Szymon Kaczanowski

• Polish Academy of Sciences

Different types of programmed cell death have been described both in unicellular and multicellular organisms. The fundamental mode of eukaryotic cell death is programmed cell death initiated by mitochondria, which is frequently referred to as apoptosis (or mitochondrial apoptosis). It is initiated by mitochondria through mitochondrial permeability...

The mechanisms initiating apoptotic programmed cell death in diverse eukaryotes are very similar. Basically, the mitochondrial permeability transition activates apoptotic proteases, DNases, and flavoproteins such as apoptosis-inducing factors (AIFs). According to the hypothesis of the endosymbiotic origin of apoptosis, these mechanisms evolved duri...

Background The impact of genetic interaction networks on evolution is a fundamental issue. Previous studies have demonstrated that the topology of the network is determined by the properties of the cellular machinery. Functionally related genes frequently interact with one another, and they establish modules, e.g., modules of protein complexes and...

Otto Warburg, a Nobel prize winner, observed that cancer cells typically “switch” from aerobic to anaerobic respiration. He hypothesized that mitochondrial damage induces neoplastic transformation. In contrast, pathological aging is observed mainly in neuron cells in neurodegenerative diseases. Oxidative respiration is particularly active in neuron...

Apoptotic cell death is a type of eukaryotic cell death. In animals, it regulates development, is involved in cancer suppression, and causes cell death during pathological aging of neuronal cells in neurodegenerative diseases such as Alzheimer's. Mitochondrial apoptotic-like cell death, a form of primordial apoptosis, also occurs in unicellular org...

In this study, we used genetic interaction (GI) and gene–chemical interaction (GCI) data to compare mutations with different dominance phenotypes. Our analysis focused primarily on Saccharomyces cerevisiae, where haploinsufficient genes (HI; genes with dominant loss-of-function mutations) were found to be participating in gene expression processes,...

In this paper we characterize the biofilm community from an ancient Złoty Stok gold and arsenic mine. Bacterial diversity was examined using a culture-independent technique based on 16S rRNA gene amplification, cloning and sequencing. We show that unexpectedly the microbial diversity of this community was extremely high (more than 190 OTUs detected...

Essentiality and ranking of known drug targets. The essentiality and ranking (from an evolutionary perspective) of known drug targets. Drug targets are ordered by drug class. Data for eight species of interest are presented in separate columns. Red: essential genes, blue: nonessential genes, grey: no data addressing essentiality, white: no ortholog...

Statistical data - pN/pS analysis. Mean pN/pS ratio for three sets of genes (ADT - drug targets, ESS - essential genes, ALL - other genes) presented. Data for eight species analyzed in the study. P-values where corrected for multiple testing with FDR (Benjamini-Yekutieli algorithm). Abbreviations: ciu - confidence interval upper limit; cil - confid...

Statistical data - dN/dS analysis. Mean dN/dS ratio for three sets of genes (ADT - drug targets, ESS - essential genes, ALL - other genes) presented. Data for eight species analyzed in the study. P-values where corrected for multiple testing with FDR (Benjamini-Yekutieli algorithm). Abbreviations: ciu - confidence interval upper limit; cil - confid...

Dn/Ds analysis - materials, methods and results. Analysis of evolutionary rate (dN/dS ratio) of known drug targets. Materials and methods as well as Results are presented in the file. Details about recombination (detection and removal procedures) can be also found.

Disease-causing organisms are notorious for fast rates of molecular evolution and the ability to adapt rapidly to changes in their ecology. Sex plays a key role in evolution, and recent studies, in humans and other multicellular organisms, document that genes expressed principally or exclusively in males exhibit the fastest rates of adaptive evolut...

Analysis of 16S rRNA sequence diversity is widely performed for characterizing the biodiversity of microbial samples. The number of determined sequences has a considerable impact on complete results. Although the cost of mass sequencing is decreasing, it is often still too high for individual projects. We applied the multi-temperature single-strand...

During cell cycle of a ciliate Tetrahymena thermophila the divisions of micro-and macronucleus, cortical morphogenesis and cytokinesis are temporarily coordinated. Cortical morphogenesis begins with proliferation of the new ciliary basal bodies (BBs) within meridional cortical rows of ciliary BBs, and with the local proliferation of BBs, which form...

Apoptosis-like programmed cell death (PCD) has recently been described in multiple taxa of unicellular protists, including the protozoan parasites Plasmodium, Trypanosoma and Leishmania. Apoptosis-like PCD in protozoan parasites shares a number of morphological features with programmed cell death in multicellular organisms. However, both the evolut...

Comparison of proteins identified in the mosquito stage proteomes of this study with the proteomes of salivary gland sporozoites (SGS) of P. falciparum as reported by Florens and colleagues [10] and the proteomes of oocysts (OOC) and SGS of P. berghei as reported by Hall and coworkers [11]. The tables contain information about proteins shared by ou...

Comparison of proteins identified in the mosquito stage proteomes with genes transcribed in sporozoites in P. berghei and P. yoelii as identified by either subtractive hybridization (SSH) or cDNA quantification methods (SAGE). S-genes: 25 sporozoite (S) genes identified in a P.yoelii SSH screen [18]. UIS-genes: 30 UIS genes (Upregulated In Sporozoi...

Information on the replacement constructs used to disrupt the different members of the 6-cys gene family (0.04 MB DOC)

Sliding window analysis of p48/45, p47 and p230 in P. berghei vs P. yoelii vs P. chabaudi (0.07 MB PDF)

Residues of P48/45, P47 and P230 under positive selection according to the Bayes Empirical Bayes (BEB) analysis (0.07 MB PDF)

Gene alignments of P. falciparum and P. berghei p230, p48/45 and p47. The one residue (861V) in P. berghei p230 that appears to be under strong positive selection by the BEB analysis is highlighted (blue) and aligned with the two non-synonymous polymorphic residues in P. falciparum (i.e. 1194Y and 1196Q; in red and highlighted in yellow; defined by...

Gene models of the different 6-cys gene family members in 6 Plasmodium species (0.04 MB DOC)

Gene expression of p230, p47 and p48/45 in mutants in which the paralogous gene has been disrupted. A. Northern analysis of transcription of p230 and p230p in mutant Δp230 showing wild type transcription of the paralog p230p. B. Northern analysis of transcription of p47 and p48/45 in the mutant Δp47, showing wild type transcription of the paralog p...

Evolutionarily related proteins have similar sequences. Such similarity is called homology and can be described using substitution matrices such as Blosum 60. Naturally occurring homologous proteins usually have similar stable tertiary structures and this fact is used in so-called homology modeling. In contrast, the artificial protein designed by t...

Advances in high-throughput technologies available to modern biology have created an increasing flood of experimentally determined facts. Ordering, managing and describing these raw results is the first step which allows facts to become knowledge. Currently there are limited ways to automatically annotate such data, especially utilizing information...

The proper theoretical description of the distribution of the node degree for yeast protein-protein interaction network was investigated to deal with the observed discrepancy between usually proposed models and the existing data. The power law or the generalized power law with exponential cut-off were shown to be inaccurate within a wide range of d...

Unlabelled: Using literature databases one can find not only known and true relations between processes but also less studied, non-obvious associations. The main problem with discovering such type of relevant biological information is 'selection'. The ability to distinguish between a true correlation (e.g. between different types of biological pro...

The aim of this study was to search for a mechanism responsible for the acquisition of cell polarity in a ciliate Tetrahymena. Homologs of the mammalian genes coding for CDC42-GSK3beta- MARK/PAR1-MAPs proteins were found in the Tetrahymena genome (Eisen et al., 2006, and this study). These proteins belong to a pathway which controls assembly and di...

It is well proved that the probability that a protein interacts with itself is higher than that it interacts with another protein. It has been recently shown that the probability of interaction is also higher for proteins with significant sequence similarity. In this paper we show that proteins sharing identical PFAM domains interact more often tha...

Using protein sequence data obtained from a calcium- and phospholipid-regulated protein kinase purified from maize (Zea mays), we isolated a cDNA encoding a calcium-dependent protein kinase (CDPK), which we designated ZmCPK11. The deduced amino acid sequence of ZmCPK11 includes the sequences of all the peptides obtained from the native protein. The...

SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin-remodeling complexes mediate ATP-dependent alterations of DNA-histone contacts. The minimal functional core of conserved SWI/SNF complexes consists of a SWI2/SNF2 ATPase, SNF5, SWP73, and a pair of SWI3 subunits. Because of early duplication of the SWI3 gene family in plants, Arabidopsis thaliana enc...

In tobacco (Nicotiana tabacum), hyperosmotic stress induces rapid activation of a 42-kD protein kinase, referred to as Nicotiana tabacum osmotic stress-activated protein kinase (NtOSAK). cDNA encoding the kinase was cloned and, based on the predicted amino acid sequence, the enzyme was assigned to the SNF1-related protein kinase type 2 (SnRK2) fami...

The availability of the complete sequence of Arabidopsis genomic DNA has allowedin-depth comparative analyses of plant proteins homologous to components of yeast and animal complexes involved in chromatin remodelling. These studies have uncovered an astonishing diversity of plant proteins that are potentially involved in ATP-dependent modulation of...

ATP‐dependent nucleosome remodeling plays a central role in the regulation of access to chromatin DNA. Swi/Snf remodeling complexes characterized in yeast, Drosophila and mammals all contain a conserved set of core subunits composed of homologs of yeast SNF2‐type DNA‐dependent ATPase, SNF5 and SWI3 proteins. So far, no complete Swi/Snf‐type complex...

Histones of the H1 group (linker histones) are abundant components of chromatin in eukaryotes, occurring on average at one molecule per nucleosome. The recent reports on the lack of a clear phenotypic effect of knock-out mutations as well as overexpression of histone H1 genes in different organisms have seriously undermined the long-held view that...