Journal of Nucleic Acids最新文献_第6页

Simultaneous Detection of Different MicroRNA Types Using the ZIP-Code Array System. 利用邮政编码阵列系统同时检测不同MicroRNA类型。

IF 2.3

Journal of Nucleic Acids Pub Date : 2013-01-01 Epub Date: 2013-09-02 DOI: 10.1155/2013/496425

Sonja U Weishaupt, Steffen Rupp, Karin Lemuth

{"title":"Simultaneous Detection of Different MicroRNA Types Using the ZIP-Code Array System.","authors":"Sonja U Weishaupt, Steffen Rupp, Karin Lemuth","doi":"10.1155/2013/496425","DOIUrl":"https://doi.org/10.1155/2013/496425","url":null,"abstract":"MicroRNAs (miRNAs) are important negative regulators of gene expression. Their implication in tumorigenesis is based on their dysregulation in many human cancer diseases. Interestingly, in tumor cells, an altered ratio of precursor and mature miRNA levels has been described. Consequently, differences in miRNA type levels have a high potential as biomarkers and comparative high-throughput-based detection might permit a more accurate characterization of subtypes, especially in the case of very heterogeneous tumor entities. Several molecular methods exist for the detection of mature and precursor miRNAs. DNA microarrays are predestinated as a high-throughput method for comprehensive miRNA detection in tumors. However, the simultaneous array-based detection of both these miRNA types is limited because the mature miRNA sequence is identically present in both forms. Here we present a ZIP-code DNA microarray-based system in combination with a novel labeling approach, which enables the simultaneous detection of precursor and mature miRNAs in one single experiment. Using synthetic miRNA templates, we demonstrate the specificity of the method for the different miRNA types, as well as the detection range up to four orders of magnitude. Moreover, mature and precursor miRNAs were detected and validated in human tumor cells. ","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2013 ","pages":"496425"},"PeriodicalIF":2.3,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/496425","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31770129","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: 6

Oligonucleotide-Based Therapy for FTD/ALS Caused by the C9orf72 Repeat Expansion: A Perspective. 基于寡核苷酸的治疗由C9orf72重复扩增引起的FTD/ALS:一个视角。

IF 1.3

Journal of Nucleic Acids Pub Date : 2013-01-01 Epub Date: 2013-11-17 DOI: 10.1155/2013/208245

Stephanie A Fernandes, Andrew G L Douglas, Miguel A Varela, Matthew J A Wood, Yoshitsugu Aoki

{"title":"Oligonucleotide-Based Therapy for FTD/ALS Caused by the C9orf72 Repeat Expansion: A Perspective.","authors":"Stephanie A Fernandes, Andrew G L Douglas, Miguel A Varela, Matthew J A Wood, Yoshitsugu Aoki","doi":"10.1155/2013/208245","DOIUrl":"10.1155/2013/208245","url":null,"abstract":"Amyotrophic lateral sclerosis (ALS) is a progressive and lethal disease of motor neuron degeneration, leading to paralysis of voluntary muscles and death by respiratory failure within five years of onset. Frontotemporal dementia (FTD) is characterised by degeneration of frontal and temporal lobes, leading to changes in personality, behaviour, and language, culminating in death within 5-10 years. Both of these diseases form a clinical, pathological, and genetic continuum of diseases, and this link has become clearer recently with the discovery of a hexanucleotide repeat expansion in the C9orf72 gene that causes the FTD/ALS spectrum, that is, c9FTD/ALS. Two basic mechanisms have been proposed as being potentially responsible for c9FTD/ALS: loss-of-function of the protein encoded by this gene (associated with aberrant DNA methylation) and gain of function through the formation of RNA foci or protein aggregates. These diseases currently lack any cure or effective treatment. Antisense oligonucleotides (ASOs) are modified nucleic acids that are able to silence targeted mRNAs or perform splice modulation, and the fact that they have proved efficient in repeat expansion diseases including myotonic dystrophy type 1 makes them ideal candidates for c9FTD/ALS therapy. Here, we discuss potential mechanisms and challenges for developing oligonucleotide-based therapy for c9FTD/ALS. ","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2013 ","pages":"208245"},"PeriodicalIF":1.3,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3855979/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31965145","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

Multipyrene tandem probes for point mutations detection in DNA. 用于 DNA 点突变检测的多芘串联探针。

IF 2.3

Journal of Nucleic Acids Pub Date : 2013-01-01 Epub Date: 2013-12-24 DOI: 10.1155/2013/860457

Svetlana A Kholodar, Darya S Novopashina, Mariya I Meschaninova, Alya G Venyaminova

引用次数: 0

Mesenchymal stem cell therapy in diabetes mellitus: progress and challenges. 间充质干细胞治疗糖尿病:进展和挑战。

IF 2.3

Journal of Nucleic Acids Pub Date : 2013-01-01 Epub Date: 2013-05-15 DOI: 10.1155/2013/194858

Nagwa El-Badri, Mohamed A Ghoneim

{"title":"Mesenchymal stem cell therapy in diabetes mellitus: progress and challenges.","authors":"Nagwa El-Badri, Mohamed A Ghoneim","doi":"10.1155/2013/194858","DOIUrl":"https://doi.org/10.1155/2013/194858","url":null,"abstract":"Advanced type 2 diabetes mellitus is associated with significant morbidity and mortality due to cardiovascular, nervous, and renal complications. Attempts to cure diabetes mellitus using islet transplantation have been successful in providing a source for insulin secreting cells. However, limited donors, graft rejection, the need for continued immune suppression, and exhaustion of the donor cell pool prompted the search for a more sustained source of insulin secreting cells. Stem cell therapy is a promising alternative for islet transplantation in type 2 diabetic patients who fail to control hyperglycemia even with insulin injection. Autologous stem cell transplantation may provide the best outcome for those patients, since autologous cells are readily available and do not entail prolonged hospital stays or sustained immunotoxic therapy. Among autologous adult stem cells, mesenchymal stem cells (MSCs) therapy has been applied with varying degrees of success in both animal models and in clinical trials. This review will focus on the advantages of MSCs over other types of stem cells and the possible mechanisms by which MSCs transplant restores normoglycemia in type 2 diabetic patients. Sources of MSCs including autologous cells from diabetic patients and the use of various differentiation protocols in relation to best transplant outcome will be discussed.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2013 ","pages":"194858"},"PeriodicalIF":2.3,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/194858","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31502709","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: 43

Immobilization of DNA aptamers on polyester cloth for antigen detection by dot blot immunoenzymatic assay (aptablot). 涤纶布上DNA适体的固定化，用于点印迹免疫酶法(aptablot)抗原检测。

IF 2.3

Journal of Nucleic Acids Pub Date : 2013-01-01 Epub Date: 2013-10-30 DOI: 10.1155/2013/936542

Sally Smiley, Maria Derosa, Burton Blais

引用次数: 7

Comparative (computational) analysis of the DNA methylation status of trinucleotide repeat expansion diseases. 三核苷酸重复扩增病DNA甲基化状态的比较(计算)分析。

IF 2.3

Journal of Nucleic Acids Pub Date : 2013-01-01 Epub Date: 2013-12-23 DOI: 10.1155/2013/689798

Mohammadmersad Ghorbani, Simon J E Taylor, Mark A Pook, Annette Payne

{"title":"Comparative (computational) analysis of the DNA methylation status of trinucleotide repeat expansion diseases.","authors":"Mohammadmersad Ghorbani, Simon J E Taylor, Mark A Pook, Annette Payne","doi":"10.1155/2013/689798","DOIUrl":"https://doi.org/10.1155/2013/689798","url":null,"abstract":"Previous studies have examined DNA methylation in different trinucleotide repeat diseases. We have combined this data and used a pattern searching algorithm to identify motifs in the DNA surrounding aberrantly methylated CpGs found in the DNA of patients with one of the three trinucleotide repeat (TNR) expansion diseases: fragile X syndrome (FRAXA), myotonic dystrophy type I (DM1), or Friedreich's ataxia (FRDA). We examined sequences surrounding both the variably methylated (VM) CpGs, which are hypermethylated in patients compared with unaffected controls, and the nonvariably methylated CpGs which remain either always methylated (AM) or never methylated (NM) in both patients and controls. Using the J48 algorithm of WEKA analysis, we identified that two patterns are all that is necessary to classify our three regions CCGG∗ which is found in VM and not in AM regions and AATT∗ which distinguished between NM and VM + AM using proportional frequency. Furthermore, comparing our software with MEME software, we have demonstrated that our software identifies more patterns than MEME in these short DNA sequences. Thus, we present evidence that the DNA sequence surrounding CpG can influence its susceptibility to be de novo methylated in a disease state associated with a trinucleotide repeat. ","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2013 ","pages":"689798"},"PeriodicalIF":2.3,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/689798","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32054320","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: 15

Expression Analysis of Sugarcane Aquaporin Genes under Water Deficit. 水分亏缺条件下甘蔗水通道蛋白基因表达分析。

IF 2.3

Journal of Nucleic Acids Pub Date : 2013-01-01 Epub Date: 2013-12-29 DOI: 10.1155/2013/763945

Manassés Daniel da Silva, Roberta Lane de Oliveira Silva, José Ribamar Costa Ferreira Neto, Ana Carolina Ribeiro Guimarães, Daniela Truffi Veiga, Sabrina Moutinho Chabregas, William Lee Burnquist, Günter Kahl, Ana Maria Benko-Iseppon, Ederson Akio Kido

{"title":"Expression Analysis of Sugarcane Aquaporin Genes under Water Deficit.","authors":"Manassés Daniel da Silva, Roberta Lane de Oliveira Silva, José Ribamar Costa Ferreira Neto, Ana Carolina Ribeiro Guimarães, Daniela Truffi Veiga, Sabrina Moutinho Chabregas, William Lee Burnquist, Günter Kahl, Ana Maria Benko-Iseppon, Ederson Akio Kido","doi":"10.1155/2013/763945","DOIUrl":"https://doi.org/10.1155/2013/763945","url":null,"abstract":"The present work is a pioneer study specifically addressing the aquaporin transcripts in sugarcane transcriptomes. Representatives of the four aquaporin subfamilies (PIP, TIP, SIP, and NIP), already described for higher plants, were identified. Forty-two distinct aquaporin isoforms were expressed in four HT-SuperSAGE libraries from sugarcane roots of drought-tolerant and -sensitive genotypes, respectively. At least 10 different potential aquaporin isoform targets and their respective unitags were considered to be promising for future studies and especially for the development of molecular markers for plant breeding. From those 10 isoforms, four (SoPIP2-4, SoPIP2-6, OsPIP2-4, and SsPIP1-1) showed distinct responses towards drought, with divergent expressions between the bulks from tolerant and sensitive genotypes, when they were compared under normal and stress conditions. Two targets (SsPIP1-1 and SoPIP1-3/PIP1-4) were selected for validation via RT-qPCR and their expression patterns as detected by HT-SuperSAGE were confirmed. The employed validation strategy revealed that different genotypes share the same tolerant or sensitive phenotype, respectively, but may use different routes for stress acclimation, indicating the aquaporin transcription in sugarcane to be potentially genotype-specific. ","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2013 ","pages":"763945"},"PeriodicalIF":2.3,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/763945","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32083493","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: 20

Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis. 通过微生物法证分析将群体测序作为马氏伯克霍尔德氏菌和假马氏伯克霍尔德氏菌进化的生物标志物。

IF 2.3

Journal of Nucleic Acids Pub Date : 2013-01-01 Epub Date: 2013-12-17 DOI: 10.1155/2013/801505

John P Jakupciak, Jeffrey M Wells, Richard J Karalus, David R Pawlowski, Jeffrey S Lin, Andrew B Feldman

{"title":"Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis.","authors":"John P Jakupciak, Jeffrey M Wells, Richard J Karalus, David R Pawlowski, Jeffrey S Lin, Andrew B Feldman","doi":"10.1155/2013/801505","DOIUrl":"10.1155/2013/801505","url":null,"abstract":"Large-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations. ","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2013 ","pages":"801505"},"PeriodicalIF":2.3,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3877622/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32054321","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

Thermodynamic and structural analysis of DNA damage architectures related to replication. 与复制相关的DNA损伤结构的热力学和结构分析。

IF 2.3

Journal of Nucleic Acids Pub Date : 2013-01-01 Epub Date: 2013-04-28 DOI: 10.1155/2013/867957

Nicholas J Amato, Christopher N Mwai, Timothy C Mueser, Amanda C Bryant-Friedrich

{"title":"Thermodynamic and structural analysis of DNA damage architectures related to replication.","authors":"Nicholas J Amato, Christopher N Mwai, Timothy C Mueser, Amanda C Bryant-Friedrich","doi":"10.1155/2013/867957","DOIUrl":"https://doi.org/10.1155/2013/867957","url":null,"abstract":"Damaged DNA, generated by the abstraction of one of five hydrogen atoms from the 2'-deoxyribose ring of the nucleic acid, can contain a variety of lesions, some of which compromise physiological processes. Recently, DNA damage, resulting from the formation of a C3'-thymidinyl radical in DNA oligomers, was found to be dependent on nucleic acid structure. Architectures relevant to DNA replication were observed to generate larger amounts of strand-break and 1-(2'-deoxy- β -D-threo-pentofuranosyl)thymidine formation than that observed for duplex DNA. To understand how this damage can affect the integrity of DNA, the impact of C3'-thymidinyl radical derived lesions on DNA stability and structure was characterized using biophysical methods. DNA architectures evaluated include duplex DNA (dsDNA), single 3' or 5'-overhangs (OvHgs), and forks. Thermal melting analysis and differential scanning calorimetry measurements indicate that an individual 3'-OvHg is more destabilizing than a 5'-OvHg. The presence of a terminal 3' or 5' phosphate decreases the ΔG 25 to the same extent, while the effect of the phosphate at the ss-dsDNA junction of OvHgs is dependent on sequence. Additionally, the effect of 1-(2'-deoxy- β -D-threo-pentofuranosyl)thymidine is found to depend on DNA architecture and proximity to the 3' end of the damaged strand.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2013 ","pages":"867957"},"PeriodicalIF":2.3,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/867957","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31459250","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: 3

Base Composition Characteristics of Mammalian miRNAs. 哺乳动物mirna的碱基组成特征。

IF 2.3

Journal of Nucleic Acids Pub Date : 2013-01-01 Epub Date: 2013-02-24 DOI: 10.1155/2013/951570

Bin Wang

引用次数: 22