Wyniki wyszukiwania - BazTech

1

Genomic Virtual Laboratory

Cegielska B., Kaliszan D., Handschuh L., Figlerowicz M., Meyer N.

Computational Methods in Science and Technology

|

2010

|

Vol. 16, No. 1

39-49

EN

In contemporary science, virtual laboratories give a chance to improve research by facilitating access to high-throughput technologies and bioinformatics methods. The Genomic Virtual Laboratory (GVL) presented here was developed for automate analysis of data retrieved from a microarray experiment. The system was implemented for R Bioconductor-based analysis of results obtained in the study on human acute myeloid leukaemia (AML). The article extends the theoretical aspects of GVL presented earlier [8] and describes how the particular elements were integrated to establish the advanced system of two-colour microarray data analysis.

2

Flexibility of Dicer Studied by Implicit Solvent Molecular Dynamics Simulations

Sarzyńska J., Mickiewicz A., Miłostan M., Łukasiak P., Błażewicz J., Figlerowicz M., Kuliński T.

Computational Methods in Science and Technology

|

2010

|

Vol. 16, No. 1

97-104

EN

Dicer is an enzyme responsible for processing double-stranded RNAs and plays a key role in an RNAi mechanism. Structural insight into the Dicer is provided by the crystal structure of eukaryotic Dicer from Giardia intestinalis. It has been proposed that the structure has three structurally rigid regions that are connected by the flexible hinges. Flexibility of the Dicer is believed to be a critical feature for its function. Spatial arrangement of the RNA-recognition and the catalytic regions is crucial for producing small RNAs of defined length. It has been suggested that in the Giardia Dicer a Platform domain may help in specific arrangement of these regions. To learn more about the role of the Platform domain in Giardia Dicer, we have performed molecular dynamics (MD) simulations of the whole Dicer (WT Dicer) and the Dicer with a deleted platform domain (delta Plf Dicer). The MD simulations were carried out in an implicit solvent model with two implementations of analytic Generalized Born (GB) solvation model in CHARMM: GBMV (Generalized Born using Molecular Volume) and GBSW (Generalized Born with simple Switching). To detect the key global motions of the Dicer, a principal component analysis (PCA) of the obtained MD trajectories has been used. To further explore the motion of the Dicer, we performed a domain motion analysis with the DYNDOM program. The simulations show that both WT Dicer and delta Plf Dicer display flexibility which can be described as a movement of two or three domains. The removal of the Platform substantially changed the flexibility and arrangement of these domains. During the MD simulations of delta Plf Dicer an large movement of the RNA-recognition domain was observed.

3

New approach to Genomics Experiments Taking Advantage of Virtual Laboratory System

Handschuh L., Lawenda M., Stępniak P., Figlerowicz M., Stroiński M., Węglarz J.

Computational Methods in Science and Technology

|

2009

|

Vol. 15, nr 1

31-40

EN

Specialized software, on-line tools and computational resources are very common in contemporary science. One of the exemplary domain is genomics – a new branch of science that developed rapidly in the last decade. As the genome research is very complex, it must be supported by professional informatics. In a microarray field the following steps cannot be performed without computational work: design of probes, quantitative analysis of hybridization results, post-processing, and finally data storage and management. Here, the general aspects of virtual laboratory systems are presented together with perspectives of their implementation in genomics in order to automate and facilitate this area of research.

4

Computational methods in diagnostics of chronic hepatitis C

Kędziora P., Figlerowicz M., Formanowicz P., Alejska M., Jackowiak P., Malinowska N., Frątczak A., Błażewicz J.

Bulletin of the Polish Academy of Sciences. Technical Sciences

|

2005

|

Vol. 53, nr 3

273-281

EN

Despite the considerable progress that has recently been made in medicine, the treatment of viral infections is still a problem remaining to be solved. This especially concerns infections caused by newly emerging patogenes such as: human immunodeficiency virus, hepatitis C virus or SARS-coronavirus. There are several lines of evidence that the unusual genetic polymorphism of these viruses is responsible for the observed therapeutic difficulties. In order to determine whether some parameters describing a very complex and variable viral population can be used as prognostic factors during antiviral treatment computational methods were applied. To this end, the structure of the viral population and virus evolution in the organisms of two patients suffering from chronic hepatitis C were analyzed. Here we demonstrated that phylogenetic trees and Hamming distances best reflect the differences between virus populations present in the organisms of patients who responded positively and negatively to the applied therapy. Interestingly, the obtained results suggest that based on the elaborated method df virus population analysis one can predict the final outcome of the treatment even before it has started.

5

The Influence of (O, N)-Deuteration on the Crystal and Molecular Structure, Thermal Stability and Spectroscopic Properties of 1,3-Propanediammonium Hydrogenphosphate Monohydrate

Bartoszak-Adamska E., Figlerowicz M., Wiewiórowski M., Gustaffson T., Olovsson I., Jaskolski M.

Polish Journal of Chemistry

|

2000

|

Vol. 74, nr 3

393-402

EN

Exchange of mobile hydrogen atoms in 1,3-propanediammonium hydrogenphosphate for deuterium (OH-OD, NH-ND) affects the thermal stability of the salt. Additionally, (O,N)-deuteration induces some unexpected changes in the -CH2-vibrations in the IR spectrum of this compound. The structure of the title compound has been determined by single crystal X-ray diffraction analysis at 290 K (protonated as well as deuterated crystals) and at 25 K (deuterated crystal). In all cases, the crystals are monoclinic, space group, P21/c. The 1,3-propanediammonium dication has the extended all-trans conformation. The structure contains a three-dimensional network of hydrogen bonds, in which all available proton donors are engaged. The phosphate groups are linked through relatively strong H bonds to form infinite chains along c. The water molecule is closely associated with these chains by donating H bonds to two consecutive phosphate units along the chain.