The Open Biochemistry Journal最新文献_第5页

Study on Certain Biomarkers of Inflammation in Psoriasis Through "OMICS" Platforms. 基于“组学”平台的银屑病炎症相关生物标志物研究

The Open Biochemistry Journal Pub Date : 2014-02-21 eCollection Date: 2014-01-01 DOI: 10.2174/1874091X01408010021

C Rodríguez-Cerdeira, A Molares-Vila, E Sánchez-Blanco, B Sánchez-Blanco

{"title":"Study on Certain Biomarkers of Inflammation in Psoriasis Through \"OMICS\" Platforms.","authors":"C Rodríguez-Cerdeira, A Molares-Vila, E Sánchez-Blanco, B Sánchez-Blanco","doi":"10.2174/1874091X01408010021","DOIUrl":"https://doi.org/10.2174/1874091X01408010021","url":null,"abstract":"Background: In recent years, research on psoriasis has focused on the identification of biomarkers for the diagnosis, pathogenesis, prognosis, or therapeutic response of the disease. These studies could provide insights into the susceptibility and natural history of psoriasis. The identification of biomarkers related to comorbidities in psoriasis, such as arthritis, cardiovascular disease, and the metabolic syndrome, is of special clinical interest.Materials and methods: We performed an extensive review on psoriasis biomarkers, including cytokine and growth factors, in the literature published between 1997 and 2013, including cross-references of any retrieved articles. We also included some data from our own studies.Results: This review presents current knowledge of soluble biomarkers in psoriasis, including cytokines, chemokines, proangiogenic mediators, growth factors, antimicrobial proteins, neuropeptides, and oxidative stress markers.Conclusion: In conclusion, a number of studies have been conducted with the aim of establishing soluble biomarkers for psoriasis. Most of the biomarkers that have been studied do not meet the criteria for a clinically useful biomarker. Further work is needed to establish a role for soluble biomarkers in the diagnosis and treatment of psoriasis, with a special focus on biomarkers for psoriasis comorbidities, such as arthritis, cardiovascular disease, and the metabolic syndrome.","PeriodicalId":515405,"journal":{"name":"The Open Biochemistry Journal","volume":"8 ","pages":"21-34"},"PeriodicalIF":0.0,"publicationDate":"2014-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/74/7f/TOBIOCJ-8-21.PMC3970352.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32225509","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

Effect of Target Length on Specificity and Sensitivity of Oligonucleotide Microarrays: A Comparison between Dendrimer and Modified PCR based Labelling Methods. 目标长度对寡核苷酸微阵列特异性和敏感性的影响:树状分子和改良PCR标记方法的比较。

The Open Biochemistry Journal Pub Date : 2014-01-24 eCollection Date: 2014-01-01 DOI: 10.2174/1874091X01408010011

Abdullah Gibriel

引用次数: 3

Unique Photobleaching Phenomena of the Twin-Arginine Translocase Respiratory Enzyme Chaperone DmsD. 双精氨酸转位酶呼吸酶伴侣DmsD独特的光漂白现象。

The Open Biochemistry Journal Pub Date : 2014-01-10 eCollection Date: 2014-01-01 DOI: 10.2174/1874091X01408010001

Fabrizio Rivardo, Thorin G H Leach, Catherine S Chan, Tara M L Winstone, Carol L Ladner, Kwabena J Sarfo, Raymond J Turner

{"title":"Unique Photobleaching Phenomena of the Twin-Arginine Translocase Respiratory Enzyme Chaperone DmsD.","authors":"Fabrizio Rivardo, Thorin G H Leach, Catherine S Chan, Tara M L Winstone, Carol L Ladner, Kwabena J Sarfo, Raymond J Turner","doi":"10.2174/1874091X01408010001","DOIUrl":"https://doi.org/10.2174/1874091X01408010001","url":null,"abstract":"DmsD is a chaperone of the redox enzyme maturation protein family specifically required for biogenesis of DMSO reductase in Escherichia coli. It exists in multiple folding forms, all of which are capable of binding its known substrate, the twin-arginine leader sequence of the DmsA catalytic subunit. It is important for maturation of the reductase and targeting to the cytoplasmic membrane for translocation. Here, we demonstrate that DmsD exhibits an irreversible photobleaching phenomenon upon 280 nm excitation irradiation. The phenomenon is due to quenching of the tryptophan residues in DmsD and is dependent on its folding and conformation. We also show that a tryptophan residue involved in DmsA signal peptide binding (W87) is important for photobleaching of DmsD. Mutation of W87, or binding of the DmsA twin-arginine signal peptide to DmsD in the pocket that includes W72, W80, and W91 significantly affects the degree of photobleaching. This study highlights the advantage of a photobleaching phenomenon to study protein folding and conformation changes within a protein that was once considered unusable in fluorescence spectroscopy. ","PeriodicalId":515405,"journal":{"name":"The Open Biochemistry Journal","volume":"8 ","pages":"1-11"},"PeriodicalIF":0.0,"publicationDate":"2014-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/87/2e/TOBIOCJ-8-1.PMC3912628.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32090710","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

Biophysical mechanisms of the neutralization of endotoxins by lipopolyamines. 脂多胺中和内毒素的生物物理机制。

The Open Biochemistry Journal Pub Date : 2013-09-30 eCollection Date: 2013-01-01 DOI: 10.2174/1874091X01307010082

Diptesh Sil, Lena Heinbockel, Yani Kaconis, Manfred Rössle, Patrick Garidel, Thomas Gutsmann, Sunil A David, Klaus Brandenburg

{"title":"Biophysical mechanisms of the neutralization of endotoxins by lipopolyamines.","authors":"Diptesh Sil, Lena Heinbockel, Yani Kaconis, Manfred Rössle, Patrick Garidel, Thomas Gutsmann, Sunil A David, Klaus Brandenburg","doi":"10.2174/1874091X01307010082","DOIUrl":"https://doi.org/10.2174/1874091X01307010082","url":null,"abstract":"Endotoxins (lipopolysaccharides, LPS) are one of the strongest immunostimulators in nature, responsible for beneficial effects at low, and pathophysiological effects at high concentrations, the latter frequently leading to sepsis and septic shock associated with high mortality in critical care settings. There are no drugs specifically targeting the pathophysiology of sepsis, and new therapeutic agents are therefore urgently needed. The lipopolyamines are a novel class of small molecules designed to sequester and neutralize LPS. To understand the mechanisms underlying the binding and neutralization of LPS toxicity, we have performed detailed biophysical analyses of the interactions of LPS with candidate lipopolyamines which differ in their potencies of LPS neutralization. We examined gel-to-liquid crystalline phase behavior of LPS and of its supramolecular aggregate structures in the absence and presence of lipopolyamines, the ability of such compounds to incorporate into different membrane systems, and the thermodynamics of the LPS:lipopolyamine binding. We have found that the mechanisms which govern the inactivation process of LPS obey similar rules as found for other active endotoxin neutralizers such as certain antimicrobial peptides. ","PeriodicalId":515405,"journal":{"name":"The Open Biochemistry Journal","volume":"7 ","pages":"82-93"},"PeriodicalIF":0.0,"publicationDate":"2013-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/1e/f6/TOBIOCJ-7-82.PMC3795406.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31813532","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: 8

Characterization of the Stoichiometry of HMGA1/DNA Complexes. HMGA1/DNA复合物的化学计量学表征。

The Open Biochemistry Journal Pub Date : 2013-09-04 eCollection Date: 2013-01-01 DOI: 10.2174/1874091X01307010073

Miki Watanabe, Shuisong Ni, Amy L Lindenberger, Junho Cho, Stuart L Tinch, Michael A Kennedy

{"title":"Characterization of the Stoichiometry of HMGA1/DNA Complexes.","authors":"Miki Watanabe, Shuisong Ni, Amy L Lindenberger, Junho Cho, Stuart L Tinch, Michael A Kennedy","doi":"10.2174/1874091X01307010073","DOIUrl":"https://doi.org/10.2174/1874091X01307010073","url":null,"abstract":"High-mobility group A1 (HMGA1) non-histone chromatin architectural transcription factors regulate gene expression, embryogenesis, cell differentiation, and adaptive immune responses by binding DNA and other transcription factors. HMGA1 has also been shown to be highly over-expressed in many human cancers and is considered to be a valuable cancer biomarker. Elevated HMGA1 expression levels also make cancer cells resistant to chemotherapy. Here, HMGA1/DNA complex formation was investigated using electrophoretic mobility shift assays (EMSA). Collectively, the EMSA results indicated that full length HMGA1 mixed with DNA containing three AT-hook binding sites formed four distinct HMGA1/DNA complexes ranging in stoichiometry from 1:2 to 3:1 in HMGA1:DNA ratio. The data indicated that the distribution of complexes with different HMGA1 to DNA stoichiometries depended on the molar ratio of HMGA1 to DNA in solution, which could have significant biological implications given that HMGA1 is highly over-expressed in human cancer cells. The two naturally occurring isoforms of HMGA1, HMGA1a and HMGA1b, the latter containing an 11 amino acid deletion between the first and second AT-hooks, were observed to have slightly different DNA binding profiles. Finally, HMGA1 binding affinity to DNA was found to be influenced by the DNA A:T segment sequence context, with higher specificity be observed in HMGA1 binding to TnAn segments, which have two local minor groove minima on either side of the TpA step, compared to An:Tn segments, which have a single minor groove minimum at the 3' end of the An run, implying AT-hook binding favors narrow minor groove structure. ","PeriodicalId":515405,"journal":{"name":"The Open Biochemistry Journal","volume":"7 ","pages":"73-81"},"PeriodicalIF":0.0,"publicationDate":"2013-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/90/8b/TOBIOCJ-7-73.PMC3778555.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31757147","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: 8

Phosphorylation of Tip60 Tyrosine 327 by Abl Kinase Inhibits HAT Activity through Association with FE65. Abl激酶磷酸化Tip60酪氨酸327通过与FE65的关联抑制HAT活性。

The Open Biochemistry Journal Pub Date : 2013-08-22 eCollection Date: 2013-01-01 DOI: 10.2174/1874091X20130621002

Sung Hwa Shin, Sang Sun Kang

引用次数: 2

Effects of redox state on the efficient uptake of cell permeable Peptide in Mammalian cells. 氧化还原状态对哺乳动物细胞有效摄取细胞渗透性肽的影响。

The Open Biochemistry Journal Pub Date : 2013-07-12 Print Date: 2013-01-01 DOI: 10.2174/1874091X20130531001

Shayne Squires, Elisabeth Christians, Michael Riedel, David Timothy, Christopher K Rodesch, James Marvin, Ivor Benjamin

{"title":"Effects of redox state on the efficient uptake of cell permeable Peptide in Mammalian cells.","authors":"Shayne Squires, Elisabeth Christians, Michael Riedel, David Timothy, Christopher K Rodesch, James Marvin, Ivor Benjamin","doi":"10.2174/1874091X20130531001","DOIUrl":"https://doi.org/10.2174/1874091X20130531001","url":null,"abstract":"We investigated whether a cell-penetrating peptide linked via a disulfide bond to a fluorophore-labeled cargo peptide can be used to interrogate changes in cellular redox state. A fluorescence resonance energy transfer (FRET) pair was constructed so that the cargo peptide was labeled with fluorescein amidite (FAM) and the cell-penetrating peptide was attached to a quencher. Incubation of cells in culture with the FRET construct was visualized using live-cell, time-lapse imaging, which demonstrated earlier cellular uptake of the construct when cells were treated with the reducing agent n-acetylcysteine (NAC). The FRET peptide construct was easily detected in cells cultured in 96-well plates using a plate-reader. Treatment of cells with various classes of reducing or oxidizing agents resulted in an increase or decrease in FAM fluorescence, respectively. Changes in FAM fluorescence correlated significantly with redox-sensitive green fluorescent protein ratios in cells treated with hydrogen peroxide but not NAC. Detection of relative changes in cellular redox state was enhanced by the fact that uptake of the cell-penetrating peptide occurred more quickly in relatively reduced compared with oxidized cells. We conclude that cell-penetrating peptides coupled via disulfide bonds to detectable cargo is a novel and specific approach for assessment of relative changes in cellular thiol redox state. ","PeriodicalId":515405,"journal":{"name":"The Open Biochemistry Journal","volume":"7 ","pages":"54-65"},"PeriodicalIF":0.0,"publicationDate":"2013-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/62/2f/TOBIOCJ-7-54.PMC3731798.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31636565","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: 2

Different redox response elicited by naturally occurring antioxidants in human endothelial cells. 天然抗氧化剂在人内皮细胞中引起的不同氧化还原反应。

The Open Biochemistry Journal Pub Date : 2013-04-19 Print Date: 2013-01-01 DOI: 10.2174/1874091X01307010044

Roberta Giordo, Annalisa Cossu, Valeria Pasciu, Phu Thi Hoa, Anna Maria Posadino, Gianfranco Pintus

{"title":"Different redox response elicited by naturally occurring antioxidants in human endothelial cells.","authors":"Roberta Giordo, Annalisa Cossu, Valeria Pasciu, Phu Thi Hoa, Anna Maria Posadino, Gianfranco Pintus","doi":"10.2174/1874091X01307010044","DOIUrl":"https://doi.org/10.2174/1874091X01307010044","url":null,"abstract":"Evidences that higher natural antioxidant (NA) intake provides protection against cardiovascular disease (CVD) are contradictory. Oxidative-induced endothelial cells (ECs) injury is the key step in the onset and progression of CVD and for this reason the cellular responses resulting from NA interaction with ECs are actively investigated. This study was designed to investigate the direct impact of different naturally occurring antioxidants on the intracellular ROS levels in cultured human ECs. NA-induced redox changes, in terms of modulation of the intracellular ROS levels, were assessed by using the ROS fluorescent probe 2',7'-dichlorodihydrofluorescein diacetate (H2DCF-DA). While caffeic and caftaric acid exerted an anti-oxidant effect, both coumaric acid and resveratrol were pro-oxidant. Anti- and pro-oxidant effects of the tested compounds were concentration dependent, showing the induction or the tendency to promote a pro-oxidant outcome with increasing concentrations. Interestingly, the anti- and pro-oxidant behavior of chlorogenic and ferulic acid was dependent on the basal intracellular redox state. Our data indicate that naturally occurring antioxidants are able to induce a rapid modification of the intracellular ROS levels in human ECs, which is dependent on both the applied concentration and the intracellular redox state.","PeriodicalId":515405,"journal":{"name":"The Open Biochemistry Journal","volume":"7 ","pages":"44-53"},"PeriodicalIF":0.0,"publicationDate":"2013-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/13/c9/TOBIOCJ-7-44.PMC3664460.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31476984","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

Activation Energy Calculations for Formamide-TiO2 and Formamide-Pt Interactions in the Presence of Water. 水存在下甲酰胺- tio2和甲酰胺- pt相互作用的活化能计算。

The Open Biochemistry Journal Pub Date : 2013-03-22 Print Date: 2013-01-01 DOI: 10.2174/1874091X01307010033

E Dushanov, Kh Kholmurodov, K Yasuoka

{"title":"Activation Energy Calculations for Formamide-TiO2 and Formamide-Pt Interactions in the Presence of Water.","authors":"E Dushanov, Kh Kholmurodov, K Yasuoka","doi":"10.2174/1874091X01307010033","DOIUrl":"https://doi.org/10.2174/1874091X01307010033","url":null,"abstract":"Formamide contains the four elements (C, H, O, and N) most required for life and it is attractive as a potential prebiotic starting material for nucleobase synthesis. In the presence of catalysts (for example, TiO2) and with moderate heating, formamide can pass surface energy barriers, yielding a complete set of nucleic bases and acyclonucleosides, and favoring both phosphorylations and transphosphorylations necessary for life. In the reaction mechanism, interaction with water seems to be an essential factor for the formamide molecule to function. In this paper, a formamide-water solution on a TiO$_2$ (anatase) surface is simulated using the molecular dynamics method, and activation energy calculations are performed for the temperature range of T = 250 K to T = 400 K. A correlation is established between the diffusion and density profiles for the formamide and water molecules on an anatase surface. Also, the calculated activation energies of the formamide-water-anatase and formamide-water-platinum systems are compared. A comparative analysis is performed of the behavior of formamide-water and ethanol-water interaction on the same (anatase and platinum) surfaces. ","PeriodicalId":515405,"journal":{"name":"The Open Biochemistry Journal","volume":"7 ","pages":"33-43"},"PeriodicalIF":0.0,"publicationDate":"2013-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2174/1874091X01307010033","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31626951","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: 2

The Stimulatory Mechanism of Hepatitis C Virus NS5A Protein on the NS5B Catalyzed Replication Reaction In Vitro. 丙型肝炎病毒NS5A蛋白对NS5B催化复制反应的体外刺激机制

The Open Biochemistry Journal Pub Date : 2013-01-01 Epub Date: 2013-01-31 DOI: 10.2174/1874091X01307010011

Elizabeth M Quezada, Caroline M Kane

引用次数: 7