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1

From sequence to function ? looking for genes and their annotations

100%
Baczkowski K., Mackiewicz P., Kowalczuk M., Banaszak J., Cebrat S.
Biotechnologia
|
2005
|
issue 3
22-44
EN
Today, we have very powerful and effective machines and methods to sequence and analyze DNA sequences. Almost every week, new genomes are added to sequence databases. However, those data are useless without additional annotations. Genes need to be found and their functions defined. Experimental work is too slow to analyze each sequence of a potential gene but computational methods facilitate such analyses. Here, we review the methodology, potential problems and constraints in genes finding and their annotation. We describe some new approaches including comparative genomics.
2

Influence of replication on organization and evolution of bacterial genomes

100%
Kowalczuk M., Mackiewicz D., Mackiewicz P., Polak N., Cebrat S.
Biotechnologia
|
2005
|
issue 3
75-90
EN
In bacterial chromosomes, strong bias in nucleotide composition has been observed between differently replicated DNA strands (leading and lagging ones), and also in many species between the regions proximal and distal to the origin of replication (ori). This bias is also reflected in composition and distribution of genes along the chromosome. Several phenomena connected with the replication of the chromosome are responsible for such polarization, especially mutational pressure, repair mechanisms and recombinations, and also selection pressure. All these phenomena are not indifferent for gene evolution and their rearrangements which are strictly connected with the organization of bacterial chromosome.
3

Asymmetry of nucleotide composition of prokaryotic chromosomes

100%
Mackiewicz P., Gierlik A., Kowalczuk M., Dudek M., Cebrat S.
Journal of Applied Genetics
|
1999
|
vol. 40
|
issue 1
1-14
EN
We have analysed the causes of asymmetry in nucleotide composition of DNA complementary strands of prokaryotic chromosomes. Analysing DNA walks we have separated the effect of replication-associated processes from the effect introduced by transcription and coding functions. The asymmetry introduced by replication switches its polarity at the origin and at the terminus of replication, which is observed in both noncoding and coding sequences and varies with respect to positions in codons. Coding functions introduce very strong trends into protein coding ORFs, which are specific for each nucleotide position in the codon. Using detrended DNA walks we have eliminated the effect of coding density and we were able to distinguish between mutational pressure associated with replication and compositional bias for genes proximal and distal to the origin of replication.
4
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The preliminary studies of a structure and electrospinning of new polyurethanes based on synthetic atactic poly[(R, S)-3-hydroxybutyrate]

86%
Sajkiewicz P., Brzeska J., Denis P., Sikorska W., Kowalczuk M., Rutkowska M.
|
2014
|
issue 1
5

High divergence rate of sequences located on different DNA strands in closely related bacterial genomes

86%
Mackiewicz P., Mackiewicz D., Kowalczuk M., Dudkiewicz M., Dudek M. R., Cebrat S.
Journal of Applied Genetics
|
2003
|
vol. 44
|
issue 4
561-584
EN
One of the common features of bacterial genomes is a strong compositional asymmetry between differently replicating DNA strands (leading and lagging). The main cause of the observed bias is the mutational pressure associated with replication. This suggests that genes translocated between differently replicating DNA strands are subjected to a higher mutational pressure, which may influence their composition and divergence rate. Analyses of groups of completely sequenced bacterial genomes have revealed that the highest divergence rate is observed for the DNA sequences that in closely related genomes are located on different DNA strands in respect to their role in replication. Paradoxically, for this group of sequences the absolute values of divergence rate are higher for closely related species than for more diverged ones. Since this effect concerns only the specific group of orthologs, there must be a specific mechanism introducing bias into the structure of chromosome by enriching the set of homologs in trans position in newly diverged species in relatively highly diverged sequences. These highly diverged sequences may be of varied nature: (1) paralogs or other fast-evolving genes under weak selection; or (2) pseudogenes that will probably be eliminated from the genome during further evolution; or (3) genes whose history after divergence is longer than the history of the genomes in which they are found. The use of these highly diverged sequences for phylogenetic analyses may influence the topology and branch length of phylogenetic trees. The changing mutational pressure may contribute to arising of genes with new functions as well.
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