Biomedical subjects

András Gyorffy

Publications and source records attributed to András Gyorffy.

4 recordsLinked to original sources

PubMed2006

[Microelectrodes and their application in diagnostic medicine].

Microelectrodes are in common use in medical detection systems. The binding of two complementary nucleic acid sequences is called hybridization. Today the major obstacle of large-scale hybridization approaches is the large time-dependency of a single reaction, which is up to 16 hours. As the DNA molecules can be electronically charged, the binding could be facilitated and confirmed using an electronic control system. The authors' team aimed to develop a microelectrode system capable for the detection and control of hybridization. A microelectrode head is immersed in small liquid drop. Here, the platinum counterelectrode is surrounded by a non-conducting quartz capillary. The reference electrode is chloridized silver immersed in saturated Ag/Cl dilution. The Ag/AgCl/1 M KCl +AgCl microelectrode in stabilized against the calomel electrode in the first hours, and remains stable between 7th and 30th hours. This can be verified by the minimal drop in the potential difference. Thus the AgCl saturated KCl electrode is usable for several days for actual measurements. The detector is controlled by an attached computer. The system can be used to detect hybridization in a micro-cell located on a gold-plate. The electrode can be dismounted and reused after repeated chloridization of the Ag wire. The microelectrode is simple, cheap; thus is best suited for application in future automated diagnostic detection systems.

Diagnostic Techniques and Procedures↗

PubMed2005

[Hybridization and their application in the DNA array technology].

Hybridization and their application in the DNA array technology. DNA hybridization arrays measure simultaneously the expression of several genes. First, a known DNA sequence (probe) is fixed on a firm basis. Then the complementer sequence (target sequence) is linked to it during the hybridization process. The target sequence extracted from biological samples is fluorescently, enzimatically or radioactively labeled before detection. Higher expression results in higher signal in the detection system. Unlabeled DNA strands can also be detected, as the electronic and optical characteristics of the DNA is altered after complementer hybridization. In this review we summarize the basics of hybridisation and its newest application area in the DNA array systems.

Animals↗

PubMed2005

[The problem of multiple testing and solutions for genome-wide studies].

The problem of multiple testing and its solutions for genome-wide studies. Even if there is no real change, the traditional p = 0.05 can cause 5% of the investigated tests being reported significant. Multiple testing corrections have been developed to solve this problem. Here the authors describe the one-step (Bonferroni), multi-step (step-down and step-up) and graphical methods. However, sometimes a correction for multiple testing creates more problems, than it solves: the universal null hypothesis is of little interest, the exact number of investigations to be adjusted for can not determined and the probability of type II error increases. For these reasons the authors suggest not to perform multiple testing corrections routinely. The calculation of the false discovery rate is a new method for genome-wide studies. Here the p value is substituted by the q value, which also shows the level of significance. The q value belonging to a measurement is the proportion of false positive measurements when we accept it as significant. The authors propose using the q value instead of the p value in genome-wide studies.

Confidence Intervals↗

PubMedDate not supplied

Comparative promoter analysis of doxorubicin resistance-associated genes suggests E47 as a key regulatory element.

Working under the assumption that up- or downregulation of genes implicated in chemoresistance may be the result of altered function of regulatory transcription factors (TF), over-represented TF-binding sites of gene lists previously associated with doxorubicin resistance were the target of our search. First, a data warehouse was set up containing 52 genes which were present in at least two gene lists; of those, proximal promoter sequences (1 kb upstream and 0.05 kb downstream of the transcriptional start sites) could be retrieved from genomic databases for 45 genes using the EZ-Retrieve. The TOUCAN tool MotifScanner, which searches the TRANSFAC database, was used to detect TF-binding sites (TFBSs) in our set of sequences. The statistics tool of the Java program TOUCAN was applied to the data with the appropriate expected frequencies file to compare the measured prevalence to a background model. The most significantly over-represented TFBS was that of E47 (p=0.00024, prevalence: 0.2 vs. background: 8.19E-6). In summary, based on the results of our analysis it is hypothesized that the E47 transcription factor may contribute to doxorubicin resistance.

Antibiotics, Antineoplastic↗