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Novel Halophyte EREBP/AP2-type DNA Binding Protein Improves Salt Tolerance in Transgenic Tobacco 被引量:11
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作者 沈义国 闫冬青 +4 位作者 张万科 杜保兴 张劲松 刘强 陈受宜 《Acta Botanica Sinica》 CSCD 2003年第1期82-87,共6页
EREBP/AP2-type proteins are members of a large DNA binding protein (DBP) family found in plants. Some members like APETALA2 and AtDREB/CBF can regulate flower development and response to environmental stresses, respec... EREBP/AP2-type proteins are members of a large DNA binding protein (DBP) family found in plants. Some members like APETALA2 and AtDREB/CBF can regulate flower development and response to environmental stresses, respectively. To characterize transcription factors involved in plant responses to salt stress, we constructed cDNA library from salt-treated halophyte (Atriplex hortensis) and isolated a novel gene encoding EREBP/AP2-type protein from this library. This cDNA contained an ORF of 723 bp and a long 3'-Untranslated-Region (UTR) of 655 bp. The deduced amino acid sequence showed one conserved DNA binding domain of EREBP/AP2, thus the corresponding gene was named AhDREB1 with a calculated molecular mass of 26.1 kD. AhDREB1 under the control of CaMV 35S promoter was then transformed into tobacco and nine independent transgenic lines were obtained and subjected to long term salt stress. The results suggested that overexpression of AhDREB1 improved the salt tolerance in transgenic tobacco through functioning as a regulatory molecule in response to salt stress. Analysis of Arabidopsis genome in database resulted in dozens of EREBP/AP2-type homologous proteins, of which seven members showed high similarity to AhDREB1. Secondary structure analysis predicted similar arrangement of a-helix in their DNA binding domains. 展开更多
关键词 Atriplex hortensis EREBP/AP2-type dna binding protein transgenic tobacco
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Taq DNA聚合酶的分子改造及其在探针法qPCR直扩体系中的应用
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作者 胡松青 袁家惠 +1 位作者 刘光毅 侯轶 《华南理工大学学报(自然科学版)》 EI CAS CSCD 北大核心 2024年第4期8-16,共9页
Taq DNA聚合酶作为实时荧光定量聚合酶链式反应(qPCR)技术的核心组分,其性能优劣直接影响qPCR技术的进一步发展。然而,野生型Taq DNA聚合酶的耐抑制剂性能差、延伸性能不足。为获得具有高性能的Taq DNA聚合酶,采用基因工程技术将双链DN... Taq DNA聚合酶作为实时荧光定量聚合酶链式反应(qPCR)技术的核心组分,其性能优劣直接影响qPCR技术的进一步发展。然而,野生型Taq DNA聚合酶的耐抑制剂性能差、延伸性能不足。为获得具有高性能的Taq DNA聚合酶,采用基因工程技术将双链DNA结合蛋白Sso7d或Sto7d融合在野生型Taq DNA聚合酶的N端或C端,构建了4个均可溶表达的改造体,再经过耐受性测试筛选较优的改造体,结果显示:改造体Taq-Sto的耐受性最高,其热稳定性不受影响,且在1 s/kbp的延伸条件下能成功扩增靶标,表明Taq-Sto具有增强的延伸性能,在TaqMan探针法qPCR体系中对腐殖酸、单宁酸、全血等抑制剂同样表现出良好的耐受性。EMSA实验发现:Taq-Sto对DNA模板的结合亲和力有所提高,有利于增强Taq-Sto对模板的竞争力;将Taq-Sto应用于非洲猪瘟病毒(ASFV)的TaqMan探针法qPCR检测,与商品化试剂相比,Taq-Sto具有更低的ASFV检出限,且在体积分数为2%~6%的猪粪便样本或猪肉样本中的检测灵敏度分别为100.0%和85.4%,说明Taq-Sto在直扩qPCR检测领域更具有优势。 展开更多
关键词 Taq dna聚合酶 双链dna结合蛋白 耐受性 聚合酶链式反应
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Endonuclease-rolling circle amplification-based method for sensitive analysis of DNA-binding protein 被引量:4
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作者 Min Li Li Dong Rui Zhou +2 位作者 Hong Zhao Jin Ke Wang Zu Hong Lu 《Chinese Chemical Letters》 SCIE CAS CSCD 2009年第11期1315-1318,共4页
A sensitive approach for the qualitative detection of DNA-binding protein on the microarray was developed. DNA complexes in which a partial duplex region is formed from a biotin-primer and a circle single strand DNA ... A sensitive approach for the qualitative detection of DNA-binding protein on the microarray was developed. DNA complexes in which a partial duplex region is formed from a biotin-primer and a circle single strand DNA (ssDNA) were spotted on a microarray. The endonuclease recognition site (ERS) and the DNA-binding sites (DBS) were arranged side by side within the duplex region. The working principle of the detection system is described as follows: when the DNA-binding protein capture the DBS, the endonuclease could not attach to the ERS, and the immobilized primer in the DNA complex could be extended along the circle ssDNA by rolling circle amplification (RCA). When no protein protects the DBS, the ERS could be attacked by the endonuclease and subsequently no rolling circle amplification occurs. Thereby we can detect the sequence specific DNA-binding activity with high-sensitivity due to the signal amplification of RCA. 展开更多
关键词 Rolling circle amplification dna-binding protein MICROARRAY
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Chromodomain-helicase-DNA binding protein 5, 7 and pronecrotic mixed lineage kinase domain-like protein serve as potential prognostic biomarkers in patients with resected pancreatic adenocarcinomas 被引量:2
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作者 Crystal S Seldon Lauren E Colbert +3 位作者 William A Hall Sarah B Fisher David S Yu Jerome C Landry 《World Journal of Gastrointestinal Oncology》 SCIE CAS 2016年第4期358-365,共8页
Pancreatic cancer is one of the deadliest cancers with a very poor prognosis. Recently, there has been a significant increase in research directed towards identifying potential biomarkers that can be used to diagnose ... Pancreatic cancer is one of the deadliest cancers with a very poor prognosis. Recently, there has been a significant increase in research directed towards identifying potential biomarkers that can be used to diagnose and provide prognostic information for pancreatic cancer. These markers can be used clinically to optimize and personalize therapy for individual patients. In this review, we focused on 3 biomarkers involved in the DNA damage response pathway and the necroptosis pathway: Chromodomainhelicase-DNA binding protein 5, chromodomain-helicaseDNA binding protein 7, and mixed lineage kinase domain-like protein. The aim of this article is to review present literature provided for these biomarkers and current studies in which their effectiveness as prognostic biomarkers are analyzed in order to determine their future use as biomarkers in clinical medicine. Based on the data presented, these biomarkers warrant further investigation,and should be validated in future studies. 展开更多
关键词 Chromodomain-helicase-dna binding protein 5 Chromodomain-helicase-dna binding protein 7 Mixed lineage kinase domain-like protein Pancreatic adenocarcinoma Biomarker
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A novel detection of single-stranded DNA binding protein based on ss-DNA modified chip using surface plasmon resonance microscopy
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作者 Jian Quan Lu Ming Bo Xu +2 位作者 Xing Wang Zhou Jin Guang Xu Qing Tao 《Chinese Chemical Letters》 SCIE CAS CSCD 2007年第4期441-444,共4页
An ss-DNA gold chip was prepared based on self-assembly of the thiol-derivatized oligonucleotide, and used for the determination of single-stranded binding protein (SSB) by surface plasmon resonance microscopy (SPR... An ss-DNA gold chip was prepared based on self-assembly of the thiol-derivatized oligonucleotide, and used for the determination of single-stranded binding protein (SSB) by surface plasmon resonance microscopy (SPR). The experiment results showed that SSB binds ss-DNA with high specificity, and relative signal of SPR response is proportional to the concentration of SSB in the range of 0.1-100 ng/mL with a detection limit (S/N = 3) of 0.07 ng/mL. 展开更多
关键词 DETECTION Single-stranded dna binding protein ss-dna Surface plasmon resonance microscopy
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Endonuclease-based Method for Detecting the Sequence Specific DNA Binding Protein on Double-stranded DNA Microarray
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作者 YunFeiBAI QinYuGE TongXiangLI JinKeWANG QuanJunLIU ZuHongLU 《Chinese Chemical Letters》 SCIE CAS CSCD 2005年第5期651-654,共4页
The double-stranded DNA (dsDNA) probe contains two different protein binding sites. One is for DNA- binding proteins to be detected and the other is for a DNA restriction enzyme. The two sites were arranged together w... The double-stranded DNA (dsDNA) probe contains two different protein binding sites. One is for DNA- binding proteins to be detected and the other is for a DNA restriction enzyme. The two sites were arranged together with no base interval. The working principle of the capturing dsDNA probe is described as follows: the capturing probe can be cut with the DNA restriction enzyme (such as EcoR I) to cause a sticky terminal, if the probe is not bound with a target protein, and the sticky terminal can be extended and labeled with Cy3-dUTP by DNA polymerase. When the probe is bound with a target protein, the probe is not capable to be cut by the restriction enzyme because of space obstruction. The amount of the target DNA binding proteins can be measured according to the variations of fluorescent signals of the corresponding probes. 展开更多
关键词 Double stranded dna microarray dna binding protein label-free detection.
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REGULATED PHOSPHORYLATION OF THE GATA-2 DNA BINDINGPROTEIN IN ENDOTHELIAL CELLS
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作者 卜昕 《Journal of Pharmaceutical Analysis》 CAS 1995年第2期174-175,共2页
Endothelin-1 and a number of other genes expressd primarily in endothelial cells(EC)require a functional GATA element in their promoter region.The widely expressed zinc finger DNA binding protein GATA-2 has been chara... Endothelin-1 and a number of other genes expressd primarily in endothelial cells(EC)require a functional GATA element in their promoter region.The widely expressed zinc finger DNA binding protein GATA-2 has been characterized as the likely GATA factor which binds these GATA elements.To understand the specificity of this interaction,and to investigate the potential for regulation of GATA-2 activity,we have studied translation and post-translational modification of the GATA-2 protein. A specific antiserum immunoprecipitated a 52kDa GATA-2 protein from [35-S] methionine-labeled EC,as well as a wide variety of cultured human cell lines which express GATA-2 mRNA. Immunoprecipitation experiments with [32-P]-orthophosphate labeled cells indicated that GATA-2 is similarly phosphorylated in EC and non-EC lines. Thus the apparent cell-specific activity of this transcription factor is not regulated by translation or phosphorylation, and must derive from the interaction of GATA-2 with other nuclear proteins in the EC.Further studies investigated the potential regulation of GATA-2 phosphorylation in EC. Phosphoamino acid analysis indicated that GATA-2 is phosphorylated on serine and threonine residues in EC.The hasal phosphorylation of GATA-2 was rapidly and markedly increased when EC were treated with calcium ionophore A23187, while phorbol ester and forskolin had no effect.Phosphopeptide map analysis showed that A23187 induced phosphorylation of at least two additional sites in GATA-2.Gel shift assays employing nuclear extracts isolated from EC that had been treated with A23187 had a different DNA binding pattern when compared to control.This regulated phosphorylation of GATA-2 may provide a signaling pathway for hormonal regulation of endothelial cell genes such as endothelin-1 which alter their rate of transcription in response to increased intracellular calcium. 展开更多
关键词 GATA-2 endothelial cell ENDOTHELIN-1 PHOSPHORYLATION dna binding protein
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Identification and characterization of GIP1,an Arabidopsis thaliana protein that enhances the DNA binding affinity and reduces the oligomeric state of G-box binding factors
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作者 Paul C.SEHNKE Beth J.LAUGHNER +2 位作者 Carla R.LYERLY LINEBARGER William B.GURLEY Robert J.FERL 《Cell Research》 SCIE CAS CSCD 2005年第8期567-575,共9页
Environmental control of the alcohol dehydrogenase(Adh)and other stress response genes in plants is in part brought about by transcriptional regulation involving the G-box cis-acting DNA element and bZIP G-box Binding... Environmental control of the alcohol dehydrogenase(Adh)and other stress response genes in plants is in part brought about by transcriptional regulation involving the G-box cis-acting DNA element and bZIP G-box Binding Factors(GBFs).The mechanisms of GBF regulation and requirements for additional factors in this control process are not well understood.In an effort to identify potential GBF binding and control partners,maize GBF1 was used as bait in a yeast two-hybrid screen of an A.thaliana cDNA library.GBF Interacting Protein 1(GIP1)arose from the screen as a 496 amino acid protein with a predicted molecular weight of 53,748 kDa that strongly interacts with GBFs.Northern analysis of A.thaliana tissue suggests a 1.8-1.9 kb GIP1 transcript,predominantly in roots.Immunolocalization studies indicate that GIP1 protein is mainly localized to the nucleus.In vitro electrophoretic mobility shift assays using an Adh G-box DNA probe and recombinant A.thaliana GBF3 or maize GBF1,showed that the presence of GIP1 resulted in a tenfold increase in GBF DNA binding activity without altering the migration,suggesting a transient association between GIP1 and GBF.Addition of GIP1 to intentionally aggregated GBF converted GBF to lower molecular weight macromolecular complexes and GIP1 also refolded denatured rhodanese in the absence of ATP.These data suggest GIP1 functions to enhance GBF DNA binding activity by acting as a potent nuclear chaperone or crowbar,and potentially regulates the multimeric state of GBFs,thereby contributing to bZIP-mediated gene regulation. 展开更多
关键词 G-box binding factor interacting protein nuclear chaperone dna binding affinity.
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急性脑出血患者血清E盒锌指结合蛋白1及DNA甲基化转移酶1与神经功能缺损和预后的相关性分析
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作者 李晓娜 牛媛媛 赵燕 《实用临床医药杂志》 CAS 2024年第8期64-69,共6页
目的探讨急性脑出血(ACH)患者血清E盒锌指结合蛋白1(ZEB1)、DNA甲基化转移酶1(DNMTl)与神经功能缺损、预后的关系。方法选取2019年7月—2022年7月本院收治的105例ACH患者为ACH组,依据ACH患者入院时美国国立卫生研究院卒中量表(NIHSS)评... 目的探讨急性脑出血(ACH)患者血清E盒锌指结合蛋白1(ZEB1)、DNA甲基化转移酶1(DNMTl)与神经功能缺损、预后的关系。方法选取2019年7月—2022年7月本院收治的105例ACH患者为ACH组,依据ACH患者入院时美国国立卫生研究院卒中量表(NIHSS)评分将其分为轻度组(n=34)、中度组(n=41)、重度组(n=30)。根据改良Rankin量表(mRS)评分将ACH患者分为预后良好组(n=65)和预后不良组(n=40)。另纳入同期105例体检健康者为对照组。选取2021年7月—2022年7月本院诊治的45例ACH患者对构建的ACH预后模型的受试者工作特征(ROC)曲线进行验证。采用酶联免疫吸附试验检测血清ZEB1、DNMT1水平;采用Spearman法分析ACH患者ZEB1、DNMT1水平与NIHSS评分的关系;采用多因素Logistic回归模型分析ACH患者预后的影响因素,采用ROC曲线评估血清ZEB1、DNMT1水平对ACH患者预后的预测价值。结果与对照组相比,ACH组血清ZEB1、DNMT1水平升高,差异有统计学意义(P<0.05)。与轻度组相比,中度组和重度组ACH患者血清ZEB1、DNMT1、NIHSS评分均升高,差异有统计学意义(P<0.05);与中度组相比,重度组ACH患者血清ZEB1、DNMT1、NIHSS评分均升高,差异有统计学意义(P<0.05)。Spearman分析结果显示,ACH患者血清ZEB1、DNMT1水平与NIHSS评分均呈正相关(r=0.569、0.763,P均<0.001)。单因素分析结果显示,与预后良好组比较,预后不良组患者NIHSS评分、血肿体积、ZEB1及DNMT1水平均升高或增大,差异有统计学意义(P<0.05)。Logistic回归分析结果显示,ZEB1、DNMT1、NIHSS评分、血肿体积增大是ACH患者预后不良的危险因素(P<0.05)。血清ZEB1、DNMT1预测ACH患者预后的曲线下面积(AUC)分别为0.834、0.854,ZEB1、DNMT1联合预测ACH患者预后的AUC为0.944,灵敏度为95.0%,特异度为86.2%。以验证组人群对预测预后的ROC曲线进行验证,结果显示AUC为0.903(95%CI:0.854~0.951),提示预后预测曲线具有较好的区分度。结论ACH患者血清ZEB1、DNMT1水平较高,二者均与ACH患者神经功能缺损、预后显著相关,且血清ZEB1、DNMT1联合可能更有利于临床评估ACH患者预后情况。 展开更多
关键词 急性脑出血 E盒锌指结合蛋白1 dna甲基化转移酶1 神经功能缺损 预后
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Role of the PEST sequence in the long-type GATA-6 DNA-binding protein expressed in human cancer cell lines
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作者 Kanako Obayashi Kayoko Takada +2 位作者 Kazuaki Ohashi Ayako Kobayashi-Ohashi Masatomo Maeda 《Advances in Bioscience and Biotechnology》 2012年第4期314-320,共7页
GATA-6 mRNA utilizes two Met-codons in frame as translational initiation codons in cultured mammalian cells. Deletion of the nucleotide sequence encoding the PEST sequence between the two initiation codons unusually r... GATA-6 mRNA utilizes two Met-codons in frame as translational initiation codons in cultured mammalian cells. Deletion of the nucleotide sequence encoding the PEST sequence between the two initiation codons unusually reduced the protein molecular size on SDS-polyacrylamide gel-electrophoresis. The reduced molecular size is ascribed to the molecular property of GATA-6, since both amino-and carboxy-lterminal tags introduced into GATA-6 were detected on the gel. This PEST sequence seems to contribute to expansion of the long-type GATA-6 molecule. The long-type GATA-6 containing the PEST sequence exhibits more activation potential than that without this sequence, the latter’s activity being similar to that of the short-type GATA-6. We further demonstrated that human colon and lung cancer cell lines express both the long-type GATA-6 and the short-type GATA-6 in their nuclei. 展开更多
关键词 dna-binding protein GATA-6 TRANSCRIPTION Factor Leaky RIBOSOME Scanning PEST Sequence Gel ELECTROPHORESIS
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基于结构模型的DBP-DNA识别及预测研究综述 被引量:2
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作者 陈凌 王飞 《计算机应用与软件》 CSCD 2011年第5期142-146,151,共6页
DNA结合蛋白DBP(DNA Binding Protein)对细胞内遗传物质的生命活动中起着至关重要的作用,包括染色体的复制、剪切及基因表达调控。DBP通过与DNA发生结合反应,行使各种不同的生物功能。因此研究DBP-DNA之间的识别规律,对基因调控分析、... DNA结合蛋白DBP(DNA Binding Protein)对细胞内遗传物质的生命活动中起着至关重要的作用,包括染色体的复制、剪切及基因表达调控。DBP通过与DNA发生结合反应,行使各种不同的生物功能。因此研究DBP-DNA之间的识别规律,对基因调控分析、蛋白功能预测和转录因子结合位点预测有着十分重要的意义。随着DBP-DNA复合物结构数据库的出现,基于结构信息的计算机分析方法为DBP与DNA之间的相互作用研究提供了新的发展契机。介绍了若干经典的DBP-DNA结构模型,简要评述了DBP-DNA结构分析方法目前的研究现状。 展开更多
关键词 蛋白质-dna识别与结合位点预测 结构模型 生物信息学
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A candidate protective factor in amyotrophic lateral sclerosis:heterogenous nuclear ribonucleoprotein G 被引量:2
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作者 Fang Yang Wen-Zhi Chen +2 位作者 Shi-Shi Jiang Xiao-Hua Wang Ren-Shi Xu 《Neural Regeneration Research》 SCIE CAS CSCD 2023年第7期1527-1534,共8页
Heterogenous nuclear ribonucleoprotein G is down-regulated in the spinal cord of the Tg(SOD1*G93A)1Gur(TG)amyotrophic lateral sclerosis mouse model.However,most studies have only examined heterogenous nuclear ribonucl... Heterogenous nuclear ribonucleoprotein G is down-regulated in the spinal cord of the Tg(SOD1*G93A)1Gur(TG)amyotrophic lateral sclerosis mouse model.However,most studies have only examined heterogenous nuclear ribonucleoprotein G expression in the amyotrophic lateral sclerosis model and heterogenous nuclear ribonucleoprotein G effects in amyotrophic lateral sclerosis pathogenesis such as in apoptosis are unknown.In this study,we studied the potential mechanism of heterogenous nuclear ribonucleoprotein G in neuronal death in the spinal cord of TG and wild-type mice and examined the mechanism by which heterogenous nuclear ribonucleoprotein G induces apoptosis.Heterogenous nuclear ribonucleoprotein G in spinal cord was analyzed using immunohistochemistry and western blotting,and cell proliferation and proteins(TAR DNA binding protein 43,superoxide dismutase 1,and Bax)were detected by the Cell Counting Kit-8 and western blot analysis in heterogenous nuclear ribonucleoprotein G siRNA-transfected PC12 cells.We analyzed heterogenous nuclear ribonucleoprotein G distribution in spinal cord in the amyotrophic lateral sclerosis model at various time points and the expressions of apoptosis and proliferation-related proteins.Heterogenous nuclear ribonucleoprotein G was mainly localized in neurons.Amyotrophic lateral sclerosis mice were examined at three stages:preonset(60-70 days),onset(90-100 days)and progression(120-130 days).The number of heterogenous nuclear ribonucleoprotein G-positive cells was significantly higher in the anterior horn of the lumbar spinal cord segment of TG mice at the preonset stage than that of control group but lower than that of the control group at the onset stage.The number of heterogenous nuclear ribonucleoprotein G-positive cells in both central canal and surrounding gray matter of the whole spinal cord of TG mice at the onset stage was significantly lower than that in the control group,whereas that of the lumbar spinal cord segment of TG mice was significantly higher than that in the control group at preonset stage and significantly lower than that in the control group at the progression stage.The numbers of heterogenous nuclear ribonucleoprotein G-positive cells in the posterior horn of cervical and thoracic segments of TG mice at preonset and progression stages were significantly lower than those in the control group.The expression of heterogenous nuclear ribonucleoprotein G in the cervical spinal cord segment of TG mice was significantly higher than that in the control group at the preonset stage but significantly lower at the progression stage.The expression of heterogenous nuclear ribonucleoprotein G in the thoracic spinal cord segment of TG mice was significantly increased at the preonset stage,significantly decreased at the onset stage,and significantly increased at the progression stage compared with the control group.heterogenous nuclear ribonucleoprotein G expression in the lumbar spinal cord segment of TG mice was significantly lower than that of the control group at the progression stage.After heterogenous nuclear ribonucleoprotein G gene silencing,PC12 cell survival was lower than that of control cells.Both TAR DNA binding protein 43 and Bax expressions were significantly increased in heterogenous nuclear ribonucleoprotein G-silenced cells compared with control cells.Our study suggests that abnormal distribution and expression of heterogenous nuclear ribonucleoprotein G might play a protective effect in amyotrophic lateral sclerosis development via preventing neuronal death by reducing abnormal TAR DNA binding protein 43 generation in the spinal cord. 展开更多
关键词 amyotrophic lateral sclerosis Bax heterogenous nuclear ribonucleoprotein G heterogenous nuclear ribonucleoprotein G-siRNA neuron death superoxide dismutase 1 TAR dna binding protein 43 TG(SOD1*G93A)1Gur mice
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Affinity chromatography-dependent selection (ACDS)of genomic DNA fragments bound specifically to bacterial synthesized Myc/Myn proteins
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作者 SHI CAN PEI WANG +1 位作者 YONGJUN HU LIAN XU. (Oncogene Group, Laboratory of Molecular and Cellular Oncology, Shanghai Institute of Cell Biology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China) 《Cell Research》 SCIE CAS CSCD 1995年第1期25-34,共10页
This paper describes an approach to seek for mouse c-Myc/Myn proteins-bound specific sequences among ge-nomic DNA. cDNA fragment of myn gene was obtained through RT-PCR technique from RNA of NIH3T3 cells. DNA fragment... This paper describes an approach to seek for mouse c-Myc/Myn proteins-bound specific sequences among ge-nomic DNA. cDNA fragment of myn gene was obtained through RT-PCR technique from RNA of NIH3T3 cells. DNA fragments encoding BR/HLH/LZ structure of Myc and Myn proteins were cloned in frame into pGEX-2T vec-tor respectively Fusion GST-Myc and GST-Myn synthe-sized in E.coli hosts showed affinity to CACGTG E-boxDNA and subsequently interacted with genomic fragments prepared through whole-genome-PCR. A PCR-assisted procedure which combines protein-DNA interaction and affinity chromatography was designed to enrich Myc/Myn bound DNA. At least two genomic DNA fragments ob- tained exhibit specifical binding capacity to Myc/Myn complex but not to GST alone. Significance of the work and of the technique itself as well as identification of the DNAs are discussed. 展开更多
关键词 Myc/Myn proteins ACDS genomic dna binding
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基于Transformer-BiLSTM特征融合的DNA结合蛋白预测方法
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作者 钟来民 陆卫忠 +3 位作者 傅启明 马洁明 崔志明 吴宏杰 《微电子学与计算机》 2023年第12期1-9,共9页
蛋白质与生命活动密切相关,脱氧核糖核酸(DNA)结合蛋白作为一种特殊的蛋白质,在生命活动中有着不可替代的作用.因此,研究DNA结合蛋白有很重要的现实意义,这个课题的研究前景十分广阔.传统生物技术虽然精度较高,但其成本十分的昂贵,效率... 蛋白质与生命活动密切相关,脱氧核糖核酸(DNA)结合蛋白作为一种特殊的蛋白质,在生命活动中有着不可替代的作用.因此,研究DNA结合蛋白有很重要的现实意义,这个课题的研究前景十分广阔.传统生物技术虽然精度较高,但其成本十分的昂贵,效率比较低,设备要求极高,并不适合现代社会大量研究蛋白质的需求.机器学习的方法在一定程度上弥补了生物实验技术的不足,但是在数据处理方面远不如深度学习技术来的高效与便捷.在本研究中提出了一种基于双向平行长短期记忆神经网络(BiLSTM)和Transformer的深度学习框架来预测DNA结合蛋白.该模型不仅可以进一步提取蛋白质序列的信息和特征,还可以进一步提取进化信息的特征,最后,将这两个特征融合起来进行训练和测试.该模型拓展了研究人员在蛋白质特征提取方面的研究思路,为使用Transformer编码器块提取蛋白质全局特征提供参考.在PDB2272数据集上,与PDBP_Fusion模型相比,精度(ACC)和Matthew相关系数(MCC)分别提高了2.64%和5.51%.该模型的实验结果具有一定的优势. 展开更多
关键词 TRANSFORMER 双向长短期记忆网络 dna结合蛋白 特征提取 深度学习
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Isolation and identification of proteins binding to the major breakpoint region(mbr) of bcl2 gene
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作者 Nan Yang Yujie Sun Changyan Ma 《Journal of Nanjing Medical University》 2009年第4期236-240,共5页
Objective: We have previously found that mbr is a regulatory element of the bcl2 gene. The objective of this study is to isolate and identify the proteins binding to the 37 mbr in the 3 ' -end of the mbr. Methods: ... Objective: We have previously found that mbr is a regulatory element of the bcl2 gene. The objective of this study is to isolate and identify the proteins binding to the 37 mbr in the 3 ' -end of the mbr. Methods: Streptavidin magnetic particles were ligated to concatameric oligonucleotides of 37 mbr and incubated with the nuclear extracts of Jurkat cells. The DNA-binding proteins were eluted and then resolved by SDS-PAGE. After silver staining, the protein bands were excised and subjected to MALDI-TOF MS. Results: Several protein bands were detected after the isolation with magnetic particles, and Splicing factor, proline- and glutamine-rich(SFPQ), Poly(ADP-ribose) polymerase I(PARP), and promyelocytic leukemia protein(PML) were identified by MALDI-TOF MS. Conclusion: Several proteins were isolated and identified from the 37 mbr-protein complex. Results of this study establish a foundation for further study of the mechanisms by which mbr executes its regulatory function. 展开更多
关键词 bcl2 gene 37 mbr dna-binding protein
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Presence/Absence of Two Types of Z-DNA Binding Domains in the Genomes of Organisms from Archaea, Bacteria, and Eukaryotes and Its Implications
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作者 Hiroshi Nakashima 《Journal of Biomedical Science and Engineering》 2019年第1期1-9,共9页
We conducted genome sequence analysis to examine the presence/absence of two types of Z-DNA binding domains in various organisms. We examined 68 organisms from archaea, 914 organisms from bacteria, and 199 organisms f... We conducted genome sequence analysis to examine the presence/absence of two types of Z-DNA binding domains in various organisms. We examined 68 organisms from archaea, 914 organisms from bacteria, and 199 organisms from eukaryotes. RecA protein from Escherichia coli has a Z-DNA binding domain and this protein promotes homologous recombination. All the organisms examined had this domain. This result indicated that this domain is essential for all the organisms. RNA editing enzyme, adenosine deaminase from human has another type of Z-DNA binding domain. This domain was observed in some organisms of archaea, bacteria, and eukaryotes. The presence/absence of Z-DNA binding domain in adenosine deaminase indicated that gain and loss of this domain had occurred in the process of evolution. The implication of presence and absence of this domain is discussed in this study. 展开更多
关键词 Z-dna binding Domain RECA protein Adenosine DEAMINASE Acting on RNA Genome Sequence Analysis
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甲基化SIM2、GNA12、CTGF在子痫前期孕妇中表达水平及其对疾病的预测价值 被引量:1
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作者 张阔 陈莹 +1 位作者 刘丹 汪俊红 《国际检验医学杂志》 CAS 2024年第1期44-48,共5页
目的 探究子痫前期孕妇血浆中甲基化DNA的表达水平及对子痫前期发生的预测价值。方法 纳入2022年1-12月在该院确诊的82例子痫前期孕妇作为观察组,另外纳入82例健康孕妇作为对照组。提取患者游离总DNA,经过DNA亚硫酸氢盐修饰后通过实时... 目的 探究子痫前期孕妇血浆中甲基化DNA的表达水平及对子痫前期发生的预测价值。方法 纳入2022年1-12月在该院确诊的82例子痫前期孕妇作为观察组,另外纳入82例健康孕妇作为对照组。提取患者游离总DNA,经过DNA亚硫酸氢盐修饰后通过实时荧光定量PCR反应(qRT-PCR)检测患者血浆中甲基化单意同源物2(SIM2)、结缔组织生长因子(CTGF)及鸟嘌呤核苷酸结合蛋白(GNA12)基因的相对表达水平,并采用相关性分析及受试者工作特征(ROC)曲线对各甲基化DNA预测子痫前期发生的价值进行评估。结果 观察组血浆甲基化SIM2、GNA12、CTGF相对表达水平均高于对照组(P<0.05),且重度子痫前期孕妇各甲基化DNA相对表达水平更高(P<0.05)。相关性分析结果表明,血浆甲基化SIM2、GNA12、CTGF相对表达水平与孕妇发生子痫前期均呈正相关(P<0.05)。ROC曲线分析结果表明,血浆甲基化SIM2、GNA12、CTGF相对表达水平单独及联合检测对预测孕妇子痫前期的效能均较好,且三者联合检测的预测效能最高(曲线下面积为0.888,95%CI:0.827~0.949)。结论 相较于健康孕妇,子痫前期孕妇血浆中甲基化SIM2、GNA12、CTGF相对表达水平均较高,且其与孕妇子痫前期的发生率呈正相关,血浆甲基化SIM2、GNA12及CTGF相对表达水平有望成为判断子痫前期是否发生的重要指标。 展开更多
关键词 子痫前期 甲基化dna 单意同源物2 鸟嘌呤核苷酸结合蛋白 结缔组织生长因子
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补阳还五汤提高血管性痴呆大鼠海马CREB、C/EBP的DNA结合活性 被引量:11
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作者 张泓波 高维娟 +2 位作者 钱涛 唐敬龙 李君 《中国药理学通报》 CAS CSCD 北大核心 2011年第8期1166-1170,共5页
目的观察补阳还五汤对血管性痴呆大鼠海马CREB(cAMP反应元件结合蛋白)、C/EBP(CCAAT/增强子结合蛋白)DNA结合活性的影响。方法实验分为假手术组、模型组、补阳还五汤组和尼莫地平组。采用改良的4血管法制备血管性痴呆模型,分别给予生理... 目的观察补阳还五汤对血管性痴呆大鼠海马CREB(cAMP反应元件结合蛋白)、C/EBP(CCAAT/增强子结合蛋白)DNA结合活性的影响。方法实验分为假手术组、模型组、补阳还五汤组和尼莫地平组。采用改良的4血管法制备血管性痴呆模型,分别给予生理盐水、补阳还五汤、尼莫地平灌胃干预,用凝胶电泳迁移率改变分析法(EMSA)测定各组大鼠CREB和C/EBP的DNA结合活性。结果与假手术组比较,模型组大鼠海马组织CREB的DNA结合活性明显降低(P<0.01);与模型组比较,尼莫地平组与补阳还五汤组明显升高(P<0.01);尼莫地平组与补阳还五汤组之间差异无显著性(P>0.05)。结论补阳还五汤可提高VD大鼠海马组织CREB、C/EBP与DNA的结合活性。 展开更多
关键词 补阳还五汤 血管性痴呆 海马组织 CAMP反应元件结合蛋白 CCAAT/增强子结合蛋白 dna结合活性
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日本血吸虫DNA多价疫苗pVIVO_2SjFABP-23的构建及其保护性免疫 被引量:9
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作者 李春艳 余龙江 +4 位作者 刘智 朱路 朱晓华 胡媛 石佑恩 《中国人兽共患病学报》 CAS CSCD 北大核心 2006年第2期122-126,共5页
目的构建日本血吸虫多价DNA疫苗pVIVO2SjFABP-23,并观察其在小鼠抗血吸虫感染中的免疫保护作用。方法根据Sj FABP和Sj23的基因序列合成两对特异性引物,利用重组PCR技术将日本血吸虫Sj FABP和Sj23的基因片段进行拼接,得到融合基因SjFABP-... 目的构建日本血吸虫多价DNA疫苗pVIVO2SjFABP-23,并观察其在小鼠抗血吸虫感染中的免疫保护作用。方法根据Sj FABP和Sj23的基因序列合成两对特异性引物,利用重组PCR技术将日本血吸虫Sj FABP和Sj23的基因片段进行拼接,得到融合基因SjFABP-23,再将该片段重组于p GEM-T载体中,进行PCR扩增及DNA序列测定。然后经双酶切将目的片段SjFABP-23克隆到pVIVO2的一个多克隆位点上转化E.coliGT 110获得重组质粒pVIVO2SjFABP-23,免疫小鼠进行免疫保护性实验。结果PCR扩增出一条大小约为1.1Kb的目的片段。免疫小鼠获得52.14%减虫率(P<0.01)和60.93%的减卵率(P<0.01),且均高于单价疫苗pVIVO2Sj23(P<0.05)。结论PCR成功扩增SjFABP-23的基因片段,血吸虫DNA多价疫苗pVI-VO2SjFABP-23构建成功,该疫苗在小鼠抗血吸虫感染中具有比单价疫苗pVIVO2Sj23更好的免疫保护作用。 展开更多
关键词 日本血吸虫 23K Da膜蛋白 脂肪酸结合蛋白 多价dna疫苗 免疫保护
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日本血吸虫脂肪酸结合蛋白DNA疫苗诱导小鼠保护性免疫力的研究 被引量:13
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作者 朱晓华 石佑恩 +2 位作者 胡萍 宁长修 朱红刚 《中国血吸虫病防治杂志》 CAS CSCD 2005年第1期4-8,共5页
目的构建日本血吸虫脂肪酸结合蛋白(Sj14FABP)重组质粒,并观察其在小鼠体内诱导的抗日本血吸虫感染保护作用。方法RT-PCR特异性扩增Sj14FABP基因,将其克隆入真核表达载体pVIVO2,通过PCR、双酶切及测序鉴定。获得的重组质粒pVIVO2-Sj14F... 目的构建日本血吸虫脂肪酸结合蛋白(Sj14FABP)重组质粒,并观察其在小鼠体内诱导的抗日本血吸虫感染保护作用。方法RT-PCR特异性扩增Sj14FABP基因,将其克隆入真核表达载体pVIVO2,通过PCR、双酶切及测序鉴定。获得的重组质粒pVIVO2-Sj14FABP转染HepG2细胞,间接免疫荧光(IFA)检测蛋白表达;并免疫BALB/c小鼠,30d后攻击感染,感染后45天剖杀,计数检获成虫数和肝脏虫卵数。结果RT-PCR扩增出大小为440bp的Sj14FABP片段,重组质粒经PCR和双酶切后均获得目的片段,转染细胞IFA结果显示有较强荧光。重组质粒免疫小鼠后分别获得24.1%减虫率和27.2%减卵率。结论成功构建和表达重组质粒pVIVO2-Sj14FABP,该核酸疫苗能够诱导小鼠产生部分抗血吸虫感染的保护力。 展开更多
关键词 日本血吸虫 脂肪酸结合蛋白 核酸疫苗 真核表达 免疫保护性
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