ISRN molecular biology最新文献_第3页

Isolation of Alcohol Dehydrogenase cDNA and Basal Regulatory Region from Metroxylon sagu. 杉木醇脱氢酶cDNA的分离及其基础调控区。

ISRN molecular biology Pub Date : 2012-08-26 eCollection Date: 2012-01-01 DOI: 10.5402/2012/839427

Ching Ching Wee, Hairul Azman Roslan

{"title":"Isolation of Alcohol Dehydrogenase cDNA and Basal Regulatory Region from Metroxylon sagu.","authors":"Ching Ching Wee, Hairul Azman Roslan","doi":"10.5402/2012/839427","DOIUrl":"https://doi.org/10.5402/2012/839427","url":null,"abstract":"Alcohol dehydrogenase (Adh) is a versatile enzyme involved in many biochemical pathways in plants such as in germination and stress tolerance. Sago palm is plant with much importance to the state of Sarawak as one of the most important crops that bring revenue with the advantage of being able to withstand various biotic and abiotic stresses such as heat, pathogens, and water logging. Here we report the isolation of sago palm Adh cDNA and its putative promoter region via the use of rapid amplification of cDNA ends (RACE) and genomic walking. The isolated cDNA was characterized and determined to be 1464 bp long encoding for 380 amino acids. BLAST analysis showed that the Adh is similar to the Adh1 group with 91% and 85% homology with Elaeis guineensis and Washingtonia robusta, respectively. The putative basal msAdh1 regulatory region was further determined to contain promoter signals of TATA and AGGA boxes and predicted amino acids analyses showed several Adh-specific motifs such as the two zinc-binding domains that bind to the adenosine ribose of the coenzyme and binding to alcohol substrate. A phylogenetic tree was also constructed using the predicted amino acid showed clear separation of Adh from bacteria and clustered within the plant Adh group. ","PeriodicalId":89785,"journal":{"name":"ISRN molecular biology","volume":"2012 ","pages":"839427"},"PeriodicalIF":0.0,"publicationDate":"2012-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890887/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34493549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Real-Time PCR-Coupled CE-SELEX for DNA Aptamer Selection. 实时pcr耦合CE-SELEX用于DNA适体选择。

ISRN molecular biology Pub Date : 2012-08-08 eCollection Date: 2012-01-01 DOI: 10.5402/2012/939083

Patrick Ruff, Rekha B Pai, Francesca Storici

{"title":"Real-Time PCR-Coupled CE-SELEX for DNA Aptamer Selection.","authors":"Patrick Ruff, Rekha B Pai, Francesca Storici","doi":"10.5402/2012/939083","DOIUrl":"https://doi.org/10.5402/2012/939083","url":null,"abstract":"Aptamers are short nucleic acid or peptide sequences capable of binding to a target molecule with high specificity and affinity. Also known as \"artificial antibodies,\" aptamers provide many advantages over antibodies. One of the major hurdles to aptamer isolation is the initial time and effort needed for selection. The systematic evolution of ligands by exponential enrichment (SELEX) is the traditional procedure for generating aptamers, but this process is lengthy and requires a large quantity of target and starting aptamer library. A relatively new procedure for generating aptamers using capillary electrophoresis (CE), known as CE-SELEX, is faster and more efficient than SELEX but requires laser-induced fluorescence (LIF) to detect the aptamer-target complexes. Here, we implemented an alternative system without LIF using real-time- (RT-) PCR to indirectly measure aptamer-target complexes. In three rounds of selection, as opposed to ten or more rounds common in SELEX protocols, a specific aptamer for bovine serum albumin (BSA) was obtained. The specificity of the aptamer to BSA was confirmed by electrophoretic mobility shift assays (EMSAs), an unlabeled competitor assay, and by a supershift assay. The system used here provides a cost effective and a highly efficient means of generating aptamers. ","PeriodicalId":89785,"journal":{"name":"ISRN molecular biology","volume":"2012 ","pages":"939083"},"PeriodicalIF":0.0,"publicationDate":"2012-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890860/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34506131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 26

Receptor Binding by Cholera Toxin B-Subunit and Amino Acid Modification Improves Minimal Peptide Immunogenicity. 霍乱毒素b亚基受体结合和氨基酸修饰提高最小肽免疫原性。

ISRN molecular biology Pub Date : 2012-07-15 eCollection Date: 2012-01-01 DOI: 10.5402/2012/170676

Andreas Boberg, Alexandra Stålnacke, Andreas Bråve, Jorma Hinkula, Britta Wahren, Nils Carlin

{"title":"Receptor Binding by Cholera Toxin B-Subunit and Amino Acid Modification Improves Minimal Peptide Immunogenicity.","authors":"Andreas Boberg, Alexandra Stålnacke, Andreas Bråve, Jorma Hinkula, Britta Wahren, Nils Carlin","doi":"10.5402/2012/170676","DOIUrl":"https://doi.org/10.5402/2012/170676","url":null,"abstract":"We increase our understanding of augmenting a cellular immune response, by using an HIV-1 protease-derived epitope (PR75-84), and variants thereof, coupled to the C-terminal, of the B subunit of cholera toxin (CTB). Fusion proteins were used for immunizations of HLA-A0201 transgenic C57BL/6 mice. We observed different capacities to elicit a cellular immune response by peptides with additions of five to ten amino acids to the PR epitope. There was a positive correlation between the magnitude of the elicited cellular immune response and the capacity of the fusion protein to bind GM-1. This binding capacity is affected by its ability to form natural pentamers of CTB. Our results suggest that functional CTB pentamers containing a foreign amino acid-modified epitope is a novel way to overcome the limited cellular immunogenicity of minimal peptide antigens. This way of using a functional assay as readout for improved cellular immunogenicity might become highly valuable for difficult immunogens such as short peptides (epitopes). ","PeriodicalId":89785,"journal":{"name":"ISRN molecular biology","volume":"2012 ","pages":"170676"},"PeriodicalIF":0.0,"publicationDate":"2012-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34604827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ion Transporters and Abiotic Stress Tolerance in Plants. 离子转运体与植物的非生物抗逆性。

ISRN molecular biology Pub Date : 2012-06-03 eCollection Date: 2012-01-01 DOI: 10.5402/2012/927436

Faïçal Brini, Khaled Masmoudi

{"title":"Ion Transporters and Abiotic Stress Tolerance in Plants.","authors":"Faïçal Brini, Khaled Masmoudi","doi":"10.5402/2012/927436","DOIUrl":"https://doi.org/10.5402/2012/927436","url":null,"abstract":"Adaptation of plants to salt stress requires cellular ion homeostasis involving net intracellular Na(+) and Cl(-) uptake and subsequent vacuolar compartmentalization without toxic ion accumulation in the cytosol. Sodium ions can enter the cell through several low- and high-affinity K(+) carriers. Some members of the HKT family function as sodium transporter and contribute to Na(+) removal from the ascending xylem sap and recirculation from the leaves to the roots via the phloem vasculature. Na(+) sequestration into the vacuole depends on expression and activity of Na(+)/H(+) antiporter that is driven by electrochemical gradient of protons generated by the vacuolar H(+)-ATPase and the H(+)-pyrophosphatase. Sodium extrusion at the root-soil interface is presumed to be of critical importance for the salt tolerance. Thus, a very rapid efflux of Na(+) from roots must occur to control net rates of influx. The Na(+)/H(+) antiporter SOS1 localized to the plasma membrane is the only Na(+) efflux protein from plants characterized so far. In this paper, we analyze available data related to ion transporters and plant abiotic stress responses in order to enhance our understanding about how salinity and other abiotic stresses affect the most fundamental processes of cellular function which have a substantial impact on plant growth development. ","PeriodicalId":89785,"journal":{"name":"ISRN molecular biology","volume":"2012 ","pages":"927436"},"PeriodicalIF":0.0,"publicationDate":"2012-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907263/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34556365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 87

K-Ras Mutations in Non-Small-Cell Lung Cancer: Prognostic and Predictive Value. 非小细胞肺癌的K-Ras突变:预后和预测价值。

ISRN molecular biology Pub Date : 2012-05-14 eCollection Date: 2012-01-01 DOI: 10.5402/2012/837306

Manolo D'Arcangelo, Federico Cappuzzo

{"title":"K-Ras Mutations in Non-Small-Cell Lung Cancer: Prognostic and Predictive Value.","authors":"Manolo D'Arcangelo, Federico Cappuzzo","doi":"10.5402/2012/837306","DOIUrl":"10.5402/2012/837306","url":null,"abstract":"Non-small-cell lung cancer (NSCLC) is a heterogeneous disease due to the presence of different clinically relevant molecular subtypes. Until today, several biological events have been identified in lung adenocarcinoma, including epidermal growth factor receptor (EGFR) mutations and anaplastic lymphoma kinase (ALK) translocations, offering new hopes to patients with metastatic disease. Unfortunately, in approximately 50% of adenocarcinoma and for those harbouring K-RAS mutations, the most frequent mutation in Caucasian lung adenocarcinoma, so far no specific drug demonstrated efficacy. The rat sarcoma (RAS) genes, including H-RAS, K-RAS, and N-RAS, encode a family of proteins regulating cell growth, differentiation, and apoptosis. K-RAS mutations are present in 20-30% of NSCLC and occur most commonly, but not exclusively, in adenocarcinoma histology and life-long smokers. Although in colorectal cancer patients K-RAS mutations represent a validated negative predictive biomarker for treatment with anti-EGFR monoclonal antibodies, their role in selecting specific treatment for NSCLC patients remains undefined. Aim of the present paper is to critically analyze the prognostic and predictive value of K-RAS mutations in NSCLC. ","PeriodicalId":89785,"journal":{"name":"ISRN molecular biology","volume":"2012 ","pages":"837306"},"PeriodicalIF":0.0,"publicationDate":"2012-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.5402/2012/837306","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34556363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 35

Nucleotide Sequencing and SNP Detection of Toll-Like Receptor-4 Gene in Murrah Buffalo (Bubalus bubalis). 穆拉水牛（Bubalus bubalis）Toll-Like Receptor-4 基因的核苷酸测序和 SNP 检测。

ISRN molecular biology Pub Date : 2012-03-29 eCollection Date: 2012-01-01 DOI: 10.5402/2012/659513

M Mitra, S Taraphder, G S Sonawane, A Verma

{"title":"Nucleotide Sequencing and SNP Detection of Toll-Like Receptor-4 Gene in Murrah Buffalo (Bubalus bubalis).","authors":"M Mitra, S Taraphder, G S Sonawane, A Verma","doi":"10.5402/2012/659513","DOIUrl":"10.5402/2012/659513","url":null,"abstract":"Toll-like receptor-4 (TLR-4) has an important pattern recognition receptor that recognizes endotoxins associated with gram negative bacterial infections. The present investigation was carried out to study nucleotide sequencing and SNP detection by PCR-RFLP analysis of the TLR-4 gene in Murrah buffalo. Genomic DNA was isolated from 102 lactating Murrah buffalo from NDRI herd. The amplified PCR fragments of TLR-4 comprised of exon 1, exon 2, exon 3.1, and exon 3.2 were examined to RFLP. PCR products were obtained with sizes of 165, 300, 478, and 409 bp. TLR-4 gene of investigated Murrah buffaloes was highly polymorphic with AA, AB, and BB genotypes as revealed by PCR-RFLP analysis using Dra I, Hae III, and Hinf I REs. Nucleotide sequencing of the amplified fragment of TLR-4 gene of Murrah buffalo was done. Twelve SNPs were identified. Six SNPs were nonsynonymous resulting in change in amino acids. Murrah is an indigenous Buffalo breed and the presence of the nonsynonymous SNP is indicative of its unique genomic architecture. Sequence alignment and homology across species using BLAST analysis revealed 97%, 97%, 99%, 98%, and 80% sequence homology with Bos taurus, Bos indicus, Ovis aries, Capra hircus, and Homo sapiens, respectively. ","PeriodicalId":89785,"journal":{"name":"ISRN molecular biology","volume":"2012 ","pages":"659513"},"PeriodicalIF":0.0,"publicationDate":"2012-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908255/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34556360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural Modeling and Analysis of Pregnancy-Associated Glycoprotein-1 of Buffalo (Bubalus bubalis). 水牛妊娠相关糖蛋白-1的结构建模与分析。

ISRN molecular biology Pub Date : 2012-03-12 eCollection Date: 2012-01-01 DOI: 10.5402/2012/481539

Jerome Andonissamy, S K Singh, S K Agarwal

{"title":"Structural Modeling and Analysis of Pregnancy-Associated Glycoprotein-1 of Buffalo (Bubalus bubalis).","authors":"Jerome Andonissamy, S K Singh, S K Agarwal","doi":"10.5402/2012/481539","DOIUrl":"https://doi.org/10.5402/2012/481539","url":null,"abstract":"The present study was conducted to design and analyze the structural model of buffalo pregnancy-associated glycoprotein-1 (PAG-1) using bioinformatics. Structural modeling of the deduced buffalo PAG-1 protein was done using PHYRE, CONSURF servers and its structure was subsequently constructed using MODELLER 9.9 and PyMOL softwares Buffalo PAG-1 structural conformity was analyzed using PROSA, WHATIF, and 3D-PSSM servers. Designed buffalo PAG-1 protein structure on BLAST analysis retrieved protein structures belonging to aspartic proteinase family. Moreover in silico analysis revealed buffalo PAG-1 protein retained bilobed structure with pepstatin-binding clefts near the active sites by docking studies with pepstatin A using PatchDock server. Structural studies revealed that the amino and carboxy terminal containing aspartic residues are highly conserved and buried within the protein structure. Structural conformity studies showed that more than 90% of the residues lie inside favored and allowed regions. It was also deduced that buffalo PAG-1 possesses low and high energy zones with a very low threshold for proteolysis ascertaining the stableness of the buffalo PAG-1 protein structure. This study depicts the structural conformity and stability of buffalo PAG-1 protein.","PeriodicalId":89785,"journal":{"name":"ISRN molecular biology","volume":"2012 ","pages":"481539"},"PeriodicalIF":0.0,"publicationDate":"2012-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890903/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34556359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Central Role of Ubiquitination in Genome Maintenance: DNA Replication and Damage Repair. 泛素化在基因组维持中的核心作用:DNA复制和损伤修复。

ISRN molecular biology Pub Date : 2012-02-08 eCollection Date: 2012-01-01 DOI: 10.5402/2012/146748

Soma Ghosh, Tapas Saha

{"title":"Central Role of Ubiquitination in Genome Maintenance: DNA Replication and Damage Repair.","authors":"Soma Ghosh, Tapas Saha","doi":"10.5402/2012/146748","DOIUrl":"https://doi.org/10.5402/2012/146748","url":null,"abstract":"Faithful transmission of genetic information through generations ensures genomic stability and integrity. However, genetic alterations occur every now and then during the course of genome duplication. In order to repair these genetic defects and lesions, nature has devised several repair pathways which function promptly to prevent the cell from accumulating permanent mutations. These repair mechanisms seem to be significantly impacted by posttranslational modifications of proteins like phosphorylation and ubiquitination. Protein ubiquitination is emerging as a critical regulatory mechanism of DNA damage response. Non-proteolytic, proteasome-independent functions of ubiquitin involving monoubiquitination and polyubiquitination of DNA repair proteins contribute significantly to the signaling of DNA repair pathways. In this paper, we will particularly highlight the work on ubiquitin-mediated signaling in the repair processes involving the Fanconi anemia pathway, translesional synthesis, nucleotide excision repair, and repair of double-strand breaks. We will also discuss the role of ubiquitin ligases in regulating checkpoint mechanisms, the role of deubiquitinating enzymes, and the growing possibilities of therapeutic intervention in this ubiquitin-conjugation system. ","PeriodicalId":89785,"journal":{"name":"ISRN molecular biology","volume":"2012 ","pages":"146748"},"PeriodicalIF":0.0,"publicationDate":"2012-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908256/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34544338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12

Increased Phospho-Keratin 8 Isoforms in Colorectal Tumors Associated with EGFR Pathway Activation and Reduced Apoptosis. 结直肠肿瘤中磷酸化角蛋白8亚型的增加与EGFR通路激活和细胞凋亡减少有关。

ISRN molecular biology Pub Date : 2012-01-31 eCollection Date: 2012-01-01 DOI: 10.5402/2012/706545

Georgia Arentz, Tim Chataway, Mark R Condina, Timothy J Price, Peter Hoffmann, Jennifer E Hardingham

{"title":"Increased Phospho-Keratin 8 Isoforms in Colorectal Tumors Associated with EGFR Pathway Activation and Reduced Apoptosis.","authors":"Georgia Arentz, Tim Chataway, Mark R Condina, Timothy J Price, Peter Hoffmann, Jennifer E Hardingham","doi":"10.5402/2012/706545","DOIUrl":"https://doi.org/10.5402/2012/706545","url":null,"abstract":"Hyperphosphorylated keratin (K) 8 acts as a phosphate \"sponge\" for stress-activated protein kinases thereby inhibiting pro-apoptotic molecules and thus apoptosis. MAP kinase/ERK1 has increased activity in colorectal cancer (CRC) and is known to phosphorylate K8. The aims were to identify the K8 isoforms abundantly present in colon tumors, using 2D difference gel electrophoresis (DIGE), to identify the modifications using mass spectrometry, and to validate the differential abundance of these isoforms in tumors relative to matched normal mucosae. 2D DIGE showed 3 isoforms of K8 significantly increased in tumor ≥2-fold in 6/8 pairs. Metal oxide affinity chromatography mass spectrometry and bioinformatics were used to identify phosphorylated serine residues. Levels of PS24, PS432, and PS74 by western blotting were found to be significantly increased in tumor versus matched normal. Blocking of EGFR signaling in Caco2 cells showed a significant decrease (P < 0.0001) in K8 PS74 and PS432 levels by 59% and 66%, respectively, resulting in increased apoptosis. ","PeriodicalId":89785,"journal":{"name":"ISRN molecular biology","volume":"2012 ","pages":"706545"},"PeriodicalIF":0.0,"publicationDate":"2012-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908239/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34556361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Functional Characterization of a Small-Molecule Inhibitor of the DKK1-LRP6 Interaction. DKK1-LRP6相互作用小分子抑制剂的功能表征

ISRN molecular biology Pub Date : 2012-01-23 eCollection Date: 2012-01-01 DOI: 10.5402/2012/823875

Sara Iozzi, Rosaria Remelli, Barbara Lelli, Daniela Diamanti, Silvia Pileri, Luisa Bracci, Renza Roncarati, Andrea Caricasole, Simonetta Bernocco

引用次数: 28