FS)on vascular insufficiency conditions.METHODS RNA sequencing of three different Panax notoginseng tissues was performed using next generation DNA sequencing and differential gene expression was validated by real-time PCR.In order to determine pro-angiogenic and therapeutic effects of FS on myocardial infraction(MI),FS was examined on the endothelial cell migration assay,vascular insufficiency model in zebrafish and MI model in rats.RESULTS After assembling the high quality sequencing reads into 107 340 unigenes,biochemical pathways were predicted and 9 908 unigenes were assigned to 135 KEGG pathways.Among them,270 unigenes were identified to be involved in triterpene saponin biosynthesis as well as 350 and 342unigenes were predicted to encode cytochrome P450 sand glycosyltransferases,respectively.One unigene was annotated as CYP716A53v2,probably participates in the formation of protopanaxatriol from protopanaxadiol and the differential expression of this gene was confirmed by real-time PCR.In addition,the pharmacological evaluation demonstrate that FS significantly promoted vascular endothelial growth factor(VEGF)induced the migration of human umbilical vein endothelial cells(HUVECs)and partially restored defective intersegmental vessels in a chemically induced vascular insufficiency model of zebrafish larva.Moreover,the two week posttreatment of the rat MI model with FS(25-50mg·kg-1·d-1)induced approximately 3-fold upregulation of VEGF mRNA expression,with a concomitant increase in blood vessel density in the peri-infarct area of the heart by 50.7%,compared to 41.4%in the MI group.Furthermore,TUNEL analysis indicates a reduction in the mean apoptotic nuclei per field in peri-infarct myocardium upon FS treatment.CONCLUSION We have established a global transcriptome dataset for Panax notoginseng and provided additional genetic information for further genome-wide research and analyses.Candidate genes involved in ginsenoside biosynthesis,including putative cytochrome P450 sand glycosyltransferases were obtained.The transcriptomes in different plant tissues also provide invaluable resources for future study of the differences in physiological processes and secondary metabolites in different parts of P.notoginseng.And the significant pro-angiogenic effect of FS in multiple experimental models renders the purified saponin preparation as potential preventive and therapeutic agent for cardiovascular diseases yet to be developed.
基金the financial support from the American Heart Association ( 16SDG31020038)
文摘Cells actively modulate mechanobiological circuitry against external perturbations to stabilize whole cell/tissue physiology.The dynamic adaption of cells to mechanical force is critical for cells to perform vital biological functions,from single cell migration to embryonic development.Dysregulation of such dynamics has been associated with pathophysiological conditions in cardiovascular diseases,cancer,aging,and developmental disorders[1].Therefore,a direct understanding of cell’s biomechanical adaptive/maladaptive behaviors and the trigger factors causing the transformation of healthy adaption to maladaptation can help reveal the regulatory role of single cell mechanosensitive dynamics in the progression of various degenerative diseases and aging.However,current efforts for uncovering fundamental associations between disease and cell architecture have been focusing on'static'measurements of biophysical properties,which is limited by the requirement of large sample sizes to obtain statistically significant data.We therefore developed a single and highly integrated platform with mechanical stimulation and fine spatiotemporal sensing functions to probe the single cell mechanical dynamics at subcellular level to determine cell’s mechanophenotypes in healthy and disease conditions.We developed an integrated micromechanical system composed of an’ultrasound tweezer’stimulator[2]and a PDMS micropillar array [3] cellular force sensor to in situ noninvasively probe and monitor single cell mechanical dynamics.Vascular smooth muscle cells(VSMCs)from healthy mouse and mouse with induced abdominal aorta aneurysm(AAA)were used for cell mechanobiological study.An ultrasound transducer(V312-SM,Olympus)was used to generate ultrasound pulses to excite lipid-encapsulated microbubbles(Targeson)binding to cell membrane through an RGD-integrin linkage to apply a transient nanonewton force to VSMCs seeded on the PDMS micropillar array.PDMS micropillar array was fabricated and functionalized as previously described [3] and acts as the mechanical force sensor in our platform.Upon a 1 HZ and 10-second ultrasound stimulation,calcium influx was clearly detected in both healthy and AAA-VSMCs by using the fluo-4 calcium sensor,suggesting the microbubble-integrin-actin cytoskeleton(CSK)linkage can serve as a mechanosensory to sense the ultrasound stimulation.We then examined how healthy and AAA VSMCs would exhibit adaptions to mechanical stimulation at a global cellular scale.After the onset of a 10-second ultrasound stimulation,control and AAA-VSMCs displayed distinct dynamics of CSK tension within 30 mins,in which the CSK tension of healthy VSMCs increased within the reinforcement period(0-5 min)and restored to their ground state with the relaxation period(5-10 min);yet AAA-VSMCs displayed compromised dynamics of such CSK tension upon calcium influx.Quantitative analysis and theoretical modelling revealed the critical roles of myosin motor contraction,F-actin filament polymerization in regulating cell mechanosensitive dynamics in response to a transient mechanical perturbation.The distinct force and CSK dynamics in healthy and AAA conditions indicates that the force-dependent CSK molecular kinetics is a critical factor governing the distinct mechanosensitive dynamics of cells under pathologically dysfunctional conditions.Our results reveal that the mechanical adaptive process of cells to mechanical stimulus can measure the cellular mechanobiological phenotypes featured in both pathologically healthy and diseased context.We demonstrated that an altered mechanobiological phenotype,i.e.AAA-VSMCs with distinct actomyosin-CSK properties potentiates a mechanical maladaptation that reflects progressive accumulation of cellular damage and dysfunction.This may further reveal the pathogenic contexts and their physical mediators featuring biophysical dysregulation in cardiovascular diseases.
基金Macao Science and Technology Development Fund(017/2015/AMJ134/2014/A3).
文摘OBJECTIVE Palythoa caribaeorum(class Anthozoa) is a zoanthid that together jellyfishes,hydra,and sea anemones,which are venomous and predatory,belongs to the Phyllum Cnidaria.The distinguished feature in these marine animals is the cnidocytes in the body tissues,responsible for toxin production and injection that are used majorly for prey capture and defense.With exception for other anthozoans,the toxin cocktails of zoanthids have been scarcely studied and are poorly known.METHODS Based on the analysis of P.caribaeorum transcriptome,numerous predicted venom-featured polypeptides were identified,including allergens,neuro-toxins,membrane-active and Kunitz-like peptides(PcKuz).The three predicted PcKuz isotoxins(1 to 3) were selected for functional studies.Through computational processing comprising structural phylogenetic analysis,molecular docking,and dynamics simulation,PcKuz3 was shown to be a potential voltage gated potassium-channel inhibitor.RESULTS PcKuz3 fitted well as new functional Kunitz-type toxins with strong anti-locomotor activity as in vivo assessed in zebrafish larvae,with weak inhibitory effect toward proteases,as evaluated in vitro.Notably,PcKuz3 can suppress,at low concentration,the 6-OHDA-induced neurotoxicity on the locomotive behavior of zebrafish,which indicated PcKuz3 may have a neuroprotective effect.CONCLUSION Taken together,PcK uz3 figures as a novel neurotoxin structure which differs from known homologous peptides expressed in sea anemone.Moreover,the novel PcKuz3 provides an insightful hint for bio-drug development for prospective neurodegenerative disease treatment.
文摘In this project,we aim to elucidate the molecular mechanism controlling initiation and elongation of tetraploid Gossypium hirsutum fiber cells by setting up a high throughput custom-designed
基金Supported by the National Natural Science Foundation of China(31801386,31371650)the Ministry of Science and Technology of China(2016YFD0100500)+2 种基金Funding from Harbin Science and Technology Bureau(2016RQYXJ018,2017RAQXJ104)Heilongjiang Natural Science Foundation(LC2018008)the Key Laboratory of Soybean Biology in the Chinese Ministry of Education,Northeast Agricultural University(SB17A01)。
文摘Soybean mutants withα-nullβ-conglycinin are associated with high nutritional value and low allergenic risk.Although long noncoding RNAs(lncRNAs)are increasingly recognized as functional regulatory components affecting eukaryotic gene expression,little is known about lnc RNA profiles inα-null-type hypoallergenic soybeans.In this study,a genome-wide integrative analysis of lncRNAs,m RNAs and epigenomic data in the soybean cgy-2(confirmedα-null)near-isogenic line(NIL)and its recurrent parent Dongnong47(DN47)was conducted.Nineteen novel lncRNAs that were differentially expressed(DE)only in the NIL at 18 days after flowering(i.e.,α-null-associated DE lncRNAs)were delected.Sixteen putative soybean stress-responsive lncRNAs were identified,and observed to regulate 257 stress-related genes DE in the NIL.This result indicated that theα-null allele might represent an intrinsic defect stress that altered the expression of various stress-related genes inα-null-type hypoallergenic soybean.Additionally,25 epigenetic-related lncRNAs regulated 831 DE epigenetic-related genes and simultaneously initiated multiple epigenetic activities,including ubiquitination,methylation and acetylation.Kyoto encyclopedia of genes and genomes(KEGG)analysis indicated that the biosynthesis of amino acids pathway was enriched with 83 DE genes regulated by nine DE lncRNAs.Changes in the expression of these lncRNAs and genes might be the reason for the altered amino acid composition in the NIL.Among all detected DE lncRNAs,MSTRG.12518 was the most conspicuousα-null-specific cis/trans-lnc RNA that played an efficient,versatile and vital role in the NIL.The data indicated that the lnc RNA profile differed between the NIL and DN47.Variations in lncRNAs,gene expression levels and DNA methylation states likely contributed to the intrinsic defect stress response mechanism inα-null-type hypoallergenic soybeans.
文摘Fiber cell initiation is a complex process involving many pathways,including phytohormones and components for transcriptional and posttranscriptional regulation.Here we report expression
基金supported by Jiangxi′s Major International Science and Technology Cooperation Projects(20151BDH80020)
文摘OBJECTIVE o facilitate the basic acquaintance with the bioactive lycodine-type alkaloids biosynthetic pathways,we conducted the transcriptome analysis of L.casuarinoides by illumina sequencing.METHODS The plant of L.casuarinoides was collected and was subjected to RNA isolation,cDNA library construction,and illumina sequencing before bioinformatics analysis.After sequencing,the clean reads were obtained for de novo assembly by using Trinity software,and then further processed with TGICL sequencing clustering software to generate unigenes,The unigenes are aligned by Blast X alignment to six public protein database.In addition,all unigenes are functionally annotated by GO,KEGG and characterized putative genes involved in lycopodium alkaloids biosynthesis.RESULTS In total,124,524 high-quality unigenes were obtained with an average sequence length of 601 bp.Among the L.casuarinoides transcripts,61,304 showed significant similarity(E-value<1 e-5) to the known proteins in the public database.Among the total 124 524 unigenes,47,538 open reading frame(ORFs) were predicted.Based on the bioinformatics analysis,all possible enzymes involved in the Lycodine-type alkaloids biosynthetic pathway of L.casuarinoides were identified,including primary amine oxidase(PAO),and Malonly-CoA decarboxylase.In addition,a total of 64 putative cytochrome P450(CYP450) and 827 transcription factors were selected as the candidates of Lycodine-type alka.loids modifiers.Furthermore,a total of 13 352 simple sequence repeats(SSRs) were identified from the 124,524 unigenes,of which dinucleotide motifs AG/CT(50.1%),were the most abundant.CONCLU.SION This transcriptome analysis of L.casuarinoides,provides many valuable candidate genes involv.ing in the biosynthesis of novel secondary metabolites but also lays the foundation for genetic diversity analysis via SSRs markers in L.casuarinoides.
基金supported by the Key Research and Development Program of Hunan Province(2023SK2038)the Natural Science Foundation of Hunan Province(2024JJ8121),China。
文摘Objective:Pelvic organ prolapse(POP)is a common condition in postmenopausal women,with an increasing prevalence due to aging.Some women experience POP recurrence after surgical treatment,significantly affecting their physical and mental health.The uterosacral ligament is a critical pelvic support structure.This study aims to investigate the molecular pathological changes in the uterosacral ligament of postmenopausal women with recurrent POP using transcriptomic analysis.Methods:Transcriptomic data of uterosacral ligament tissues were obtained from the public dataset GSE28660,which includes samples from 4 postmenopausal women with recurrent POP,4 with primary POP,and 4 without POP.Differentially expressed genes(DEGs)were identified between recurrent POP and both primary and non-POP groups.Further analysis included intersection analysis of DEGs,gene ontology enrichment,protein protein interaction(PPI)network construction,gene set enrichment analysis(GSEA),single-sample GSEA,and xCell immune cell infiltration analysis to explore molecular pathological changes in recurrent POP.Additionally,histological and molecular differences in the uterosacral ligament were compared between simulated vaginal delivery(SVD)rat models with and without ovariectomy.Results:Compared with primary POP and non-POP groups,recurrent POP exhibited activation of adipogenesis and inflammation-related pathways,while pathways related to muscle proliferation and contraction were downregulated in the uterosacral ligament.Nine key DEGs(ADIPOQ,FABP4,IL-6,LIPE,LPL,PCK1,PLIN1,PPARG,and CD36)were identified,with most enriched in the peroxisome proliferator-activated receptor(PPAR)signaling pathway.These genes were significantly correlated with lipid accumulation,monocyte infiltration,and neutrophil infiltration in the uterosacral ligament.Urodynamic testing revealed that the bladder leak point pressure was significantly higher in ovariectomized SVD rats,both of which had higher values than the sham group.Masson staining showed pronounced adipogenesis in the uterosacral ligament of ovariectomized SVD rats,along with reduced collagen and muscle fibers compared to the sham and non ovariectomized SVD groups.Furthermore,real-time RT-PCR confirmed significantly elevated expression of key DEGs,including ADIPOQ,IL-6,PCK1,and PLIN1,in the uterosacral ligaments of ovariectomized SVD rats.Conclusion:Adipogenesis and inflammation in the uterosacral ligament may contribute to its reduced supportive function,potentially leading to recurrence POP in postmenopausal women.
文摘为初步解析马尾松花粉对超低温保存的生理响应及相关代谢机制,该文以马尾松花粉为研究对象,在-196℃液氮进行超低温保存并分析冷存过程中[冻存前(CK)、液氮冻存后(LD)、化冻后(HD)]与活性氧(ROS)相关的生理指标及转录组数据。结果表明:(1)马尾松花粉超低温保存的最适含水量为3.96%,该含水量下将花粉直接投入液氮保存至少48 h,冻存前后花粉存活率分别为78.54%和73.80%。(2)超氧化物歧化酶(SOD),抗坏血酸过氧化物酶(GSH),谷胱甘肽(APX),抑制羟自由基能力4个指标在冻存前后差异显著。(3)转录组测序共获得65.60 Gb过滤数据,有38505个基因比对到参考基因组(47.84%),CK vs LD、CK vs HD、LD vs HD的差异表达基因(DEGs数量分别为232个、268个、218个)。GO和KEGG分析表明,应激响应(response to stimulus)和抗氧化活性(antioxidant activity)等GO term显著富集;植物激素信号转导、MAPK信号途径、淀粉和蔗糖代谢、果糖和甘露醇代谢、过氧化物酶体等KEGG途径显著富集,从这些途径中进一步筛选到10个可能与冷冻保存过程中损伤和修复有关的基因。该研究结果为马尾松种质资源高效利用和安全保存提供了技术手段,也为进一步解析冷冻保存损伤的分子机制提供参考。
