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At least 19 recordsLinked to original sources
PubMed1992

Conservation analysis and structure prediction of the SH2 family of phosphotyrosine binding domains.

Src homology 2 (SH2) regions are short (approximately 100 amino acids), non-catalytic domains conserved among a wide variety of proteins involved in cytoplasmic signaling induced by growth factors. It is thought that SH2 domains play an important role in the intracellular response to growth factor stimulation by binding to phosphotyrosine containing proteins. In this paper we apply the techniques of multiple sequence alignment, secondary structure prediction and conservation analysis to 67 SH2 domain amino acid sequences. This combined approach predicts seven core secondary structure regions with the pattern beta-alpha-beta-beta-beta-beta-alpha, identifies those residues most likely to be buried in the hydrophobic core of the native SH2 domain, and highlights patterns of conservation indicative of secondary structural elements. Residues likely to be involved in phosphotyrosine binding are shown and orientations of the predicted secondary structures suggested which could enable such residues to cooperate in phosphate binding. We propose a consensus pattern that encapsulates the principal conserved features of the SH2 domains. Comparison of the proposed SH2 domain of akt to this pattern shows only 12/40 matches, suggesting that this domain may not exhibit SH2-like properties.

Amino Acid Sequence↗
PubMed2025

Whole-Genome Conservation Analysis for the Specific and Accurate Detection of Influenza A and B Viruses and Respiratory Syncytial Virus by Quadruplex RT-qPCR.

Influenza virus (Flu) and respiratory syncytial virus (RSV) are the primary pathogens responsible for acute respiratory infections. Both viruses are prone to mutations due to the seasonal epidemic, leading to an increasing rate of false-negative results. In this study, comprehensive meta-analyses of the genomes focusing on most conserved fragments have been performed for the four seasonal influenza viruses (two subtypes of Flu A: H1N1 and H3N2; two subtypes of Flu B: Yamagata and Victoria) and the two types of RSV: RSVA and RSVB), respectively. The most conserved sequences of 200 bp were identified as targets of the designed primer/probe sets for RT-qPCR were screened and optimized. Good sensitivities of the optimized primer/probe sets were obtained with the limits of detections of 2.95, 2.82, 1.57, 2.8, 1.19, and 2.12 copies/reaction for H1N1, H3N2, Yamagata, Victoria, RSVA and RSVB, respectively. Eventually, quadruplex qPCR using the four designed primer/probe sets can achieve simultaneous screening of the four viruses at a single tube. Furthermore, the assay's good performance in detecting target viruses from clinical throat swab samples demonstrated its potential for diagnosis of these viruses. The method, based on the identified conserved sequences and primer/probe sets, can effectively reduce false-negative results and rapidly respond to these viruses during respiratory disease outbreaks, or even before their widespread emergence, which aid in preventing outbreaks and guiding clinical treatment.

Humans↗
PubMed1992

Clinical usefulness of computerized colposcopy: image analysis and conservative management of mild dysplasia.

OBJECTIVES: The purposes of this study were to evaluate the clinical usefulness of computerized colposcopy and image analysis, to investigate the correlation between lesion size and grade of dysplasia, and to examine and record the colposcopic changes associated with progression or regression of cervical dysplasia. METHODS: Sixty-eight patients with a fully visualized squamocolumnar junction and a histopathologic diagnosis of mild dysplasia were serially monitored for a period of 1 year using computerized colposcopy and image analysis. All patients had baseline computer-assisted measurements of their cervical lesions and repeat measurements at 3-month intervals. RESULTS: The mean age of the patients was 31 years, and the mean size of the colposcopically visualized lesions was 58 mm2. During the 12-month observation, 5.9% of the lesions increased in size, 32.4% decreased in size, 13.2% remained unchanged, 20.6% disappeared, and 27.9% completely changed location. In patients with an increase in lesion size (N = 4), a repeat biopsy was performed, revealing a progression to moderate dysplasia. Treatment was withheld from patients whose lesions disappeared (N = 14), decreased in size (N = 22), or remained unchanged (N = 9). Active therapy was unnecessary in 66% of cases and repeat biopsy was avoided in 94.1%. CONCLUSIONS: Computerized colposcopy provides objective information and may be an adjunct to cytology and histopathology in some cases. Computerized colposcopy replaces subjective colposcopic evaluation with objective computer assessment and may hold promise for conservative management of cervical dysplasia.

Adult↗
PubMed1991

Analysis of conserved domains identifies a unique structural feature of a chloroplast heat shock protein.

A low molecular weight heat shock protein which localizes to chloroplasts has been identified in several plant species. This protein belongs to a eukaryotic superfamily of small HSPs, all of which contain a conserved carboxyl-terminal domain. To investigate further the structure of this HSP, we isolated and sequenced cDNA clones for the chloroplast LMW HSPs from Petunia hybrida and Arabidopsis thaliana. The cloning of chloroplast HSPs from these two species enabled us to compare the amino acid sequences of this protein from plant species (petunia, Arabidopsis, pea, soybean and maize) that represent evolutionarily divergent taxonomic subclasses. Three conserved regions were identified, which are designated as regions I, II and III. Regions I and II are also shared by cytoplasmic LMW HSPs and therefore are likely to have functional roles common to all eukaryotic LMW HSPs. In contrast, consensus region III is not found in other LMW HSPs. Secondary structure analysis predicts that this region forms an amphipathic alpha-helix with high conservation of methionine residues on the hydrophobic face and 100% conservation of residues on the hydrophilic face. This structure is similar to three helices, termed "methionine bristles", which are found in a methionine-rich domain of a 54 kDa protein component of signal recognition particle (SRP54). The conservation of regions I and II among LMW cytoplasmic and chloroplast HSPs suggests that these HSPs perform related functions in different cellular compartments. However, identification of the methionine bristle domain suggests that chloroplast HSPs also have unique functions or substrates within the special environment of the chloroplast or other plastids.

Amino Acid Sequence↗
PubMed1992

Mutational analysis of conserved positions potentially important for initiator tRNA function in Saccharomyces cerevisiae.

The conserved positions of the eukaryotic cytoplasmic initiator tRNA have been suggested to be important for the initiation of protein synthesis. However, the role of these positions is not known. We describe in this report a functional analysis of the yeast initiator methionine tRNA (tRNA(iMet)), using a novel in vivo assay system which is not dependent on suppressor tRNAs. Strains of Saccharomyces cerevisiae with null alleles of the four initiator methionine tRNA (IMT) genes were constructed. Consequently, growth of these strains was dependent on tRNA(iMet) encoded from a plasmid-derived gene. We used these strains to investigate the significance of the conserved nucleosides of yeast tRNA(iMet) in vivo. Nucleotide substitutions corresponding to the nucleosides of the yeast elongator methionine tRNA (tRNA(MMet)) have been made at all conserved positions to identify the positions that are important for tRNA(iMet) to function in the initiation process. Surprisingly, nucleoside changes in base pairs 3-70, 12-23, 31-39, and 29-41, as well as expanding loop I by inserting an A at position 17 (A17) had no effect on the tester strain. Nucleotide substitutions in positions 54 and 60 to cytidines and guanosines (C54, G54, C60, and G60) did not prevent cell growth. In contrast, the double mutation U/rT54C60 blocked cell growth, and changing the A-U base pair 1-72 to a G-C base pair was deleterious to the cell, although these tRNAs were synthesized and accepted methionine in vitro. From our data, we suggest that an A-U base pair in position 1-72 is important for tRNA(iMet) function, that the hypothetical requirement for adenosines at positions 54 and 60 is invalid, and that a U/rT at position 54 is an antideterminant distinguishing an elongator from an initiator tRNA in the initiation of translation.

Base Sequence↗
PubMed1976

[Working time analysis in conservative dentistry (dental filling therapy)].

The purpose of the present paper was to determine the time required for filling therapy. The authors deal briefly with the subdivision of time adopted for the present study. Conclusions as to planning in dental practice may be drawn from the results obtained only if values determined by different dentists are available for comparison.

Dental Restoration, Permanent↗
PubMed1992

[Review of results and clinical analysis of conservative partial surgery associated with postoperative radiotherapy in operable breast cancers stages I amd II].

Over the last 25 years, conservative forms of treatment have been used for the locoregional treatment of early breast cancer, stages I and II (< 3 cm in diameter). At present, the same carcinological results are obtained with conservative surgery and radiation therapy as with radical surgery, and the aesthetic and functional results have improved. Several parameters should be taken into account, ie tumour volume, breast volume, multifocal nature and histologic type. A number of questions still remain unanswered namely: what is the most appropriate conservative surgery (quadrantectomy, tumourectomy or local excision)? What is the most appropriate total irradiation dose (50 Gy over 5 weeks: or 45 Gy over 4.5 weeks)? What is the value of radiation boost in patients with negative resection margins? What is the value of radiation boost in patients with a high local risk of recurrence? What is the most appropriate radiation technique for boost in the primary tumour bed (electrons or iridium implants)? Does the external irradiation of regional lymph nodes improve survival rate? Is it possible to extend conservative treatment to a 4-cm diameter tumour? What is the impact of adjuvant systemic chemotherapy and/or hormonotherapy on the risk of isolated breast cancer recurrence?

Adult↗
PubMed1992

Analysis of conserved domains and sequence motifs in cellular regulatory proteins and locus control regions using new software tools for multiple alignment and visualization.

With the tremendous expansion of molecular sequence data in recent years, multiple alignment is arguably one of the two most important analytic techniques (the other being fast database searching). A number of useful approaches to this problem have previously been developed, but often they are limited to only a subset of multiple-alignment applications and cannot easily deal with the complex structural organization seen in an increasing number of sequences. For example, a single sequence may contain several domains of different evolutionary origins, and the multiplicities and relative ordering of these domains may be quite different among related sequences. Here we describe an integrated set of interactive Unix tools that combines several multiple-alignment techniques with traditional "dot-plot" visualization to provide a flexible environment for approaching complex sequence analysis problems. We apply these tools to the identification and characterization of "catalytic" domains in ras and rho/rac GTPase-activating proteins, to "Src homology" (SH2, SH3) domains in cytoplasmic signaling proteins, to repetitive sequence motifs in the alpha and beta subunits of protein prenyltransferases, and to regulatory DNA sequences in the locus control region of the beta-globin gene cluster.

Alkyl and Aryl Transferases↗
PubMed1992

Mutational analysis of conserved N-linked glycosylation sites of human immunodeficiency virus type 1 gp41.

Amino acid substitutions were introduced into four conserved N-linked glycosylation sites of the human immunodeficiency virus type 1 envelope transmembrane glycoprotein, gp41, to alter the canonical N-linked glycosylation sequences. One altered site produced a severe impairment of viral infectivity, which raises the possibility that N-linked sugars at this site may have an important role in the human immunodeficiency virus type 1 life cycle.

Animals↗
PubMed1990

Mutational analysis of conserved nucleotides in a self-splicing group I intron.

We have constructed all single base substitutions in almost all of the highly conserved residues of the Tetrahymena self-splicing intron. Mutation of highly conserved residues almost invariably leads to loss of enzymatic activity. In many cases, activity could be regained by making additional mutations that restored predicted base-pairings; these second site suppressors in general confirm the secondary structure derived from phylogenetic data. At several positions, our suppression data can be most readily explained by assuming non-Watson-Crick base-pairings. In addition to the requirements imposed by the secondary structure, the sequence of the intron is constrained by "negative interactions", the exclusion of particular nucleotide sequences that would form undesirable secondary structures. A comparison of genetic and phylogenetic data suggests sites that may be involved in tertiary structural interactions.

Animals↗
PubMed2026

Comparative analysis of conserved non-coding elements identifies gene regulatory networks rewired during the water-to-land transition in vertebrates.

The conquest of land by vertebrates has been a pivotal moment in evolutionary history. Adapting to the new habitats necessitated numerous changes in vertebrate anatomy and physiology, creating an enduring imprint on the developmental gene regulatory networks (GRNs) of tetrapods. The increase of high-quality genomic resources over the past decade has made it possible to study the genomic legacy of the water-to-land transition. While much attention has been given to the highly conserved non-coding elements (CNEs) of the genome that share high levels of similarity across evolutionarily diverged clades, recent evidence suggests that perhaps comparable attention should be given to "missing" CNE-s, conserved sequence patches present in extant stem gnathostomes and actinopterygian fishes that have become undetectable in tetrapods during the adaptation to terrestrial life, whether through true sequence loss or divergence beyond alignability. These sequences could help us reveal the relaxation of certain developmental constraints, related to the aquatic lifestyle, that made reaching new adaptive peaks in the developmental landscape possible. In this paper, we search for such CNEs and characterize them in comparison with pan-Gnathostome CNEs, using the zebrafish (Danio rerio) genome as a reference. Our results suggest that the rewiring of developmental networks related to pigmentation and muscle structure formation has left the largest genomic imprint. We also find that components of canonical Wnt and Hedgehog signalling, are enriched among CNEs retained in fish.

cis-regulatory evolution↗
PubMed1992

[An analysis of conservative therapy in 376 patients with paraplegia after injuries of the spine].

In 376 cases of paraplegia after lesions of the vertebral column which had been treated exclusively by conservative methods we were interested in changes of the neurological status, if any, during inpatient treatment, as well as in the rate of complications, the stability of the vertebral column and the immobilisation time and period of hospitalisation. 70.7% of the patients were primarily completely paralysed at admission to hospital; 6.4% of them displayed neurological improvement, compared to 49.5% of the primarily not fully paralysed patients. With decreasing height of the site of lesion of the vertebral column the rate of neurological improvement increased to a statistically significant extent. The neurological status did not deteriorate in any of the patients. Instabilities of the vertebral column were rare in our patient material, occurring in only 0.8% of the exclusively conservatively treated lesions of the thoracic and lumbar vertebral column. The average rate of complications was 13.9%, the immobilisation time approx. 10.8 weeks and the hospitalisation period on the average 25.6 weeks.

Adolescent↗
PubMed1991

Mutational analysis of conserved residues in the tyrosine kinase domain of the human trk oncogene.

The human trk oncogene (originally identified in a colon carcinoma) was activated by a genetic rearrangement which resulted in replacement of the extracellular ligand-binding domain of the proto-trk transmembrane receptor by non-muscle tropomyosin sequences. The product of the trk oncogene, a protein of 70 kDa (p70trk), possesses tyrosine-specific protein kinase activity, is autophosphorylated in vitro on tyrosine and is phosphorylated on serine, threonine and tyrosine residues in trk-transformed cells. By site-directed mutagenesis of trk oncogene cDNA, the codon for lysine (367) at the putative ATP-binding site was changed to that for methionine and the codons for tyrosines (503 and 504) at the putative autophosphorylation sites were changed to those for phenylalanine. Replacement of Lys-367 by methionine results in a biologically inactive, kinase-negative mutant. Phe-ala mutants of trk showed drastically reduced ability to induce morphologic transformation, anchorage-independent growth and tumorigenicity in mouse NIH3T3 cells and showed reduced in vitro tyrosine kinase activity when assayed by autophosphorylation and phosphorylation of histone as exogenous substrate. The present study indicates the role of these specific conserved residues in regulating the biochemical and biological properties of p70trk oncoprotein.

3T3 Cells↗
PubMed1977

[Comparative analysis of conservative and surgical treatment of the imminent myocardial infarct].

It is reported on 108 patients with the symptoms of the impending myocardial infarction, of whom 80 patients were treated conservatively. 51 patients developed a fresh definitive myocardial infarction. 28 patients were surgically treated, 5 of them died. Therefore, in patients with instable angina pectoris the possibility of an early coronary-surgical intervention should be taken into consideration to prevent the development of a definitive myocardial infarction.

Acute Disease↗
PubMed1979

A retrospective analysis of conservative versus active management in severe open myelomeningocele.

88 patients with thoraco-lumbar myelomeningocele not operated upon in the 1976-1977 period were compared with 76 patients with the same condition operated upon in the 1964-1971 period. There was no significant difference in sex and hydrocephalus at birth in the two groups. Mortality was less in the surgically treated group only after the age of three months. Ventriculitis appeared to be related to the incidence of hydrocephalus in the surgically treated group. There was a reduced risk of developing progressive hydrocephalus after birth in the untreated group, and the neurological status of the survivors at one year was the same in both groups. Interpreting the results as indicating that early surgery increased the incidence of progressive hydrocephalus and ventriculitis, and might increase survival of more disabled infants, then non-surgical treatment is justified since survivors are no worse as a result of this non-active approach.

Cerebral Ventricles↗