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Biomedical subjects

M Szymanski

Publications and source records attributed to M Szymanski.

18 recordsLinked to original sources
PubMed2003

Delayed facial palsy following laser stapedectomy: in vitro study of facial nerve temperature.

Delayed facial palsy following conventional stapes surgery is a rare event, but this complication appears to be more common when a laser is used. We have investigated the temperature in the facial canal during stapes surgery using a KTP laser or a microdrill in preserved human temporal bones. Thermocouples were placed in the facial canal and under the foot plate. The results show maximum rises in temperature of between 1.4 degrees C and 15.2 degrees C in the facial canal during laser surgery (mean 6.1 degrees C, SD 4.5 degrees C), but only between 0.45 degrees C and 2 degrees C during procedures in which a microdrill was used (mean 0.9 degrees C, SD 0.9 degrees C) (P = < 0.009). In addition, the facial nerve undergoes repeated heating and cooling cycles during the laser surgery. We conclude that heating of the facial nerve during laser surgery causes oedema, which in turn leads to compression of the nerve within its bony canal.

Adult↗
PubMed2001

The non-coding RNAs as riboregulators.

The non-coding RNAs database (http://biobases.ibch.poznan.pl/ncRNA/) contains currently available data on RNAs, which do not have long open reading frames and act as riboregulators. Non-coding RNAs are involved in the specific recognition of cellular nucleic acid targets through complementary base pairing to control cell growth and differentiation. Some of them are connected with several well known developmental and neuro-behavioral disorders. We have divided them into four groups. This paper is a short introduction to the database and presents its latest, updated edition.

Animals↗
PubMed2001

Aminoacyl-tRNA synthetases database.

Aminoacyl-tRNA synthetases (AARSs) are at the center of the question of the origin of life. They constitute a family of enzymes integrating the two levels of cellular organization: nucleic acids and proteins. AARSs arose early in evolution and are believed to be a group of ancient proteins. They are responsible for attaching amino acid residues to their cognate tRNA molecules, which is the first step in the protein synthesis. The role they play in a living cell is essential for the precise deciphering of the genetic code. The analysis of AARSs evolutionary history was not possible for a long time due to a lack of a sufficiently large number of their amino acid sequences. The emerging picture of synthetases' evolution is a result of recent achievements in genomics [Woese,C., Olsen,G.J., Ibba,M. and Söll,D. (2000) Microbiol. Mol. Biol. Rev., 64, 202-236]. In this paper we present a short introduction to the AARSs database. The updated database contains 1047 AARS primary structures from archaebacteria, eubacteria, mitochondria, chloroplasts and eukaryotic cells. It is the compilation of amino acid sequences of all AARSs known to date, which are available as separate entries via the WWW at http://biobases.ibch.poznan.pl/aars/.

Amino Acid Sequence↗
PubMed2000

5S ribosomal RNA database Y2K.

This paper presents the updated version (Y2K) of the database of ribosomal 5S ribonucleic acids (5S rRNA) and their genes (5S rDNA), http://rose.man/poznan.pl/5SData/index.html. This edition of the database contains 1985primary structures of 5S rRNA and 5S rDNA. They include 60 archaebacterial, 470 eubacterial, 63 plastid, nine mitochondrial and 1383 eukaryotic sequences. The nucleotide sequences of the 5S rRNAs or 5S rDNAs are divided according to the taxonomic position of the source organisms.

Databases, Factual↗
PubMed2000

Non-coding, mRNA-like RNAs database Y2K.

In last few years much data has accumulated on various non-translatable RNA transcripts that are synthesised in different cells. They are lacking in protein coding capacity and it seems that they work mainly or exclusively at the RNA level. All known non-coding RNA transcripts are collected in the database: http://www. man.poznan.pl/5SData/ncRNA/index.html

Databases, Factual↗
PubMed2000

Aminoacyl-tRNA synthetases database Y2K.

The aminoacyl-tRNA synthetases (AARS) are a diverse group of enzymes that ensure the fidelity of transfer of genetic information from DNA into protein. They catalyse the attachment of amino acids to transfer RNAs and thereby establish the rules of the genetic code by virtue of matching the nucleotide triplet of the anticodon with its cognate amino acid. Currently, 818 AARS primary structures have been reported from archaebacteria, eubacteria, mitochondria, chloro-plasts and eukaryotic cells. The database is a compilation of the amino acid sequences of all AARSs, known to date, which are available as separate entries or alignments of related proteins via the WWW at http://rose.man.poznan.pl/aars/index.html

Amino Acyl-tRNA Synthetases↗
PubMed2000

Lessons from sequenced genomes. Overlapping genes in Methanococcus jannaschii?

This paper describes our finding on overlapping genes in Methanococcus jannaschii genome. We found that one of the open reading frames (ORFs) within the M. jannaschii genome contains the nucleotide sequence of tRNA(Ser), which raises a serious question of the correctness of the initiation codon assignment for that ORF. We suggest that there are two other possible AUG initiation codons downstream from the TTG triplet, which was initially considered as a translation start site. Only one of the AUG triplets is preceded by the Shine-Dalgarno sequence that seems to be required for binding the ribosome and initiation of translation.

Amino Acid Sequence↗
PubMed1999

5S Ribosomal RNA Data Bank.

This paper presents the updated version of the data base of ribosomal 5S ribonucleic acids (5S rRNA) and their genes (5S rDNA). This edition of the data bank contains 1889 primary structures of 5S rRNA and 5S rDNA. These include 60 archaebacterial, 439 eubacterial, 63 plastid, 9 mitochondrial and 1318 eukaryotic sequences. The nucleotide sequences of 5S rRNAs or 5S rDNAs are divided according to the taxonomic position of organisms. The sequences stored in the database can be viewed and retrieved using the taxonomic browser at the URL: http://rose.man.poznan.pl/5SData/5SRNA.html++ +

Animals↗
PubMed1999

Collection of mRNA-like non-coding RNAs.

In last few years much data has accumulated which shows that in different cells various RNA transcripts are synthesized. They lack protein coding capacity and do not produce mature protein. It seems that they work mainly or exclusively on the RNA level. Their function and mechanism of action is poorly understood. In this paper we have collected all known RNA transcript and prepared a database for further structural and functional studies. This is the first collection of the nucleotide sequences of RNAs of this kind. The data can be accessed via WWW at: http://www.man.poznan.pl/5SData/ncRNA/inde x.html

Animals↗
PubMed1999

The aminoacyl-tRNA Synthetase Data Bank (AARSDB).

Aminoacyl-tRNA synthetases (AARSs) are the key components of the protein biosynthesis machinery. They are responsible for maintaining the fidelity of transfer of genetic information from DNA into protein. The database is a compilation of amino acid sequences of all aminoacyl-tRNA synthetases known to date. It contains 422 primary structures of the AARSs available as separate entries or alignments of related proteins. The database is available via the World Wide Web at http://rose.man.poznan.pl/aars/index.html

Amino Acid Sequence↗
PubMed1999

Preparation of HIV TAR RNA with RNA scissors.

Two hammerhead ribozymes derived from plant pathogenic RNAs were used to cut off the HIV TAR RNA from the T7 RNA transcript through a cis cleavage reaction. Stem I of the (+)vLTSV ribozyme comprises 8 nucleotides of the 5' terminus of TAR RNA, but stem III of the (+)sTRSV ribozyme consists of 8 nucleotides of the 3' end of TAR RNA. The construct containing two GUC hammerhead ribozyme target sequences identified the cleavage sites to cut off a required RNA molecule. This method was applied for preparation of 35 nt long TAR RNA. Its activity was proved by the complex formation with the Tat protein. It seems that this approach based on RNA scissors can also be used for the generation of required RNA molecules, RNA decoys or RNA aptamers in vivo.

Bacteriophage T7↗
PubMed1998

5S rRNA Data Bank.

In this paper we present the updated version of the compilation of 5S rRNA and 5S rDNA nucleotide sequences. It contains 1622 primary structures of 5S rRNAs and 5S rRNA genes from 888 species. These include 58 archaeal, 427 eubacterial, 34 plastid, nine mitochondrial and 1094 eukaryotic DNA or RNA nucleotide sequences. The sequence entries are divided according to the taxonomic position of the organisms. All individual sequences deposited in the 5S rRNA Database can be retrieved using the WWW-based, taxonomic browser at http://rose.man.poznan.pl/5SData/5SRNA.html++ + or http://www.chemie. fu-berlin.de/fb_chemie/agerdmann/5S_rRNA.html . The files with complete sets of data as well as sequence alignments are available via anonymous ftp.

Animals↗
PubMed1998

Modular subdivisions of dolphin insular cortex: does evolutionary history repeat itself?

The structural organization of the insular cortex in the bottlenose dolphin was investigated by examining Nissl- and myelin-stained tissue that was sectioned coronally and tangentially. An uneven distribution of cell clusters that coincided with myelin-light zones was observed in layer II. When the present observations were compared to descriptions of modules in other animals, we found that the range of module size is restricted, while the size of the brain, particularly the neocortex, varies dramatically. Indeed, despite the tremendous expansion of the cetacean neocortex, the size of the modules in the insular cortex is similar to that described for small-brained mammals like the mouse, suggesting that module size is evolutionarily stable across species. Selection for optimal-size processing units, in terms of the lengths of connections within and between them, is a likely source of this stability.

Animals↗
PubMed1997

Compilation of 5S rRNA and 5S rRNA gene sequences.

The compilation of 5S rRNA and 5S rRNA gene nucleotide sequences as of 30 September 1996, contains a total of 1661 primary structures of 5S rRNAs or their genes, which is an increase of 928 new sequence entries over the last compilation. It covers sequences from 54 archaea, 449 eubacteria, 34 plastids, nine mitochondria and 430 eukaryotes. The databank uses the format of the EMBL Nucleotide Sequence Data Library complemented by a Sequence Alignment (SA) field including secondary structure information. The taxonomic classification of organisms was totally updated. Now the database is also available via anonymous FTP or WWW.

Base Sequence↗
PubMed1995

The primary structure of Harpalus rufipes 5S ribosomal RNA: a contribution for understanding insect evolution.

The nucleotide sequence of 5S ribosomal RNA from the beetle Harpalus rufipes was determined and compared with primary structures of other insect 5S rRNAs. Sequence differences between two beetle 5S rRNAs may represent phylogenetic markers specific for two groups of Coleoptera - Adephaga and Polyphaga. Analysis of all insect sequences using parsimony allowed us to infer a phylogenetic tree of insects, which is consistent with morphological and paleobiological data.

Animals↗
PubMed1995

Modified Bondy technique.

Bondy operation is a type of modified radical mastoidectomy in which the mastoid cavity is exteriorized without disturbing the intact ossicular chain and pars tensa. It is indicated in cases of epitympanic cholesteatoma with intact ossicular chain, normal pars tensa, and good hearing. The advantages of the technique are one-stage surgery with preservation of preoperative hearing levels, which is not possible with any other procedure. This article presents the indications, technique, results, and complications.

Adolescent↗
PubMed1995

Are 5S ribosomal RNA primary transcripts edited?

Comparative analysis of the nucleotide sequences of plant 5S rRNA genes shows numerous discrepancies with the mature 5S rRNAs. Detailed inspection of these differences revealed that they are mainly due to single nucleotide substitutions, insertions and deletions. In several cases also longer insertions were found, two of which are particularly interesting. Their location in loops resembles tRNA introns. One of these insertions is 79 nucleotides long and can potentially form a tRNA-like structure, with 50% homology to plant tRNAGly. This observation led us to propose that, in the maturation of some 5S rDNA transcripts, editing and splicing mechanisms may be involved.

Base Sequence↗