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Andrzej M Kierzek

Publications and source records attributed to Andrzej M Kierzek.

10 recordsLinked to original sources
PubMed2006

XQTav: an XQuery processor for Taverna environment.

UNLABELLED: Taverna workbench is an environment for construction, visualization and execution of bioinformatic workflows that integrate specialized tools available through the internet. It is gaining popularity fast, because of supporting the most important bioinformatic services and its simple, yet robust graphical notation. Here we present XQTav-an extension of Taverna that provides full integration with XQuery (the query language for XML) engine. XQTav allows execution of XQuery scripts in Taverna workflow diagrams. All existing Taverna processors can be accessed in the XQuery scripts. This provides an alternative way of specifying subworkflows in Taverna and is useful when one deals with query-like algorithms (e.g. filters and inner joins). Moreover, XQtav may be used to automatically generate an XQuery script that is equivalent to Taverna's workflow. This constitutes another way of creating and enacting bioinformatic workflows: overall structure of a diagram is drawn in Taverna environment, XQuery code is generated and possibly adjusted by hand. It can be executed by XQuery engines or incorporated into other software environments. AVAILABILITY: XQtav is an open source software. It may be downloaded from http://xqtav.sourceforge.net/. The page also contains various tutorials and examples, including the one described in this report.

Algorithms↗
PubMed2004

Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis.

A large number of cDNA inserts were sequenced from a high-quality library of chicken bursal lymphocyte cDNAs. Comparisons to public gene databases indicate that the cDNA collection represents more than 2,000 new, full-length transcripts. This resource defines the structure and the coding potential of a large fraction of B-cell specific and housekeeping genes whose function can be analyzed by disruption in the chicken DT40 B-cell line.

Animals↗
PubMed2004

Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line.

BACKGROUND: The understanding of whole genome sequences in higher eukaryotes depends to a large degree on the reliable definition of transcription units including exon/intron structures, translated open reading frames (ORFs) and flanking untranslated regions. The best currently available chicken transcript catalog is the Ensembl build based on the mappings of a relatively small number of full length cDNAs and ESTs to the genome as well as genome sequence derived in silico gene predictions. RESULTS: We use Long Serial Analysis of Gene Expression (LongSAGE) in bursal lymphocytes and the DT40 cell line to verify the quality and completeness of the annotated transcripts. 53.6% of the more than 38,000 unique SAGE tags (unitags) match to full length bursal cDNAs, the Ensembl transcript build or the genome sequence. The majority of all matching unitags show single matches to the genome, but no matches to the genome derived Ensembl transcript build. Nevertheless, most of these tags map close to the 3' boundaries of annotated Ensembl transcripts. CONCLUSIONS: These results suggests that rather few genes are missing in the current Ensembl chicken transcript build, but that the 3' ends of many transcripts may not have been accurately predicted. The tags with no match in the transcript sequences can now be used to improve gene predictions, pinpoint the genomic location of entirely missed transcripts and optimize the accuracy of gene finder software.

Animals↗
PubMed2004

RDM1, a novel RNA recognition motif (RRM)-containing protein involved in the cell response to cisplatin in vertebrates.

A variety of cellular proteins has the ability to recognize DNA lesions induced by the anti-cancer drug cisplatin, with diverse consequences on their repair and on the therapeutic effectiveness of this drug. We report a novel gene involved in the cell response to cisplatin in vertebrates. The RDM1 gene (for RAD52 Motif 1) was identified while searching databases for sequences showing similarities to RAD52, a protein involved in homologous recombination and DNA double-strand break repair. Ablation of RDM1 in the chicken B cell line DT40 led to a more than 3-fold increase in sensitivity to cisplatin. However, RDM1-/- cells were not hypersensitive to DNA damages caused by ionizing radiation, UV irradiation, or the alkylating agent methylmethane sulfonate. The RDM1 protein displays a nucleic acid binding domain of the RNA recognition motif (RRM) type. By using gel-shift assays and electron microscopy, we show that purified, recombinant chicken RDM1 protein interacts with single-stranded DNA as well as double-stranded DNA, on which it assembles filament-like structures. Notably, RDM1 recognizes DNA distortions induced by cisplatin-DNA adducts in vitro. Finally, human RDM1 transcripts are abundant in the testis, suggesting a possible role during spermatogenesis.

Amino Acid Sequence↗
PubMed2004

Identification of new genes regulated by the Crt1 transcription factor, an effector of the DNA damage checkpoint pathway in Saccharomyces cerevisiae.

The Crt1 (RFX1) protein in Saccharomyces cerevisiae is an effector of the DNA damage checkpoint pathway. It recognizes a 13-bp cis-regulatory element in the 5'-untranslated region (5'-UTR) of the ribonucleotide reductase genes RNR2, RNR3, and RNR4; the HUG1 gene; and itself. We calculated the weight matrix representing the Crt1p binding site motif according to analysis of the 5'-UTR sequences of the genes that are under its regulation. We subsequently searched the 5'-UTR sequences of all the genes in the yeast genome for the occurrence of this motif. The motif was found in regulatory regions of 30 genes. A statistical analysis showed that it is unlikely that a random gene cluster contains the motif conserved as well as the Crt1p binding site. Analysis of microarray data provided supporting evidence for five putative Crt1p targets: FSH3, YLR345W, UBC5, NDE2, and NTH2. We used reverse transcription-PCR to compare the expression levels of these genes in wild-type and crt1Delta strains. Our results indicated that FSH3, YLR345W, and NTH2 are indeed under the regulation of Crt1p. Sequence analysis of the FSH3p indicated that this protein may be involved in folate metabolism either by carrying serine hydrolase activity required for the novel metabolic pathway involving dihydrofolate reductase (DHFR) or by directly interacting with the DHFR enzyme. We postulate that Crt1p may influence deoxyribonucleotide synthesis not only by regulating expression of the RNR genes but also by modulating DHFR activity. FSH3p shares significant sequence similarity with the product of the human tumor suppressor gene OVCA2. YLR345Wp and NTH2p are enzymes involved in the central metabolism under stress conditions.

DNA Damage↗
PubMed2004

Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks.

The biochemical reaction networks include elementary reactions differing by many orders of magnitude in the numbers of molecules involved. The kinetics of reactions involving small numbers of molecules can be studied by exact stochastic simulation. This approach is not practical for the simulation of metabolic processes because of the computational cost of accounting for individual molecular collisions. We present the "maximal time step method," a novel approach combining the Gibson and Bruck algorithm with the Gillespie tau-leap method. This algorithm allows stochastic simulation of systems composed of both intensive metabolic reactions and regulatory processes involving small numbers of molecules. The method is applied to the simulation of glucose, lactose, and glycerol metabolism in Escherichia coli. The gene expression, signal transduction, transport, and enzymatic activities are modeled simultaneously. We show that random fluctuations in gene expression can propagate to the level of metabolic processes. In the cells switching from glucose to a mixture of lactose and glycerol, random delays in transcription initiation determine whether lactose or glycerol operon is induced. In a small fraction of cells severe decrease in metabolic activity may also occur. Both effects are epigenetically inherited by the progeny of the cell in which the random delay in transcription initiation occurred.

Biochemistry↗
PubMed2003

Chemical rearrangement and repair pathways of 1,N6-ethenoadenine.

1,N(6)-Ethenoadenine (epsilonA) is an exocyclic DNA adduct introduced to DNA by vinyl chloride and related compounds as well as in the consequence of oxidative stress and lipid peroxidation (LPO). This highly genotoxic DNA damage is chemically unstable and either depurinates or converts into pyrimidine ring-opened secondary lesions. We have studied the structures of derivatives formed during epsilonA chemical rearrangement and identified enzymes repairing one of the rearrangement products. Rearrangement involves a water molecule addition to the C(2)-N(3) bond of epsilonA, resulting in formation of pyrimidine ring-closed B1 product, which is in equilibrium with pyrimidine ring-opened B2 compound. B2 further deformylates to yield compound C. N-Glycosidic bond of compound C is unstable and C depurinates, yielding compound D. These secondary lesions are not repaired by alkylpurine DNA N-glycosylase, which excises the parental epsilon A. Compound B, when paired with thymine and cytosine is efficiently excised by Escherichia coli formamidopirymidine DNA N-glycosylase (Fpg), and thymine glycol DNA N-glycosylases from E. coli (Nth) and Saccharomyces cerevisiae (Ntg2). B is eliminated from B:G pair only by Nth and Ntg2 glycosylases, however none of the enzymes studied is excising B from B:A pair. This enables finishing of rearrangement, formation of AP sites and subsequently DNA strand breaks. During in vitro translesion synthesis, C is much easier bypassed by DNA polymerases, than compound B, and also than the parental epsilonA as well as than the AP site. This bypass beyond C proceeds mainly by misinsertion of adenine and guanine, or by insertion of thymine, the latter restoring the parental A:T pair. Alternatively, looping out of adducted nucleotide alone or with adjacent one generates one- or two-nucleotide deletions. This may explain the previously reported 20-fold higher mutagenic potency of product C in comparison to epsilon A in E. coli [Biochemistry 32 (1993) 12793].

Adenine↗
PubMed2003

The structure of full-length LysR-type transcriptional regulators. Modeling of the full-length OxyR transcription factor dimer.

The LysR-type transcriptional regulators (LTTRs) comprise the largest family of prokaryotic transcription factors. These proteins are composed of an N-terminal DNA binding domain (DBD) and a C-terminal cofactor binding domain. To date, no structure of the DBD has been solved. According to the SUPERFAMILY and MODBASE databases, a reliable homology model of LTTR DBDs may be built using the structure of the Escherichia coli ModE transcription factor, containing a winged helix- turn-helix (HTH) motif, as a template. The remote, but statistically significant, sequence similarity between ModE and LTTR DBDs and an alignment generated using SUPERFAMILY and MODBASE methods was independently confirmed by alignment of sequence profiles representing ModE and LTTR family DBDs. Using the crystal structure of the E.coli OxyR C-terminal domain and the DBD alignments we constructed a structural model of the full-length dimer of this LTTR family member and used it to investigate the mode of protein-DNA interaction. We also applied the model to interpret, in a structural context, the results of numerous biochemical studies of mutated LTTRs. A comparison of the LTTR DBD model with the structures of other HTH proteins also provides insights into the interaction of LTTRs with the C-terminal domain of the RNA polymerase alpha subunit.

Amino Acid Sequence↗
PubMed2002

STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm.

MOTIVATION: The availability of a huge amount of molecular data concerning various biochemical reactions provoked numerous attempts to study the dynamics of cellular processes by means of kinetic models and computer simulations. Biochemical processes frequently involve small numbers of molecules (e.g. a few molecules of a transcriptional regulator binding to one 'molecule' of a DNA regulatory region). Such reactions are subject to significant stochastic fluctuations. Monte Carlo methods must be employed to study the functional consequences of the fluctuations and simulate processes that cannot be modelled by continuous fluxes of matter. This provides the motivation to develop software dedicated to Monte Carlo simulations of cellular processes with the rigorously proven Gillespie algorithm. RESULTS: STOCKS, software for the stochastic kinetic simulation of biochemical processes is presented. The program uses a rigorously derived Gillespie algorithm that has been shown to be applicable to the study of prokaryotic gene expression. Features dedicated to the study of cellular processes are implemented, such as the possibility to study a process in the range of several cell generations with the application of a simple cell division model. Taking expression of Escherichia coli beta-galactosidase as an example, it is shown that the program is able to simulate systems composed of reactions varying in several orders of magnitude by means of reaction rates and the numbers of molecules involved. AVAILABILITY: The software is available at ftp://ibbrain.ibb.waw.pl/stocksand http://www.ibb.waw.pl/stocks. SUPPLEMENTARY INFORMATION: Parameters of the model of prokaryotic gene expression are available in example files of software distribution.

Algorithms↗