Piotr Weglenski - Academia.edu (original) (raw)
Papers by Piotr Weglenski
Gene, 2015
The kaeA(KAE1) (suDpro) gene, which was identified in Aspergillus nidulans as a suppressor of pro... more The kaeA(KAE1) (suDpro) gene, which was identified in Aspergillus nidulans as a suppressor of proline auxotrophic mutations, encodes the orthologue of Saccharomyces cerevisiae Kae1p, a member of the evolutionarily conserved KEOPS/EKC (Kinase, Endopeptidase and Other Proteins of Small size/Endopeptidase-like and Kinase associated to transcribed Chromatin) complex. In yeast, this complex has been shown to be involved in tRNA modification, transcription, and genome maintenance. In A. nidulans, mutations in kaeA result in several phenotypic effects, the derepression of arginine catabolism genes, and changes in the expression levels of several others, including genes involved in amino acid and siderophore metabolism, sulfate transport, carbon/energy metabolism, translation, and transcription regulation, such as rcoA(TUP1), which encodes the global transcriptional corepressor.
Article history: Available online xxx a b s t r a c t
The vast majority of fossil remains in Late Pleistocene deposits from Niedźwiedzia Cave in Kletno... more The vast majority of fossil remains in Late Pleistocene deposits from Niedźwiedzia Cave in Kletno, Sudetes, Poland, belong to the cave bear. Phylogenetic analyses based on a fragment of the mitochondrial D-loop region extracted from two cave bear samples unambiguously showed their close relationship with the Ursus ingressus haplogroup. This taxonomic affiliation of the cave bear remains from Niedźwiedzia Cave was further confirmed by biometrical analyses of molar teeth and skulls. Our results represent the first record of U. ingressus north of the Carpathian Arch, while radiocarbon dating (> 49,000 yr BP) of the samples indicates that they represent some of the oldest specimens of this cave bear taxon known so far. Multi-method phylogenetic analyses including numerous publicly available cave bear sequences allowed analysing the relationships among these samples in details, including the significance of particular clades, and discussing some aspects of cave bear phylogeography. The sequences of U. ingressus from Poland are most closely related to specimens from the Ural Mountains and next to Slovenia, which may indicate migrations between Central and Eastern European populations. The internal placement of Ural samples among European specimens in phylogenetic trees and the older age of Polish samples than those from Urals suggest that the eastward expansion of U. ingressus may have started from Central Europe.
American Journal of Physical Anthropology, 2014
The common practice of resettlement and the development of administrative and ceremonial systems ... more The common practice of resettlement and the development of administrative and ceremonial systems shaped the population landscape of the Andean region under the Inca rule. The area surrounding Coropuna and Solimana volcanoes, in the Arequipa region (Peru), carried a high-density, multiethnic population. We studied the genetic variation among three pre-Columbian populations from three functionally diverse archaeological sites excavated in this region. By analyzing the genetic composition of a large ceremonial center (Acchaymarca), an isolated pastoral settlement (Tompullo 2), and an agricultural settlement characterized by architectural features rare in the region (Puca), we investigated the patterns of population movements and the distribution of genetic diversity. We obtained mitochondrial DNA sequences for
1998 IEEE International Conference on Evolutionary Computation Proceedings. IEEE World Congress on Computational Intelligence (Cat. No.98TH8360), 1998
Abstract In this paper we present a novel application of molecular computing to problems of exper... more Abstract In this paper we present a novel application of molecular computing to problems of expert systems. A biocliemical reaction on DNA strands is used to realise the backward chaining algoritlim. Knowledge base for the expert systern is based on the sticker model; memory ...
Fungal Genetics and Biology, 2003
The arginine catabolism gene otaA encoding ornithine transaminase (OTAse) is specifically induced... more The arginine catabolism gene otaA encoding ornithine transaminase (OTAse) is specifically induced by arginine and is under the control of the broad-domain carbon and nitrogen repression systems. Arginine induction is mediated by a product of arcA gene coding for Zn2C6 activator. We have identified a region responsible for arginine induction in the otaA promoter (AnUASarg). Deletions within this region result
Future Generation Computer Systems, 2001
Self-assembly of DNA is considered a fundamental operation in realization of molecular logic circ... more Self-assembly of DNA is considered a fundamental operation in realization of molecular logic circuits. We propose a new approach to implementation of data flow logical operations based on manipulating DNA strands. In our method the logic gates, input, and output signals are represented by DNA molecules. Each logical operation is carried out as soon as the operands are ready. This
Polar Biology, 2002
Comparison of partial mitochondrial 12S and 16S rDNA sequences from non-Antarctic notothenioid fi... more Comparison of partial mitochondrial 12S and 16S rDNA sequences from non-Antarctic notothenioid fishes - an icefish Champsocephalus esox and two members of the genus Patagonotothen - and their sister species from the Southern Ocean suggests that their divergence took place 1.7 and 6.6-7 million years ago, respectively, i.e. much later than the formation of the Antarctic Polar Front (20-25 million
Soil Biology and Biochemistry, 2001
... The number of colony forming bacteria (CFU) was estimated by the plate method on full strengt... more ... The number of colony forming bacteria (CFU) was estimated by the plate method on full strength nutrient agar (NA), appropriated for the isolation of ... bacteria (CFU±SD×10 6 g −1 dry wt n=3), relative daily increment CFU on agar (RDI×10 6 ), average cell volume (ACV), organic C ...
Quaternary International, 2013
Article history: Available online xxx a b s t r a c t
The Emine-Bair-Khosar Cave (EBK), situated on the northern edge of the Lower Plateau of the Chaty... more The Emine-Bair-Khosar Cave (EBK), situated on the northern edge of the Lower Plateau of the Chatyrdag Massif (Crimean Mountains) is rich in palaeontological material accumulated over most of the Pleistocene. mtDNA was isolated from bones of three specimens of red deer (Cervus elaphus) dated to the late Pleistocene (MIS 3). These are the first ancient DNA sequences obtained for this species. The position of the three red deer individuals on the phylogeographic tree is based on mtDNA sequences of contemporary representatives of the Cervinae inhabiting the Northern Hemisphere. The results confirm the notion that the Crimean Peninsula was the north-easternmost refugium in Europe, and that during and after the Late Pleistocene it played a major role in recolonisation and dispersal of temperate species in the whole Eurasian continent.
Fungal Genetics and Biology, 2007
Expression of Aspergillus nidulans arginine catabolism genes, agaA and otaA, is regulated at the ... more Expression of Aspergillus nidulans arginine catabolism genes, agaA and otaA, is regulated at the level of transcription by a specific induction and two global carbon and nitrogen repression systems. Post-transcriptional and/or post-translational mechanisms have also been proposed to operate additionally. Gene tagging with transposon impala allowed us to select the rrmA gene. RRMA protein contains three conserved RRM domains, typical for RNA-binding proteins. The gene has a complex structure with several potential transcription start sites, an exceptionally long intron in 5 0 UTR and few uORFs in the intron. RRMA is highly conserved among fungi. Its homologues, Csx1p of Schizosaccharomyces pombe and Ngr1p of Saccharomyces cerevisiae, participate in the post-transcriptional regulation of specific genes by modifying transcript stability. Levels of otaA and agaA transcripts in the rrmA::impala loss of function mutant grown under inducing conditions are significantly higher than in the wild type strain. We propose that RRMA participates in a mechanism promoting agaA and otaA mRNA degradation. The rrmA::impala mutation has pleiotropic character and results in a slow growth phenotype indicating that rrmA functions are not limited to the regulation of arginine catabolism.
The Late Pleistocene has been a period of significant population and species turnover and extinct... more The Late Pleistocene has been a period of significant population and species turnover and extinctions among the large mammal fauna. Massive climatic and environmental changes during Pleistocene significantly influenced the distribution and also genetic diversity of plants and animals. The model of glacial refugia and habitat contraction to southern peninsulas in Europe as areas for the survival of temperate animal
FEMS Microbiology Ecology, 2000
The total number of bacteria and culturable bacteria in Adélie penguin (Pygoscelis adeliae) guano... more The total number of bacteria and culturable bacteria in Adélie penguin (Pygoscelis adeliae) guano was determined during 42 days of decomposition in a location adjacent to the rookery in Admiralty Bay, King George Island, Antarctica. Of the culturable bacteria, 72 randomly selected colonies were described using 49 morpho-physiological tests, 27 of which were subsequently considered significant in characterizing and differentiating the isolates. On the basis of the nucleotide sequence of a fragment of the 16S rRNA gene in each of 72 pure isolates, three major phylogenetic groups were identified, namely the Moraxellaceae/Pseudomonadaceae (29 isolates), the Flavobacteriaceae , and the Micrococcaceae (29). Grouping of the isolates on the basis of morpho-physiological tests (whether 49 or 27 parameters) showed similar results to those based on 16S rRNA gene sequences. Clusters were characterized by considerable intra-cluster variation in both 16S rRNA gene sequences and morpho-physiological responses. High diversity in abundance and morphometry of total bacterial communities during penguin guano decomposition was supported by image analysis of epifluorescence micrographs. The results indicate that the bacterial community in penguin guano is not only one of the richest in Antarctica, but is extremely diverse, both phylogenetically and morpho-physiologically.
Current Genetics, 1999
The ornithine transaminase (otaA) gene of Aspergillus nidulans has been cloned by transformation ... more The ornithine transaminase (otaA) gene of Aspergillus nidulans has been cloned by transformation of the A. nidulans pro-ota- mutant strain with a cosmid gene library. The otaA gene contains two introns and potentially codes for a 453-aa-long protein. The deduced amino-acid sequence is homologous to known ornithine transaminases from Saccharomyces cerevisiae, Plasmodium falciparum, Vigna aconitifolia, rat, mouse and man, particularly in the pyridoxal phosphate-binding domain. The expression of the otaA gene is specifically induced by arginine, and is also under the control of nitrogen-metabolite and carbon-catabolite repression. Regulation of the gene occurs at both transcriptional and post-transcriptional levels. The promoter region of otaA contains putative AREA and CREA binding-sites. Fusion proteins containing AREA or CREA DNA-binding domains bind some of these sites. CREA binding-sites correspond very well to the CREA-binding consensus sequence which is SYGGRG. AREA binding-sites are composed of GATT sequences which are not typical binding sites for the GATA - binding family of transcription factors.
Biological Chemistry, 2000
Aspergillus nidulans is subject to complex transcriptional and post-transcriptional regulation. A... more Aspergillus nidulans is subject to complex transcriptional and post-transcriptional regulation. Arginase mRNA has a long 59-UTR sequence. Analysis of this sequence in silico revealed its putative complex secondary structure, the presence of arginine-binding motifs (arginine aptamers) and a short intron with two potential 39 splicing sites. In this report we present evidence that L-arginine (i) binds directly to the arginase 59-UTR; (ii) invokes drastic changes in the secondary structure of the 59-UTR, unlike several other L-amino acids and D-arginine; and (iii) forces the selection of one of two 39 splice sites of an intron present in the 59-UTR. We postulate that expression of the eukaryotic structural gene coding for arginase in A. nidulans is regulated at the level of mRNA stability, depending on riboswitch-mediated alternative splicing of the 59-UTR intron.
Molecular Microbiology, 2013
Differential regulation of transcript stability is an effective means by which an organism can mo... more Differential regulation of transcript stability is an effective means by which an organism can modulate gene expression. A well-characterized example is glutamine signalled degradation of specific transcripts in Aspergillus nidulans. In the case of areA, which encodes a wide-domain transcription factor mediating nitrogen metabolite repression, the signal is mediated through a highly conserved region of the 3′ UTR. Utilizing this RNA sequence we isolated RrmA, an RNA recognition motif protein. Disruption of the respective gene led to loss of both glutamine signalled transcript degradation as well as nitrate signalled stabilization of niaD mRNA. However, nitrogen starvation was shown to act independently of RrmA in stabilizing certain transcripts. RrmA was also implicated in the regulation of arginine catabolism gene expression and the oxidative stress responses at the level of mRNA stability. ΔrrmA mutants are hypersensitive to oxidative stress. This phenotype correlates with destabilization of eifE and dhsA mRNA. eifE encodes eIF5A, a translation factor within which a conserved lysine is post-translationally modified to hypusine, a process requiring DhsA. Intriguingly, for specific transcripts RrmA mediates both stabilization and destabilization and the specificity of the signals transduced is transcript dependent, suggesting it acts in consort with other factors which differ between transcripts.
Gene, 2015
The kaeA(KAE1) (suDpro) gene, which was identified in Aspergillus nidulans as a suppressor of pro... more The kaeA(KAE1) (suDpro) gene, which was identified in Aspergillus nidulans as a suppressor of proline auxotrophic mutations, encodes the orthologue of Saccharomyces cerevisiae Kae1p, a member of the evolutionarily conserved KEOPS/EKC (Kinase, Endopeptidase and Other Proteins of Small size/Endopeptidase-like and Kinase associated to transcribed Chromatin) complex. In yeast, this complex has been shown to be involved in tRNA modification, transcription, and genome maintenance. In A. nidulans, mutations in kaeA result in several phenotypic effects, the derepression of arginine catabolism genes, and changes in the expression levels of several others, including genes involved in amino acid and siderophore metabolism, sulfate transport, carbon/energy metabolism, translation, and transcription regulation, such as rcoA(TUP1), which encodes the global transcriptional corepressor.
Article history: Available online xxx a b s t r a c t
The vast majority of fossil remains in Late Pleistocene deposits from Niedźwiedzia Cave in Kletno... more The vast majority of fossil remains in Late Pleistocene deposits from Niedźwiedzia Cave in Kletno, Sudetes, Poland, belong to the cave bear. Phylogenetic analyses based on a fragment of the mitochondrial D-loop region extracted from two cave bear samples unambiguously showed their close relationship with the Ursus ingressus haplogroup. This taxonomic affiliation of the cave bear remains from Niedźwiedzia Cave was further confirmed by biometrical analyses of molar teeth and skulls. Our results represent the first record of U. ingressus north of the Carpathian Arch, while radiocarbon dating (> 49,000 yr BP) of the samples indicates that they represent some of the oldest specimens of this cave bear taxon known so far. Multi-method phylogenetic analyses including numerous publicly available cave bear sequences allowed analysing the relationships among these samples in details, including the significance of particular clades, and discussing some aspects of cave bear phylogeography. The sequences of U. ingressus from Poland are most closely related to specimens from the Ural Mountains and next to Slovenia, which may indicate migrations between Central and Eastern European populations. The internal placement of Ural samples among European specimens in phylogenetic trees and the older age of Polish samples than those from Urals suggest that the eastward expansion of U. ingressus may have started from Central Europe.
American Journal of Physical Anthropology, 2014
The common practice of resettlement and the development of administrative and ceremonial systems ... more The common practice of resettlement and the development of administrative and ceremonial systems shaped the population landscape of the Andean region under the Inca rule. The area surrounding Coropuna and Solimana volcanoes, in the Arequipa region (Peru), carried a high-density, multiethnic population. We studied the genetic variation among three pre-Columbian populations from three functionally diverse archaeological sites excavated in this region. By analyzing the genetic composition of a large ceremonial center (Acchaymarca), an isolated pastoral settlement (Tompullo 2), and an agricultural settlement characterized by architectural features rare in the region (Puca), we investigated the patterns of population movements and the distribution of genetic diversity. We obtained mitochondrial DNA sequences for
1998 IEEE International Conference on Evolutionary Computation Proceedings. IEEE World Congress on Computational Intelligence (Cat. No.98TH8360), 1998
Abstract In this paper we present a novel application of molecular computing to problems of exper... more Abstract In this paper we present a novel application of molecular computing to problems of expert systems. A biocliemical reaction on DNA strands is used to realise the backward chaining algoritlim. Knowledge base for the expert systern is based on the sticker model; memory ...
Fungal Genetics and Biology, 2003
The arginine catabolism gene otaA encoding ornithine transaminase (OTAse) is specifically induced... more The arginine catabolism gene otaA encoding ornithine transaminase (OTAse) is specifically induced by arginine and is under the control of the broad-domain carbon and nitrogen repression systems. Arginine induction is mediated by a product of arcA gene coding for Zn2C6 activator. We have identified a region responsible for arginine induction in the otaA promoter (AnUASarg). Deletions within this region result
Future Generation Computer Systems, 2001
Self-assembly of DNA is considered a fundamental operation in realization of molecular logic circ... more Self-assembly of DNA is considered a fundamental operation in realization of molecular logic circuits. We propose a new approach to implementation of data flow logical operations based on manipulating DNA strands. In our method the logic gates, input, and output signals are represented by DNA molecules. Each logical operation is carried out as soon as the operands are ready. This
Polar Biology, 2002
Comparison of partial mitochondrial 12S and 16S rDNA sequences from non-Antarctic notothenioid fi... more Comparison of partial mitochondrial 12S and 16S rDNA sequences from non-Antarctic notothenioid fishes - an icefish Champsocephalus esox and two members of the genus Patagonotothen - and their sister species from the Southern Ocean suggests that their divergence took place 1.7 and 6.6-7 million years ago, respectively, i.e. much later than the formation of the Antarctic Polar Front (20-25 million
Soil Biology and Biochemistry, 2001
... The number of colony forming bacteria (CFU) was estimated by the plate method on full strengt... more ... The number of colony forming bacteria (CFU) was estimated by the plate method on full strength nutrient agar (NA), appropriated for the isolation of ... bacteria (CFU±SD×10 6 g −1 dry wt n=3), relative daily increment CFU on agar (RDI×10 6 ), average cell volume (ACV), organic C ...
Quaternary International, 2013
Article history: Available online xxx a b s t r a c t
The Emine-Bair-Khosar Cave (EBK), situated on the northern edge of the Lower Plateau of the Chaty... more The Emine-Bair-Khosar Cave (EBK), situated on the northern edge of the Lower Plateau of the Chatyrdag Massif (Crimean Mountains) is rich in palaeontological material accumulated over most of the Pleistocene. mtDNA was isolated from bones of three specimens of red deer (Cervus elaphus) dated to the late Pleistocene (MIS 3). These are the first ancient DNA sequences obtained for this species. The position of the three red deer individuals on the phylogeographic tree is based on mtDNA sequences of contemporary representatives of the Cervinae inhabiting the Northern Hemisphere. The results confirm the notion that the Crimean Peninsula was the north-easternmost refugium in Europe, and that during and after the Late Pleistocene it played a major role in recolonisation and dispersal of temperate species in the whole Eurasian continent.
Fungal Genetics and Biology, 2007
Expression of Aspergillus nidulans arginine catabolism genes, agaA and otaA, is regulated at the ... more Expression of Aspergillus nidulans arginine catabolism genes, agaA and otaA, is regulated at the level of transcription by a specific induction and two global carbon and nitrogen repression systems. Post-transcriptional and/or post-translational mechanisms have also been proposed to operate additionally. Gene tagging with transposon impala allowed us to select the rrmA gene. RRMA protein contains three conserved RRM domains, typical for RNA-binding proteins. The gene has a complex structure with several potential transcription start sites, an exceptionally long intron in 5 0 UTR and few uORFs in the intron. RRMA is highly conserved among fungi. Its homologues, Csx1p of Schizosaccharomyces pombe and Ngr1p of Saccharomyces cerevisiae, participate in the post-transcriptional regulation of specific genes by modifying transcript stability. Levels of otaA and agaA transcripts in the rrmA::impala loss of function mutant grown under inducing conditions are significantly higher than in the wild type strain. We propose that RRMA participates in a mechanism promoting agaA and otaA mRNA degradation. The rrmA::impala mutation has pleiotropic character and results in a slow growth phenotype indicating that rrmA functions are not limited to the regulation of arginine catabolism.
The Late Pleistocene has been a period of significant population and species turnover and extinct... more The Late Pleistocene has been a period of significant population and species turnover and extinctions among the large mammal fauna. Massive climatic and environmental changes during Pleistocene significantly influenced the distribution and also genetic diversity of plants and animals. The model of glacial refugia and habitat contraction to southern peninsulas in Europe as areas for the survival of temperate animal
FEMS Microbiology Ecology, 2000
The total number of bacteria and culturable bacteria in Adélie penguin (Pygoscelis adeliae) guano... more The total number of bacteria and culturable bacteria in Adélie penguin (Pygoscelis adeliae) guano was determined during 42 days of decomposition in a location adjacent to the rookery in Admiralty Bay, King George Island, Antarctica. Of the culturable bacteria, 72 randomly selected colonies were described using 49 morpho-physiological tests, 27 of which were subsequently considered significant in characterizing and differentiating the isolates. On the basis of the nucleotide sequence of a fragment of the 16S rRNA gene in each of 72 pure isolates, three major phylogenetic groups were identified, namely the Moraxellaceae/Pseudomonadaceae (29 isolates), the Flavobacteriaceae , and the Micrococcaceae (29). Grouping of the isolates on the basis of morpho-physiological tests (whether 49 or 27 parameters) showed similar results to those based on 16S rRNA gene sequences. Clusters were characterized by considerable intra-cluster variation in both 16S rRNA gene sequences and morpho-physiological responses. High diversity in abundance and morphometry of total bacterial communities during penguin guano decomposition was supported by image analysis of epifluorescence micrographs. The results indicate that the bacterial community in penguin guano is not only one of the richest in Antarctica, but is extremely diverse, both phylogenetically and morpho-physiologically.
Current Genetics, 1999
The ornithine transaminase (otaA) gene of Aspergillus nidulans has been cloned by transformation ... more The ornithine transaminase (otaA) gene of Aspergillus nidulans has been cloned by transformation of the A. nidulans pro-ota- mutant strain with a cosmid gene library. The otaA gene contains two introns and potentially codes for a 453-aa-long protein. The deduced amino-acid sequence is homologous to known ornithine transaminases from Saccharomyces cerevisiae, Plasmodium falciparum, Vigna aconitifolia, rat, mouse and man, particularly in the pyridoxal phosphate-binding domain. The expression of the otaA gene is specifically induced by arginine, and is also under the control of nitrogen-metabolite and carbon-catabolite repression. Regulation of the gene occurs at both transcriptional and post-transcriptional levels. The promoter region of otaA contains putative AREA and CREA binding-sites. Fusion proteins containing AREA or CREA DNA-binding domains bind some of these sites. CREA binding-sites correspond very well to the CREA-binding consensus sequence which is SYGGRG. AREA binding-sites are composed of GATT sequences which are not typical binding sites for the GATA - binding family of transcription factors.
Biological Chemistry, 2000
Aspergillus nidulans is subject to complex transcriptional and post-transcriptional regulation. A... more Aspergillus nidulans is subject to complex transcriptional and post-transcriptional regulation. Arginase mRNA has a long 59-UTR sequence. Analysis of this sequence in silico revealed its putative complex secondary structure, the presence of arginine-binding motifs (arginine aptamers) and a short intron with two potential 39 splicing sites. In this report we present evidence that L-arginine (i) binds directly to the arginase 59-UTR; (ii) invokes drastic changes in the secondary structure of the 59-UTR, unlike several other L-amino acids and D-arginine; and (iii) forces the selection of one of two 39 splice sites of an intron present in the 59-UTR. We postulate that expression of the eukaryotic structural gene coding for arginase in A. nidulans is regulated at the level of mRNA stability, depending on riboswitch-mediated alternative splicing of the 59-UTR intron.
Molecular Microbiology, 2013
Differential regulation of transcript stability is an effective means by which an organism can mo... more Differential regulation of transcript stability is an effective means by which an organism can modulate gene expression. A well-characterized example is glutamine signalled degradation of specific transcripts in Aspergillus nidulans. In the case of areA, which encodes a wide-domain transcription factor mediating nitrogen metabolite repression, the signal is mediated through a highly conserved region of the 3′ UTR. Utilizing this RNA sequence we isolated RrmA, an RNA recognition motif protein. Disruption of the respective gene led to loss of both glutamine signalled transcript degradation as well as nitrate signalled stabilization of niaD mRNA. However, nitrogen starvation was shown to act independently of RrmA in stabilizing certain transcripts. RrmA was also implicated in the regulation of arginine catabolism gene expression and the oxidative stress responses at the level of mRNA stability. ΔrrmA mutants are hypersensitive to oxidative stress. This phenotype correlates with destabilization of eifE and dhsA mRNA. eifE encodes eIF5A, a translation factor within which a conserved lysine is post-translationally modified to hypusine, a process requiring DhsA. Intriguingly, for specific transcripts RrmA mediates both stabilization and destabilization and the specificity of the signals transduced is transcript dependent, suggesting it acts in consort with other factors which differ between transcripts.