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Targeting neuronal PAS domain protein 2 and KN motif/ankyrin repeat domains 1:Advances in type 2 diabetes therapy
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作者 Chun-Han Cheng Wen-Rui Hao Tzu-Hurng Cheng 《World Journal of Diabetes》 SCIE 2024年第11期2173-2176,共4页
This editorial summarizes the latest literature on the roles of neuronal PAS domain protein 2 and KN motif/ankyrin repeat domain 1 in type 2 diabetes(T2D).We highlight their involvement inβ-cell dysfunction,explore t... This editorial summarizes the latest literature on the roles of neuronal PAS domain protein 2 and KN motif/ankyrin repeat domain 1 in type 2 diabetes(T2D).We highlight their involvement inβ-cell dysfunction,explore their potential as therapeutic targets,and discuss the implications for new treatment strategies.We offer valuable insights into relevant gene regulation and cellular mechanisms relevant for the targeted management of T2D. 展开更多
关键词 Type 2 diabetes Neuronal PAS domain protein 2 KN motif and ankyrin repeat domain 1 β-cell dysfunction Therapeutic target
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Docking of Human Band 3 Anion Transporter Proteins with Their Plasmodium falciparum Interactors Based on Short Linear Motifs
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作者 Fatoumata Gniné Fofana Ayoub Ksouri +7 位作者 Cheickna Cisse Oussema Souiai Alia Benkahla Hedmon Okella Mamadou Sangare Jeffrey G. Shaffer Seydou Doumbia Mamadou Wele 《American Journal of Molecular Biology》 CAS 2024年第4期187-200,共14页
Plasmodium (P.) falciparum is a pathogen that causes severe forms of malaria. Protein interactions have been shown to occur between P. falciparum and human erythrocytes in human blood. The Band 3 Anion Transporter (B3... Plasmodium (P.) falciparum is a pathogen that causes severe forms of malaria. Protein interactions have been shown to occur between P. falciparum and human erythrocytes in human blood. The Band 3 Anion Transporter (B3AT) protein is considered the main invasive pathway for the parasite in erythrocytes that causes clinical symptoms for malaria in humans. The interactions between P. falciparum parasites and erythrocytes along this receptor have previously been explored. Short linear motifs (SLIMs) are short linear mediator sequences that involve several biological processes, acting as mediators of protein interactions identifiable by computational tools such as SLiMFinder. For a given protein, the identification of SLIMs allows predicting its interactors. Using the SLIMs approach, protein-protein interaction network analyses between P. falciparum and its human host, were used to identify a tryptophan-rich protein, A5K5E5_PLAVS as an essential interactor of B3AT. To better understand the interaction mechanism, a guided protein-protein docking approach based on SLIM motifs was performed for human B3AT and A5K5E5_PLAVS. The highlights of this important interaction between P. falciparum and its human host have the potential to pave the way to identify new therapeutic candidates. 展开更多
关键词 MALARIA protein-protein Docking protein-protein Interaction Short Linear motifs
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Regulation of different light conditions for efficient biomass production and protein accumulation of Spirulina platensis
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作者 Yufei ZHANG Xianjun LI +9 位作者 Yuhui LI Shiqi LIU Yanrui CHEN Miao JIA Xin WANG Lu ZHANG Qiping GAO Liang ZHANG Daoyong YU Baosheng GE 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2024年第1期174-186,共13页
Light plays an important role in the photosynthesis and metabolic process of microalgae.However,how different light conditions regulate the biomass production and protein accumulation of microalgae is mostly unknown.I... Light plays an important role in the photosynthesis and metabolic process of microalgae.However,how different light conditions regulate the biomass production and protein accumulation of microalgae is mostly unknown.In this study,the influence of different light conditions,including light colors,densities,and light:dark cycles on the cell growth and biochemical composition of Spirulina platensis was symmetrically characterized.Under different colored lights,S.platensis all shows an increase trend within the increased light intensity ranges;however,each showing different optimal light intensities.At the same light intensity,different colored lights show different growth rate of S.platensis following the sequence of red>white>green>yellow>blue.The maximum growth rate and protein accumulation were determined as 21.88 and 5.10 mg/(L·d)when illuminated under red LED.The energy efficiency of different light sources was calculated and ranked as red>white>blue≈green>yellow.Transcriptomic analysis suggests that red light can promote cell growth and protein accumulation by upregulating genes related to photosynthesis,carbon fixation,and C-N metabolism pathways.This study provides a conducive and efficient way to promote biomass production and protein accumulation of S.platensis by regulating light conditions. 展开更多
关键词 MICROALGAE light emitting diode protein accumulation biomass production transcriptomic analysis
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Basic regulatory science behind drug substance and drug product specifications of monoclonal antibodies and other protein therapeutics
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作者 Patanachai K.Limpikirati Sorrayut Mongkoltipparat +7 位作者 Thinnaphat Denchaipradit Nathathai Siwasophonpong Wudthipong Pornnopparat Parawan Ramanandana Phumrapee Pianpaktr Songsak Tongchusak Maoxin Tim Tian Trairak Pisitkun 《Journal of Pharmaceutical Analysis》 SCIE CAS CSCD 2024年第6期785-804,共20页
In this review,we focus on providing basics and examples for each component of the protein therapeutic specifications to interested pharmacists and biopharmaceutical scientists with a goal to strengthen understanding ... In this review,we focus on providing basics and examples for each component of the protein therapeutic specifications to interested pharmacists and biopharmaceutical scientists with a goal to strengthen understanding in regulatory science and compliance.Pharmaceutical specifications comprise a list of important quality attributes for testing,references to use for test procedures,and appropriate acceptance criteria for the tests,and they are set up to ensure that when a drug product is administered to a patient,its intended therapeutic benefits and safety can be rendered appropriately.Conformance of drug substance or drug product to the specifications is achieved by testing an article according to the listed tests and analytical methods and obtaining test results that meet the acceptance criteria.Quality attributes are chosen to be tested based on their quality risk,and consideration should be given to the merit of the analytical methods which are associated with the acceptance criteria of the specifications.Acceptance criteria are set forth primarily based on efficacy and safety profiles,with an increasing attention noted for patient-centric specifications.Discussed in this work are related guidelines that support the biopharmaceutical specification setting,how to set the acceptance criteria,and examples of the quality attributes and the analytical methods from 60 articles and 23 pharmacopeial monographs.Outlooks are also explored on process analytical technologies and other orthogonal tools which are on-trend in biopharmaceutical characterization and quality control. 展开更多
关键词 Biopharmaceutical analysis Biopharmaceutical quality control Biopharmaceutical specifications Monoclonal antibodies protein therapeutics Regulatory science
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Molecular Cloning and Bioinformatics Analysis of sucC Gene of Vibrio alginolyticus Strain HY9901
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作者 Yingzhu WEI Zhiqing WEI +2 位作者 Xuelian LIN Huanying PANG Na WANG 《Asian Agricultural Research》 2024年第8期32-37,共6页
[Objectives]To clone the sucC gene of Vibrio alginolyticus strain HY9901 and conduct the bioinformatics analysis.[Methods]Based on the sucC gene of V.alginolyticus strain HY9901,specific primers were designed to ampli... [Objectives]To clone the sucC gene of Vibrio alginolyticus strain HY9901 and conduct the bioinformatics analysis.[Methods]Based on the sucC gene of V.alginolyticus strain HY9901,specific primers were designed to amplify the full length sequence by PCR and make further analysis.[Results]The theoretical molecular weight of SucC protein was about 41528.45 Da,and the full length was 1167 bp,encoding 388 amino acids.It has no signal peptide and transmembrane region,and has a variety of functional sites.It is predicted that it is mainly located in the cytoplasm,and the ubiquitin and lactate modification sites overlap,and it has high gene homology with Vibrio parahaemolyticus.Theα-helix,random coil and extended strand are the main secondary structures.The similarity between the constructed three-level structure model and the template is high.[Conclusions]This study reveals the structural characteristics and functional potential of SucC protein,and provides a theoretical basis for the study of drug resistance mechanism and prevention strategies. 展开更多
关键词 VIBRIO ALGINOLYTICUS GENE amplification sucC GENE Succinyl-Coa SYNTHETASE protein POST-TRANSLATIONAL modification Bioinformatics analysis
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基于Motif的图采样算法
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作者 石俊豪 王欣 +2 位作者 邹杰军 方宇 蒋星 《南京大学学报(自然科学版)》 CAS CSCD 北大核心 2024年第4期552-565,共14页
图采样通过对图数据进行约简操作,获得比原图的规模更小的图结构,进而服务于图谱分析、图可视化等下游任务.现有的图采样算法侧重于保留图中显著的结构特征而忽略了节点属性,导致采样图在许多下游任务如频繁模式挖掘等,难以取得预期效果... 图采样通过对图数据进行约简操作,获得比原图的规模更小的图结构,进而服务于图谱分析、图可视化等下游任务.现有的图采样算法侧重于保留图中显著的结构特征而忽略了节点属性,导致采样图在许多下游任务如频繁模式挖掘等,难以取得预期效果.为此,提出基于Motif的节点有偏采样算法(Motif-Based Node Biased Sampling,MNBS),利用频繁Motif结构重新定义图中节点的重要性,随后进行有偏节点采样,实现融合节点属性与结构特征的采样.为了快速识别频繁Motif模式,设计了具有“提前终止”特性的Motif模式快速发现算法(Fast Motif-Pattern Discovery,FMPD),能高效且准确地发现Motif模式以支持图采样.实验表明,MNBS采样算法在多项指标上优于其他基线算法,其对数归一化累积组相关性指标平均降低0.54,使用包含“提前终止”特性策略的FMPD算法的时间消耗和内存消耗比基线算法分别降低56.1%和29.8%. 展开更多
关键词 图采样 图数据挖掘 网络分析 motif结构
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Cloning and expression analysis of a long type peptidoglycan recognition protein(PGRP-L) from Xenopus tropicalis 被引量:2
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作者 齐志涛 张启焕 +4 位作者 王资生 王爱民 黄贝 昌鸣先 聂品 《Zoological Research》 CAS CSCD 北大核心 2011年第4期371-378,共8页
Peptidoglycan recognition proteins(PGRPs) are a family of pattern recognition receptors(PRRs) of the immune system,which bind and hydrolyze bacterial peptidoglycan.Here,a long type PGRP(PGRP-L) was first cloned ... Peptidoglycan recognition proteins(PGRPs) are a family of pattern recognition receptors(PRRs) of the immune system,which bind and hydrolyze bacterial peptidoglycan.Here,a long type PGRP(PGRP-L) was first cloned in the lower vertebrate species Xenopus tropicalis(Xt).The XtPGRP-L possessed a conserved genomic structure with five exons and four introns.The alignment and phylogenetic analysis indicated that XtPGRP-L might be a type of amidase-like PGRP.The 3-D model showed that XtPGRP-L possessed a conserved structure compared with the Drosophila PGRP-Lb.During embryonic development,XtPGRP-L was not expressed until the 72 h tadpole stage.In adult tissues,it was strongly expressed in the liver,lung,intestine,and stomach.Furthermore,after LPS stimulation,the expression of XtPGRP-L was up-regulated significantly in the liver,intestine and spleen,indicating that XtPGRP-L may play an important role in the innate immunity of Xenopus tropicalis. 展开更多
关键词 Peptidoglycan recognition protein Gene clone Expression analysis Xenopus tropicalis
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Analysis of the Conditional Correlations from Different Genetic Systems Between the Protein Content and the Appearance Quality Traits of Indica Rice 被引量:4
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作者 葛国科 郑希 +2 位作者 吴建国 叶子弘 石春海 《Journal of Genetics and Genomics》 SCIE CAS CSCD 北大核心 2007年第2期129-137,共9页
A factorial mating design in two environments was conducted using 7 cytoplasmic male sterile lines (A) and 5 restorer lines (R) along with their F1 (A × R) and F2 populations. The unconditional and conditio... A factorial mating design in two environments was conducted using 7 cytoplasmic male sterile lines (A) and 5 restorer lines (R) along with their F1 (A × R) and F2 populations. The unconditional and conditional analyses of genetic models and the corresponding statistic methods, including endospermic, cytoplasmic, and maternal plant genetic systems, were used to analyze the genetic relationships between protein content (PC) and the appearance quality traits of indica rice (Oryza sativa L.). The results from unconditional analysis indicated that PC was significantly correlated with the appearance quality traits of rice, except for the brown rice thickness (BRT). Only the genetic covariance between PC and the brown rice width (BRW) was positively correlative, whereas all the other pairwise traits were negatively correlative. The results from conditional analysis revealed that the weight of brown rice (WBR) or the amylose content (AC) could significantly affect the relationships between PC and the appearance quality traits of indica rice. The conditional analysis showed that WBR might negatively affect the relationships between PC and the brown rice length (BRL), BRW, or BRT through the geuotype x environmental (GE) interaction effects, but positively affected the relationships between PC and the ratio of brown rice length to width (RLW) or the ratio of brown rice length to thickness (RLT). The amylase content could positively affect the relationships between PC and BRL, RLW, RLT through the cytoplasmic effects and maternal additive effects, but negatively affected the relationships between PC and BRW. 展开更多
关键词 indica rice (Oryza sativa L.) COVARIANCE unconditional and conditional analysis methods protein content amylose content appearance quality
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Cloning and Sequence Analysis of HN and F Protein Genes from a Strain of Goose Paramyxovirus 被引量:2
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作者 易春华 潘杰 +3 位作者 付薇 颜健华 徐贤坤 熊毅 《Agricultural Science & Technology》 CAS 2009年第4期75-78,共4页
[ Objective] The study was to clone HN and F genes from GX1 strain of goose paramyxovirus and analyze their sequences. [ Method] According to the full nucleotide sequence of GPV-SF02 strain of goose paramyxovirus, two... [ Objective] The study was to clone HN and F genes from GX1 strain of goose paramyxovirus and analyze their sequences. [ Method] According to the full nucleotide sequence of GPV-SF02 strain of goose paramyxovirus, two pairs of pdmers were designed to amplify the HN and F genes from GX1 strain of goose paramyxovirus isolated from diseased goose in Guangxi Zhuang Autonomous Region; the amplified products were ligated into pMD18-T vector and sequenced. [ Result ] HN and F genes of this strain tested were 1 716 and 1 662 bp in full nucleotide length, respectively; both showed the homologues of about 97.3% with GPV- SF02 strain, of 80.3% -97.5% with strains LaSota, F48E9 and JS, of just 84.8% with Miyadera strain. [ Conclusion] The results show that isolated strain BX1 matches to virulent APMV-1 strain, belonging to genotype Ⅶ of APMV-1 strain. 展开更多
关键词 Goose paramyxovirus HN protein gene F protein gene CLONING Sequence analysis
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Cloning and Expression Analysis of PtFATB Gene Encoding the Acyl-acyl Carrier Protein Thioesterase in Populus tomentosa Carr 被引量:1
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作者 周洲 张德强 卢孟柱 《Journal of Genetics and Genomics》 SCIE CAS CSCD 北大核心 2007年第3期267-274,共8页
Acyl-ACP thioesterases (FATs) terminates the fatty acid synthesis and allow the transport of fatty acids out of the plastids, which are the important determinants of cellular metabolism. FATB is a member of FAT enzy... Acyl-ACP thioesterases (FATs) terminates the fatty acid synthesis and allow the transport of fatty acids out of the plastids, which are the important determinants of cellular metabolism. FATB is a member of FAT enzymes that has been described previously in most of the plants. In silico cloning is a new method that utilizes the bioinformatics on the complete genome and available EST database. In this study, a full-length cDNA clone of PtFATB gene was isolated from Populus tomentosa using this approach. It is 1,450 bp in length and the open reading frame encodes a peptide of 421 amino acids. The predicted amino acid sequence shows significant homology with those from other plant species, which contain typical domains owned by FATB proteins. The transcripts of PtFATB were abundant in leaves, and less in roots detected by using semiquantitative RT-PCR. When the shoots were subjected to the stress treatments (cold, dry, NaC1) and ABA (Abscisic acid), the expression of PtFATB was only slightly reduced under the treatment of low temperature. This suggests that the expression of PtFATB is in a constitutive fashion. This study provides the basis not only for the identification and characterization of this gene but also for the improvement of cold tolerance by controlling the expression of the PtFATB gene in trees in near future. 展开更多
关键词 Populus tomentosa Carr. Acyl-acyl carrier protein thioesterase (PtFATB) in silico and molecular cloning RT-PCR expression analysis
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The Immuno-fluorescence Quantity Analysis of α-Tubulin and γ-Tubulin Protein in Precancerous Lesion and Carcinoma of the Breast and Its Significance 被引量:1
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作者 牛昀 张彤文 +3 位作者 王颖 韦丽 魏锡胤 牛瑞芳 《Chinese Journal of Clinical Oncology》 CSCD 2008年第1期16-21,共6页
OBJECTIVE To investigate the changes and values of the expression of α-tubulin and γ-tubulin in atypical ductal hyperplasia (ADH), ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC) of the bre... OBJECTIVE To investigate the changes and values of the expression of α-tubulin and γ-tubulin in atypical ductal hyperplasia (ADH), ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC) of the breast. The relationship between centrosome abnormalities and breast tumor development was further discussed. METHODS There were three groups including ADH, DCIS and IDC with 30 cases in each group. They were analyzed by immuno-fiuorescence quantity analysis. The expression levels of α-tubulin and γ-tubulin protein in these tissues were detected by flow cytometry immuno-fiuorescence analysis and compared with the results from normal tissues. Immunohistochemistry was also performed in this research. RESULTS The results showed significant differences of the average of the positive (FITC labeled) cells (P=0.000) among the four groups. The level of the IDC group was the highest, while normal breast tissue showed the lowest level. The results suggested that the expression levels of α-tubulin and γ-tubulin both increased as the grade of cellular proliferation and differentiation increased. The expressions showed significant differences among all the groups, except between the ADH and DCIS. There were no significant differences between α-tubulin and γ-tubulin expression in each group (P〈0.05), as there was agreement in the immuno-fluorescence and immunohistochemical analysis for protein expression. CONCLUSION There is abnormal expression of centrosome tubulin as an early event in the development of breast tumor. Furthermore these aberrations may play a key role during oncogenesis and promote cellular transformation to malignancy. The immuno-fiuorescence quantitive analysis and immunohistochemistry can complement each other. 展开更多
关键词 centrosome α-tubulin protein centrosome γ-tubulin protein precancerous lesion breast carcinoma immuno-fluorescence quantity analysis.
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Analysis of the autophagy gene expression profile of pancreatic cancer based on autophagy-related protein microtubule-associated protein 1A/1B-light chain 3 被引量:15
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作者 Yan-Hui Yang Yu-Xiang Zhang +3 位作者 Yang Gui Jiang-Bo Liu Jun-Jun Sun Hua Fan 《World Journal of Gastroenterology》 SCIE CAS 2019年第17期2086-2098,共13页
BACKGROUND Pancreatic cancer is a highly invasive malignant tumor. Expression levels of the autophagy-related protein microtubule-associated protein 1 A/1 B-light chain 3(LC3) and perineural invasion(PNI) are closely ... BACKGROUND Pancreatic cancer is a highly invasive malignant tumor. Expression levels of the autophagy-related protein microtubule-associated protein 1 A/1 B-light chain 3(LC3) and perineural invasion(PNI) are closely related to its occurrence and development. Our previous results showed that the high expression of LC3 was positively correlated with PNI in the patients with pancreatic cancer. In this study, we further searched for differential genes involved in autophagy of pancreatic cancer by gene expression profiling and analyzed their biological functions in pancreatic cancer, which provides a theoretical basis for elucidating the pathophysiological mechanism of autophagy in pancreatic cancer and PNI.AIM To identify differentially expressed genes involved in pancreatic cancer autophagy and explore the pathogenesis at the molecular level.METHODS Two sets of gene expression profiles of pancreatic cancer/normal tissue(GSE16515 and GSE15471) were collected from the Gene Expression Omnibus.Significance analysis of microarrays algorithm was used to screen differentially expressed genes related to pancreatic cancer. Gene Ontology(GO) analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis were used to analyze the functional enrichment of the differentially expressed genes. Protein interaction data containing only differentially expressed genes was downloaded from String database and screened. Module mining was carried out by Cytoscape software and ClusterOne plug-in. The interaction relationship between the modules was analyzed and the pivot nodes between the functional modules were determined according to the information of the functional modules and the data of reliable protein interaction network.RESULTS Based on the above two data sets of pancreatic tissue total gene expression, 6098 and 12928 differentially expressed genes were obtained by analysis of genes with higher phenotypic correlation. After extracting the intersection of the two differential gene sets, 4870 genes were determined. GO analysis showed that 14 significant functional items including negative regulation of protein ubiquitination were closely related to autophagy. A total of 986 differentially expressed genes were enriched in these functional items. After eliminating the autophagy related genes of human cancer cells which had been defined, 347 differentially expressed genes were obtained. KEGG pathway analysis showed that the pathways hsa04144 and hsa04020 were related to autophagy. In addition,65 clustering modules were screened after the protein interaction network was constructed based on String database, and module 32 contains the LC3 gene,which interacts with multiple autophagy-related genes. Moreover, ubiquitin C acts as a pivot node in functional modules to connect multiple modules related to pancreatic cancer and autophagy.CONCLUSION Three hundred and forty-seven genes associated with autophagy in human pancreatic cancer were concentrated, and a key gene ubiquitin C which is closely related to the occurrence of PNI was determined, suggesting that LC3 may influence the PNI and prognosis of pancreatic cancer through ubiquitin C. 展开更多
关键词 Pancreatic cancer Autophagy-related protein microtubule-associated protein 1A/1B-light chain 3 Perineural invasion Gene Ontology analysis Kyoto ENCYCLOPEDIA of Genes and Genomes pathway analysis Ubiquitin C
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Central role of Yes-associated protein and WW-domain-containing transcriptional co-activator with PDZ-binding motif in pancreatic cancer development 被引量:3
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作者 Enrique Rozengurt Guido Eibl 《World Journal of Gastroenterology》 SCIE CAS 2019年第15期1797-1816,共20页
Pancreatic ductal adenocarcinoma(PDAC) remains a deadly disease with no efficacious treatment options. PDAC incidence is projected to increase, which may be caused at least partially by the obesity epidemic. Significa... Pancreatic ductal adenocarcinoma(PDAC) remains a deadly disease with no efficacious treatment options. PDAC incidence is projected to increase, which may be caused at least partially by the obesity epidemic. Significantly enhanced efforts to prevent or intercept this cancer are clearly warranted. Oncogenic KRAS mutations are recognized initiating events in PDAC development, however, they are not entirely sufficient for the development of fully invasive PDAC.Additional genetic alterations and/or environmental, nutritional, and metabolic signals, as present in obesity, type-2 diabetes mellitus, and inflammation, are required for full PDAC formation. We hypothesize that oncogenic KRAS increases the intensity and duration of the growth-promoting signaling network.Recent exciting studies from different laboratories indicate that the activity of the transcriptional co-activators Yes-associated protein(YAP) and WW-domaincontaining transcriptional co-activator with PDZ-binding motif(TAZ) play a critical role in the promotion and maintenance of PDAC operating as key downstream target of KRAS signaling. While initially thought to be primarily an effector of the tumor-suppressive Hippo pathway, more recent studies revealed that YAP/TAZ subcellular localization and co-transcriptional activity is regulated by multiple upstream signals. Overall, YAP has emerged as a central node of transcriptional convergence in growth-promoting signaling in PDAC cells. Indeed, YAP expression is an independent unfavorable prognostic marker for overall survival of PDAC. In what follows, we will review studies implicating YAP/TAZ in pancreatic cancer development and consider different approaches to target these transcriptional regulators. 展开更多
关键词 Pancreatic cancer Yes-associated protein and WW-domain-containing TRANSCRIPTIONAL CO-ACTIVATOR with PDZ-binding motif Oncogenic Kras Obesity Signaling network and LOOPS
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Protein profile of human hepatocarcinoma cell line SMMC-7721:Identification and functional analysis 被引量:8
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作者 Yi Feng Zhong-Min Tian Ming-Xi Wan Zhao-Bin Zheng 《World Journal of Gastroenterology》 SCIE CAS CSCD 2007年第18期2608-2614,共7页
AIM: TO investigate the protein profile of human hepatocarcinoma cell line SMMC-7721, to analyze the specific functions of abundant expressed proteins in the processes of hepatocarcinoma genesis, growth and metastasi... AIM: TO investigate the protein profile of human hepatocarcinoma cell line SMMC-7721, to analyze the specific functions of abundant expressed proteins in the processes of hepatocarcinoma genesis, growth and metastasis, to identify the hepatocarcinoma-specific biomarkers for the early prediction in diagnosis, and to explore the new drug targets for liver cancer therapy. METHODS: Total proteins from human hepatocarcinoma cell line SMMC-7721 were separated by two-dimensional electrophoresis (2DE). The silver-stained gel was analyzed by 2DE software Image Master 2D Elite. Interesting protein spots were identified by peptide mass fingerprinting based on matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and database searching. RESULTS: We obtained protein profile of human hepatocarcinoma cell line SMMC-7721. Among the twenty-one successfully identified proteins, mitofilin, endoplasmic reticulum protein ERp29, ubiquinol-cytochrome C reductase complex core protein I, peroxisomal enoyl CoA hydratase, peroxiredoxin-4 and probable 3-oxoacid CoA transferase 1 precursor were the six novel proteins identified in human hepatocarcinoma cells or tissues. Specific functions of the identified heat-shock proteins were analyzed in detail, and the results suggested that these proteins might promote tumorigenesis via inhibiting cell death induced by several cancer-related stresses or via inhibiting apoptosis at multiple points in the apoptotic signal pathway. Other identified chaperones and cancer-related proteins were also analyzed.CONCLUSION: Based on the protein profile of SMMC-7721 cells, functional analysis suggests that the identified chaperones and cancer-related proteins have their own pathways to contribute to the tumorigenesis, tumor growth and metastasis of liver cancer. Furthermore, proteomic analysis is indicated to be feasible in the cancer study. 展开更多
关键词 Human hepatocarcinoma cell line SMMC-7721 protein identification Functional analysis Heat-shockprotein Tumorigenesis
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Genome-wide analysis of the barley non-specific lipid transfer protein gene family 被引量:2
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作者 Mengyue Zhang Yujin Kim +5 位作者 Jie Zong Hong Lin Anne Dievart Huanjun Li Dabing Zhang Wanqi Liang 《The Crop Journal》 SCIE CAS CSCD 2019年第1期65-76,共12页
Non-specific lipid transfer proteins(nsLTPs) are small, basic proteins that are characterized by an eight-cysteine motif. The biological functions of these proteins have been reported to involve plant reproduction and... Non-specific lipid transfer proteins(nsLTPs) are small, basic proteins that are characterized by an eight-cysteine motif. The biological functions of these proteins have been reported to involve plant reproduction and biotic or abiotic stress response. With the completion of the barley genome sequence, a genome-wide analysis of nsLTPs in barley(Hordeum vulgare L.)(HvLTPs) will be helpful for understanding the function of nsLTPs in plants. We performed a genome-wide analysis of the nsLTP gene family in barley and identified 70 nsLTP genes,which can be divided into five types(1, 2, C, D, and G). Each type of nsLTPs shares similar exon and intron gene structures. Expression analysis showed that barley nsLTPs have diverse expression patterns, revealing their various roles. Our results shed light on the phylogenetic relationships and potential functions of barley nsLTPs and will be useful for future studies of barley development and molecular breeding. 展开更多
关键词 LIPID TRANSFER protein BARLEY Classification SEQUENCE analysis GENE expression
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Analysis of correlated mutations, stalk motifs, and phylogenetic relationship of the 2009 influenza A virus neuraminidase sequences 被引量:4
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作者 Wei Hu 《Journal of Biomedical Science and Engineering》 2009年第7期550-558,共9页
The 2009 H1N1 influenza pandemic has attracted worldwide attention. The new virus first emerged in Mexico in April, 2009 was identified as a unique combination of a triple- reassortant swine influenza A virus, compose... The 2009 H1N1 influenza pandemic has attracted worldwide attention. The new virus first emerged in Mexico in April, 2009 was identified as a unique combination of a triple- reassortant swine influenza A virus, composed of genetic information from pigs, hu- mans, birds, and a Eurasian swine influenza virus. Several recent studies on the 2009 H1N1 virus util-ized small datasets to conduct analysis. With new sequences available up to date, we were able to extend the previous research in three areas. The first was finding two networks of co-mutations that may po-tentially affect the current flu-drug binding sites on neuraminidase (NA), one of the two surface proteins of flu virus. The second was discovering a special stalk motif, which was dominant in the H5N1 strains in the past, in the 2009 H1N1 strains for the first time. Due to the high virulence of this motif, the second finding is significant in our current research on 2009 H1N1. The third was updating the phylogenetic an- alysis of current NA sequences of 2009 H1N1 and H5N1, which demonstrated that, in clear contrast to previous findings, the N1 sequences in 2009 are di-verse enough to cover different major branches of the phylogenetic tree of those in previous years. As the novel influenza A H1N1 virus continues to spread globally, our results highlighted the importance of performing timely analysis on the 2009 H1N1 virus. 展开更多
关键词 Entropy Co-mutation MUTATION Mutual Information NEURAMINIDASE Phylogenetic analysis Random Forest STALK motif Swine Flu
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The structural analysis of protein sequences based on the quasi-amino acids code 被引量:2
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作者 朱平 唐旭清 徐振源 《Chinese Physics B》 SCIE EI CAS CSCD 2009年第1期363-369,共7页
Proteomics is the study of proteins and their interactions in a cell. With the successful completion of the Human Cenome Project, it comes the postgenome era when the proteomics technology is emerging. This paper stud... Proteomics is the study of proteins and their interactions in a cell. With the successful completion of the Human Cenome Project, it comes the postgenome era when the proteomics technology is emerging. This paper studies protein molecule from the algebraic point of view. The algebraic system (∑, +, *) is introduced, where ∑ is the set of 64 codons. According to the characteristics of (∑, +, *), a novel quasi-amino acids code classification method is introduced and the corresponding algebraic operation table over the set ZU of the 16 kinds of quasi-amino acids is established. The internal relation is revealed about quasi-amino acids. The results show that there exist some very close correlations between the properties of the quasi-amino acids and the codon. All these correlation relationships may play an important part in establishing the logic relationship between codons and the quasi-amino acids during the course of life origination. According to Ma F et al (2003 J. Anhui Agricultural University 30 439), the corresponding relation and the excellent properties about amino acids code are very difficult to observe. The present paper shows that (ZU, +,×) is a field. Furthermore, the operational results display that the eodon tga has different property from other stop codons. In fact, in the mitochondrion from human and ox genomic codon, tga is just tryptophane, is not the stop codon like in other genetic code, it is the case of the Chen W C et al (2002 Acta Biophysiea Siniea 18(1) 87). The present theory avoids some inexplicable events of the 20 kinds of amino acids code, in other words it solves the problem of 'the 64 codon assignments of mRNA to amino acids is probably completely wrong' proposed by Yang (2006 Progress in Modern Biomedicine 6 3). 展开更多
关键词 algebraic operation quasi-amino acids code protein sequences structural analysis
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Analysis of Two-Dimensional Gel Electrophoresis Images of Protein from Posterior Silk Gland of Silkworm (Bombyx mori) on Day 1 and Day 4 in the 5th Instar Stage 被引量:2
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作者 WU Wei-cheng GAOQi-kang +7 位作者 CHEN Jin-e YE Jian QIAN Yang-wen LI Jian-ying LU Hua-yun MENG Zhi-qi NI Chun-xiao ZHONG Bo-xiong 《Agricultural Sciences in China》 CAS CSCD 2007年第2期249-254,共6页
The posterior silk gland (PSG) of silkworm is an important organ where fibroin is synthesized and secreted exclusively. Because fibroin constitutes 75-80% of the silk filament, the mechanism governing fibroin secret... The posterior silk gland (PSG) of silkworm is an important organ where fibroin is synthesized and secreted exclusively. Because fibroin constitutes 75-80% of the silk filament, the mechanism governing fibroin secretion, quality and yield of cocoon can be elucidated by the study on the PSG. Using two-dimensional gel electrophoresis (2-DE) and image analysis system, the changes in the protein composition in the PSG cell were investigated on the day 1 (D1) and day 4 (D4) in the 5th instar stage from five different strains of silkworm (Bombyx mori). While differences at protein level between days and strains were far less than those observed at the gene level using EST analysis. The change trends in protein composition from D1 to D4 were diverse among the different strains. The results suggest that the secretion of fibroin is regulated by multiple proteins. The site of regulation and the proteins responsible for the regulation vary with the strain, which leads to differences between strains in the capacity of fibroin secretion in the PSG cell. 展开更多
关键词 silkworm (Bombyx mori) silk gland protein 2-DE image analysis
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Identification of distant co-evolving residues in antigen 85C from Mycobacterium tuberculosis using statistical coupling analysis of the esterase family proteins 被引量:2
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作者 Veeky Baths Utpal Roy 《The Journal of Biomedical Research》 CAS 2011年第3期165-169,共5页
A fundamental goal in cellular signaling is to understand allosteric communication, the process by which sig-nals originating at one site in a protein propagate reliably to affect distant functional sites. The general... A fundamental goal in cellular signaling is to understand allosteric communication, the process by which sig-nals originating at one site in a protein propagate reliably to affect distant functional sites. The general principles of protein structure that underlie this process remain unknown. Statistical coupling analysis (SCA) is a statistical technique that uses evolutionary data of a protein family to measure correlation between distant functional sites and suggests allosteric communication. In proteins, very distant and small interactions between collections of amino acids provide the communication which can be important for signaling process. In this paper, we present the SCA of protein alignment of the esterase family (pfam ID: PF00756) containing the sequence of antigen 85C secreted by Mycobacterium tuberculosis to identify a subset of interacting residues. Clustering analysis of the pairwise correlation highlighted seven important residue positions in the esterase family alignments. These resi-dues were then mapped on the crystal structure of antigen 85C (PDB ID: 1DQZ). The mapping revealed corre-lation between 3 distant residues (Asp38, Leu123 and Met125) and suggests allosteric communication between them. This information can be used for a new drug against this fatal disease. 展开更多
关键词 antigen 85C Mycobacterium tuberculosis clustering analysis COVARIANCE statistical coupling analy-sis esterase family multiple sequence alignments PFAM protein Data Bank.
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Analysis on the Variation Expression of Difficult-Dissolved-Proteins of Diapause Eggs After Activating by Acid Treatment 被引量:1
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作者 ZHAO Feng LIN Jian-rong HUO Yong-kang MAO Li-ming KONG Qing-ming XU Qiu-yun ZHONG Yang-sheng WANG Ye-yuan 《Agricultural Sciences in China》 CAS CSCD 2008年第12期1474-1480,共7页
Using HCl to activate the diapause eggs is a traditional technique of artificial hatching applied in silkworm egg production. Its mechanism has not yet been clarified. This experiment explored the effect of HCl on the... Using HCl to activate the diapause eggs is a traditional technique of artificial hatching applied in silkworm egg production. Its mechanism has not yet been clarified. This experiment explored the effect of HCl on the termination of diapause of silkworm eggs cold-stored for 45 days from the point of proteomes. Two-dimensional electrophoresis techniques and ESI- MS-MS were used to compare and analyze the variation expression of difficult-dissolved-proteins of diapause eggs coldstored for 45 days before and after acid treatment. Through analysis on the two-dimensional electrophoretogram, there were 296 dots before acid treatment and 302 after the treatment, respectively. Amongst them 265 dots were matchable. The matchability reached 88.6%. There were 31 specific protein dots before acid treatment and 37 after acid treatment, respectively. ESI-MS-MS analysis was conducted for two specific protein-rich dots which disappeared after acid treatment. The results indicated that the sequence of No. 1 protein dot had 55 amino acids' peptide matched with those of chorion protein (Bombyx mori). While the sequence of No. 2 protein dot had only 15 amino acids' peptide matched with those of heat shock protein hsp 19.9 (Bombyx mori), and it was presumed to be an unknown protein. The difficult-dissolvedproteins of diapause eggs have variation expression after acid treatment. Some proteins before and after acid treatment are changed in MW. 展开更多
关键词 silkworm egg acid treatment protein ELECTROPHORESIS image analysis
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