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1

Ethylene and plant defense response

100%
Handschuh L.
Biotechnologia
|
1999
|
issue 3
86-93
EN
The simplest plant growth and development hormone, ethylene, belongs (together with S.A. and JA) to key molecules governing the plant defense response. Production of ethylene is stimulated by wounding, flooding, metal ions, senescense and abscission processes, pathogene attack and ethylene itself. High level of ethylene induces the expression of many classes of pathogenesis-related proteins (PR). In order to properly function, ethylene must be precisely regulated, especially at the biosynthesis and signalling pathways. Two main enzymes involved in ethylene biosynthesis are ACC synthase and ACC oxidase. The ethylene signal transduction pathway is very complicated and needs to be further investigated. Ethylene binds to its receptors ETRs, then the signal is transduced to CTR1 and through phosforylating kinases cascades to EINs and EREBPs, directly binding to DNA GCC boxes. As a consequence, many PR proteins are activated.
2

DNA microarrays in medical diagnostics

51%
Handschuh L., Magacz T., Figlerowicz M.
Biotechnologia
|
2009
|
issue 2
95-112
EN
Many techniques of molecular biology have already been successfully applied in medicine. It seems that in the nearest future, DNA microarrays can also become a usefull tool in medical practice. They enable early and precise diagnostics, help to identify disease, predict its outcome and monitor its treatment. DNA microarrays are most frequently applied in medical sciences to detect chromosomal aberrations (CGH arrays), screen single nucleotide mutations (SNP arrays), identify pathogens and profile gene expression. Recently, especially designed DNA microarrays have been introduced to profile the expression of microRNA genes. The majority of projects involving DNA microarr tcWUWF ays have been devoted to cancer research. Here, the most prominent examples are described.
3

DNA microarrays in structural and functional genomics

51%
Zmienko A., Handschuh L., Goralski M., Figlerowicz M.
Biotechnologia
|
2008
|
issue 4
39-53
EN
DNA microarrays or DNA chips were introduced in the middle nineties and have developed as a very powerful tool for structural and functional analysis of genomes. With thousands to millions of probes deposited on each microarray, it is now possible to perform various kinds of analysis on the genome-wide scale. The basic use of microarrays is gene expression profiling. For this purpose, both one- and two-color labeling methods are used. More sophisticated DNA microarrays allow for analyzing alternative splicing, DNA-protein interactions, chromatine modifications and many more. Currently, DNA microarrays represent an indispensable tool in biology and medicine.
4

DNA microarray data anlysis

51%
Stepniak P., Handschuh L., Figlerowicz M.
|
EN
The paper gives an overview of common methods applied in microarray data analysis. High density oligonucleotide and low density home made microarray types are being considered. Presented exploration procedures follow preprocessing and higher analysis steps, including example methods. Describing higher analysis algorithms we focus on implementation of pattern search and machine learning approaches.
5

DNA microarray probe design

45%
Formanowicz P., Urbaniak R., Handschuh L., Formanowicz D., Figlerowicz M.
Biotechnologia
|
2008
|
issue 4
54-67
EN
DNA microarrays are widely used in many areas of biological research. They are an efficient tool for gene expression analysis due to a high level of parallelism, what means that they allow for simultaneous measuring of the transcriptional activity of all genes present in the studied genome. The quality of the results obtained using microarrays depends among other factors on the proper design of probes. Two general features which should characterize each probe are sensitivity and specificity. Since designing a set of probes having both of these properties is usually a complex task, many algorithms supporting this process have been developed and implemented. However, the designing method should be carefully chosen such that the results will match the requirements following from the nature of the biological problem to be solved. In this paper the criteria used for DNA microarray design are described and some computer based approaches are presented.
6

Blood proliferative diseases ? application of the DNA microarrays for transcriptome analysis

45%
Handschuh L., Lewandowski K., Kazmierczak M., Komarnicki M., Figlerowicz M.
Biotechnologia
|
2009
|
issue 3
22-43
EN
Hematopoiesis is a complex process precisely regulated by a wide spectrum of cooperating factors. Dysfunction of hematopoietic cell proliferation, differentiation or maturation usually leads to the malignant transformation. The DNA microarray-based transcriptome analysis helped to revise the traditional classification of hematological disorders, predict their outcome, test potential therapeutic agents and better understand basic mechanisms underlying cancer origin and development. Here, the results of gene expression profiling in myelo- and lymphoproliferative diseases such as leukemia, lymphoma and myelodysplastic syndromes, are presented. Two microarray technologies were applied in this area of research: Affymetrix gene chips and cDNA microarrays. Among them, Lymphochip is a prominent example of a specialized cDNA microarray tool designed to investigate gene expression in the immunological system and hematological diseases. It seems that typical problems connected with microarray results analysis ? small number of patients, loss of reproducibility can be overcome by increasing the number of samples and application of identical protocols, equipment and reagents in different laboratories.
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