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PubMed2000

Phylogenetic analysis of Trypanosomatina (Protozoa: Kinetoplastida) based on minicircle conserved regions.

Phylogenetic relationships within the suborder Trypanosomatina were inferred from the kinetoplast DNA minicircle conserved region sequences. Trees built using distance-matrix (Neighbor-Joining) and maximum parsimony methods showed that the minicircle conserved regions (CRs) provide a sensitive and specific molecular marker suitable for phylogenetic analyses of subspecies and strains of trypanosomatid flagellates, as testified by the subdivision of the genus Leishmania into the subgenera Leishmania. Viannia and Sauroleishmania. However, since Phytomonas and monogenetic parasites of insects represent the earliest diverging groups, the CRs do not seem to be useful for inference of relationships among major lineages of the order Kinetoplastida.

Animals↗
PubMedDate not supplied

[Comparative analysis of the efficacy of some methods of conservative treatment of accomodation spasms and myopia in children].

A study was carried out of short- and long-term results in treatment of accommodation spasms and myopia of mild and moderate degrees in children with equipment having different operating mechanism. 171 patients aged 6-15 years were examined (30 persons made up a control group). Electrostimulation, laser stimulation and treatment on "Ambliokor" equipment were used. It was found out that these procedures give a good immediate effect in treatment of accommodation spasm and myopia but 5-6 months later the obtained results deteriorated in 2/3 of children and therefore it is recommended to repeat the treatment in the above period. Using "Ambliokor" equipment provides the best short-term effect. The highest effectiveness of treatment was obtained in combined method comprising all three procedures which made it possible to reduce the rate of myopia progression 2-fold and more compared with the similar index in the control group.

Accommodation, Ocular↗
PubMed1994

Analysis of human T cell clones specific for conserved peptide sequences within malaria proteins. Paucity of clones responsive to intact parasites.

T cells are thought to be of central importance in malaria immunity. Peptides copying malaria protein sequences often stimulate human CD4+ T cells and it was thought that they represented T cell epitopes present in the parasite and may thus have particular relevance to malaria vaccine development. To verify whether synthetic peptides representing highly conserved regions of parasite Ags may contribute to a malaria vaccine, we searched the data bank for conserved regions of Plasmodium falciparum malaria proteins that were not homologous to known self (human) proteins. We synthesized 24 such peptides representing 11 of the cloned and sequenced malaria asexual stage Ags, which were predicted by algorithms to represent T cell epitopes, and 6 peptides not predicted to be T cell epitopes and used these to generate T cell clones from individuals with an extensive previous history of malaria exposure. The T cell clones responded vigorously to many peptides but only a single clone, specific for a peptide within merozoite surface protein-1, 20-39, VTHESYQELVKKLEALEDAV, and not previously defined to be a T cell epitope responded to malaria parasites by proliferation and secretion of IFN-gamma. This epitope was not revealed by studying parasite-induced T cell lines and is thus subdominant. The clone was able to significantly inhibit parasite growth in vitro. The final step in the inhibition of parasite growth appears to be nonspecific because other activated clones (not specific for malaria sequences) can inhibit parasite growth. Our data suggest that few conserved peptides within malaria parasites can be processed from the intact parasite. However, such peptides that can be processed from malaria parasites may be expected to stimulate parasite-specific T cells that could inhibit parasite growth and as such may be lead candidates for a vaccine aimed at inducing cellular immunity to malaria.

Adult↗
PubMed1994

Specificity of coenzyme binding in thiamin diphosphate-dependent enzymes. Crystal structures of yeast transketolase in complex with analogs of thiamin diphosphate.

The three-dimensional structures of complexes of yeast apotransketolase with the coenzyme analogs 6'-methyl, N1'-pyridyl, and N3'-pyridyl thiamin diphosphate, respectively, were determined with protein crystallographic methods. All three coenzyme analogs bind to the enzyme in a fashion highly similar to the cofactor thiamin diphosphate. Thus, either one of the hydrogen bonds of the pyrimidine ring nitrogens to the protein is sufficient for proper binding and positioning of the cofactor. The lack of catalytic activity of the N3'-pyridyl analog is not due to incorrect orientation of the pyrimidine ring, but results from the absence of the hydrogen bond between the N1' nitrogen atom and the conserved residue Glu418. The structure analysis provides further evidence for the importance of this conserved interaction for enzymatic thiamin catalysis.

Coenzymes↗
PubMed2007

DNA-DNA hybridization values and their relationship to whole-genome sequence similarities.

DNA-DNA hybridization (DDH) values have been used by bacterial taxonomists since the 1960s to determine relatedness between strains and are still the most important criterion in the delineation of bacterial species. Since the extent of hybridization between a pair of strains is ultimately governed by their respective genomic sequences, we examined the quantitative relationship between DDH values and genome sequence-derived parameters, such as the average nucleotide identity (ANI) of common genes and the percentage of conserved DNA. A total of 124 DDH values were determined for 28 strains for which genome sequences were available. The strains belong to six important and diverse groups of bacteria for which the intra-group 16S rRNA gene sequence identity was greater than 94 %. The results revealed a close relationship between DDH values and ANI and between DNA-DNA hybridization and the percentage of conserved DNA for each pair of strains. The recommended cut-off point of 70 % DDH for species delineation corresponded to 95 % ANI and 69 % conserved DNA. When the analysis was restricted to the protein-coding portion of the genome, 70 % DDH corresponded to 85 % conserved genes for a pair of strains. These results reveal extensive gene diversity within the current concept of "species". Examination of reciprocal values indicated that the level of experimental error associated with the DDH method is too high to reveal the subtle differences in genome size among the strains sampled. It is concluded that ANI can accurately replace DDH values for strains for which genome sequences are available.

Bacterial Typing Techniques↗
PubMed1999

Structural features of the glutamate transporter family.

Neuronal and glial glutamate transporters remove the excitatory neurotransmitter glutamate from the synaptic cleft and thus prevent neurotoxicity. The proteins belong to a large and widespread family of secondary transporters, including bacterial glutamate, serine, and C4-dicarboxylate transporters; mammalian neutral-amino-acid transporters; and an increasing number of bacterial, archaeal, and eukaryotic proteins that have not yet been functionally characterized. Sixty members of the glutamate transporter family were found in the databases on the basis of sequence homology. The amino acid sequences of the carriers have diverged enormously. Homology between the members of the family is most apparent in a stretch of approximately 150 residues in the C-terminal part of the proteins. This region contains four reasonably well-conserved sequence motifs, all of which have been suggested to be part of the translocation pore or substrate binding site. Phylogenetic analysis of the C-terminal stretch revealed the presence of five subfamilies with characterized members: (i) the eukaryotic glutamate transporters, (ii) the bacterial glutamate transporters, (iii) the eukaryotic neutral-amino-acid transporters, (iv) the bacterial C4-dicarboxylate transporters, and (v) the bacterial serine transporters. A number of other subfamilies that do not contain characterized members have been defined. In contrast to their amino acid sequences, the hydropathy profiles of the members of the family are extremely well conserved. Analysis of the hydropathy profiles has suggested that the glutamate transporters have a global structure that is unique among secondary transporters. Experimentally, the unique structure of the transporters was recently confirmed by membrane topology studies. Although there is still controversy about part of the topology, the most likely model predicts the presence of eight membrane-spanning alpha-helices and a loop-pore structure which is unique among secondary transporters but may resemble loop-pores found in ion channels. A second distinctive structural feature is the presence of a highly amphipathic membrane-spanning helix that provides a hydrophilic path through the membrane. Recent data from analysis of site-directed mutants and studies on the mechanism and pharmacology of the transporters are discussed in relation to the structural model.

ATP-Binding Cassette Transporters↗
PubMed2006

Conserved motifs in voltage-sensing and pore-forming modules of voltage-gated ion channel proteins.

Voltage-gated ion channels (VGCs) mediate selective diffusion of ions across cell membranes to enable many vital cellular processes. Three-dimensional structure data are lacking for VGC proteins; hence, to better understand their function, there is a need to identify the conserved motifs using sequence analysis methods. In this study, we have used a profile-to-profile alignment method to identify several new conserved motifs specific to each transmembrane segment (TMS) of the voltage-sensing and the pore-forming modules of Ca2+, Na+, and K+ channel subfamilies. For Ca2+ and Na+, the functional theme of motif conservation is similar in all segments while they differ with those of the K+ channel proteins. Nevertheless, the conservation is strikingly similar in the S4 segment of the voltage-sensing module across all subfamilies. In each subfamily and for each TMS, we have identified conserved motifs/residues and correlated their functional significance and disease associations in human, using mutational data from the literature.

Amino Acid Motifs↗
PubMed1993

Neurological outcome from conservative or surgical treatment of cervical spinal cord injured patients.

This is an analysis of the results of treatment of 1761 patients with traumatic injury of cervical spinal cord, admitted to hospital within the first hours or days after injury. Analysis of the results of conservative treatment in 798 patients and of surgical treatment in 963 patients has shown that the results are to a large extent dependent on the method of treatment and when specialist treatment was started.

Humans↗
PubMed1996

Comparison of the canine and human acid beta-galactosidase gene.

Several canine cDNA libraries were screened with human beta-galactosidase cDNA as probe. Seven positive clones were isolated and sequenced yielding a partial (2060 bp) canine beta-galactosidase cDNA with 86% identity to the human beta-galactosidase cDNA. Preliminary analysis of a canine genomic library indicated conservation of exon number and size. Analysis by Northern blotting disclosed a single mRNA of 2.4 kb in fibroblasts and liver from normal dogs and dogs affected with GM1 gangliosidosis. Although incomplete, these results indicate canine GM1 gangliosidosis is a suitable animal model of the human disease and should further efforts to devise a gene therapy strategy for its treatment.

Amino Acid Sequence↗
PubMed1998

Gene-based anchoring of the rat genetic linkage and cytogenetic maps: new regional localizations, orientation of the linkage groups, and insights into mammalian chromosome evolution.

In order to generate anchor points connecting the rat cytogenetic and genetic maps, the cytogenetic position of 62 rat markers (including 55 genes) already localized genetically was determined by fluorescence in situ hybridization. Whenever possible, markers located near one end of the linkage groups were included. These new localizations allowed us to unambiguously orient the 20 autosomal and the X chromosome linkage groups. The position of the centromere in the linkage map could also be determined in the case of several metacentric chromosomes. In addition, the regional localization of 15 other rat genes was determined. These new data bring useful information with respect to comparative mapping with the mouse and the human and to mammalian evolution. They illustrate, for instance, that groups of genes can remain syntenic during mammalian evolution while being subjected to intrachromosomal rearrangements in some lineages (synteny is conserved while gene order is not). This analysis also disclosed cases of synteny conservation in one the two rodent species and the human, while the synteny is split in the other rodent species: such configurations are likely examples of lineage-specific interchromosomal rearrangements associated with speciation.

Animals↗
PubMed1997

Mutations in the GAP-related domain impair the ability of neurofibromin to associate with microtubules.

The neurofibromatosis 1 (NF1) gene encodes a cytoplasmic protein with structural and functional homology to GTPase activating proteins (GAPs) for p21-ras. Double-labeling immunofluorescence experiments using neurofibromin antibodies and in vitro microtubule assembly have demonstrated that the NF1 gene product, neurofibromin, interacts with cytoplasmic microtubules. The region critical for this interaction was shown to reside within the NF1-GAP-related domain (NF1GRD). Examination of the NFIGRD reveals a number of residues that are highly conserved amongst all GAP molecules. Mutational analysis of a representative number of these conserved residues demonstrated differential effects on NF1GRD p21-ras GAP activity. In this study, we examined the effect of these selected NF1GRD mutations on the ability of neurofibromin to associate with microtubules. Mutations at residues R1391, P1400 and K1423 disrupted microtubule association. In contrast, mutations at residues E1264, Q1426 and the insertion of exon 23a, critical for p21-ras regulation, did not impair microtubule association. These results demonstrate that some residues important for p21-ras regulation are also required for microtubule binding while other residues within the NF1GRD differentially affect p21-ras regulation and microtubule association.

Animals↗
PubMed2005

SVC: structured visualization of evolutionary sequence conservation.

We have developed a web application for the detailed analysis and visualization of evolutionary sequence conservation in complex vertebrate genes. Given a pair of orthologous genes, the protein-coding sequences are aligned. When these sequences are mapped back onto their encoding exons in the genomes, a scaffold of the conserved gene structure naturally emerges. Sequence similarity between exons and introns is analysed and embedded into the gene structure scaffold. The visualization on the SVC server provides detailed information about evolutionarily conserved features of these genes. It further allows concise representation of complex splice patterns in the context of evolutionary conservation. A particular application of our tool arises from the fact that around mRNA editing sites both exonic and intronic sequences are highly conserved. This aids in delineation of these sites. SVC is available at http://svc.molgen.mpg.de.

Animals↗
PubMed2006

Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire.

We constructed and applied an open source informatic framework called Cistematic in an effort to predict the target gene repertoire for transcription factors with large binding sites. Cistematic uses two different evolutionary conservation-filtering algorithms in conjunction with several analysis modules. Beginning with a single conserved and biologically tested site for the neuronal repressor NRSF/REST, Cistematic generated a refined PSFM (position specific frequency matrix) based on conserved site occurrences in mouse, human, and dog genomes. Predictions from this model were validated by chromatin immunoprecipitation (ChIP) followed by quantitative PCR. The combination of transfection assays and ChIP enrichment data provided an objective basis for setting a threshold for membership and rank-ordering a final gene cohort model consisting of 842 high-confidence sites in the human genome associated with 733 genes. Statistically significant enrichment of NRSE-associated genes was found for neuron-specific Gene Ontology (GO) terms and neuronal mRNA expression profiles. A more extensive evolutionary survey showed that NRSE sites matching the PSFM model exist in roughly similar numbers in all fully sequenced vertebrate genomes but are notably absent from invertebrate and protochordate genomes, as is NRSF itself. Some NRSF/REST sites reside in repeats, which suggests a mechanism for both ancient and modern dispersal of NRSEs through vertebrate genomes. Multiple predicted sites are located near neuronal microRNA and splicing-factor genes, and these tested positive for NRSF/REST occupancy in vivo. The resulting network model integrates post-transcriptional and translational controllers, including candidate feedback loops on NRSF and its corepressor, CoREST.

Animals↗
PubMed1975

[Outcome of conservative treatment of traumatic hip dislocation].

The authors report an analysis of the results obtained after conservative therapy for femoral dislocations. Reduction of luxations was accomplished after the Djanalidze and Kocher method with subsequent immobilization of the extremity by means of skeletal extension, plaster cast and bandaging one leg to the other. The results proved to be different depending on the technic of reduction employed, fixation of the extremity and its duration, and the start of the weight-bearing on the injured extremity. Some recommendations on prophylaxis of arthroses immediately after femoral dislocation are given.

Bandages↗
PubMed2006

Analysis of the binding of the N-terminal conserved domain of yeast Cbf5p to a box H/ACA snoRNA.

During ribosome biogenesis, the RNA precursor to mature rRNAs undergoes numerous post-transcriptional chemical modifications of bases, including conversions of uridines to pseudouridines. In archaea and eukaryotes, these conversions are performed by box H/ACA small ribonucleoprotein particles (box H/ACA RNPs), which contain a small guide RNA responsible for the selection of substrate uridines and four proteins, including the pseudouridine synthase, Cbf5p. So far, no in vitro reconstitution of eukaryotic box H/ACA RNPs from purified components has been achieved, principally due to difficulties in purifying recombinant eukaryotic Cbf5p. In this study, we present the purification of a truncated derivative of yeast Cbf5p (Cbf5(Delta)p) that retains the highly conserved TRUB and PUA domains. We have used band retardation assays to show that Cbf5(Delta)p on its own binds to box H/ACA small nucleolar (sno)RNAs. We demonstrate that the conserved H and ACA boxes enhance the affinity of the protein for the snoRNA. Furthermore, like its archaeal homologs, Cbf5(Delta)p can bind to a single stem-loop-box ACA RNA. Finally, we report the first enzymatic footprinting analysis of a Cbf5-RNA complex. Our results are compatible with the view that two molecules of Cbf5p interact with a binding platform constituted by the 5' end of the RNA, the single-stranded hinge domain containing the conserved H box, and the 3' end of the molecule, including the conserved ACA box.

Amino Acid Sequence↗
PubMed2002

One operation after percutaneous diagnosis of nonpalpable breast cancer: frequency and associated factors.

OBJECTIVE: The purpose of this study was to determine the frequency of and factors associated with performing one therapeutic operation after percutaneous diagnosis of nonpalpable breast cancer. MATERIALS AND METHODS: Retrospective review was performed of records of 350 consecutive women who had therapeutic surgery after percutaneous imaging-guided core biopsy diagnosis of nonpalpable breast cancer. Records were reviewed to determine the frequency of performing one operation and associated factors. Statistical analysis was performed. RESULTS: One operation was performed in 283 (80.9%) of 350 women, including 106 (95.5%) of 111 women who had mastectomy and 177 (74.1%) of 239 women who had breast conserving surgery. At bivariate analysis, one operation was significantly more likely in women who had no underestimation (p < 0.001), mastectomy rather than breast conservation (p < 0.001), axillary dissection during the first operation (p < 0.001), percutaneous diagnosis of infiltrating carcinoma (p = 0.001), or mammographic mass (p = 0.006). At multivariate analysis, one operation was significantly more likely if underestimation was absent (odds ratio [OR] = 10.1, 95% confidence interval [CI] = 4.2-24.7) or if mastectomy was performed (OR = 8.7, 95% CI = 3.2-23.5); for women who had breast-conserving surgery, one operation was significantly more likely if underestimation was absent (OR = 11.4, 95% CI = 3.9-33.2) or if a mammographic mass was present (OR = 2.4, 95% CI = 1.3-4.6). CONCLUSION: One operation was performed in 80.9% of women with percutaneously proven nonpalpable breast cancer, including 74.1% of women who had breast-conserving surgery and 95.5% of women who had mastectomy. Among women who had breast conservation, one operation was significantly more likely if histologic underestimation was absent or if a mammographic mass was present.

Adult↗