TY - JOUR A1 - Luo, Ting A1 - Chen, Xiaoyi A1 - Zeng, Shufei A1 - Guan, Baozhang A1 - Hu, Bo A1 - Meng, Yu A1 - Liu, Fanna A1 - Wong, Taksui A1 - Lu, Yongpin A1 - Yun, Chen A1 - Hocher, Berthold A1 - Yin, Lianghong T1 - Bioinformatic identification of key genes and analysis of prognostic values in clear cell renal cell carcinoma JF - Oncology Letters N2 - The present study aimed to identify new key genes as potential biomarkers for the diagnosis, prognosis or targeted therapy of clear cell renal cell carcinoma (ccRCC). Three expression profiles (GSE36895, GSE46699 and GSE71963) were collected from Gene Expression Omnibus. GEO2R was used to identify differentially expressed genes (DEGs) in ccRCC tissues and normal samples. The Database for Annotation, Visualization and Integrated Discovery was utilized for functional and pathway enrichment analysis. STRING v10.5 and Molecular Complex Detection were used for protein-protein interaction (PPI) network construction and module analysis, respectively. Regulation network analyses were performed with the WebGestal tool. UALCAN web-portal was used for expression validation and survival analysis of hub genes in ccRCC patients from The Cancer Genome Atlas (TCGA). A total of 65 up- and 164 downregulated genes were identified as DEGs. DEGs were enriched with functional terms and pathways compactly related to ccRCC pathogenesis. Seventeen hub genes and one significant module were filtered out and selected from the PPI network. The differential expression of hub genes was verified in TCGA patients. Kaplan-Meier plot showed that high mRNA expression of enolase 2 (ENO2) was associated with short overall survival in ccRCC patients (P=0.023). High mRNA expression of cyclin D1 (CCND1) (P<0.001), fms related tyrosine kinase 1 (FLT1) (P=0.004), plasminogen (PLG) (P<0.001) and von Willebrand factor (VWF) (P=0.008) appeared to serve as favorable factors in survival. These findings indicate that the DEGs may be key genes in ccRCC pathogenesis and five genes, including ENO2, CCND1, PLT1, PLG and VWF, may serve as potential prognostic biomarkers in ccRCC. KW - clear cell renal cell carcinoma KW - bioinformatics KW - differentially expressed genes KW - biomarkers KW - Kaplan-Meier plot Y1 - 2018 U6 - https://doi.org/10.3892/ol.2018.8842 SN - 1792-1074 SN - 1792-1082 VL - 16 IS - 2 SP - 1747 EP - 1757 PB - Spandidos publ LTD CY - Athens ER - TY - GEN A1 - Choi, Youngeun A1 - Schmidt, Carsten A1 - Tinnefeld, Philip A1 - Bald, Ilko A1 - Rödiger, Stefan T1 - A new reporter design based on DNA origami nanostructures for quantification of short oligonucleotides using microbeads T2 - Postprints der Universität Potsdam : Mathematisch-naturwissenschaftliche Reihe N2 - The DNA origami technique has great potential for the development of brighter and more sensitive reporters for fluorescence based detection schemes such as a microbead-based assay in diagnostic applications. The nanostructures can be programmed to include multiple dye molecules to enhance the measured signal as well as multiple probe strands to increase the binding strength of the target oligonucleotide to these nanostructures. Here we present a proof-of-concept study to quantify short oligonucleotides by developing a novel DNA origami based reporter system, combined with planar microbead assays. Analysis of the assays using the VideoScan digital imaging platform showed DNA origami to be a more suitable reporter candidate for quantification of the target oligonucleotides at lower concentrations than a conventional reporter that consists of one dye molecule attached to a single stranded DNA. Efforts have been made to conduct multiplexed analysis of different targets as well as to enhance fluorescence signals obtained from the reporters. We therefore believe that the quantification of short oligonucleotides that exist in low copy numbers is achieved in a better way with the DNA origami nanostructures as reporters. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 705 KW - nucleic-acids KW - hybridization KW - microrna KW - flourescence KW - biomarkers KW - platform KW - particle KW - binding KW - array KW - gene Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-428271 SN - 1866-8372 IS - 705 ER - TY - JOUR A1 - Choi, Youngeun A1 - Schmidt, Carsten A1 - Tinnefeld, Philip A1 - Bald, Ilko A1 - Rödiger, Stefan T1 - A new reporter design based on DNA origami nanostructures for quantification of short oligonucleotides using microbeads JF - Scientific Reports N2 - The DNA origami technique has great potential for the development of brighter and more sensitive reporters for fluorescence based detection schemes such as a microbead-based assay in diagnostic applications. The nanostructures can be programmed to include multiple dye molecules to enhance the measured signal as well as multiple probe strands to increase the binding strength of the target oligonucleotide to these nanostructures. Here we present a proof-of-concept study to quantify short oligonucleotides by developing a novel DNA origami based reporter system, combined with planar microbead assays. Analysis of the assays using the VideoScan digital imaging platform showed DNA origami to be a more suitable reporter candidate for quantification of the target oligonucleotides at lower concentrations than a conventional reporter that consists of one dye molecule attached to a single stranded DNA. Efforts have been made to conduct multiplexed analysis of different targets as well as to enhance fluorescence signals obtained from the reporters. We therefore believe that the quantification of short oligonucleotides that exist in low copy numbers is achieved in a better way with the DNA origami nanostructures as reporters. KW - nucleic-acids KW - hybridization KW - microrna KW - flourescence KW - biomarkers KW - platform KW - particle KW - binding KW - array KW - gene Y1 - 2019 U6 - https://doi.org/10.1038/s41598-019-41136-x SN - 2045-2322 IS - 9 PB - Macmillan Publishers Limited CY - London ER - TY - JOUR A1 - Romero-Viana, Lidia A1 - Kienel, Ulrike A1 - Sachse, Dirk T1 - Lipid biomarker signatures in a hypersaline lake on Isabel Island (Eastern Pacific) as a proxy for past rainfall anomaly (1942-2006 AD) JF - Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences N2 - Isabel Lake is a hypersaline crater-lake on Isabel Island, Mexico, situated in the eastern tropical Pacific, an area highly sensitive to hydrological changes. Today, annual rainfall mostly occurs during the wet season, from June to October, when the northern edge of the Intertropical Convergence Zone (ITCZ) extends over the island. In order to evaluate the potential of sedimentary lipid biomarker signatures as a proxy of past hydro-climatic variability we have performed a calibration analysis comparing changes in biomarker distribution in the upper 16 cm of the sediment core with a regional instrumental data set. Annual laminations present in the sediment sequence allow for precise chronological control (1942-2006), More than 80 different lipid compounds were identified in the sediment and could be assigned to three major groups of source organisms: (1) algal populations; (2) a mixed community of ciliates, bacteria and cyanobacteria; and (3) photosynthetic sulfur bacteria. We found that the observed changes in the. relative contribution of the different lipid biomarkers to the sediment record were determined by the regional rainfall variability over the last 65 years. The planktonic community of Isabel Lake was highly sensitive to salinity fluctuations related to rainfall variability; seasonal precipitation results in freshwater input into the lake, driving an annual algal bloom and a relative decrease in the abundance of the more halotolerant populations of (cyano) bacteria and ciliates. Consequently, the concentration ratio between the two most abundant biomarkers in the Isabel Lake sediments, n-alkyl diols and tetrahymanol (which we define as the DiTe index), representing algal and ciliate planktonic populations, respectively, was significantly correlated with the seasonal rainfall anomaly (r = 0.68, p < 0.01). We propose that the DiTe index is a proxy of changes in the aquatic ecosystem of Isabel Lake and, by extension, regional hydrological changes in a sensitive climatic area of the eastern tropical Pacific. KW - Lipid KW - biomarkers KW - Diol KW - Tetrahymanol KW - ENSO KW - Salinity KW - Paleoclimate KW - Mexico Y1 - 2012 U6 - https://doi.org/10.1016/j.palaeo.2012.06.011 SN - 0031-0182 VL - 350 IS - 18 SP - 49 EP - 61 PB - Elsevier CY - Amsterdam ER -