Background:Heterosis is an important biological phenomenon that has been extensively utilized in agricultural breeding.However,negative heterosis is also pervasively observed in nature,which can cause unfavorable impa...Background:Heterosis is an important biological phenomenon that has been extensively utilized in agricultural breeding.However,negative heterosis is also pervasively observed in nature,which can cause unfavorable impacts on production performance.Compared with systematic studies of positive heterosis,the phenomenon of negative heterosis has been largely ignored in genetic studies and breeding programs,and the genetic mechanism of this phenomenon has not been thoroughly elucidated to date.Here,we used chickens,the most common agricultural animals worldwide,to determine the genetic and molecular mechanisms of negative heterosis.Results:We performed reciprocal crossing experiments with two distinct chicken lines and found that the body weight presented widely negative heterosis in the early growth of chickens.Negative heterosis of carcass traits was more common than positive heterosis,especially breast muscle mass,which was over−40%in reciprocal progenies.Genome-wide gene expression pattern analyses of breast muscle tissues revealed that nonadditivity,including dominance and overdominace,was the major gene inheritance pattern.Nonadditive genes,including a substantial number of genes encoding ATPase and NADH dehydrogenase,accounted for more than 68%of differentially expressed genes in reciprocal crosses(4257 of 5587 and 3617 of 5243,respectively).Moreover,nonadditive genes were significantly associated with the biological process of oxidative phosphorylation,which is the major metabolic pathway for energy release and animal growth and development.The detection of ATP content and ATPase activity for purebred and crossbred progenies further confirmed that chickens with lower muscle yield had lower ATP concentrations but higher hydrolysis activity,which supported the important role of oxidative phosphorylation in negative heterosis for growth traits in chickens.Conclusions:These findings revealed that nonadditive genes and their related oxidative phosphorylation were the major genetic and molecular factors in the negative heterosis of growth in chickens,which would be beneficial to future breeding strategies.展开更多
ObjectiveTo investigate the gene expression changes in normal and degeneration lumbar intervertebral disc in humans, providing information for clinical. MethodsThe PCR products of 4096 human genes were spotted onto a ...ObjectiveTo investigate the gene expression changes in normal and degeneration lumbar intervertebral disc in humans, providing information for clinical. MethodsThe PCR products of 4096 human genes were spotted onto a kind of chemical-material-coated-glass slides. The total RNAs were isolated from the tissues. Both the mRNAs from the degeneration and normal lumbar intervertebral disc in humans were reversely transcribed to the cDNAs, which used as the hybridization probes with the incorporations of fluorescent dUTP. The mixed probes were then hybridized to the cDNA microarray. After high-stringent washing, the cDNA microarray was scanned for the fluorescent signals and analyzed with computer image analysis. ResultsAmong the 4096 targets, there were 706 genes whose expression levels differed between the degeneration and normal lumbar intervertebral disc in all cases, comprising 298 up-regulated and 358 down-regulated ones. ConclusionDNA microarray technology is an effective technique in screening for differently expressed genes between the degeneration and normal lumbar intervertebral disc. Cell apoptosis plays an important role in the process of lumbar intervertebral disc degeneration.展开更多
Baculoviruses are effective biological control agents for many insect pests. They not only efficiently challenge the host immune system but also make them hyperactive for better virus dispersal. Some investigations ha...Baculoviruses are effective biological control agents for many insect pests. They not only efficiently challenge the host immune system but also make them hyperactive for better virus dispersal. Some investigations have focused on the viral mechanisms for induction of such altered response from the host. However, there are no current studies monitoring changes in gene expression during this altered phenotype in infected larvae. The L. dispar multiple nucleopolyhedrovirus(Ld MNPV) induces hyperactivity in third instar L. dispar larvae at 3-days post infection(dpi), to continued till 6 dpi. The transcriptome profiles of the infected and uninfected larvae at these time points were analyzed to provide new clues on the response of the larvae towards infection during hyperactivity. Gene ontology enrichment analysis revealed, most of the differentially expressed genes(DEGs) were involved in proteolysis, extracellular region, and serine-type endopeptidase activity. Similarly, Kyoto Encyclopedia of Genes and Genome enrichment analysis showed maximum enrichment of 487 genes of the signal transduction category and neuroactive ligand–receptor interaction sub-category with 85 annotated genes. In addition, enrichment map visualization of gene set enrichment analysis showed the coordinated response of neuroactive ligand–receptor interaction genes with other functional gene sets, as an important signal transduction mechanism during the hyperactive stage. Interestingly all the DEGs in neuroactive ligand–receptor interactions were serine proteases, their differential expression during the hyperactive stage correlated with their conceivable involvement in disease progression and the resulting altered phenotype during this period. The outcome provides a basic understanding of L. dispar larval responses to Ld MNPV infection during the hyperactive stage and helps to determine the important host factors involved in this process.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
Auxin plays important roles in various aspects of plant growth and development （Zhao, 2010）. In Arabidopsis, a number of YUCCA （YUC） genes, which are involved in auxin biosyn- thesis, have been identified （Zhao e...Auxin plays important roles in various aspects of plant growth and development （Zhao, 2010）. In Arabidopsis, a number of YUCCA （YUC） genes, which are involved in auxin biosyn- thesis, have been identified （Zhao et al., 2001; Woodward et al., 2005; Cheng et al., 2006, 2007; Kim et al., 2007; Chen et al., 2014）. YUC genes encode flavin monooxygenases （FMOs） that convert indole-3-pyruvate （IPA） to indole-3-acetic acid （IAA） （Zhao, 2012）. The Arabidopsis YUC family is comprised of 11 members （Zhao et al., 2001;展开更多
Background The cellular repressor of ElA-stimulated genes(CREG) is a secreted glycoprotein that inhibits cell proliferation and/or enhances differentiation.CREG is widely expressed in adult tissues such as the brain,h...Background The cellular repressor of ElA-stimulated genes(CREG) is a secreted glycoprotein that inhibits cell proliferation and/or enhances differentiation.CREG is widely expressed in adult tissues such as the brain,heart, lungs,liver,intestines and kidneys in mice.We investigated the level of CREG expression during mouse embryogenesis and its distribution at 18.5 days post coitus(dpc).Methods Immunohistochemical staining with diaminobenzidine,western blotting and reverse transcription-polymerase chain reaction were used.Results CREG expression was rst detected in mouse embryos at 4.5 dpc.It was expressed at almost all stages up to 18.5 dpc.The level of CREG was found to increase gradually and was highest at 18.5 dpc.Western blotting showed that the CREG protein was expressed at higher levels in the brain,heart,intestines and kidneys than in the lungs and liver at 18.5 dpc.In 9.5 dpc embryos,CREG was expressed only in the endothelial cells of blood vessels,after the vascular lumen had formed.With advanced differentiation, vascular smooth muscle cells developed in the embryonic vascular structures;the expression of smooth muscle a-actin protein and CREG were positive and increased gradually in 10.5 dpc embryonic vessels.CREG expression in the embryonic blood vessels peaked at 15.5 dpc and was reduced slightly at 18.5 dpc.Conclusions These results indicate that CREG is expressed during mouse embryogenesis and might participate in the differentiation of these organs during embryogenesis.展开更多
Maize （Zea raays L.） is one of the most important crops because of the remarkable properties of its hybrid, which is responsible for the high commercial value of hybrid maize. The genetic basis of heterosis （hybrid...Maize （Zea raays L.） is one of the most important crops because of the remarkable properties of its hybrid, which is responsible for the high commercial value of hybrid maize. The genetic basis of heterosis （hybrid vigor） is not well understood. A differential display technique was performed to identify genes with differential expression across twelve maize inbred lines and thirty-three hybrids during ear development. An incomplete diallel design was used to investigate the relationship between the global framework of differential gene expression and heterosis. It was found that the genes belonging to MONO pattern （i.e., genes expressed in both parental lines and in hybrid） was the highest in percentage among the total five patterns and illustrated that the properties of differentially expressed genes are not entirely responsible for heterosis. Furthermore,a larger number of differentially expressed genes in hybrid, which serves as a major reservoir for generating novel phenotypes that exhibit heterosis of certain agronomic traits during early development and differentiation of maize ear. Moreover, there were some silent genesin hybrids that are responsible for the arrest or abortion of spikelets and for the increase in kernels weight.展开更多
In this study, we examined the effect of elevated temperature on the expression patterns of genes, i.e., nacrein, irr, n16, n19, and hsp70 in the pearl oyster Pinctada fucata. The experiment was carried out at 4 tempe...In this study, we examined the effect of elevated temperature on the expression patterns of genes, i.e., nacrein, irr, n16, n19, and hsp70 in the pearl oyster Pinctada fucata. The experiment was carried out at 4 temperatures, i.e., 20℃(ambient, control), 24, 28℃, and 32℃. The expression levels of target genes in P. fucata were assayed at 0, 6, 24, 48, and 96 h via real-time polymerase chain reaction. Results showed that the expression levels of nacrein and irr had no significant variations among different time points below 28℃, but significantly increased over time at 32℃. The expression levels of n16 and n19 did not change markedly at 20℃. The former increased significantly at 6 h and 24 h while the latter substantially decreased during 6–96 h at 24, 28 and 32℃. Among different temperatures, the level of n16 was significantly lower at 20℃ than at other temperatures during 6–96 h, and the level of n19 significantly varied among different temperatures at 48 h and 96 h. The expression level of hsp70 was significantly higher at 32℃ than at 20, 24 and 28℃ at 24 h. These results demonstrated that elevated temperature impacted the physiological processes of P. fucata and potentially influenced its adaptability to thermal stress.展开更多
Background： The SWEET （Sugars will eventually be exported transporters） gene family plays multiple roles in plant physiological activities and development process. It participates in reproductive development and in...Background： The SWEET （Sugars will eventually be exported transporters） gene family plays multiple roles in plant physiological activities and development process. It participates in reproductive development and in the process of sugar transport and absorption, plant senescence and stress responses and plant-pathogen interaction. However, thecomprehensive analysis of SWEET genes has not been reported in cotton. Results： In this study, we identified 22, 31, 55 and 60 SWEETgenes from the sequenced genomes of Gossypium orboreum, G. rairnondii, G. hirsutum and G. borbadense, respectively. Phylogenetic tree analysis showed that the SWEET genes could be divided into four groups, which were further classified into 14 sub-clades. Further analysis of chromosomal location, synteny analysis and gene duplication suggested that the orthologs showed a good collinearity and segmental duplication events played a crucial role in the expansion of the family in cotton. Specific MtN3_slv domains were highly conserved between Arabidopsis and cotton by exon-intron organization and motif analysis. In addition, the expression pattern in different tissues indicated that the duplicated genes in cotton might have acquired new functions as a result of sub-functionalization or neo-functionalization. The expression pattern of SWEET genes showed that the different genes were induced by diverse stresses. The identification and functional analysis of SWEET genes in cotton may provide more candidate genes for genetic modification. Conclusion： SWEET genes were classified into four clades in cotton. The expression patterns suggested that the duplicated genes might have experienced a functional divergence. This work provides insights into the evolution of SWEETgenes and more candidates for specific genetic modification, which will be useful in future research.展开更多
BMP2 plays crucial roles in vertebrate developmental process and acts as a bone inducer during osteogenesis. We present here the molecular cloning of bmp2 cDNA from the marine flatfish Cynoglossus semilaevis, and the ...BMP2 plays crucial roles in vertebrate developmental process and acts as a bone inducer during osteogenesis. We present here the molecular cloning of bmp2 cDNA from the marine flatfish Cynoglossus semilaevis, and the analysis of bmp2 expression profiling and promoter function. The full length of bmp2 cDNA sequence is 2 048 bp,which encodes a protein of 422 amino acids. Tissue expression distribution of bmp2 was examined in 14 tissues of mature individuals by quantitative real time PCR（qRT-PCR）. The results revealed that bmp2 was expressed ubiquitously, and the highest expression level was detected in the spinal cord. Moreover, bmp2 expression levels were detected at 15 sampling time points of early developmental stages（egg, larva, juvenile and fingerling stages）.The highest expression level of bmp2 was observed at the gastrula stage, which was about ten times higher than those at the other three embryo stages. Whole-mount in situ hybridization showed that the bmp2 signal was strongly detected at the location of the crown-like larval fin, heart and liver, and slightly expressed in the notochord at one day post hatch（dph）; then the expression of bmp2 started to be concentrated in notochord at three dph. Subsequently, we characterized the 5′-flanking region of bmp2 by testing the promoter activity by Luciferase reporter assays. Positive regulatory region was detected at the location of –179 to ＋109. The predicted transcription factor binding sites（E-box binding factors, zinc finger transcription factor, etc.） in this region might participate in the transcriptional regulation of the bmp2 gene.展开更多
Frequent drought events severely restrict global crop productivity,especially those occurring in the reproductive stages.Moderate drought priming during the earlier growth stages is a promising strategy for allowing p...Frequent drought events severely restrict global crop productivity,especially those occurring in the reproductive stages.Moderate drought priming during the earlier growth stages is a promising strategy for allowing plants to resist recurrent severe drought stress.However,the underlying mechanisms remain unclear.Here,we subjected wheat plants to drought priming during the vegetative growth stage and to severe drought stress at 10 days after anthesis.We then collected leaf samples at the ends of the drought priming and recovery periods,and at the end of drought stress for transcriptome sequencing in combination with phenotypic and physiological analyses.The drought-primed wheat plants maintained a lower plant temperature,with higher stomatal openness and photosynthesis,thereby resulting in much lower 1,000-grain weight and grain yield losses under the later drought stress than the non-primed plants.Interestingly,416 genes,including 27 transcription factors(e.g.,MYB,NAC,HSF),seemed to be closely related to the improved drought tolerance as indicated by the dynamic transcriptome analysis.Moreover,the candidate genes showed six temporal expression patterns and were significantly enriched in several stress response related pathways,such as plant hormone signal transduction,starch and sucrose metabolism,arginine and proline metabolism,inositol phosphate metabolism,and wax synthesis.These findings provide new insights into the physiological and molecular mechanisms of the long-term effects of early drought priming that can effectively improve drought tolerance in wheat,and may provide potential approaches for addressing the challenges of increasing abiotic stresses and securing food safety under global warming scenarios.展开更多
The molecular network features of spinal cord development that are integral to tissue engineering remain poorly understood in placental mammals,especially in terms of their relationships with vital biological processe...The molecular network features of spinal cord development that are integral to tissue engineering remain poorly understood in placental mammals,especially in terms of their relationships with vital biological processes such as regeneration.Here,using a large-scale temporal transcriptomic analysis of rat spinal cord from the embryonic stage to adulthood,we show that fluctuating RNA expression levels reflect highly active transcriptional regulation,which may initiate spinal cord patterning.We also demonstrate that microRNAs(miRNAs)and transcriptional factors exhibit a mosaic profile based on their expression patterns,while differential alternative splicing events reveal that alternative splicing may be a driving force for the development of the node of Ranvier.Our study also supports the existence of a negative correlation between innate immunity and intrinsic growth capacity.Epigenetic modifications appear to perform their respective regulatory functions at different stages of development,while guanine nucleotidebinding protein(G protein)-coupled receptors(including olfactory receptors(ORs))may perform pleiotropic roles in axonal growth.This study provides a valuable resource for investigating spinal cord development and complements the increasing number of single-cell datasets.These findings also provide a genetic basis for the development of novel tissue engineering strategies.展开更多
Microarray has become increasingly popular biotechnology in biological and medical researches, and has been widely applied in classification of treatment subtypes using expression patterns of biomarkers. We developed ...Microarray has become increasingly popular biotechnology in biological and medical researches, and has been widely applied in classification of treatment subtypes using expression patterns of biomarkers. We developed a statistical procedure to identify expression biomarkers for treatment subtype classification by constructing an F-statistic based on Henderson method Ⅲ. Monte Carlo simulations were conducted to examine the robustness and efficiency of the proposed method. Simulation results showed that our method could provide satisfying power of identifying differentially expressed genes （DEGs） with false discovery rate （FDR） lower than the given type I error rate. In addition, we analyzed a leukemia dataset collected from 38 leukemia patients with 27 samples diagnosed as acute lymphoblastic leukemia （ALL） and 11 samples as acute myeloid leukemia （AML）. We compared our results with those from the methods of significance analysis of microarray （SAM） and microarray analysis of variance （MAANOVA）. Among these three methods, only expression biomarkers identified by our method can precisely identify the three human acute leukemia subtypes.展开更多
The basic leucine zipper(bZIP)transcription factor family is one of the largest and most diverse families in plants,regulating plant growth and development and playing an essential role in response to abiotic and biot...The basic leucine zipper(bZIP)transcription factor family is one of the largest and most diverse families in plants,regulating plant growth and development and playing an essential role in response to abiotic and biotic stresses.However,little is known about the biological functions of bZIP proteins in yellowhorn(Xanthoceras sorbifolium).Recently,64 XsbZIP genes were identifi ed in the yellowhorn genome and found to be disproportionately distributed in linkage groups.The XsbZIP proteins clustered into 11 groups based on their phylogenetic relationships with AtbZIP,ZmbZIP and GmbZIP proteins.Five intron patterns in the basic and hinge regions and additional conserved motifs were defi ned,both supporting the group classifi cation and possibly contributing to their functional diversity.Compared to tandem duplication,the segment duplication greatly contributed to the expansion of yellowhorn bZIP genes.In addition,most XsbZIP genes harbor several stress responsive cis-elements in their promoter regions.Moreover,the RNA-seq and qRT-PCR data indicated XsbZIP genes were extensively involved in response to various stresses,including salt(NaCl),cold and abscisic acid,with possibly diff erent molecular mechanisms.These results provide a new understanding of the biological functions of bZIP transcription factors in yellowhorn.展开更多
Objectives To explore the intrinsic factors related to the pathogenesis of acute arterial thrombosis （AAT） and to elucidate the patho- genesis of AAT on the basis of differentially expressed genes. Methods Patients ...Objectives To explore the intrinsic factors related to the pathogenesis of acute arterial thrombosis （AAT） and to elucidate the patho- genesis of AAT on the basis of differentially expressed genes. Methods Patients with acute myocardial infarction （AMI）, stable angina （SA） and healthy controls （n = 20 per group） were recruited, and the whole human genome microarray analysis was performed to detect the differentially expressed genes among these subjects. Results Patients with AMI had disease-specific gene expression pattern. Biological functional analysis showed the function of T cells was significantly reduced, the mitochondrial metabolism significantly decreased, the ion metabolism was abnormal, the cell apoptosis and inflammatory reaction increased, the phagocytosis elevated, the neutrophil-mediated immunity increased and the post-traumatic repair of cells and tissues increased in AMI patients. The biological function in SA group and healthy controis remained stable and was comparable. Conclusions The reduced function ofT cell gene models in AAT showed the dysfunction of the immune system. The pathogenesis of AAT may be related to the inflammatory reaction after arterial intima infection caused by potential pathogenic microorganisms.展开更多
窖蛋白(Caveolin)是一类构成细胞膜上胞膜窖主要结构的标志蛋白,由Caveolin基因家族编码而成。Caveolin-1基因是Caveolin基因家族的成员之一。该实验采用RT-PCR与RACE(rapid amplification of cDNA ends)技术成功地克隆了家鸽Caveolin-...窖蛋白(Caveolin)是一类构成细胞膜上胞膜窖主要结构的标志蛋白,由Caveolin基因家族编码而成。Caveolin-1基因是Caveolin基因家族的成员之一。该实验采用RT-PCR与RACE(rapid amplification of cDNA ends)技术成功地克隆了家鸽Caveolin-1基因的全长cDNA。该cDNA全长2605bp,包含537bp的完整编码区,编码178个氨基酸;分析发现家鸽Caveolin-1基因编码区与牛、家犬、鸡、褐家鼠等核苷酸同源性为80.1%～93.4%,氨基酸同源性高达85.4%～97.2%;半定量RT-PCR分析表明该基因在家鸽各种组织广泛表达,脂肪中表达量最高,各种肌肉中表达量次之,肝脏中表达量最低。此结果说明家鸽Caveolin-1基因可能与脂肪、肌肉中的某些代谢途径有关。展开更多
Chronic myeloid leukemia（CML） is characterized by the accumulation of active BCR-ABL protein. Imatinib is the first-line treatment of CML; however, many patients are resistant to this drug. In this study, we aimed t...Chronic myeloid leukemia（CML） is characterized by the accumulation of active BCR-ABL protein. Imatinib is the first-line treatment of CML; however, many patients are resistant to this drug. In this study, we aimed to compare the differences in expression patterns and functions of time-series genes in imatinib-resistant CML cells under different drug treatments. GSE24946 was downloaded from the GEO database, which included 17 samples of K562-r cells with（n=12） or without drug administration（n=5）. Three drug treatment groups were considered for this study： arsenic trioxide（ATO）, AMN107, and ATO＋AMN107. Each group had one sample at each time point（3, 12, 24, and 48 h）. Time-series genes with a ratio of standard deviation/average（coefficient of variation） 〉0.15 were screened, and their expression patterns were revealed based on Short Time-series Expression Miner（STEM）. Then, the functional enrichment analysis of time-series genes in each group was performed using DAVID, and the genes enriched in the top ten functional categories were extracted to detect their expression patterns. Different time-series genes were identified in the three groups, and most of them were enriched in the ribosome and oxidative phosphorylation pathways. Time-series genes in the three treatment groups had different expression patterns and functions. Time-series genes in the ATO group（e.g. CCNA2 and DAB2） were significantly associated with cell adhesion, those in the AMN107 group were related to cellular carbohydrate metabolic process, while those in the ATO＋AMN107 group（e.g. AP2M1） were significantly related to cell proliferation and antigen processing. In imatinib-resistant CML cells, ATO could influence genes related to cell adhesion, AMN107 might affect genes involved in cellular carbohydrate metabolism, and the combination therapy might regulate genes involved in cell proliferation.展开更多
Spatial statistics are crucial for analyzing clustering patterns in various spaces,such as the distribution of trees in a forest or stars in the sky.Advances in spatial biology,such as single-cell spatial transcriptom...Spatial statistics are crucial for analyzing clustering patterns in various spaces,such as the distribution of trees in a forest or stars in the sky.Advances in spatial biology,such as single-cell spatial transcriptomics,enable researchers to map gene expression patterns within tissues,offering unprecedented insights into cellular functions and disease pathology.Common methods for deriving spatial relationships include density-based methods(quadrat analysis,kernel density estimators)and distance-based methods(nearest-neighbor distance[NND],Ripley’s K function).While density-based methods are effective for visualization,they struggle with quantification due to sensitivity to parameters and complex significance tests.In contrast,distance-based methods offer robust frameworks for hypothesis testing,quantifying spatial clustering or dispersion,and facilitating comparisons with models such as uniform random distributions or Poisson processes[1,2].展开更多
基金supported by the National Natural Science Foundation of China(No.31930105)China Agriculture Research Systems(CARS-40)China Postdoctoral Science Foundation(No.2020 M680028).
文摘Background:Heterosis is an important biological phenomenon that has been extensively utilized in agricultural breeding.However,negative heterosis is also pervasively observed in nature,which can cause unfavorable impacts on production performance.Compared with systematic studies of positive heterosis,the phenomenon of negative heterosis has been largely ignored in genetic studies and breeding programs,and the genetic mechanism of this phenomenon has not been thoroughly elucidated to date.Here,we used chickens,the most common agricultural animals worldwide,to determine the genetic and molecular mechanisms of negative heterosis.Results:We performed reciprocal crossing experiments with two distinct chicken lines and found that the body weight presented widely negative heterosis in the early growth of chickens.Negative heterosis of carcass traits was more common than positive heterosis,especially breast muscle mass,which was over−40%in reciprocal progenies.Genome-wide gene expression pattern analyses of breast muscle tissues revealed that nonadditivity,including dominance and overdominace,was the major gene inheritance pattern.Nonadditive genes,including a substantial number of genes encoding ATPase and NADH dehydrogenase,accounted for more than 68%of differentially expressed genes in reciprocal crosses(4257 of 5587 and 3617 of 5243,respectively).Moreover,nonadditive genes were significantly associated with the biological process of oxidative phosphorylation,which is the major metabolic pathway for energy release and animal growth and development.The detection of ATP content and ATPase activity for purebred and crossbred progenies further confirmed that chickens with lower muscle yield had lower ATP concentrations but higher hydrolysis activity,which supported the important role of oxidative phosphorylation in negative heterosis for growth traits in chickens.Conclusions:These findings revealed that nonadditive genes and their related oxidative phosphorylation were the major genetic and molecular factors in the negative heterosis of growth in chickens,which would be beneficial to future breeding strategies.
文摘ObjectiveTo investigate the gene expression changes in normal and degeneration lumbar intervertebral disc in humans, providing information for clinical. MethodsThe PCR products of 4096 human genes were spotted onto a kind of chemical-material-coated-glass slides. The total RNAs were isolated from the tissues. Both the mRNAs from the degeneration and normal lumbar intervertebral disc in humans were reversely transcribed to the cDNAs, which used as the hybridization probes with the incorporations of fluorescent dUTP. The mixed probes were then hybridized to the cDNA microarray. After high-stringent washing, the cDNA microarray was scanned for the fluorescent signals and analyzed with computer image analysis. ResultsAmong the 4096 targets, there were 706 genes whose expression levels differed between the degeneration and normal lumbar intervertebral disc in all cases, comprising 298 up-regulated and 358 down-regulated ones. ConclusionDNA microarray technology is an effective technique in screening for differently expressed genes between the degeneration and normal lumbar intervertebral disc. Cell apoptosis plays an important role in the process of lumbar intervertebral disc degeneration.
基金supported by NSFC Grant(31670659)Special Fund for Forest Scientific Research in the Public Welfare(201404403-09)Shaanxi Provincial Science and Technology Innovation Project(2014KTCL02-14)
文摘Baculoviruses are effective biological control agents for many insect pests. They not only efficiently challenge the host immune system but also make them hyperactive for better virus dispersal. Some investigations have focused on the viral mechanisms for induction of such altered response from the host. However, there are no current studies monitoring changes in gene expression during this altered phenotype in infected larvae. The L. dispar multiple nucleopolyhedrovirus(Ld MNPV) induces hyperactivity in third instar L. dispar larvae at 3-days post infection(dpi), to continued till 6 dpi. The transcriptome profiles of the infected and uninfected larvae at these time points were analyzed to provide new clues on the response of the larvae towards infection during hyperactivity. Gene ontology enrichment analysis revealed, most of the differentially expressed genes(DEGs) were involved in proteolysis, extracellular region, and serine-type endopeptidase activity. Similarly, Kyoto Encyclopedia of Genes and Genome enrichment analysis showed maximum enrichment of 487 genes of the signal transduction category and neuroactive ligand–receptor interaction sub-category with 85 annotated genes. In addition, enrichment map visualization of gene set enrichment analysis showed the coordinated response of neuroactive ligand–receptor interaction genes with other functional gene sets, as an important signal transduction mechanism during the hyperactive stage. Interestingly all the DEGs in neuroactive ligand–receptor interactions were serine proteases, their differential expression during the hyperactive stage correlated with their conceivable involvement in disease progression and the resulting altered phenotype during this period. The outcome provides a basic understanding of L. dispar larval responses to Ld MNPV infection during the hyperactive stage and helps to determine the important host factors involved in this process.
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.
基金financially supported by the grant from the National Plant Transgenic Program(No.2013ZX08003-003)from Ministry of Agriculture of the People’s Republic of China
文摘Auxin plays important roles in various aspects of plant growth and development （Zhao, 2010）. In Arabidopsis, a number of YUCCA （YUC） genes, which are involved in auxin biosyn- thesis, have been identified （Zhao et al., 2001; Woodward et al., 2005; Cheng et al., 2006, 2007; Kim et al., 2007; Chen et al., 2014）. YUC genes encode flavin monooxygenases （FMOs） that convert indole-3-pyruvate （IPA） to indole-3-acetic acid （IAA） （Zhao, 2012）. The Arabidopsis YUC family is comprised of 11 members （Zhao et al., 2001;
文摘Background The cellular repressor of ElA-stimulated genes(CREG) is a secreted glycoprotein that inhibits cell proliferation and/or enhances differentiation.CREG is widely expressed in adult tissues such as the brain,heart, lungs,liver,intestines and kidneys in mice.We investigated the level of CREG expression during mouse embryogenesis and its distribution at 18.5 days post coitus(dpc).Methods Immunohistochemical staining with diaminobenzidine,western blotting and reverse transcription-polymerase chain reaction were used.Results CREG expression was rst detected in mouse embryos at 4.5 dpc.It was expressed at almost all stages up to 18.5 dpc.The level of CREG was found to increase gradually and was highest at 18.5 dpc.Western blotting showed that the CREG protein was expressed at higher levels in the brain,heart,intestines and kidneys than in the lungs and liver at 18.5 dpc.In 9.5 dpc embryos,CREG was expressed only in the endothelial cells of blood vessels,after the vascular lumen had formed.With advanced differentiation, vascular smooth muscle cells developed in the embryonic vascular structures;the expression of smooth muscle a-actin protein and CREG were positive and increased gradually in 10.5 dpc embryonic vessels.CREG expression in the embryonic blood vessels peaked at 15.5 dpc and was reduced slightly at 18.5 dpc.Conclusions These results indicate that CREG is expressed during mouse embryogenesis and might participate in the differentiation of these organs during embryogenesis.
文摘Maize （Zea raays L.） is one of the most important crops because of the remarkable properties of its hybrid, which is responsible for the high commercial value of hybrid maize. The genetic basis of heterosis （hybrid vigor） is not well understood. A differential display technique was performed to identify genes with differential expression across twelve maize inbred lines and thirty-three hybrids during ear development. An incomplete diallel design was used to investigate the relationship between the global framework of differential gene expression and heterosis. It was found that the genes belonging to MONO pattern （i.e., genes expressed in both parental lines and in hybrid） was the highest in percentage among the total five patterns and illustrated that the properties of differentially expressed genes are not entirely responsible for heterosis. Furthermore,a larger number of differentially expressed genes in hybrid, which serves as a major reservoir for generating novel phenotypes that exhibit heterosis of certain agronomic traits during early development and differentiation of maize ear. Moreover, there were some silent genesin hybrids that are responsible for the arrest or abortion of spikelets and for the increase in kernels weight.
基金supported by the National Natural Science Foundation of China (41006090)Joint Program of NSFC-Guangdong (U0831001)the Funds of Knowledge Innovation Program of Chinese Academy of Sciences (ZCX2-EW-Q21)
文摘In this study, we examined the effect of elevated temperature on the expression patterns of genes, i.e., nacrein, irr, n16, n19, and hsp70 in the pearl oyster Pinctada fucata. The experiment was carried out at 4 temperatures, i.e., 20℃(ambient, control), 24, 28℃, and 32℃. The expression levels of target genes in P. fucata were assayed at 0, 6, 24, 48, and 96 h via real-time polymerase chain reaction. Results showed that the expression levels of nacrein and irr had no significant variations among different time points below 28℃, but significantly increased over time at 32℃. The expression levels of n16 and n19 did not change markedly at 20℃. The former increased significantly at 6 h and 24 h while the latter substantially decreased during 6–96 h at 24, 28 and 32℃. Among different temperatures, the level of n16 was significantly lower at 20℃ than at other temperatures during 6–96 h, and the level of n19 significantly varied among different temperatures at 48 h and 96 h. The expression level of hsp70 was significantly higher at 32℃ than at 20, 24 and 28℃ at 24 h. These results demonstrated that elevated temperature impacted the physiological processes of P. fucata and potentially influenced its adaptability to thermal stress.
基金supported by the The National Key ResearchDevelopment Program of China(2016YFD0101400,2017YFD0101600)
文摘Background： The SWEET （Sugars will eventually be exported transporters） gene family plays multiple roles in plant physiological activities and development process. It participates in reproductive development and in the process of sugar transport and absorption, plant senescence and stress responses and plant-pathogen interaction. However, thecomprehensive analysis of SWEET genes has not been reported in cotton. Results： In this study, we identified 22, 31, 55 and 60 SWEETgenes from the sequenced genomes of Gossypium orboreum, G. rairnondii, G. hirsutum and G. borbadense, respectively. Phylogenetic tree analysis showed that the SWEET genes could be divided into four groups, which were further classified into 14 sub-clades. Further analysis of chromosomal location, synteny analysis and gene duplication suggested that the orthologs showed a good collinearity and segmental duplication events played a crucial role in the expansion of the family in cotton. Specific MtN3_slv domains were highly conserved between Arabidopsis and cotton by exon-intron organization and motif analysis. In addition, the expression pattern in different tissues indicated that the duplicated genes in cotton might have acquired new functions as a result of sub-functionalization or neo-functionalization. The expression pattern of SWEET genes showed that the different genes were induced by diverse stresses. The identification and functional analysis of SWEET genes in cotton may provide more candidate genes for genetic modification. Conclusion： SWEET genes were classified into four clades in cotton. The expression patterns suggested that the duplicated genes might have experienced a functional divergence. This work provides insights into the evolution of SWEETgenes and more candidates for specific genetic modification, which will be useful in future research.
基金The Special Scientific Research Funds for Central Non-profit Institutes,Chinese Academy of Fishery Sciences under contract No.2016RC-LX02the National Natural Science Foundation of China under contract No.31201981
文摘BMP2 plays crucial roles in vertebrate developmental process and acts as a bone inducer during osteogenesis. We present here the molecular cloning of bmp2 cDNA from the marine flatfish Cynoglossus semilaevis, and the analysis of bmp2 expression profiling and promoter function. The full length of bmp2 cDNA sequence is 2 048 bp,which encodes a protein of 422 amino acids. Tissue expression distribution of bmp2 was examined in 14 tissues of mature individuals by quantitative real time PCR（qRT-PCR）. The results revealed that bmp2 was expressed ubiquitously, and the highest expression level was detected in the spinal cord. Moreover, bmp2 expression levels were detected at 15 sampling time points of early developmental stages（egg, larva, juvenile and fingerling stages）.The highest expression level of bmp2 was observed at the gastrula stage, which was about ten times higher than those at the other three embryo stages. Whole-mount in situ hybridization showed that the bmp2 signal was strongly detected at the location of the crown-like larval fin, heart and liver, and slightly expressed in the notochord at one day post hatch（dph）; then the expression of bmp2 started to be concentrated in notochord at three dph. Subsequently, we characterized the 5′-flanking region of bmp2 by testing the promoter activity by Luciferase reporter assays. Positive regulatory region was detected at the location of –179 to ＋109. The predicted transcription factor binding sites（E-box binding factors, zinc finger transcription factor, etc.） in this region might participate in the transcriptional regulation of the bmp2 gene.
基金supported by the projects of the National Key Research and Development Program of China(2023YFD2300202)the Natural Science Foundation of Jiangsu Province,China(BK20241543)+5 种基金the National Natural Science Foundation of China(32272213,32030076,U1803235,and 32021004)the Fundamental Research Funds for the Central Universities,China(XUEKEN2023013)the Jiangsu Innovation Support Program for International Science and Technology Cooperation Project,China(BZ2023049)the Jiangsu Agriculture Science and Technology Innovation Fund,China(CX(22)1006)the China Agriculture Research System(CARS-03)the Jiangsu Collaborative Innovation Center for Modern Crop Production,China(JCIC-MCP)。
文摘Frequent drought events severely restrict global crop productivity,especially those occurring in the reproductive stages.Moderate drought priming during the earlier growth stages is a promising strategy for allowing plants to resist recurrent severe drought stress.However,the underlying mechanisms remain unclear.Here,we subjected wheat plants to drought priming during the vegetative growth stage and to severe drought stress at 10 days after anthesis.We then collected leaf samples at the ends of the drought priming and recovery periods,and at the end of drought stress for transcriptome sequencing in combination with phenotypic and physiological analyses.The drought-primed wheat plants maintained a lower plant temperature,with higher stomatal openness and photosynthesis,thereby resulting in much lower 1,000-grain weight and grain yield losses under the later drought stress than the non-primed plants.Interestingly,416 genes,including 27 transcription factors(e.g.,MYB,NAC,HSF),seemed to be closely related to the improved drought tolerance as indicated by the dynamic transcriptome analysis.Moreover,the candidate genes showed six temporal expression patterns and were significantly enriched in several stress response related pathways,such as plant hormone signal transduction,starch and sucrose metabolism,arginine and proline metabolism,inositol phosphate metabolism,and wax synthesis.These findings provide new insights into the physiological and molecular mechanisms of the long-term effects of early drought priming that can effectively improve drought tolerance in wheat,and may provide potential approaches for addressing the challenges of increasing abiotic stresses and securing food safety under global warming scenarios.
基金This work was supported by the National Natural Science Foundation of China(31730031)the National Key Research and Development Program of China(2017YFA0104700 and 2016YFC1101603)the Jiangsu Provincial Key Medical Center and Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD).
文摘The molecular network features of spinal cord development that are integral to tissue engineering remain poorly understood in placental mammals,especially in terms of their relationships with vital biological processes such as regeneration.Here,using a large-scale temporal transcriptomic analysis of rat spinal cord from the embryonic stage to adulthood,we show that fluctuating RNA expression levels reflect highly active transcriptional regulation,which may initiate spinal cord patterning.We also demonstrate that microRNAs(miRNAs)and transcriptional factors exhibit a mosaic profile based on their expression patterns,while differential alternative splicing events reveal that alternative splicing may be a driving force for the development of the node of Ranvier.Our study also supports the existence of a negative correlation between innate immunity and intrinsic growth capacity.Epigenetic modifications appear to perform their respective regulatory functions at different stages of development,while guanine nucleotidebinding protein(G protein)-coupled receptors(including olfactory receptors(ORs))may perform pleiotropic roles in axonal growth.This study provides a valuable resource for investigating spinal cord development and complements the increasing number of single-cell datasets.These findings also provide a genetic basis for the development of novel tissue engineering strategies.
基金Project partly supported by the National Basic Research Program(973) of China (No. 2004CB117306) and the National Natural Sci-ence Foundation of China (No. 2002AA234031)
文摘Microarray has become increasingly popular biotechnology in biological and medical researches, and has been widely applied in classification of treatment subtypes using expression patterns of biomarkers. We developed a statistical procedure to identify expression biomarkers for treatment subtype classification by constructing an F-statistic based on Henderson method Ⅲ. Monte Carlo simulations were conducted to examine the robustness and efficiency of the proposed method. Simulation results showed that our method could provide satisfying power of identifying differentially expressed genes （DEGs） with false discovery rate （FDR） lower than the given type I error rate. In addition, we analyzed a leukemia dataset collected from 38 leukemia patients with 27 samples diagnosed as acute lymphoblastic leukemia （ALL） and 11 samples as acute myeloid leukemia （AML）. We compared our results with those from the methods of significance analysis of microarray （SAM） and microarray analysis of variance （MAANOVA）. Among these three methods, only expression biomarkers identified by our method can precisely identify the three human acute leukemia subtypes.
基金the fundamental research funds for the Central Universities(2572018BS01)the innovation project of state key laboratory of tree genetics and breeding(Northeast Forestry University)(Grant No.2019A02).
文摘The basic leucine zipper(bZIP)transcription factor family is one of the largest and most diverse families in plants,regulating plant growth and development and playing an essential role in response to abiotic and biotic stresses.However,little is known about the biological functions of bZIP proteins in yellowhorn(Xanthoceras sorbifolium).Recently,64 XsbZIP genes were identifi ed in the yellowhorn genome and found to be disproportionately distributed in linkage groups.The XsbZIP proteins clustered into 11 groups based on their phylogenetic relationships with AtbZIP,ZmbZIP and GmbZIP proteins.Five intron patterns in the basic and hinge regions and additional conserved motifs were defi ned,both supporting the group classifi cation and possibly contributing to their functional diversity.Compared to tandem duplication,the segment duplication greatly contributed to the expansion of yellowhorn bZIP genes.In addition,most XsbZIP genes harbor several stress responsive cis-elements in their promoter regions.Moreover,the RNA-seq and qRT-PCR data indicated XsbZIP genes were extensively involved in response to various stresses,including salt(NaCl),cold and abscisic acid,with possibly diff erent molecular mechanisms.These results provide a new understanding of the biological functions of bZIP transcription factors in yellowhorn.
文摘Objectives To explore the intrinsic factors related to the pathogenesis of acute arterial thrombosis （AAT） and to elucidate the patho- genesis of AAT on the basis of differentially expressed genes. Methods Patients with acute myocardial infarction （AMI）, stable angina （SA） and healthy controls （n = 20 per group） were recruited, and the whole human genome microarray analysis was performed to detect the differentially expressed genes among these subjects. Results Patients with AMI had disease-specific gene expression pattern. Biological functional analysis showed the function of T cells was significantly reduced, the mitochondrial metabolism significantly decreased, the ion metabolism was abnormal, the cell apoptosis and inflammatory reaction increased, the phagocytosis elevated, the neutrophil-mediated immunity increased and the post-traumatic repair of cells and tissues increased in AMI patients. The biological function in SA group and healthy controis remained stable and was comparable. Conclusions The reduced function ofT cell gene models in AAT showed the dysfunction of the immune system. The pathogenesis of AAT may be related to the inflammatory reaction after arterial intima infection caused by potential pathogenic microorganisms.
文摘窖蛋白(Caveolin)是一类构成细胞膜上胞膜窖主要结构的标志蛋白,由Caveolin基因家族编码而成。Caveolin-1基因是Caveolin基因家族的成员之一。该实验采用RT-PCR与RACE(rapid amplification of cDNA ends)技术成功地克隆了家鸽Caveolin-1基因的全长cDNA。该cDNA全长2605bp,包含537bp的完整编码区,编码178个氨基酸;分析发现家鸽Caveolin-1基因编码区与牛、家犬、鸡、褐家鼠等核苷酸同源性为80.1%～93.4%,氨基酸同源性高达85.4%～97.2%;半定量RT-PCR分析表明该基因在家鸽各种组织广泛表达,脂肪中表达量最高,各种肌肉中表达量次之,肝脏中表达量最低。此结果说明家鸽Caveolin-1基因可能与脂肪、肌肉中的某些代谢途径有关。
基金supported by Natural Science Foundation of Heilongjiang Province of China(No.D201252)
文摘Chronic myeloid leukemia（CML） is characterized by the accumulation of active BCR-ABL protein. Imatinib is the first-line treatment of CML; however, many patients are resistant to this drug. In this study, we aimed to compare the differences in expression patterns and functions of time-series genes in imatinib-resistant CML cells under different drug treatments. GSE24946 was downloaded from the GEO database, which included 17 samples of K562-r cells with（n=12） or without drug administration（n=5）. Three drug treatment groups were considered for this study： arsenic trioxide（ATO）, AMN107, and ATO＋AMN107. Each group had one sample at each time point（3, 12, 24, and 48 h）. Time-series genes with a ratio of standard deviation/average（coefficient of variation） 〉0.15 were screened, and their expression patterns were revealed based on Short Time-series Expression Miner（STEM）. Then, the functional enrichment analysis of time-series genes in each group was performed using DAVID, and the genes enriched in the top ten functional categories were extracted to detect their expression patterns. Different time-series genes were identified in the three groups, and most of them were enriched in the ribosome and oxidative phosphorylation pathways. Time-series genes in the three treatment groups had different expression patterns and functions. Time-series genes in the ATO group（e.g. CCNA2 and DAB2） were significantly associated with cell adhesion, those in the AMN107 group were related to cellular carbohydrate metabolic process, while those in the ATO＋AMN107 group（e.g. AP2M1） were significantly related to cell proliferation and antigen processing. In imatinib-resistant CML cells, ATO could influence genes related to cell adhesion, AMN107 might affect genes involved in cellular carbohydrate metabolism, and the combination therapy might regulate genes involved in cell proliferation.
基金Daniel Shafiee Kermany,Ju Young Ahn,Matthew Vasquez,Lin Wang,Kai Liu,Raksha Raghunathan,Jianting Sheng,Hong Zhao,and Stephen Tin Chi Wong are supported by NCI U01CA252553,NCI R01CA238727,NCI R01CA177909,NCI R01CA244413John S.Dunn Research Foundation,and Ting Tsung and Wei Fong Chao Foundation+3 种基金Xiang Hong-Fei Zhang,Zhan Xu,Xiaoxin Hao,Weijie Zhang are supported by US Department of Defense DAMD W81XWH-16-1-0073(Era of Hope Scholarship)NCI R01CA183878,NCI R01CA251950,NCI U01CA252553,DAMD W81XWH-20-1-0375Breast Cancer Research Foundation,and McNair Medical Institute.Vahid Afshar-Kharghan,Min Soon Cho,Wendolyn Carlos-AlcaldeHani Lee are supported by NCI R01CA177909,NCI R01CA016672,NCI R01CA275762,and NCI P50CA217685.
文摘Spatial statistics are crucial for analyzing clustering patterns in various spaces,such as the distribution of trees in a forest or stars in the sky.Advances in spatial biology,such as single-cell spatial transcriptomics,enable researchers to map gene expression patterns within tissues,offering unprecedented insights into cellular functions and disease pathology.Common methods for deriving spatial relationships include density-based methods(quadrat analysis,kernel density estimators)and distance-based methods(nearest-neighbor distance[NND],Ripley’s K function).While density-based methods are effective for visualization,they struggle with quantification due to sensitivity to parameters and complex significance tests.In contrast,distance-based methods offer robust frameworks for hypothesis testing,quantifying spatial clustering or dispersion,and facilitating comparisons with models such as uniform random distributions or Poisson processes[1,2].
