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D Evers

Publications and source records attributed to D Evers.

8 recordsLinked to original sources
PubMed2000

Conservation of the 3'-untranslated region of the Rab1a gene in amniote vertebrates: exceptional structure in marsupials and possible role for posttranscriptional regulation.

The YPT1/RAB1 protein, a key regulator of the intracellular vesicle transport in eukaryotes, is highly conserved in function and amino acid sequence. Here we report that the most highly conserved nucleotide sequence of the Rab1a gene of amniote vertebrates corresponds to the 3'-untranslated region (3'-UTR) of the mRNA. Sequences of 27 species ranging from mammals to sauropsida are >91% identical in this region. Secondary structure prediction procedures applied to the 3'-UTR sequences between positions 750 and 984 and 1428 (mouse cDNA: Y00094), respectively, of the RAB1a mRNAs revealed families of alternative structures around nucleotide position 800 as recurrent features. The two hairpin loops are also predicted for marsupials, despite of their exceptional extension of the A-rich sequence in between. Yet, sequence conservation is much higher than required to conserve secondary structure. Implications for posttranscriptional regulation and protein binding are discussed.

3' Untranslated Regions↗
PubMed1999

RNA movies: visualizing RNA secondary structure spaces.

MOTIVATION: RNA Movies is a system for the visualization of RNA secondary structure spaces. Its input is a script consisting of primary and secondary structure information. From this script, the system fully automatically generates animated graphical structure representations. In this way, it creates the impression of an RNA molecule exploring its own two-dimensional structure space. RESULTS: RNA Movies has been used to generate animations of a switching structure in the spliced leader RNA of Leptomonas collosoma and sequential foldings of potato spindle tuber viroid transcripts. AVAILABILITY: Demonstrations of the animations mentioned in this paper can be viewed on our Bioinformatics web server under the following address: http://BiBiServ.TechFak.Uni-Bielefeld. DE/rnamovies/. The RNA Movies software is available upon request from the authors.

Algorithms↗
PubMed1998

Rose: generating sequence families.

MOTIVATION: We present a new probabilistic model of the evolution of RNA-, DNA-, or protein-like sequences and a software tool, Rose, that implements this model. Guided by an evolutionary tree, a family of related sequences is created from a common ancestor sequence by insertion, deletion and substitution of characters. During this artificial evolutionary process, the 'true' history is logged and the 'correct' multiple sequence alignment is created simultaneously. The model also allows for varying rates of mutation within the sequences, making it possible to establish so-called sequence motifs. RESULTS: The data created by Rose are suitable for the evaluation of methods in multiple sequence alignment computation and the prediction of phylogenetic relationships. It can also be useful when teaching courses in or developing models of sequence evolution and in the study of evolutionary processes. AVAILABILITY: Rose is available on the Bielefeld Bioinformatics WebServer under the following URL: http://bibiserv.TechFak.Uni-Bielefeld.DE/rose/ The source code is available upon request. CONTACT: folker@TechFak.Uni-Bielefeld.DE

Algorithms↗
PubMed1997

Generating benchmarks for multiple sequence alignments and phylogenetic reconstructions.

We present a new probabilistic model of evolution of RNA-, DNA-, or protein-like sequences and a tool rose that implements this model. By insertion, deletion and substitution of characters, a family of sequences is created from a common ancestor. During this artificial evolutionary process, the "true" history is logged and the "correct" multiple sequence alignment is created simultaneously. We also allow for varying rates of mutation within the sequences making it possible to establish so-called sequence motifs. The results are suitable for the evaluation of methods in multiple sequence alignment computation and the prediction of phylogenetic relationships.

Amino Acid Sequence↗
PubMed1992

Echocardiographic proof of pulmonary hypertension with irreversible increased resistance in the pulmonary circulation as a complication after placement of a ventriculo-atrial shunt for internal hydrocephalus.

Increased resistance in the pulmonary vessels in children with ventriculo-atrial shunts is a rare and often unrecognized permanent complication. We report 2 children in whom this diagnosis was detected by two-dimensional echocardiography. The first patient received a ventriculo-atrial shunt at age 9 days for congenital internal hydrocephalus. At 17 months it had to be replaced because of infection of the efferent catheter limb. At 22 months at a routine follow-up the echocardiographic diagnosis of pulmonary hypertension was made. Invasive studies confirmed the presence of irreversible increased resistance in the pulmonary circulation. The second patient received a ventriculo-atrial shunt at age 13 months because of a cerebral cyst. After repeated catheter infections, at 28 months a ventriculo-peritoneal shunt was placed. At age 4 years the diagnosis of pulmonary hypertension was made by routine echocardiography. This finding was confirmed by invasive studies. The left pulmonary artery was completely occluded. Both patients had developed microemboli, caused or aggravated by catheter sepsis, in the second case probably through contiguous clot growth up to complete occlusion of the left pulmonary artery. Therapeutic measures seemed not to be indicated. Two-dimensional echocardiography proved to be a reliable method for diagnosing increased resistance and pulmonary hypertension. We recommend routine echocardiography for follow-up in all children with ventriculo-atrial shunts.

Cerebrospinal Fluid Shunts↗
PubMed1984

Sialoglycoconjugate changes during 2-acetylaminofluorene-induced hepatocarcinogenesis in the rat.

Previous studies indicated a reproducible pattern of altered glycosphingolipid biosynthesis accompanying late stages of liver tumorigenesis in the rat induced by the carcinogen 2-acetylaminofluorene. The sequence began with a dramatic elevation in CMP-sialic acid:lactosylceramide sialyltransferase and was followed by sequential elevations and eventual depressions in other enzymes catalyzing sugar transfers to glycolipid acceptors. The present study focused on the early events of glycolipid biosynthesis during the first 11 weeks of 2-acetylaminofluorene administration according to the same feeding schedule as used previously. Transient elevations in CMP-sialic acid synthetase and elevations in neutral glycosphingolipid precursors to gangliosides were found to precede the major elevations in CMP-sialic acid:lactosylceramide sialyltransferase (GM3 synthetase) noted earlier. Two cycles of response were observed prior to the initiation of the sustained enhancement of biosynthesis of precursor ganglioside, GM3, and/or a significant increase in total or lipid-soluble sialic acid. In vitro rates of sialyl transfer from CMP-sialic acid to endogenous protein acceptors were not altered. The results suggest that the previous observations of altered ganglioside biosynthesis following 2-acetylaminofluorene administration are not an isolated occurrence but may represent late events in a sequence or 'cascade' of biochemical change involving, as well, biosynthesis of ganglioside precursors, CMP-sialic acid and neutral glycosphingolipids.

2-Acetylaminofluorene↗
PubMed1984

Protein on the cell surface of the moderately halophilic phototrophic bacterium Rhodospirillum salexigens.

A cell surface protein (Mr 68,000) of the moderately but obligately halophilic phototrophic bacterium Rhodospirillum salexigens was identified by two independent methods: first, by labeling the cell surface with radioactive iodine and lactoperoxidase, and second, by washing cells in 30% sucrose to remove proteins attached to the cell surface by ionic bonds. The identified protein very likely represents the outermost layer of the cell envelope of R. salexigens as observed by electron microscopy. The protein was isolated. Its isoelectric point was determined to be 4.4; the excess of acidic over basic amino acids was found to be 18.3 mol%; and its average hydrophobicity was 2.26 kJ per residue.

Cell Membrane↗