@article{LuoChenZengetal.2018, author = {Luo, Ting and Chen, Xiaoyi and Zeng, Shufei and Guan, Baozhang and Hu, Bo and Meng, Yu and Liu, Fanna and Wong, Taksui and Lu, Yongpin and Yun, Chen and Hocher, Berthold and Yin, Lianghong}, title = {Bioinformatic identification of key genes and analysis of prognostic values in clear cell renal cell carcinoma}, series = {Oncology Letters}, volume = {16}, journal = {Oncology Letters}, number = {2}, publisher = {Spandidos publ LTD}, address = {Athens}, issn = {1792-1074}, doi = {10.3892/ol.2018.8842}, pages = {1747 -- 1757}, year = {2018}, abstract = {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.}, language = {en} } @misc{ChoiSchmidtTinnefeldetal.2019, author = {Choi, Youngeun and Schmidt, Carsten and Tinnefeld, Philip and Bald, Ilko and R{\"o}diger, Stefan}, title = {A new reporter design based on DNA origami nanostructures for quantification of short oligonucleotides using microbeads}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-naturwissenschaftliche Reihe}, number = {705}, issn = {1866-8372}, doi = {10.25932/publishup-42827}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-428271}, pages = {8}, year = {2019}, abstract = {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.}, language = {en} } @article{ChoiSchmidtTinnefeldetal.2019, author = {Choi, Youngeun and Schmidt, Carsten and Tinnefeld, Philip and Bald, Ilko and R{\"o}diger, Stefan}, title = {A new reporter design based on DNA origami nanostructures for quantification of short oligonucleotides using microbeads}, series = {Scientific Reports}, journal = {Scientific Reports}, number = {9}, publisher = {Macmillan Publishers Limited}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-019-41136-x}, pages = {8}, year = {2019}, abstract = {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.}, language = {en} } @article{RomeroVianaKienelSachse2012, author = {Romero-Viana, Lidia and Kienel, Ulrike and Sachse, Dirk}, title = {Lipid biomarker signatures in a hypersaline lake on Isabel Island (Eastern Pacific) as a proxy for past rainfall anomaly (1942-2006 AD)}, series = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, volume = {350}, journal = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences}, number = {18}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0031-0182}, doi = {10.1016/j.palaeo.2012.06.011}, pages = {49 -- 61}, year = {2012}, abstract = {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.}, language = {en} }