Background. Our previous studies indicated that the increased arginine vasopressin(AVP) in ischemic brain regions of gerbils could exacerbate the ischemic brain edema. This experiments is further clarify the relation ...Background. Our previous studies indicated that the increased arginine vasopressin(AVP) in ischemic brain regions of gerbils could exacerbate the ischemic brain edema. This experiments is further clarify the relation between AVP and cerebral ischemia at the molecular level. Methods. The contents of AVP, AVP mRNA, AVP immunoreactive(ir) neurons in supraoptic nucleus(SON) and paraventricular nucleus(PVN) after cerebral ischemia and reperfusion were respectively determined by radioimmunoassay(RIA), immunocytochemistry(ⅡC), situ hybridization and computed image pattern analysis. Results. The contents of AVP in SON, PVN were increased, and the AVP ir positive neurons in SON and PVN were also significantly increased as compared with the controls after ischemia and reperfusion. And there were very light staining of AVP ir positive neurons in the other brain areas such as suprachiasmatic nucleus (SC) and periventricular hypothalamic nucleus (PE), but these have no significant changes as compared with the controls. During different periods of cerebral ischemia (30～120 min) and reperfusion (30 min), AVP mRNA expression in SON and PVN were more markedly increased than the controls. Conclusions. The transcription of AVP gene elevated, then promoting synthesis and release of AVP in SON, PVN. Under the specific condition of cerebral ischemia and reperfusion, the activity and contents of central AVP increased abnormally is one of the important factors which causes ischemia brain damage.展开更多
Following extensive bowel resection, the intestinal tract undergoes a variety of adaptive responses to enhance bowel function. The purpose of this study was to determine the effect of glutamine-supplemented parenteral...Following extensive bowel resection, the intestinal tract undergoes a variety of adaptive responses to enhance bowel function. The purpose of this study was to determine the effect of glutamine-supplemented parenteral nutrition on mucosal cellularity and gut function. In addition, enterocyte gene expression of two relevant systems was also characterized and related to the structural and functional changes that occurred. Male Wistar rats underwent a 60% small bowel resection and jugular vein catheterization and were randomized into two groups. The control group (n = 10) received a standard intravenous nutritional solution and the study group (n = 10) received a similar solution but enriched with alanylglutamine dipeptide. After 7 days blood was taken for amino acid analysis, and bowel was harvested to determine mucosal morphology and expression of mucosal cell glutaminase and IGF-I mRNA. Mesentery lymphnodes were cultured to determine the presence of bacteria and thus access bacteria translocation. Serum glutamine concentration and mucosal architecture were maintained in the study group compared to the controls. Seventy percent of lymphnodes were cultured positive in control vs. only 20% in the study group (P展开更多
Objective: To formulate criteria of multidrug resistance (mdr1) gene expression for predicting chemotherapy response and prognosis. Methods: Using reverse transcriptionpolymerase chain reaction (RTPCR) assay, the exp...Objective: To formulate criteria of multidrug resistance (mdr1) gene expression for predicting chemotherapy response and prognosis. Methods: Using reverse transcriptionpolymerase chain reaction (RTPCR) assay, the expression of mdr1 gene in 82 breast cancer samples were detected. Results: The data were treated by statistic analysis system (SAS)singlevariate analysis. It showed that the level of mdr1 gene expression clearly deviated from normal to right distribution (P<0.0001), and thus might be divided by quantiles P50 (mdr1/β 2MG=0.2) and P75 (mdr1/β 2MG=0.6), which were taken as the preliminary criteria for analyzing 56 patients' chemosensitivity to ADM、VDS and VCR in vitro and 32 relapsed metastatic patients' chemotherapy response in vivo, seperately. When mdr1/( 2MG(0.2, the ratios of resistance gradually escalated, but there were about 30%～50% of the cases who showed sensitive to the drugs in vitro and effective to chemotherapy in vivo. When mdr1/β 2MG≥0.6, the most of patients showed drug resistance both in vitro and in vivo. Conclusion: According to the abovementioned results, criteria of evaluating mdr1 gene expression level was formulated: the mdr1/β 2MG<0.2 (P50) was considered as negative expression, the ratio≥02～<0.6 (P75) was weakly positive expression, ≥0.6 was strongly positive expression. This indicated that different levels of mdr1 gene expression may reflect objectively drug resistance in vitro and chemotherapy response in vivo.展开更多
The primary role of the gastrointestinal tract in broiler chickens is nutrient assimilation,with transporter proteins facilitating the uptake of amino acids,peptides,monosaccharides,fatty acids,and minerals across the...The primary role of the gastrointestinal tract in broiler chickens is nutrient assimilation,with transporter proteins facilitating the uptake of amino acids,peptides,monosaccharides,fatty acids,and minerals across the intestinal epithelium.Among these nutrient transporters,members of the solute carrier family are particularly important,and gene expression analyses targeting these transporters have provided informative insights into how birds adapt to diverse dietary,environmental,and physiological challenges to maintain nutrient homeostasis.These transporters are expressed either at the brush border membrane,where they facilitate the absorption of nutrients from the gut lumen into enterocytes,or at the basolateral membrane,where they mediate the transfer of nutrients from the enterocytes into the bloodstream.The expression of these transporters is influenced by a range of factors,including bird age,sex,intestinal segment,dietary substrate availability and source,as well as external stressors such as heat stress and pathogen exposure.While upregulation of transporter genes often suggests an enhanced capacity for nutrient uptake,it does not always correlate with improved growth performance,due to compensatory physiological responses and fluctuations in nutrient bioavailability.Understanding the regulation and functional dynamics of nutrient transporters presents valuable opportunities to develop targeted dietary and management strategies aimed at optimizing nutrient utilization and improving bird performance.This review summarizes current knowledge on the classification,function,and regulation of key nutrient transporters in broilers,highlights factors influencing their expression,and explores their implications for nutrition and production efficiency.展开更多
[Objectives]The present study was conducted to investigate the change rule ofβ-fructofuranosidase gene expression and its enzyme activity in the midgut of 5 th instar silkworm(Bombyx mori),in order to provide a refer...[Objectives]The present study was conducted to investigate the change rule ofβ-fructofuranosidase gene expression and its enzyme activity in the midgut of 5 th instar silkworm(Bombyx mori),in order to provide a reference for illustrating the enzymatic mechanism of usingβ-fructofuranosidase to absorb sucrose nutrition from mulberry leaves.[Methods]Real-time fluorescent quantitative PCR was applied to analyze the expression of BmSuc1 and BmSuc2 in midgut of 5 th-instar silkworm larvae,meanwhile the activities ofβ-fructofuranosidase was determined.[Results]BmSuc1 was expressed in the midgut of 5 th-instar silkworm larvae at different developmental stages.Its expression was upregulated at the beginning of the 5 th instar and during the peak feeding period,whereas BmSuc2 expression remained very low throughout the entire 5 th instar.The activity ofβ-fructofuranosidase was relatively high during the peak feeding period of 5 th-instar larvae,showing a trend of increasing first and then decreasing.[Conclusions]The expression pattern of the BmSuc1 gene and the changes inβ-fructofuranosidase activity were generally consistent with the physiological process of sugar nutrient absorption and utilization from mulberry leaves in 5 th-instar silkworms.It suggests that BmSuc1,as a sucrose hydrolase gene,plays a major role in the digestion and absorption of sucrose nutrients from mulberry leaves in the midgut tissue.展开更多
[Objectives]To investigate the structure and function of the lipoxygenase(LOX)gene family in Physcomitrella patens.[Methods]This study employed bioinformatics methods to identify and predict LOX gene family members.Qu...[Objectives]To investigate the structure and function of the lipoxygenase(LOX)gene family in Physcomitrella patens.[Methods]This study employed bioinformatics methods to identify and predict LOX gene family members.Quantitative real-time PCR(qRT-PCR)was utilized to analyze the expression patterns of LOX genes at different stages of Botrytis cinerea infection.[Results]The P.patens LOX gene family comprises eight putative proteins,including two 12-LOX-type members and six 13-LOX-type members.Among the eight LOX proteins,PpLOX7 exhibited the lowest molecular weight and shortest amino acid sequence.PpLOX7 was identified as a basic protein with an isoelectric point(pI)of 8.54,while all other members were acidic.Subcellular localization analysis indicated that PpLOX7 was localized to the chloroplast,whereas the remaining members were distributed in the cytoplasm.Secondary structure prediction showed that all eight proteins were predominantly composed of random coils andα-helixes.Chromosomal mapping revealed that the LOX genes were distributed across 7 of the 27 chromosomes in P.patens,with PpLOX1 and PpLOX2 tandemly arranged on chromosome 15.The qRT-PCR analysis demonstrated distinct expression patterns among the eight PpLOX genes following B.cinerea infection.PpLOX1-3 and PpLOX7 were upregulated to varying degrees,suggesting their potential involvement in the early defense response of P.patens against B.cinerea.Notably,PpLOX2 exhibited highly significant differential expression,making it a key candidate for further investigation.[Conclusions]This study provides foundational insights into the functional roles of the LOX gene family in P.patens during biotic stress responses.展开更多
Due to the unique microstructure and diverse opsin genes of the trinocular compound eye,stomatopoda possess an extraordinary ability to perceive multiple properties of light.They not only can detect natural light(NL)a...Due to the unique microstructure and diverse opsin genes of the trinocular compound eye,stomatopoda possess an extraordinary ability to perceive multiple properties of light.They not only can detect natural light(NL)and linearly polarized light(LPL),but also are the only animals capable of recognizing circularly polarized light(CPL).Here,we integrated single-cell RNA sequencing,previously published Illumina data,and in-situ hybridization(ISH)to quantify and localize functional opsin genes in Oratosquilla oratoria,a common stomatopoda species in the China Sea.A total of high-quality 31777 cells were captured for the first time in the O.oratoria compound eye,which were classified into 25 cell subpopulations,and hypothesized that cluster 22 is a critical cell subpopulation responsible for light(whether NL,LPL,or CPL)response in O.oratoria.Furthermore,we propose that the long-wavelengthsensitive opsin gene(lws)gene family,retinol dehydrogenase(rdh),voltage-gated ion channel(vgic),arrestin(arr),and myosin(myo)collectively mediate the light response in O.oratoria.Considering that very few vision-related opsin genes show differential expression in right-handed CPL(RCPL)-vs.-dark(DL),which provides additional evidence that stomatopoda cannot recognize RCPL.Meanwhile,we believe that UV-stimulated scaffold protein A(uvssa)and red pigment concentrating hormone(rpch)play special contributions in the left-handed CPL(LCPL)environment response.ISH revealing that 16 lws,6 middle-wavelength-sensitive(mws),and 2 ultraviolet(uv)opsin genes were expressed in the photoreceptors of the O.oratoria compound eye.Although the inability to determine the functional types of cell subpopulations limits the resolution of opsin genes,these findings systematically elucidate the specific expression patterns of opsin genes in O.oratoria and represent a significant step toward refining the visual ecological theory of O.oratoria and other stomatopod species.展开更多
The prognostic and therapeutic roles of biological markers in early-stage breast cancer(eBC)warrant further investigation.Non-Breast Cancer(BRCA)genes,along with moderate-and low-penetrance breast cancer risk variant ...The prognostic and therapeutic roles of biological markers in early-stage breast cancer(eBC)warrant further investigation.Non-Breast Cancer(BRCA)genes,along with moderate-and low-penetrance breast cancer risk variant genes,are crucial formaintaining genome stability,yet their prognostic significance in eBCremains unclear.This study aimed to evaluate the impact of non-BRCA genes on clinical outcomes in eBC patients.Significant correlations were observed between the messenger ribonucleic acid(mRNA)expression levels of the genes Ataxia-telangiectasia mutated(ATM),Bloom helicase gene(BLM),and WRN RecQ Like Helicase(WRN)and patient prognosis.High mRNA expression of ATM was associated with longer metastasis-free survival(MFS).Conversely,lower mRNA expression of BLM correlated with favorable outcomes,particularly in triple-negative tumors.Additionally,high levels of WRN mRNA expression were linked to significantly longer MFS compared to low expression levels.This study highlights the prognostic significance of ATM,BLM,and WRN in predicting survival outcomes in eBC patients.Background:The prognostic significance of various biological and non-BRCA genetic in early-stage breast cancer(eBC)remains unclear and warrants further investigation.This study therefore aimed to evaluate the prognostic impact of these genes on clinical outcomes in breast cancer.Methods:Patients included in this study were subdivided into two groups based on low and high messenger ribonucleic acid(mRNA)expression levels.Statistical analysis,including Kaplan-Meier curves,univariable,andmultivariable Cox regression analyses,was performed to assess metastasis-free survival(MFS)of mRNA expression of non-BRCA genes.Subgroup analyses were also conducted among four different molecular subtypes of eBC.Results:Our analysis revealed significant correlations between mRNA-expression levels of Ataxiatelangiectasia mutated(ATM),Bloom helicase gene(BLM),and WRN RecQ Like Helicase(WRN)and patient prognosis.High mRNA expression of ATM correlated with longer MFS in the entire cohort(p=0.022,Log Rank),and in luminal-B-like tumors(p=0.036).Lower mRNA expression of BLM was associated with favorable outcomes(p=0.011,Log Rank),particularly in triple-negative eBC(p=0.030,Log Rank).Finally,high levels of WRN mRNA expression correlated with significantly longerMFS compared to lowmRNA expression levels(p=0.009,Log Rank).Conclusions:This study underscores the prognostic significance of moderate penetrance breast cancer risk variant genes,such as ATM,BLM,and WRN,for survival outcomes in eBC.展开更多
Drugs and pesticide residues in broiler feed can compromise the therapeutic and production benefits of antibiotic(ANT)application and affect gene expression.In this study,we analyzed the expression of 13 key pancreati...Drugs and pesticide residues in broiler feed can compromise the therapeutic and production benefits of antibiotic(ANT)application and affect gene expression.In this study,we analyzed the expression of 13 key pancreatic genes and blood physiology parameters after administering one maximum residue limit of herbicide glyphosate(GLY),two ANTs,and one anticoccidial drug(AD).A total of 260 Ross 308 broilers aged 1-40 d were divided into the following four groups of 65 birds each:control group,which was fed the main diet(MD),and three experimental groups,which were fed MD supplemented with GLY,GLY+ANTs(enrofloxacin and colistin methanesulfonate),and GLY+AD(ammonium maduramicin),respectively.The results showed that the addition of GLY,GLY+ANTs,and GLY+AD caused significant changes in the expression of several genes of physiological and economic importance.In particular,genes related to inflammation and apoptosis(interleukin 6(IL6),prostaglandin-endoperoxide synthase 2(PTGS2),and caspase 6(CASP6))were downregulated by up to 99.1%,and those related to antioxidant protection(catalase(CAT),superoxide dismutase 1(SOD1)and peroxiredoxin 6(PRDX6))by up to 98.6%,compared to controls.There was also a significant decline in the values of immunological characteristics in the blood serum observed in the experimental groups,and certain changes in gene expression were concordant with changes in the functioning of the pancreas and blood.The changes revealed in gene expression and blood indices in response to GLY,ANTs,and AD provide insights into the possible mechanisms of action of these agents at the molecular level.Specifically,these changes may be indicative of physiological mechanisms to overcome the negative effects of GLY,GLY+ANTs,and GLY+AD in broilers.展开更多
Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression...Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression in rice remains unclear.Here,we construct a map of 137,629 polymorphic STRs in the rice(Oryza sativa L.)genome using a population-scale resequencing dataset.A genome-wide survey encompassing 4726 accessions shows that the occurrence frequency,mutational patterns,chromosomal distribution,and functional properties of STRs are correlated with the sequences and lengths of repeat motifs.Leveraging a transcriptome dataset from 127 rice accessions,we identify 44,672 expression STRs(eSTRs)by modeling gene expression in response to the length variation of STRs.These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures.Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1726 tagged STRs that may be associated with agronomic traits.By editing the(ACT)_(7) STR in OsFD1 promoter,we further experimentally validate its role in regulating gene expression and phenotype.Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.展开更多
Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive...Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive thyroid-related cell lines cultured under simulated microgravity.Methods:Five thyroid-related cell lines—normal thyrocytes(Nthy-ori 3-1),papillary thyroid cancer(PTC)cells(SNU-790,TPC-1),poorly differentiated thyroid cancer cell(BCPAP),and anaplastic thyroid cancer cell(SNU-80)—were cultured under simulated microgravity(10-3 g)using a clinostat.Differentially expressed genes(DEGs)were analyzed using cDNA microarray,followed by functional annotation and assessment of aggressiveness via Transwell migration and invasion assays.Results:DEG analysis under simulated microgravity revealed distinct gene expression profiles by gravity condition,with 2980 DEGs in SNU-790,1033 in BCPAP,562 in TPC-1,477 in Nthy-ori 3-1,and 246 in SNU-80,as confirmed by hierarchical clustering.In PTC cell lines(SNU-790,TPC-1),G2–M phase–related genes were upregulated.In non-PTC cell lines(BCPAP,SNU-80),genes associated with innate immune response,Toll-like receptor signaling,were upregulated,whereas Hypoxia-Inducible Factor 1-alpha(HIF-1α)signaling-related genes were downregulated.Additionally,under simulated microgravity,significant migration was observed in SNU-790(3×104 cells)and BCPAP(2×104 and 3×104),while significant invasion occurred in SNU-790,Nthy-ori 3-1,and BCPAP at a seeding density of 2×104.Other conditions showed no significant differences.Conclusion:This study comprehensively evaluates the effects of simulated microgravity using a diverse panel of thyroid-related cell lines.Thesefindings provide valuable insight into how microgravity could influence cancer biology,emphasizing the importance of further research on cancer behavior in space environments and its implications for human health during long-term space missions.展开更多
Gallbladder cancer(GBC)is a lethal biliary tract malignancy,which is infrequent in most developed countries,but common in many developing countries in specific geographical regions of the world.Non-specific symptoms l...Gallbladder cancer(GBC)is a lethal biliary tract malignancy,which is infrequent in most developed countries,but common in many developing countries in specific geographical regions of the world.Non-specific symptoms leading to late diagnosis is one of the primary factors contributing to poor prognosis in GBC.An understanding of the complex relationship between molecular genetics and epidemiological variances in the incidence rates of GBC is thus of utmost importance.Present review summarizes recent updates on population-specific dysregulated genetic expressions in the genesis of GBC,highlighting the pattern of ethno-geographic variations and on advances in targeted therapies conducted till date;points out the lacunae that deserve further attention and suggest possible new directions for future clinical trials in GBC.The review calls for the need of genetic screening of each GBC patients and for more extensive clinical trials on targeted therapies to move towards the goal of personalized medicine,bringing about more favourable survival outcomes.展开更多
Highlights●Natural variations in the SGT3 promoter TATA box repeats directly modulate gene expression and SGAs content in tubers,providing a novel molecular marker for low-steroidal glycoalkaloids(SGAs)breeding.●The...Highlights●Natural variations in the SGT3 promoter TATA box repeats directly modulate gene expression and SGAs content in tubers,providing a novel molecular marker for low-steroidal glycoalkaloids(SGAs)breeding.●The SGT3 promoter haplotype with(TA)10exhibits signifcantly higher transcriptional activity,correlating with high SGAs content,while the(TA)13haplotype is linked to low SGAs in natural germplasms.展开更多
Urea is a major end product of nitrogen catabolism,serving as an osmolyte to regulate osmotic stress in fish exposed to varying water environments.It has been well known that urea transporters(UTs)facilitate the rapid...Urea is a major end product of nitrogen catabolism,serving as an osmolyte to regulate osmotic stress in fish exposed to varying water environments.It has been well known that urea transporters(UTs)facilitate the rapid movement of urea across cell membranes.However,researches on ut genes were predominantly focused on elasmobranchs and early developmental stages of fish.In this investigation,a total of three ut genes were identified in spotted sea bass.Phylogenetic,homology,and syntenic analyses were conducted to validate the annotation and assess the evolutionary relationships among ut genes.Both ut-a and ut-b genes have retained their evolutionary stability,demonstrating a significant level of homology between them.To gain deeper insights into the evolution of ut genes in spotted sea bass,we performed selective pressure analysis using site,branch,and branch-site models.The results suggested that positive selection likely played a significant role in shaping the evolution of the ut gene family.Furthermore,tissue-specific expression analyses revealed high expression levels of ut genes in osmoregulatory tissues such as the gill and kidney.Additionally,all three ut genes exhibited salinity-related expression patterns in gill and kidney tissues during both seawater-to-freshwater(SF)and freshwater-to-seawater(FS)adaptation.In situ hybridization results demonstrated the localization of both ut-a and ut-c mRNAs on the gill lamellae and adjacent gill filament epithelium.In summary,our study establishes a solid foundation for future research elucidating the evolutionary relationships and functional significance of ut genes during salinity acclimation in spotted sea bass and other teleost species.展开更多
N^(6)-Methyladenosine(m^(6)A)is the most common modification in the transcriptome of biological RNA and plays roles that include maintaining the stability and transportation of mRNA,mRNA precursor shearing,polyadenyla...N^(6)-Methyladenosine(m^(6)A)is the most common modification in the transcriptome of biological RNA and plays roles that include maintaining the stability and transportation of mRNA,mRNA precursor shearing,polyadenylation,and the initiation of translation.With the improving understanding of RNA methylation,m^(6)A modification is known to play vital roles in plant development and growth.The multi-petalization of flowering plants has high ornamental and research value in horticultural landscapes.However,the mechanism of RNA methylation in flower formation in Magnolia wufengensis,a classical multi-petalizational plant,remains unclear.This study compared and analyzed RNA m^(6)A methylation and the transcriptome in floral buds of two varieties with large differences in tepal number at the early stage of development.It was found that the degree of RNA m^(6)A methylation and relative expression levels of MawuAGL6-2,MawuPI-4,and MawuAGL9 in‘Jiaodan’with 36 tepals were significantly higher than those in‘Jiaohong’with 9 tepals during the development of floral organ primordia.Combined with quantitative real-time PCR,the expression levels of MawuAGL6-2,MawuPI-4,and MawuAGL9were positively correlated with the number of tepals.Transgenic experiments showed that MawuAGL6-1/2,and MawuPI-4 can increase the number of petals in Arabidopsis.Moreover,MawuAGL6-2 and MawuPI-4 can restore the missing petal phenotype of mutant Arabidopsis.Yeast two hybrid and yeast three hybrid indicated that MawuAGL6-2,MawuAP3-1/2,and MawuPI-4 could interact with each other under the mediation of the class E protein MawuAGL9.Based on these results,it is hypothesized that m^(6)A methylation influences the multi-petalization of Magnolia wufengensis by affecting the expression levels of MawuAGL6-2,MawuAP3-1/2,MawuPI-4,and MawuAGL9.These findings provide a better understanding of the molecular mechanisms of epigenetic modifications in flower developmental diversity.展开更多
DNA microarray technology is an extremely effective technique for studying gene expression patterns in cells, and the main challenge currently faced by this technology is how to analyze the large amount of gene expres...DNA microarray technology is an extremely effective technique for studying gene expression patterns in cells, and the main challenge currently faced by this technology is how to analyze the large amount of gene expression data generated. To address this, this paper employs a mixed-effects model to analyze gene expression data. In terms of data selection, 1176 genes from the white mouse gene expression dataset under two experimental conditions were chosen, setting up two conditions: pneumococcal infection and no infection, and constructing a mixed-effects model. After preprocessing the gene chip information, the data were imported into the model, preliminary results were calculated, and permutation tests were performed to biologically validate the preliminary results using GSEA. The final dataset consists of 20 groups of gene expression data from pneumococcal infection, which categorizes functionally related genes based on the similarity of their expression profiles, facilitating the study of genes with unknown functions.展开更多
Hydrangea macrophylla is a popular ornamental shrub with a lot of economic and aesthetic value.It is known for its different flower shapes(lacecap and mophead)and the way its flowers change color depending on the pH o...Hydrangea macrophylla is a popular ornamental shrub with a lot of economic and aesthetic value.It is known for its different flower shapes(lacecap and mophead)and the way its flowers change color depending on the pH of the soil.Even though it is important for gardening,we still don’t know much about the molecular processes that lead to flower growth.The purpose of this study was to find and study SNP-related genes and transcription factors that are connected to the growth of H.macrophylla flowers.Genome-wide SNP analysis identified 11 SNPs associated with MYB transcription factors and 10 SNPs linked to a MADS-box SEP1 gene,highlighting their potential role in inflorescence-type regulation.These SNPs provide genomic resources for functional validation and markerassisted breeding in Hydrangea macrophylla.We found the MYB and MADS-box gene families,which are important for pigmentation and flower organ identity,through an analysis of the transcriptome and gene expression.The MYB family has 731R-MYBs,105 R2R3-MYBs,and 43R-MYBs.TheMADS-box family had 42 Type I(M-type)members and 36 Type II(MIKC-type)members.Motif and phylogenetic analysis showed that certain domains were preserved.For example,R2R3-MYBs and MIKC-type MADS genes are grouped with Arabidopsis orthologs,which suggests that their functions are also preserved.There was a clear link between the greatest expression ofMADS-box genes and the distinct phases of floral bud differentiation.Some MYB genes,on the other hand,showed alternative expression patterns that may help petals or sepals develop.qRT-PCR validation of representative MYB and MADS-box genes corroborated the transcriptome-based expression profiles,supporting their role in flower development and inflorescence-type regulation.展开更多
Objectives:Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells(ASCs),their genetic and molecular mechanisms remain incompletely understood.Methods:In this study,we analyz...Objectives:Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells(ASCs),their genetic and molecular mechanisms remain incompletely understood.Methods:In this study,we analyzed the global gene expression profile of adipose-derived mesenchymal stem cells(ASCs)using microarray analysis and compared it with stromal vascular fraction(SVF)cells.Results:Microarray analysis revealed that ASCs express elevated levels of genes related to the extracellular matrix(ECM;extracellular matrix)and collagen,which are critical components of tissue remodeling and wound healing.Additionally,genes associated with cell growth,differentiation,motility,and plasticity were highly expressed.When compared to stromal vascular fraction(SVF)cells,ASCs demonstrated enrichment of genes involved in anti-inflammatory responses,immune modulation,tissue repair,cell adhesion,and migration processes.Gene Set Enrichment Analysis(GSEA;Gene Set Enrichment Analysis)showed activation of pathways related to angiogenesis,such as vascular endothelial growth factor(VEGF),Integrin,Wnt signaling pathways,transforming growth factor-beta(TGF-β),extracellular matrix(ECM),and matrix metalloproteinase(MMP),highlighting the significant angiogenic potential of ASCs.Gene Ontology(GO;Gene Ontology)analysis further linked ASCs to biological processes associated with the regulation of cell proliferation and muscle cell differentiation.Conclusion:These findings collectively underscore the suitability of adipose-derived mesenchymal stem cells(ASCs)as a promising candidate for regenerative medicine,particularly in applications involving tissue repair,immune modulation,and promotion of angiogenesis.展开更多
Background Mobile element variants(MEVs)have a significant and complex impact on genomic diversity and phe-notypic traits.However,the quantity,distribution,and relationship with gene expression and complex traits of M...Background Mobile element variants(MEVs)have a significant and complex impact on genomic diversity and phe-notypic traits.However,the quantity,distribution,and relationship with gene expression and complex traits of MEVs in the pig genome remain poorly understood.Results We constructed the most comprehensive porcine MEV library based on high-depth whole genome sequencing(WGS)data from 747 pigs across 59 breeds worldwide.This database identified a total of 147,993 poly-morphic MEVs,including 121,099 short interspersed nuclear elements(SINEs),26,053 long interspersed nuclear elements(LINEs),802 long terminal repeats(LTRs),and 39 other transposons,among which 54%are newly discovered.We found that MEVs are unevenly distributed across the genome and are strongly influenced by negative selec-tion effects.Importantly,we identified 514,530,and 584 candidate MEVs associated with population differentiation,domestication,and breed formation,respectively.For example,a significantly differentiated MEV is located in the ATRX intron between Asian and European pigs,whereas ATRX is also differentially expressed between Asian and European pigs in muscle tissue.In addition,we identified 4,169 expressed MEVs(eMEVs)significantly associated with gene expression and 6,914 splicing MEVs(sMEVs)associated with gene splicing based on RNA-seq data from 266 porcine liver tissues.These eMEVs and sMEVs explain 6.24%and 9.47%,respectively,of the observed cis-heritability and high-light the important role of MEVs in the regulation of gene expression.Finally,we provide a high-quality SNP–MEV reference haplotype panel to impute MEV genotypes from genome-wide SNPs.Notably,we identified a candidate MEV significantly associated with total teat number,demonstrating the functionality of this reference panel.Conclusions The present investigation demonstrated the importance of MEVs in pigs in terms of population diversity,gene expression and phenotypic traits,which may provide useful resources and theoretical support for pig genetics and breeding.展开更多
Glutathione-S-transferase(GST,EC2.5.1.18)multifunctional protease is important for detoxification,defense against biotic and abiotic stresses,and secondary metabolic material transport for plant growth and development...Glutathione-S-transferase(GST,EC2.5.1.18)multifunctional protease is important for detoxification,defense against biotic and abiotic stresses,and secondary metabolic material transport for plant growth and development.In this study,71 members of the BpGST family were identified from the entire Betula platyphylla Suk.genome.Most of the members encode proteins with amino acid lengths ranging from 101 to 875 and were localized to the cytoplasm by a prediction.BpGSTs can be divided into seven subfamilies,with a majority of birch U and F subfamily members according to gene structure,conserved motifs and evolutionary analysis.GST family genes showed collinearity with 22 genes in Oryza sativa L.,and three genes in Arabidopsis thaliana;promoter cis-acting elements predicted that the GST gene family is functional in growth,hormone regulation,and abiotic stress response.Most members of the F subfamily of GST(BpGSTFs)were expressed in roots,stems,leaves,and petioles,with the most expression observed in leaves.On the basis of the expression profiles of F subfamily genes(BpGSTF1 to BpGSTF13)during salt,mannitol and ABA stress,BpGSTF proteins seem to have multiple functions depending on the type of abiotic stress;for instance,BpGSTs may function at different times during abiotic stress.This study enhances understanding of the GST gene family and provides a basis for further exploration of their function in birch.展开更多
文摘Background. Our previous studies indicated that the increased arginine vasopressin(AVP) in ischemic brain regions of gerbils could exacerbate the ischemic brain edema. This experiments is further clarify the relation between AVP and cerebral ischemia at the molecular level. Methods. The contents of AVP, AVP mRNA, AVP immunoreactive(ir) neurons in supraoptic nucleus(SON) and paraventricular nucleus(PVN) after cerebral ischemia and reperfusion were respectively determined by radioimmunoassay(RIA), immunocytochemistry(ⅡC), situ hybridization and computed image pattern analysis. Results. The contents of AVP in SON, PVN were increased, and the AVP ir positive neurons in SON and PVN were also significantly increased as compared with the controls after ischemia and reperfusion. And there were very light staining of AVP ir positive neurons in the other brain areas such as suprachiasmatic nucleus (SC) and periventricular hypothalamic nucleus (PE), but these have no significant changes as compared with the controls. During different periods of cerebral ischemia (30～120 min) and reperfusion (30 min), AVP mRNA expression in SON and PVN were more markedly increased than the controls. Conclusions. The transcription of AVP gene elevated, then promoting synthesis and release of AVP in SON, PVN. Under the specific condition of cerebral ischemia and reperfusion, the activity and contents of central AVP increased abnormally is one of the important factors which causes ischemia brain damage.
文摘Following extensive bowel resection, the intestinal tract undergoes a variety of adaptive responses to enhance bowel function. The purpose of this study was to determine the effect of glutamine-supplemented parenteral nutrition on mucosal cellularity and gut function. In addition, enterocyte gene expression of two relevant systems was also characterized and related to the structural and functional changes that occurred. Male Wistar rats underwent a 60% small bowel resection and jugular vein catheterization and were randomized into two groups. The control group (n = 10) received a standard intravenous nutritional solution and the study group (n = 10) received a similar solution but enriched with alanylglutamine dipeptide. After 7 days blood was taken for amino acid analysis, and bowel was harvested to determine mucosal morphology and expression of mucosal cell glutaminase and IGF-I mRNA. Mesentery lymphnodes were cultured to determine the presence of bacteria and thus access bacteria translocation. Serum glutamine concentration and mucosal architecture were maintained in the study group compared to the controls. Seventy percent of lymphnodes were cultured positive in control vs. only 20% in the study group (P
文摘Objective: To formulate criteria of multidrug resistance (mdr1) gene expression for predicting chemotherapy response and prognosis. Methods: Using reverse transcriptionpolymerase chain reaction (RTPCR) assay, the expression of mdr1 gene in 82 breast cancer samples were detected. Results: The data were treated by statistic analysis system (SAS)singlevariate analysis. It showed that the level of mdr1 gene expression clearly deviated from normal to right distribution (P<0.0001), and thus might be divided by quantiles P50 (mdr1/β 2MG=0.2) and P75 (mdr1/β 2MG=0.6), which were taken as the preliminary criteria for analyzing 56 patients' chemosensitivity to ADM、VDS and VCR in vitro and 32 relapsed metastatic patients' chemotherapy response in vivo, seperately. When mdr1/( 2MG(0.2, the ratios of resistance gradually escalated, but there were about 30%～50% of the cases who showed sensitive to the drugs in vitro and effective to chemotherapy in vivo. When mdr1/β 2MG≥0.6, the most of patients showed drug resistance both in vitro and in vivo. Conclusion: According to the abovementioned results, criteria of evaluating mdr1 gene expression level was formulated: the mdr1/β 2MG<0.2 (P50) was considered as negative expression, the ratio≥02～<0.6 (P75) was weakly positive expression, ≥0.6 was strongly positive expression. This indicated that different levels of mdr1 gene expression may reflect objectively drug resistance in vitro and chemotherapy response in vivo.
文摘The primary role of the gastrointestinal tract in broiler chickens is nutrient assimilation,with transporter proteins facilitating the uptake of amino acids,peptides,monosaccharides,fatty acids,and minerals across the intestinal epithelium.Among these nutrient transporters,members of the solute carrier family are particularly important,and gene expression analyses targeting these transporters have provided informative insights into how birds adapt to diverse dietary,environmental,and physiological challenges to maintain nutrient homeostasis.These transporters are expressed either at the brush border membrane,where they facilitate the absorption of nutrients from the gut lumen into enterocytes,or at the basolateral membrane,where they mediate the transfer of nutrients from the enterocytes into the bloodstream.The expression of these transporters is influenced by a range of factors,including bird age,sex,intestinal segment,dietary substrate availability and source,as well as external stressors such as heat stress and pathogen exposure.While upregulation of transporter genes often suggests an enhanced capacity for nutrient uptake,it does not always correlate with improved growth performance,due to compensatory physiological responses and fluctuations in nutrient bioavailability.Understanding the regulation and functional dynamics of nutrient transporters presents valuable opportunities to develop targeted dietary and management strategies aimed at optimizing nutrient utilization and improving bird performance.This review summarizes current knowledge on the classification,function,and regulation of key nutrient transporters in broilers,highlights factors influencing their expression,and explores their implications for nutrition and production efficiency.
基金Supported by General Project of Yunnan Provincial Agricultural Basic Research Joint Special Project(202301BD070001-229)Yunnan Provincial Key R&D Program(202403AK140075)+1 种基金Modern Sericulture Industry Technology System of Yunan Province(KJTX-07)Honghe Comprehensive Test Station of National Sericulture Industry Technology System(CARS-18).
文摘[Objectives]The present study was conducted to investigate the change rule ofβ-fructofuranosidase gene expression and its enzyme activity in the midgut of 5 th instar silkworm(Bombyx mori),in order to provide a reference for illustrating the enzymatic mechanism of usingβ-fructofuranosidase to absorb sucrose nutrition from mulberry leaves.[Methods]Real-time fluorescent quantitative PCR was applied to analyze the expression of BmSuc1 and BmSuc2 in midgut of 5 th-instar silkworm larvae,meanwhile the activities ofβ-fructofuranosidase was determined.[Results]BmSuc1 was expressed in the midgut of 5 th-instar silkworm larvae at different developmental stages.Its expression was upregulated at the beginning of the 5 th instar and during the peak feeding period,whereas BmSuc2 expression remained very low throughout the entire 5 th instar.The activity ofβ-fructofuranosidase was relatively high during the peak feeding period of 5 th-instar larvae,showing a trend of increasing first and then decreasing.[Conclusions]The expression pattern of the BmSuc1 gene and the changes inβ-fructofuranosidase activity were generally consistent with the physiological process of sugar nutrient absorption and utilization from mulberry leaves in 5 th-instar silkworms.It suggests that BmSuc1,as a sucrose hydrolase gene,plays a major role in the digestion and absorption of sucrose nutrients from mulberry leaves in the midgut tissue.
基金Supported by the Science and Technology Program of Guizhou Provence(Qiankehejichu-ZK[2023]Yiban 271).
文摘[Objectives]To investigate the structure and function of the lipoxygenase(LOX)gene family in Physcomitrella patens.[Methods]This study employed bioinformatics methods to identify and predict LOX gene family members.Quantitative real-time PCR(qRT-PCR)was utilized to analyze the expression patterns of LOX genes at different stages of Botrytis cinerea infection.[Results]The P.patens LOX gene family comprises eight putative proteins,including two 12-LOX-type members and six 13-LOX-type members.Among the eight LOX proteins,PpLOX7 exhibited the lowest molecular weight and shortest amino acid sequence.PpLOX7 was identified as a basic protein with an isoelectric point(pI)of 8.54,while all other members were acidic.Subcellular localization analysis indicated that PpLOX7 was localized to the chloroplast,whereas the remaining members were distributed in the cytoplasm.Secondary structure prediction showed that all eight proteins were predominantly composed of random coils andα-helixes.Chromosomal mapping revealed that the LOX genes were distributed across 7 of the 27 chromosomes in P.patens,with PpLOX1 and PpLOX2 tandemly arranged on chromosome 15.The qRT-PCR analysis demonstrated distinct expression patterns among the eight PpLOX genes following B.cinerea infection.PpLOX1-3 and PpLOX7 were upregulated to varying degrees,suggesting their potential involvement in the early defense response of P.patens against B.cinerea.Notably,PpLOX2 exhibited highly significant differential expression,making it a key candidate for further investigation.[Conclusions]This study provides foundational insights into the functional roles of the LOX gene family in P.patens during biotic stress responses.
基金Supported by the Natural Science Foundation of Shandong Province(No.ZR2021QD110)the National Natural Science Foundation of China(No.42106128)。
文摘Due to the unique microstructure and diverse opsin genes of the trinocular compound eye,stomatopoda possess an extraordinary ability to perceive multiple properties of light.They not only can detect natural light(NL)and linearly polarized light(LPL),but also are the only animals capable of recognizing circularly polarized light(CPL).Here,we integrated single-cell RNA sequencing,previously published Illumina data,and in-situ hybridization(ISH)to quantify and localize functional opsin genes in Oratosquilla oratoria,a common stomatopoda species in the China Sea.A total of high-quality 31777 cells were captured for the first time in the O.oratoria compound eye,which were classified into 25 cell subpopulations,and hypothesized that cluster 22 is a critical cell subpopulation responsible for light(whether NL,LPL,or CPL)response in O.oratoria.Furthermore,we propose that the long-wavelengthsensitive opsin gene(lws)gene family,retinol dehydrogenase(rdh),voltage-gated ion channel(vgic),arrestin(arr),and myosin(myo)collectively mediate the light response in O.oratoria.Considering that very few vision-related opsin genes show differential expression in right-handed CPL(RCPL)-vs.-dark(DL),which provides additional evidence that stomatopoda cannot recognize RCPL.Meanwhile,we believe that UV-stimulated scaffold protein A(uvssa)and red pigment concentrating hormone(rpch)play special contributions in the left-handed CPL(LCPL)environment response.ISH revealing that 16 lws,6 middle-wavelength-sensitive(mws),and 2 ultraviolet(uv)opsin genes were expressed in the photoreceptors of the O.oratoria compound eye.Although the inability to determine the functional types of cell subpopulations limits the resolution of opsin genes,these findings systematically elucidate the specific expression patterns of opsin genes in O.oratoria and represent a significant step toward refining the visual ecological theory of O.oratoria and other stomatopod species.
文摘The prognostic and therapeutic roles of biological markers in early-stage breast cancer(eBC)warrant further investigation.Non-Breast Cancer(BRCA)genes,along with moderate-and low-penetrance breast cancer risk variant genes,are crucial formaintaining genome stability,yet their prognostic significance in eBCremains unclear.This study aimed to evaluate the impact of non-BRCA genes on clinical outcomes in eBC patients.Significant correlations were observed between the messenger ribonucleic acid(mRNA)expression levels of the genes Ataxia-telangiectasia mutated(ATM),Bloom helicase gene(BLM),and WRN RecQ Like Helicase(WRN)and patient prognosis.High mRNA expression of ATM was associated with longer metastasis-free survival(MFS).Conversely,lower mRNA expression of BLM correlated with favorable outcomes,particularly in triple-negative tumors.Additionally,high levels of WRN mRNA expression were linked to significantly longer MFS compared to low expression levels.This study highlights the prognostic significance of ATM,BLM,and WRN in predicting survival outcomes in eBC patients.Background:The prognostic significance of various biological and non-BRCA genetic in early-stage breast cancer(eBC)remains unclear and warrants further investigation.This study therefore aimed to evaluate the prognostic impact of these genes on clinical outcomes in breast cancer.Methods:Patients included in this study were subdivided into two groups based on low and high messenger ribonucleic acid(mRNA)expression levels.Statistical analysis,including Kaplan-Meier curves,univariable,andmultivariable Cox regression analyses,was performed to assess metastasis-free survival(MFS)of mRNA expression of non-BRCA genes.Subgroup analyses were also conducted among four different molecular subtypes of eBC.Results:Our analysis revealed significant correlations between mRNA-expression levels of Ataxiatelangiectasia mutated(ATM),Bloom helicase gene(BLM),and WRN RecQ Like Helicase(WRN)and patient prognosis.High mRNA expression of ATM correlated with longer MFS in the entire cohort(p=0.022,Log Rank),and in luminal-B-like tumors(p=0.036).Lower mRNA expression of BLM was associated with favorable outcomes(p=0.011,Log Rank),particularly in triple-negative eBC(p=0.030,Log Rank).Finally,high levels of WRN mRNA expression correlated with significantly longerMFS compared to lowmRNA expression levels(p=0.009,Log Rank).Conclusions:This study underscores the prognostic significance of moderate penetrance breast cancer risk variant genes,such as ATM,BLM,and WRN,for survival outcomes in eBC.
基金supported by the Russian Science Foundation(No.22-16-00128),“Investigation of the Toxic Effect of Glyphosates on the Functional State of the Bird Intestinal Microbial Community,Their Growth and Development,and the Development of a Biological Product Based on the Glyphosate Degrading Strain”.
文摘Drugs and pesticide residues in broiler feed can compromise the therapeutic and production benefits of antibiotic(ANT)application and affect gene expression.In this study,we analyzed the expression of 13 key pancreatic genes and blood physiology parameters after administering one maximum residue limit of herbicide glyphosate(GLY),two ANTs,and one anticoccidial drug(AD).A total of 260 Ross 308 broilers aged 1-40 d were divided into the following four groups of 65 birds each:control group,which was fed the main diet(MD),and three experimental groups,which were fed MD supplemented with GLY,GLY+ANTs(enrofloxacin and colistin methanesulfonate),and GLY+AD(ammonium maduramicin),respectively.The results showed that the addition of GLY,GLY+ANTs,and GLY+AD caused significant changes in the expression of several genes of physiological and economic importance.In particular,genes related to inflammation and apoptosis(interleukin 6(IL6),prostaglandin-endoperoxide synthase 2(PTGS2),and caspase 6(CASP6))were downregulated by up to 99.1%,and those related to antioxidant protection(catalase(CAT),superoxide dismutase 1(SOD1)and peroxiredoxin 6(PRDX6))by up to 98.6%,compared to controls.There was also a significant decline in the values of immunological characteristics in the blood serum observed in the experimental groups,and certain changes in gene expression were concordant with changes in the functioning of the pancreas and blood.The changes revealed in gene expression and blood indices in response to GLY,ANTs,and AD provide insights into the possible mechanisms of action of these agents at the molecular level.Specifically,these changes may be indicative of physiological mechanisms to overcome the negative effects of GLY,GLY+ANTs,and GLY+AD in broilers.
基金supported by the National Natural Science Foundation of China(32172010)the Major Program of Guangdong Basic and Applied Basic Research(2019B030302006).
文摘Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression in rice remains unclear.Here,we construct a map of 137,629 polymorphic STRs in the rice(Oryza sativa L.)genome using a population-scale resequencing dataset.A genome-wide survey encompassing 4726 accessions shows that the occurrence frequency,mutational patterns,chromosomal distribution,and functional properties of STRs are correlated with the sequences and lengths of repeat motifs.Leveraging a transcriptome dataset from 127 rice accessions,we identify 44,672 expression STRs(eSTRs)by modeling gene expression in response to the length variation of STRs.These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures.Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1726 tagged STRs that may be associated with agronomic traits.By editing the(ACT)_(7) STR in OsFD1 promoter,we further experimentally validate its role in regulating gene expression and phenotype.Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.
文摘Background:With growing interest in space exploration,understanding microgravity’s impact on human health is essential.This study aims to investigate gene expression changes and migration and invasion potential infive thyroid-related cell lines cultured under simulated microgravity.Methods:Five thyroid-related cell lines—normal thyrocytes(Nthy-ori 3-1),papillary thyroid cancer(PTC)cells(SNU-790,TPC-1),poorly differentiated thyroid cancer cell(BCPAP),and anaplastic thyroid cancer cell(SNU-80)—were cultured under simulated microgravity(10-3 g)using a clinostat.Differentially expressed genes(DEGs)were analyzed using cDNA microarray,followed by functional annotation and assessment of aggressiveness via Transwell migration and invasion assays.Results:DEG analysis under simulated microgravity revealed distinct gene expression profiles by gravity condition,with 2980 DEGs in SNU-790,1033 in BCPAP,562 in TPC-1,477 in Nthy-ori 3-1,and 246 in SNU-80,as confirmed by hierarchical clustering.In PTC cell lines(SNU-790,TPC-1),G2–M phase–related genes were upregulated.In non-PTC cell lines(BCPAP,SNU-80),genes associated with innate immune response,Toll-like receptor signaling,were upregulated,whereas Hypoxia-Inducible Factor 1-alpha(HIF-1α)signaling-related genes were downregulated.Additionally,under simulated microgravity,significant migration was observed in SNU-790(3×104 cells)and BCPAP(2×104 and 3×104),while significant invasion occurred in SNU-790,Nthy-ori 3-1,and BCPAP at a seeding density of 2×104.Other conditions showed no significant differences.Conclusion:This study comprehensively evaluates the effects of simulated microgravity using a diverse panel of thyroid-related cell lines.Thesefindings provide valuable insight into how microgravity could influence cancer biology,emphasizing the importance of further research on cancer behavior in space environments and its implications for human health during long-term space missions.
文摘Gallbladder cancer(GBC)is a lethal biliary tract malignancy,which is infrequent in most developed countries,but common in many developing countries in specific geographical regions of the world.Non-specific symptoms leading to late diagnosis is one of the primary factors contributing to poor prognosis in GBC.An understanding of the complex relationship between molecular genetics and epidemiological variances in the incidence rates of GBC is thus of utmost importance.Present review summarizes recent updates on population-specific dysregulated genetic expressions in the genesis of GBC,highlighting the pattern of ethno-geographic variations and on advances in targeted therapies conducted till date;points out the lacunae that deserve further attention and suggest possible new directions for future clinical trials in GBC.The review calls for the need of genetic screening of each GBC patients and for more extensive clinical trials on targeted therapies to move towards the goal of personalized medicine,bringing about more favourable survival outcomes.
基金financially supported by the Guangdong Major Project of Basic and Applied Basic Research,China(2021B0301030004)the National Natural Science Foundation of China(32360757,U2202206 and 32361143517)the Yunnan Fundamental Research Projects,China(202201AT070037,202501AS070012)。
文摘Highlights●Natural variations in the SGT3 promoter TATA box repeats directly modulate gene expression and SGAs content in tubers,providing a novel molecular marker for low-steroidal glycoalkaloids(SGAs)breeding.●The SGT3 promoter haplotype with(TA)10exhibits signifcantly higher transcriptional activity,correlating with high SGAs content,while the(TA)13haplotype is linked to low SGAs in natural germplasms.
基金supported by the National Natural Science Foundation of China(No.32072947)the China Agriculture Research System(No.CARS-47)。
文摘Urea is a major end product of nitrogen catabolism,serving as an osmolyte to regulate osmotic stress in fish exposed to varying water environments.It has been well known that urea transporters(UTs)facilitate the rapid movement of urea across cell membranes.However,researches on ut genes were predominantly focused on elasmobranchs and early developmental stages of fish.In this investigation,a total of three ut genes were identified in spotted sea bass.Phylogenetic,homology,and syntenic analyses were conducted to validate the annotation and assess the evolutionary relationships among ut genes.Both ut-a and ut-b genes have retained their evolutionary stability,demonstrating a significant level of homology between them.To gain deeper insights into the evolution of ut genes in spotted sea bass,we performed selective pressure analysis using site,branch,and branch-site models.The results suggested that positive selection likely played a significant role in shaping the evolution of the ut gene family.Furthermore,tissue-specific expression analyses revealed high expression levels of ut genes in osmoregulatory tissues such as the gill and kidney.Additionally,all three ut genes exhibited salinity-related expression patterns in gill and kidney tissues during both seawater-to-freshwater(SF)and freshwater-to-seawater(FS)adaptation.In situ hybridization results demonstrated the localization of both ut-a and ut-c mRNAs on the gill lamellae and adjacent gill filament epithelium.In summary,our study establishes a solid foundation for future research elucidating the evolutionary relationships and functional significance of ut genes during salinity acclimation in spotted sea bass and other teleost species.
基金supported by the National Natural Science Foundation of China(Grant No.31570651)。
文摘N^(6)-Methyladenosine(m^(6)A)is the most common modification in the transcriptome of biological RNA and plays roles that include maintaining the stability and transportation of mRNA,mRNA precursor shearing,polyadenylation,and the initiation of translation.With the improving understanding of RNA methylation,m^(6)A modification is known to play vital roles in plant development and growth.The multi-petalization of flowering plants has high ornamental and research value in horticultural landscapes.However,the mechanism of RNA methylation in flower formation in Magnolia wufengensis,a classical multi-petalizational plant,remains unclear.This study compared and analyzed RNA m^(6)A methylation and the transcriptome in floral buds of two varieties with large differences in tepal number at the early stage of development.It was found that the degree of RNA m^(6)A methylation and relative expression levels of MawuAGL6-2,MawuPI-4,and MawuAGL9 in‘Jiaodan’with 36 tepals were significantly higher than those in‘Jiaohong’with 9 tepals during the development of floral organ primordia.Combined with quantitative real-time PCR,the expression levels of MawuAGL6-2,MawuPI-4,and MawuAGL9were positively correlated with the number of tepals.Transgenic experiments showed that MawuAGL6-1/2,and MawuPI-4 can increase the number of petals in Arabidopsis.Moreover,MawuAGL6-2 and MawuPI-4 can restore the missing petal phenotype of mutant Arabidopsis.Yeast two hybrid and yeast three hybrid indicated that MawuAGL6-2,MawuAP3-1/2,and MawuPI-4 could interact with each other under the mediation of the class E protein MawuAGL9.Based on these results,it is hypothesized that m^(6)A methylation influences the multi-petalization of Magnolia wufengensis by affecting the expression levels of MawuAGL6-2,MawuAP3-1/2,MawuPI-4,and MawuAGL9.These findings provide a better understanding of the molecular mechanisms of epigenetic modifications in flower developmental diversity.
文摘DNA microarray technology is an extremely effective technique for studying gene expression patterns in cells, and the main challenge currently faced by this technology is how to analyze the large amount of gene expression data generated. To address this, this paper employs a mixed-effects model to analyze gene expression data. In terms of data selection, 1176 genes from the white mouse gene expression dataset under two experimental conditions were chosen, setting up two conditions: pneumococcal infection and no infection, and constructing a mixed-effects model. After preprocessing the gene chip information, the data were imported into the model, preliminary results were calculated, and permutation tests were performed to biologically validate the preliminary results using GSEA. The final dataset consists of 20 groups of gene expression data from pneumococcal infection, which categorizes functionally related genes based on the similarity of their expression profiles, facilitating the study of genes with unknown functions.
基金funded by Science and Technology Research Project of Shanghai Greening and City Appearance Administration in 2023(G232406).
文摘Hydrangea macrophylla is a popular ornamental shrub with a lot of economic and aesthetic value.It is known for its different flower shapes(lacecap and mophead)and the way its flowers change color depending on the pH of the soil.Even though it is important for gardening,we still don’t know much about the molecular processes that lead to flower growth.The purpose of this study was to find and study SNP-related genes and transcription factors that are connected to the growth of H.macrophylla flowers.Genome-wide SNP analysis identified 11 SNPs associated with MYB transcription factors and 10 SNPs linked to a MADS-box SEP1 gene,highlighting their potential role in inflorescence-type regulation.These SNPs provide genomic resources for functional validation and markerassisted breeding in Hydrangea macrophylla.We found the MYB and MADS-box gene families,which are important for pigmentation and flower organ identity,through an analysis of the transcriptome and gene expression.The MYB family has 731R-MYBs,105 R2R3-MYBs,and 43R-MYBs.TheMADS-box family had 42 Type I(M-type)members and 36 Type II(MIKC-type)members.Motif and phylogenetic analysis showed that certain domains were preserved.For example,R2R3-MYBs and MIKC-type MADS genes are grouped with Arabidopsis orthologs,which suggests that their functions are also preserved.There was a clear link between the greatest expression ofMADS-box genes and the distinct phases of floral bud differentiation.Some MYB genes,on the other hand,showed alternative expression patterns that may help petals or sepals develop.qRT-PCR validation of representative MYB and MADS-box genes corroborated the transcriptome-based expression profiles,supporting their role in flower development and inflorescence-type regulation.
基金supported through National Research Foundation(NRF)of Korea grants funded by the Korean Government(No.NRF-2022R1F1A1064405)the research fund of Catholic Kwandong University and Catholic Kwandong University International St.Mary’s Hospital for S.-W Kim.
文摘Objectives:Despite the considerable regenerative capacity exhibited by adipose-derived mesenchymal stem cells(ASCs),their genetic and molecular mechanisms remain incompletely understood.Methods:In this study,we analyzed the global gene expression profile of adipose-derived mesenchymal stem cells(ASCs)using microarray analysis and compared it with stromal vascular fraction(SVF)cells.Results:Microarray analysis revealed that ASCs express elevated levels of genes related to the extracellular matrix(ECM;extracellular matrix)and collagen,which are critical components of tissue remodeling and wound healing.Additionally,genes associated with cell growth,differentiation,motility,and plasticity were highly expressed.When compared to stromal vascular fraction(SVF)cells,ASCs demonstrated enrichment of genes involved in anti-inflammatory responses,immune modulation,tissue repair,cell adhesion,and migration processes.Gene Set Enrichment Analysis(GSEA;Gene Set Enrichment Analysis)showed activation of pathways related to angiogenesis,such as vascular endothelial growth factor(VEGF),Integrin,Wnt signaling pathways,transforming growth factor-beta(TGF-β),extracellular matrix(ECM),and matrix metalloproteinase(MMP),highlighting the significant angiogenic potential of ASCs.Gene Ontology(GO;Gene Ontology)analysis further linked ASCs to biological processes associated with the regulation of cell proliferation and muscle cell differentiation.Conclusion:These findings collectively underscore the suitability of adipose-derived mesenchymal stem cells(ASCs)as a promising candidate for regenerative medicine,particularly in applications involving tissue repair,immune modulation,and promotion of angiogenesis.
基金National Key Research and Development Program of China(2022YFF1000103)Postdoctoral Fellowship Program of CPSF under Grant Number GZC20240620.
文摘Background Mobile element variants(MEVs)have a significant and complex impact on genomic diversity and phe-notypic traits.However,the quantity,distribution,and relationship with gene expression and complex traits of MEVs in the pig genome remain poorly understood.Results We constructed the most comprehensive porcine MEV library based on high-depth whole genome sequencing(WGS)data from 747 pigs across 59 breeds worldwide.This database identified a total of 147,993 poly-morphic MEVs,including 121,099 short interspersed nuclear elements(SINEs),26,053 long interspersed nuclear elements(LINEs),802 long terminal repeats(LTRs),and 39 other transposons,among which 54%are newly discovered.We found that MEVs are unevenly distributed across the genome and are strongly influenced by negative selec-tion effects.Importantly,we identified 514,530,and 584 candidate MEVs associated with population differentiation,domestication,and breed formation,respectively.For example,a significantly differentiated MEV is located in the ATRX intron between Asian and European pigs,whereas ATRX is also differentially expressed between Asian and European pigs in muscle tissue.In addition,we identified 4,169 expressed MEVs(eMEVs)significantly associated with gene expression and 6,914 splicing MEVs(sMEVs)associated with gene splicing based on RNA-seq data from 266 porcine liver tissues.These eMEVs and sMEVs explain 6.24%and 9.47%,respectively,of the observed cis-heritability and high-light the important role of MEVs in the regulation of gene expression.Finally,we provide a high-quality SNP–MEV reference haplotype panel to impute MEV genotypes from genome-wide SNPs.Notably,we identified a candidate MEV significantly associated with total teat number,demonstrating the functionality of this reference panel.Conclusions The present investigation demonstrated the importance of MEVs in pigs in terms of population diversity,gene expression and phenotypic traits,which may provide useful resources and theoretical support for pig genetics and breeding.
基金supported by the National Key Research and Development Program of China(No.2021YFD2200304)FundamentalResearch Funds for the Central Universities(2572022DQ08)the National Natural Science Foundation of China(No32171738).
文摘Glutathione-S-transferase(GST,EC2.5.1.18)multifunctional protease is important for detoxification,defense against biotic and abiotic stresses,and secondary metabolic material transport for plant growth and development.In this study,71 members of the BpGST family were identified from the entire Betula platyphylla Suk.genome.Most of the members encode proteins with amino acid lengths ranging from 101 to 875 and were localized to the cytoplasm by a prediction.BpGSTs can be divided into seven subfamilies,with a majority of birch U and F subfamily members according to gene structure,conserved motifs and evolutionary analysis.GST family genes showed collinearity with 22 genes in Oryza sativa L.,and three genes in Arabidopsis thaliana;promoter cis-acting elements predicted that the GST gene family is functional in growth,hormone regulation,and abiotic stress response.Most members of the F subfamily of GST(BpGSTFs)were expressed in roots,stems,leaves,and petioles,with the most expression observed in leaves.On the basis of the expression profiles of F subfamily genes(BpGSTF1 to BpGSTF13)during salt,mannitol and ABA stress,BpGSTF proteins seem to have multiple functions depending on the type of abiotic stress;for instance,BpGSTs may function at different times during abiotic stress.This study enhances understanding of the GST gene family and provides a basis for further exploration of their function in birch.
