Piotr Borsuk

Organization of the ribosomal RNA gene cluster in Aspergillus nidulans

DNA coding for ribosomal RNA in Aspergillus nidulans was found to consist of a unit 7.8 kb in size which is tandemly repeated in the genome and codes for 5.8S, 18S and 26S rRNA. The repeat unit has been cloned, and its restriction map and the location of the individual rRNA coding sequences within the unit have been established.

Recent origin of sub-Antarctic notothenioids

Abstract. 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 years ago).

Bacterial diversity in Adélie penguin, Pygoscelis adeliae, guano: molecular and morpho‐physiological approaches

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 (14), 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.

l-Arginine influences the structure and function of arginase mRNA in Aspergillus nidulans

Abstract Expression of the arginase structural gene (agaA) in Aspergillus nidulans is subject to complex transcriptional and post-transcriptional regulation. Arginase mRNA has a long 5′-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 3′ splicing sites. In this report we present evidence that L-arginine (i) binds directly to the arginase 5′-UTR; (ii) invokes drastic changes in the secondary structure of the 5′-UTR, unlike several other L-amino acids and D-arginine; and (iii) forces the selection of one of two 3′ splice sites of an intron present in the 5′-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 5′-UTR intron.

Culturable bacteria community development in postglacial soils of Ecology Glacier, King George Island, Antarctica

Glacier forelands are excellent sites in which to study microbial succession because conditions change rapidly in the emerging soil. Development of the bacterial community was studied along two transects on lateral moraines of Ecology Glacier, King George Island, by culture-dependent and culture-independent approaches (denaturating gradient gel electrophoresis). Environmental conditions such as cryoturbation and soil composition affected both abundance and phylogenetic diversity of bacterial communities. Microbiocenosis structure along transect 1 (severe cryoturbation) differed markedly from that along transect 2 (minor cryoturbation). Soil physical and chemical factors changed along the chronosequence (time since exposure) and influenced the taxonomic diversity of cultivated bacteria, particularly along transect 2. Arthrobacter spp. played a pioneer role and were present in all soil samples, but were most abundant along transect 1. Cultivated bacteria isolated from transect 2 were taxonomically more diverse than those cultivated from transect 1; those from transect 1 tended to express a broader range of enzyme and assimilation activities. Our data suggest that cryoturbation is a major factor in controlling bacterial community development in postglacial soils, shed light on microbial succession in glacier forelands, and add a new parameter to models that describe succession phenomena.

Two different species of Euglena, E. geniculata and E. myxocylindracea (euglenophyceae), are virtually genetically and morphologically identical

We investigated the similarity of a single Euglena myxocylindracea strain, isolated originally by Bold and MacEntee, to several Euglena geniculata strains on both morphological and DNA levels. We found the three DNA stretches, consisting of fragments coding for the parts of cytoplasmic and chloroplast small subunit rRNA, and the internal transcribed spacer (ITS2) of cytoplasmic rDNA, with the combined length of 4332 nucleotides, are identical in E. myxocylindracea and E. geniculata, strain SAG 1224‐4b. Morphological differences between E. myxocylindracea and any E. geniculata strain examined were well within the range of E. geniculata variability as well. The only difference behind the distinction of E. myxocylindracea from E. geniculata is the presence of the second chloroplast in the latter. However, we were able to induce the appearance of the second chloroplast in the cells of E. myxocylindracea and its disappearance in the cells of E. geniculata by changing the composition of the culture media. We therefore conclude that E. myxocylindracea Bold and MacEntee should be regarded as an environmental form of E. geniculata Dujardin. For the first time the morphology of E. geniculata chloroplasts was shown as revealed by confocal laser microscopy.

DNA computing: implementation of data flow logical operations

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 technique employs standard operations of genetic engineering including radioactive labeling as well as digestion by the second class restriction nuclease and polymerase chain reaction (PCR). To check practical utility of the method a series of genetic engineering experiments have been performed. The obtained information confirms interesting properties of the DNA-based molecular data flow logic gates. Some experimental results demonstrating implementation of a single logic NAND gate and only in one vessel calculation of a tree-like Boolean function with the help of the PCR are provided. These techniques may be utilized in massively parallel computers and on DNA chips.

Aspergillus nidulans 5S rRNA genes and pseudogenes

SummaryThe sequence of four Aspergillus nidulans 5S rRNA genes and of two pseudogenes has been determined. A conserved sequence about 100 by upstream of the 5S rRNA coding sequences has been found in three genes and one pseudogene. The two pseudogenes correspond to the 5′ half of the 5S rRNA coding sequence and their 3′ flanking sequences which are not homologous to 5S rRNA are strongly conserved.

Studies on Ephelota sp., an epizoic suctorian found on Antarctic krill

Abstract. The anatomy, morphology and life-cycle of ciliates living on Antarctic krill are described. All ciliates found on the bodies of several thousand individual krill belong to one species of the genus Ephelota. Analysis of small subunit rDNA (SS rDNA) sequences from different Ephelota individuals in various stages of their life-cycle confirmed this result and proved that even the cysts found in great numbers in the filtering baskets of krill represent the resting stage of Ephelota. DNA studies have also shown that Antarctic and non-Antarctic species of Ephelota diverged much earlier than Antarctic and non-Antarctic species of krill.

Unusual Evolutionary Conservation of 5S rRNA Pseudogenes in Aspergillus nidulans: Similarity of the DNA Sequence Associated with the Pseudogenes with the Mouse Immunoglobulin Switch Region

SummaryAllAspergillus nidulans 5S rRNA pseudogenes known so far are the result of integration of an approx. 0.2-kbp-long DNA sequence into the 5S rRNA genes. This sequence, called block C, is present in at least five copies in theA. nidulans genome and seems to be associated either with 5S rRNA genes or pseudogenes. In contrast to the 78% sequence conservation of the C-block in pseudogenes, the truncated 5′ halves of the pseudogenes are very highly conserved (96.9–100%). We postulate that the 5S rRNA pseudogenes are still a subject of concerted evolution. The C-block sequence shows similarity to the switch region of the mouse heavy chain immunoglobulin gene. A characteristic motif GGGTGAG is repeated several times in both sequences; the sequence conservation is 63%.