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ABSTRACT: The aim of the study was to evaluate the prognostic value of the vascular endothelial growth factor A (VEGF-A) and hepatocyte growth factor receptor (HGFR, c-met) expressions in homogenous group of breast cancer patients. Tumor samples were collected from 98 patients with invasive ductal breast carcinoma stage II treated with primary surgery. We have observed a strong correlation between VEGF-A and c-met. No correlations were found between VEGF-A or HGFR expressions and clinical parameters (tumor size, grade, axillary lymph node status, age), 5- and 10-years DFS or OS. Our study did not reveal any prognostic value of c-met or VEGF. In addition they are not useful to separate a patients' subgroup with poor prognosis. Unlike in other authors' studies, our patients' group is very homogenous which might tribute to obtained results.
Folia Histochemica et Cytobiologica 01/2010; 48(1):78-83. · 0.81 Impact Factor
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ABSTRACT: One of hypotheses explaining the origin of the genetic code assumes that its evolution has minimised the deleterious effects
of mutations in coded proteins. To estimate the level of such optimization, we calculated optimal codes for genes located
on differently replicating DNA strands separately assuming the rate of amino acid substitutions in proteins as a measure of
code’s susceptibility to errors. The optimal code for genes located on one DNA strand was simultaneously worse than the universal
code for the genes located on the other strand. Furthermore, we generated 20 million random codes of which only 23 were better
than the universal one for genes located on both strands simultaneously while about two orders of magnitude more codes were
better for each of the two strands separately. The result indicates that the existing universal code, the mutational pressure,
the codon and amino acid compositions are highly optimised for the both differently replicating DNA strands.
Keywordsgenetic code–error minimization–adaptation–asymmetric mutational pressure–amino acid usage–leading strand–lagging strand
06/2008: pages 100-109;
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ABSTRACT: In a simple computer model of population evolution, we have shown that frequency of recombination between haplotypes during the gamete production influences the effectiveness of the reproduction strategy. High recombination rates keeps the fraction of defective alleles low while low recombination rate or uneven distributed recombination spots change the strategy of genomes' evolution and result in the accumulation of heterozygous loci in the genomes. Even short fragment of chromosome with restricted recombination influences the genetic structure of neighboring regions.
Theory in Biosciences 05/2007; 125(2):123-32. · 0.98 Impact Factor
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ABSTRACT: The distribution of isoelectric point (pI) of proteins in a proteome is universal for all organisms. It is bimodal dividing the proteome into two sets of acidic and basic proteins. Different species however have different abundance of acidic and basic proteins that may be correlated with taxonomy, subcellular localization, ecological niche of organisms and proteome size.
We have analysed 1784 proteomes encoded by chromosomes of Archaea, Bacteria, Eukaryota, and also mitochondria, plastids, prokaryotic plasmids, phages and viruses. We have found significant correlation in more than 95% of proteomes between the protein length and pI in proteomes--positive for acidic proteins and negative for the basic ones. Plastids, viruses and plasmids encode more basic proteomes while chromosomes of Archaea, Bacteria, Eukaryota, mitochondria and phages more acidic ones. Mitochondrial proteomes of Viridiplantae, Protista and Fungi are more basic than Metazoa. It results from the presence of basic proteins in the former proteomes and their absence from the latter ones and is related with reduction of metazoan genomes. Significant correlation was found between the pI bias of proteomes encoded by prokaryotic chromosomes and proteomes encoded by plasmids but there is no correlation between eukaryotic nuclear-coded proteomes and proteomes encoded by organelles. Detailed analyses of prokaryotic proteomes showed significant relationships between pI distribution and habitat, relation to the host cell and salinity of the environment, but no significant correlation with oxygen and temperature requirements. The salinity is positively correlated with acidicity of proteomes. Host-associated organisms and especially intracellular species have more basic proteomes than free-living ones. The higher rate of mutations accumulation in the intracellular parasites and endosymbionts is responsible for the basicity of their tiny proteomes that explains the observed positive correlation between the decrease of genome size and the increase of basicity of proteomes. The results indicate that even conserved proteins subjected to strong selectional constraints follow the global trend in the pI distribution.
The distribution of pI of proteins in proteomes shows clear relationships with length of proteins, subcellular localization, taxonomy and ecology of organisms. The distribution is also strongly affected by mutational pressure especially in intracellular organisms.
BMC Genomics 02/2007; 8:163. · 4.07 Impact Factor
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ABSTRACT: Abstract
Background
The distribution of isoelectric point (pI) of proteins in a proteome is universal for all organisms. It is bimodal dividing the proteome into two sets of acidic and basic proteins. Different species however have different abundance of acidic and basic proteins that may be correlated with taxonomy, subcellular localization, ecological niche of organisms and proteome size.
Results
We have analysed 1784 proteomes encoded by chromosomes of Archaea, Bacteria, Eukaryota, and also mitochondria, plastids, prokaryotic plasmids, phages and viruses. We have found significant correlation in more than 95% of proteomes between the protein length and pI in proteomes – positive for acidic proteins and negative for the basic ones. Plastids, viruses and plasmids encode more basic proteomes while chromosomes of Archaea, Bacteria, Eukaryota, mitochondria and phages more acidic ones. Mitochondrial proteomes of Viridiplantae, Protista and Fungi are more basic than Metazoa. It results from the presence of basic proteins in the former proteomes and their absence from the latter ones and is related with reduction of metazoan genomes. Significant correlation was found between the pI bias of proteomes encoded by prokaryotic chromosomes and proteomes encoded by plasmids but there is no correlation between eukaryotic nuclear-coded proteomes and proteomes encoded by organelles. Detailed analyses of prokaryotic proteomes showed significant relationships between pI distribution and habitat, relation to the host cell and salinity of the environment, but no significant correlation with oxygen and temperature requirements. The salinity is positively correlated with acidicity of proteomes. Host-associated organisms and especially intracellular species have more basic proteomes than free-living ones. The higher rate of mutations accumulation in the intracellular parasites and endosymbionts is responsible for the basicity of their tiny proteomes that explains the observed positive correlation between the decrease of genome size and the increase of basicity of proteomes. The results indicate that even conserved proteins subjected to strong selectional constraints follow the global trend in the pI distribution.
Conclusion
The distribution of pI of proteins in proteomes shows clear relationships with length of proteins, subcellular localization, taxonomy and ecology of organisms. The distribution is also strongly affected by mutational pressure especially in intracellular organisms.
BMC Genomics. 01/2007;
