Journal of Nucleic Acids最新文献_第2页

Genetic Clearness Novel Strategy of Group I Bacillus Species Isolated from Fermented Food and Beverages by Using Fibrinolytic Enzyme Gene Encoding a Serine-Like Enzyme. 利用编码丝氨酸样酶的纤维蛋白溶解酶基因清除从发酵食品和饮料中分离出来的 I 组芽孢杆菌的新策略。

IF 1.3

Journal of Nucleic Acids Pub Date : 2019-05-20 eCollection Date: 2019-01-01 DOI: 10.1155/2019/5484896

Moïse Doria Kaya-Ongoto, Christian Aimé Kayath, Etienne Nguimbi, Aimé Augustin Lebonguy, Stech Anomène Eckzechel Nzaou, Paola Sandra Elenga Wilson, Gabriel Ahombo

{"title":"Genetic Clearness Novel Strategy of Group I Bacillus Species Isolated from Fermented Food and Beverages by Using Fibrinolytic Enzyme Gene Encoding a Serine-Like Enzyme.","authors":"Moïse Doria Kaya-Ongoto, Christian Aimé Kayath, Etienne Nguimbi, Aimé Augustin Lebonguy, Stech Anomène Eckzechel Nzaou, Paola Sandra Elenga Wilson, Gabriel Ahombo","doi":"10.1155/2019/5484896","DOIUrl":"10.1155/2019/5484896","url":null,"abstract":"Fibrinolytic enzyme gene (fibE) is widely conserved among Bacillus spp. belonging to group I species. This is encoding a serine-like enzyme (FibE) secreted in extracellular medium. This present work aims to assess the molecular usefulness of this novel conserved housekeeping gene among group I Bacillus spp. to identify and discriminate some related strains in traditional fermented food and beverages in Republic of Congo. First of all 155 isolates have been screened for enzymatic activities using caseinolytic assays. PCR techniques and nested PCR method using specific primers and correlated with 16S RNA sequencing were used. Blotting techniques have been performed for deep comparison with molecular methods. As a result B. amyloliquefaciens (1), B. licheniformis (1), B. subtilis (1), B. pumilus (3), B. altitudinis (2), B. atrophaeus (1), and B. safensis (3) have been specifically identified among 155 isolates found in fermented food and beverages. Genetic analysis and overexpression of glutathione S-transferases (GSTs) fused to mature protein of FibE in Escherichia coli BL21 and TOP10 showed 2-fold higher enzymatic activities by comparison with FibE wild type one. Immunodetection should be associated but this does not clearly discriminate Bacillus belonging to group I.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2019-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6545797/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37359286","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

Inactivation of XPF Sensitizes Cancer Cells to Gemcitabine. XPF的失活使癌细胞对吉西他滨敏感。

IF 2.3

Journal of Nucleic Acids Pub Date : 2019-03-03 eCollection Date: 2019-01-01 DOI: 10.1155/2019/6357609

Joseph W George, Mika Bessho, Tadayoshi Bessho

引用次数: 2

Netrin Family: Role for Protein Isoforms in Cancer. Netrin家族:蛋白质亚型在癌症中的作用。

IF 2.3

Journal of Nucleic Acids Pub Date : 2019-02-24 eCollection Date: 2019-01-01 DOI: 10.1155/2019/3947123

Caroline Suzanne Bruikman, Huayu Zhang, Anneli Maite Kemper, Janine Maria van Gils

引用次数: 22

DNA Ligase IV Prevents Replication Fork Stalling and Promotes Cellular Proliferation in Triple Negative Breast Cancer. DNA连接酶IV阻止三阴性乳腺癌的复制叉停滞并促进细胞增殖。

IF 2.3

Journal of Nucleic Acids Pub Date : 2019-01-31 eCollection Date: 2019-01-01 DOI: 10.1155/2019/9170341

Rashmi R Joshi, Sk Imran Ali, Amanda K Ashley

{"title":"DNA Ligase IV Prevents Replication Fork Stalling and Promotes Cellular Proliferation in Triple Negative Breast Cancer.","authors":"Rashmi R Joshi, Sk Imran Ali, Amanda K Ashley","doi":"10.1155/2019/9170341","DOIUrl":"https://doi.org/10.1155/2019/9170341","url":null,"abstract":"DNA damage is a hallmark of cancer, and mutation and misregulation of proteins that maintain genomic fidelity are associated with the development of multiple cancers. DNA double strand breaks are arguably considered the most deleterious type of DNA damage. The nonhomologous end-joining (NHEJ) pathway is one mechanism to repair DNA double strand breaks, and proteins involved in NHEJ may also regulate DNA replication. We previously established that DNA-PKcs, a NHEJ protein, promotes genomic stability and cell viability following cellular exposure to replication stress; we wanted to discern whether another NHEJ protein, DNA ligase IV (Lig4), shares this phenotype. Our investigations focused on triple negative breast cancer cells, as, compared to nonbasal breast cancer, LIG4 is frequently amplified, and an increased gene dose is associated with higher Lig4 expression. We depleted Lig4 using siRNA and confirmed our knockdown by qPCR and western blotting. Cell survival diminished with Lig4 depletion alone, and this was associated with increased replication fork stalling. Checkpoint protein Chk1 activation and dephosphorylation were unchanged in Lig4-depleted cells. Lig4 depletion resulted in sustained DNA-PKcs phosphorylation following hydroxyurea exposure. Understanding the effect of Lig4 on genomic replication and the replication stress response will clarify the biological ramifications of inhibiting Lig4 activity. In addition, Lig4 is an attractive clinical target for directing CRISPR/Cas9-mediated repair towards homology-directed repair and away from NHEJ, thus understanding of how diminishing Lig4 impacts cell biology is critical.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2019-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2019/9170341","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37027930","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: 9

SERPINA1 mRNA as a Treatment for Alpha-1 Antitrypsin Deficiency. SERPINA1 mRNA治疗α -1抗胰蛋白酶缺乏症。

IF 2.3

Journal of Nucleic Acids Pub Date : 2018-06-13 eCollection Date: 2018-01-01 DOI: 10.1155/2018/8247935

Brendan Connolly, Cleo Isaacs, Lei Cheng, Kirtika H Asrani, Romesh R Subramanian

{"title":"SERPINA1 mRNA as a Treatment for Alpha-1 Antitrypsin Deficiency.","authors":"Brendan Connolly, Cleo Isaacs, Lei Cheng, Kirtika H Asrani, Romesh R Subramanian","doi":"10.1155/2018/8247935","DOIUrl":"https://doi.org/10.1155/2018/8247935","url":null,"abstract":"Alpha-1-antitrypsin (AAT) deficiency is a genetic disorder that produces inactive/defective AAT due to mutations in the SERPINA1 gene encoding AAT. This disease is associated with decreased activity of AAT in the lungs and deposition of excessive defective AAT protein in the liver. Currently there is no specific treatment for liver disease associated with AAT deficiency. AAT lung disease is often treated with one of several serum protein replacement products; however, long-term studies of the effectiveness of SerpinA1 replacement therapy are not available, and it does not reduce liver damage in AAT deficiency. mRNA therapy could potentially target both the liver and lungs of AAT deficient patients. AAT patient fibroblasts and AAT patient fibroblast-derived hepatocytes were transfected with SERPINA1-encoding mRNA and cell culture media were tested for SerpinA1 expression. Our data demonstrates increased SerpinA1 protein in culture media from treated AAT patient fibroblasts and AAT patient fibroblast-derived hepatocytes. In vivo studies in wild type mice demonstrate SERPINA1 mRNA biodistribution in liver and lungs, as well as SerpinA1 protein expression in these two target organs which are critically affected in AAT deficiency. Taken together, our data suggests that SerpinA1 mRNA therapy has the potential to benefit patients suffering from AAT deficiency.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2018-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2018/8247935","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36313204","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: 33

Effects of 5-Hydroxymethylcytosine Epigenetic Modification on the Stability and Molecular Recognition of VEGF i-Motif and G-Quadruplex Structures. 5-Hydroxymethylcytosine 表观遗传修饰对血管内皮生长因子 i-Motif 和 G-四联结构的稳定性和分子识别的影响

IF 2.3

Journal of Nucleic Acids Pub Date : 2018-05-16 eCollection Date: 2018-01-01 DOI: 10.1155/2018/9281286

Rhianna K Morgan, Michael M Molnar, Harshul Batra, Bethany Summerford, Randy M Wadkins, Tracy A Brooks

{"title":"Effects of 5-Hydroxymethylcytosine Epigenetic Modification on the Stability and Molecular Recognition of VEGF i-Motif and G-Quadruplex Structures.","authors":"Rhianna K Morgan, Michael M Molnar, Harshul Batra, Bethany Summerford, Randy M Wadkins, Tracy A Brooks","doi":"10.1155/2018/9281286","DOIUrl":"10.1155/2018/9281286","url":null,"abstract":"Promoters often contain asymmetric G- and C-rich strands, in which the cytosines are prone to epigenetic modification via methylation (5-mC) and 5-hydroxymethylation (5-hmC). These sequences can also form four-stranded G-quadruplex (G4) or i-motif (iM) secondary structures. Although the requisite sequences for epigenetic modulation and iM/G4 formation are similar and can overlap, they are unlikely to coexist. Despite 5-hmC being an oxidization product of 5-mC, the two modified bases cluster at distinct loci. This study focuses on the intersection of G4/iM formation and 5-hmC modification using the vascular endothelial growth factor (VEGF) gene promoter's CpG sites and examines whether incorporation of 5-hmC into iM/G4 structures had any physicochemical effect on formation, stability, or recognition by nucleolin or the cationic porphyrin, TMPyP4. No marked changes were found in the formation or stability of iM and G4 structures; however, changes in recognition by nucleolin or TMPyP4 occurred with 5-hmC modification wherein protein and compound binding to 5-hmC modified G4s was notably reduced. G4/iM structures in the VEGF promoter are promising therapeutic targets for antiangiogenic therapy, and this work contributes to a comprehensive understanding of their governing principles related to potential transcriptional control and targeting.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2018-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5976936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36189423","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

G-Quadruplexes (GQU). G-四元组（GQU）。

IF 2.3

Journal of Nucleic Acids Pub Date : 2018-04-30 eCollection Date: 2018-01-01 DOI: 10.1155/2018/1079191

Shozeb Haider, Gary N Parkinson, Thomas C Marsh

引用次数: 3

A Sequence-Dependent DNA Condensation Induced by Prion Protein. 朊病毒蛋白诱导的序列依赖性DNA凝聚。

IF 2.3

Journal of Nucleic Acids Pub Date : 2018-02-20 eCollection Date: 2018-01-01 DOI: 10.1155/2018/9581021

Alakesh Bera, Sajal Biring

{"title":"A Sequence-Dependent DNA Condensation Induced by Prion Protein.","authors":"Alakesh Bera, Sajal Biring","doi":"10.1155/2018/9581021","DOIUrl":"https://doi.org/10.1155/2018/9581021","url":null,"abstract":"Different studies indicated that the prion protein induces hybridization of complementary DNA strands. Cell culture studies showed that the scrapie isoform of prion protein remained bound with the chromosome. In present work, we used an oxazole dye, YOYO, as a reporter to quantitative characterization of the DNA condensation by prion protein. We observe that the prion protein induces greater fluorescence quenching of YOYO intercalated in DNA containing only GC bases compared to the DNA containing four bases whereas the effect of dye bound to DNA containing only AT bases is marginal. DNA-condensing biological polyamines are less effective than prion protein in quenching of DNA-bound YOYO fluorescence. The prion protein induces marginal quenching of fluorescence of the dye bound to oligonucleotides, which are resistant to condensation. The ultrastructural studies with electron microscope also validate the biophysical data. The GC bases of the target DNA are probably responsible for increased condensation in the presence of prion protein. To our knowledge, this is the first report of a human cellular protein inducing a sequence-dependent DNA condensation. The increased condensation of GC-rich DNA by prion protein may suggest a biological function of the prion protein and a role in its pathogenesis.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2018-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2018/9581021","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36012618","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

Electrochemical and AFM Characterization of G-Quadruplex Electrochemical Biosensors and Applications. g -四联电化学生物传感器的电化学和AFM表征及其应用。

IF 2.3

Journal of Nucleic Acids Pub Date : 2018-01-31 eCollection Date: 2018-01-01 DOI: 10.1155/2018/5307106

Ana-Maria Chiorcea-Paquim, Ramon Eritja, Ana Maria Oliveira-Brett

{"title":"Electrochemical and AFM Characterization of G-Quadruplex Electrochemical Biosensors and Applications.","authors":"Ana-Maria Chiorcea-Paquim, Ramon Eritja, Ana Maria Oliveira-Brett","doi":"10.1155/2018/5307106","DOIUrl":"https://doi.org/10.1155/2018/5307106","url":null,"abstract":"Guanine-rich DNA sequences are able to form G-quadruplexes, being involved in important biological processes and representing smart self-assembling nanomaterials that are increasingly used in DNA nanotechnology and biosensor technology. G-quadruplex electrochemical biosensors have received particular attention, since the electrochemical response is particularly sensitive to the DNA structural changes from single-stranded, double-stranded, or hairpin into a G-quadruplex configuration. Furthermore, the development of an increased number of G-quadruplex aptamers that combine the G-quadruplex stiffness and self-assembling versatility with the aptamer high specificity of binding to a variety of molecular targets allowed the construction of biosensors with increased selectivity and sensitivity. This review discusses the recent advances on the electrochemical characterization, design, and applications of G-quadruplex electrochemical biosensors in the evaluation of metal ions, G-quadruplex ligands, and other small organic molecules, proteins, and cells. The electrochemical and atomic force microscopy characterization of G-quadruplexes is presented. The incubation time and cations concentration dependence in controlling the G-quadruplex folding, stability, and nanostructures formation at carbon electrodes are discussed. Different G-quadruplex electrochemical biosensors design strategies, based on the DNA folding into a G-quadruplex, the use of G-quadruplex aptamers, or the use of hemin/G-quadruplex DNAzymes, are revisited.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2018-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2018/5307106","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36019525","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: 24

Cell-SELEX Identifies a “Sticky” RNA Aptamer Sequence Cell SELEX鉴定“粘性”RNA适体序列

IF 2.3

Journal of Nucleic Acids Pub Date : 2017-01-17 DOI: 10.1155/2017/4943072

P. Ray, R. White

引用次数: 13