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At least 991 records · Page 55Linked to original sources
PubMed1988

Results of salvage surgery for mammary recurrence following breast-conserving therapy.

A retrospective analysis was performed of 118 surgically treated mammary recurrences, occurring following primary conservative excision and radiation therapy for clinical Stages I and II breast cancer. Actuarial cancer-specific survival following salvage surgery was 72% at 5 years and 58% at 10 years. With a median followup of 7 years, further local-regional recurrences were observed in 20 of the 118 patients, many of whom could be treated by further surgery. Actuarial survival after recurrence was significantly influenced by initial clinical stage, as well as by the disease-free interval following primary therapy, but was similar for both premenopausal and postmenopausal patients and for patients treated by radical or breast-conserving salvage operations. For recurrences after the fifth year, actuarial survival following salvage surgery was 83% and 68% at 5 and 10 years, respectively. Survival for Stage I patients was favorable regardless of disease-free interval. It is concluded that recurrences in the breast following primary treatment with limited surgery and irradiation have a considerably more favorable prognosis than that of local failures after primary radical surgery. Suggestions for the management of these recurrences are presented.

Age Factors↗
PubMedDate not supplied

[Structure-activity organization of the variola virus genome. III. Sequencing and analysis of the nucleotide sequence of the conserved region of HindIII-F, -N-, and -A-fragments of the India 1967 strain genome].

Computer analysis of variola major virus (VAR) genomic fragment bounded by open reading frames (ORFs) D1R and A33L which is 47,961 bp long revealed 46 potential ORFs. The VAR proteins were compared with the analogous proteins of vaccinia virus strain Copenhagen. The subunits of DNA-dependent RNA polymerase, as well as the transcription factors, mRNA capping enzymes, and proteins necessary for the virion morphogenesis proved to be highly conservative within orthopoxviruses. The most pronounced differences between the VAR genome fragment under study and the corresponding vaccinia virus fragment were revealed in the vicinity of the gene encoding the A-type inclusion body protein. The possible functions of the analyzed viral proteins are discussed.

Amino Acid Sequence↗
PubMed2005

Computational analysis of protein tyrosine phosphatases: practical guide to bioinformatics and data resources.

The exponential growth of sequence data has become a challenge to database curators and end-users alike and biologists seeking to utilize the data effectively are faced with numerous analysis methods. Here, with practical examples from our bioinformatics analysis of the protein tyrosine phosphatases (PTPs), we show how computational analysis can be exploited to fuel hypothesis-driven experimental research through the exploration of online databases. We cover the following elements: (i) similarity searches and strategies to collect a non-redundant database of tyrosine-specific PTP domains; (ii) utilization of this database to classify human, fly, and worm PTPs (based on alignments and phylogenetic analysis); (iii) three-dimensional structural analysis to identify conserved regions (structure-function) and non-conserved selectivity-determining regions (substrate specificity); and (iv) genomic analysis, including mapping of exon structure, identification of pseudogenes, and exploration of disease databases. We discuss the importance of manual curation, illustrating examples in which pseudogenes give rise to predicted proteins in GenBank and note that domain servers, such as PFAM and SMART, erroneously include dual-specificity and lipid phosphatases in their collection of tyrosine-specific PTPs. To capitalize on our annotated set of 402 PTP domains (from 47 species and five phyla), we identify sequence conservation across taxonomic categories and explore structure-function relationships among tandem domain receptor-like PTPs. We define three Src homology 2 domain-containing PTP genes in stingray, zebrafish, and fugu and speculate on their evolutionary relationship with human pseudogenes. Our annotated sequences, along with a web service for phylogenetic classification of PTP domains, are available online (http://ptp.cshl.edu and http://science.novonordisk.com/ptp).

Amino Acid Sequence↗
PubMed1994

Cloning and sequence analysis of bovine bone sialoprotein cDNA: conservation of acidic domains, tyrosine sulfation consensus repeats, and RGD cell attachment domain.

We isolated and sequenced a cDNA encoding bovine bone sialoprotein (BSP) using a bovine cDNA library made from mRNA isolated from bone-derived cell cultures and ligated to a phage lambda gt11. One of the cDNA clones isolated from this library had a 1800 base pair long insert and was found to contain the entire protein-encoding region. The deduced protein sequence revealed a 310 amino acid protein containing a signal peptide sequence of 16 hydrophobic amino acids. The protein sequence shows remarkable conservation with previously published human and rat sequences (more than 80% similarity for both species). The potential functional domains of BSP, including three acid amino acid-rich sequences, tyrosine sulfation consensus repeats, and the RGD cell binding sequence, are all present in the bovine sequence. Northern analysis of RNA from different bovine tissues indicated the presence of BSP message in bone but not in other nonmineralized tissues, confirming that bone is the major site of BSP message production.

Amino Acid Sequence↗
PubMed1999

A selection system for functional internal ribosome entry site (IRES) elements: analysis of the requirement for a conserved GNRA tetraloop in the encephalomyocarditis virus IRES.

Picornavirus internal ribosome entry site (IRES) elements direct cap-independent internal initiation of protein synthesis within mammalian cells. These RNA elements (about 450 nt) contain extensive secondary structure including a hairpin loop with a conserved GNRA motif. Such loops are important in RNA-RNA and RNA-protein interactions. Plasmids that express dicistronic mRNAs of the structure GUS/IRES/HOOK have been constructed. The HOOK sequence encodes a cell-surface-targeted protein (sFv); the translation of this open reading frame within mammalian cells from these dicistronic mRNAs requires a functional IRES element. Cells that express the sFv can be selected from nonexpressing cells. A pool of up to 256 mutant encephalomyocarditis virus IRES elements was generated by converting the wild-type hairpin loop sequence (GCGA) to NNNN. Following transfection of this pool of mutants into COS-7 cells, plasmids were recovered from selected sFv-expressing cells. These DNAs were amplified in Escherichia coli and transfected again into COS-7 cells for further cycles to enrich for plasmids encoding functional IRES elements. The sequence of individual selected IRES elements was determined. All functional IRES elements had a tetraloop with a 3' terminal A residue. Optimal IRES activity, assayed in vitro and within cells, was obtained from plasmids encoding an IRES with the hairpin loop sequence fitting a RNRA consensus. In contrast, IRES elements containing YCYA tetraloops were severely defective.

Animals↗
PubMed1992

Cis-analysis of a seed protein gene promoter: the conservative RY repeat CATGCATG within the legumin box is essential for tissue-specific expression of a legumin gene.

A 2.4 kb fragment containing the 5'-flanking region and the 5'-noncoding sequence of the Vicia faba legumin gene LeB4 mediates high level seed-specific expression in transgenic tobacco plants. Deleted derivatives of this legumin upstream sequence were fused to the npt-II reporter gene to determine the tissue-specific activity of the chimeric constructs in stably transformed tobacco plants. The results indicate the presence of positive regulatory, enhancer-like cis elements within 566 bp of the upstream sequence. Most importantly, however, these elements are only fully functional in conjunction with the core motif CATGCATG of the legumin box around position -95, since destruction of the motif by a 6 bp deletion in an otherwise intact 2.4 kb upstream sequence drastically reduces expression in seeds. At the same time, low level expression in leaves is observed. The occurrence of similar CATGCATG consensus cis elements with alternating purine and pyrimidine base pairs in front of several other plant genes suggests a functional role of the motif in a wider range of plant promoters.

Base Sequence↗
PubMed1982

Spectral analysis of impulse noise for hearing conservation purposes.

Damage-risk criteria for impulse noise does not presently take the spectrum of the impulse into account; however, it is known that the human auditory system is spectrally tuned. The present paper advocates the extension to impulse noise of the noise dose concept which is widely used for continuous noise. This approach is based upon sound exposure instead of sound pressure. An A-weighting filter or an octave band analysis can then be used to take the spectral content of the impulses into account. The equipment needed for applying these procedures for impulse noise is an integrating sound level meter or a digital Fourier processor. Generalized spectral methods have been evaluated by means of an impulse simulation applied to a mathematical model of the human hearing mechanism. The results of this simulation agree with the most recent experiments on impulse noise and fully support the proposed rating methods. This conclusion must be emphasized as it leads the derivation of a uniform procedure for predicting loudness and damage risk for hearing which is applicable for continuous noise as well as for impulse noise.

Environmental Exposure↗
PubMed2004

Analysis of ascidian Not genes highlights their evolutionarily conserved and derived features of structure and expression in development.

The ascidian larva is often regarded as an organism close to the ancestral form of chordates, while it is generally accepted that the Spemann's organizer is absent from ascidian embryos. Not is one of the genes expressed in the organizer to execute functions in vertebrate embryos. To address the extent of conservation of Not gene expression among ascidians and vertebrates, we examined the structure and developmental expression of Not of the two distantly related ascidian species, Halocynthia and Ciona. Putative ascidian Not proteins were noted by the absence of one of the two motifs conserved among Not proteins of sea urchin and vertebrates. Analysis by in situ hybridization revealed that Not gene expression of ascidians could be categorized into three types: expression likely to be conserved between ascidians and vertebrates, that probably unique to ascidians, and that specific to ascidian species. Expression of ascidian Not in the posterior end of the tail as well as the notochord and a small part of the anterior neural tube at the tailbud stage is reminiscent of the expression of the vertebrate counterparts in the tailbud, which is regarded as a continuation of the organizer and the pineal gland, respectively. The expression of Not in the epidermis precursors during cleavage stage may be unique to ascidians. In the light of the present findings, evolutionary aspects of Not genes are discussed.

Animals↗
PubMedDate not supplied

Interaction of silent and replacement changes in eukaryotic coding sequences.

We examined the codon usages in well-conserved and less-well-conserved regions of vertebrate protein genes and found them to be similar. Despite this similarity, there is a statistically significant decrease in codon bias in the less-well-conserved regions. Our analysis suggests that although those codon changes initially fixed under amino acid replacements tend to follow the overall codon usage pattern, they also reduce the bias in codon usage. This decrease in codon bias leads one to predict that the rate of change of synonymous codons should be greater in those regions that are less well conserved at the amino acid level than in the better-conserved regions. Our analysis supports this prediction. Furthermore, we demonstrate a significantly elevated rate of change of synonymous codons among the adjacent codons 5' to amino acid replacement positions. This provides further support for the idea that there are contextual constraints on the choice of synonymous codons in eukaryotes.

Cell Physiological Phenomena↗
PubMed1996

Conservative management of mechanical neck pain: systematic overview and meta-analysis.

OBJECTIVE: To review the efficacy of conservative management of mechanical neck disorders. METHODS: Published and unpublished reports were identified through computerised and manual searches of bibliographical databases, reference lists from primary articles, and letters to authors, agencies, foundations, and content experts. Selection criteria were applied to blinded articles, and selected articles were scored for methodological quality. Effect sizes were calculated from raw pain scores and combined by using meta-analytic techniques when appropriate. RESULTS: Twenty four randomised clinical trials met the selection criteria and were categorised by type of intervention: nine used manual treatments; 12 physical medicine methods; four drug treatment; and three education of patients (four trials investigated more than one form of intervention). The intervention strategies were summarised separately. Pooling of studies was considered only within each category. Five of the nine trials that used manual treatment in combination with other treatments were combined. One to four weeks after treatment the pooled effect size was -0.6 (95% confidence interval -0.9 to -0.4), equivalent to an improvement of 16 (6.9 to 23.1) points on a 100 point scale. Sensitivity analyses on study quality, chronicity, and data imputation did not alter this estimate. For other interventions, studies could not be combined to arrive at pooled estimates of effect. CONCLUSIONS: There is little information available from clinical trials to support many of the treatments for mechanical neck pain. In general, conservative interventions have not been studied in enough detail to assess efficacy or effectiveness adequately.

Anti-Inflammatory Agents↗
PubMed2004

Conservative management for postprostatectomy urinary incontinence.

BACKGROUND: Urinary incontinence is common after both radical prostatectomy and transurethral resection. Conservative management includes pelvic floor muscle training, biofeedback, electrical stimulation, compression devices (penile clamps), lifestyle changes, extra-corporeal magnetic innervation or a combination of methods. OBJECTIVES: To assess the effects of conservative managements for urinary incontinence prostatectomy. SEARCH STRATEGY: We searched the Cochrane Incontinence Group trials register (searched 2 July 2003), MEDLINE (January 1966 to January 2004), EMBASE (January 1988 to January 2004), CINAHL (January 1982 to January 2004), PsycLIT (January 1984 to January 2004), ERIC (January 1984 to January 2004), the reference lists of relevant articles, handsearched conference proceedings and contacted investigators to locate studies. SELECTION CRITERIA: Randomised controlled trials evaluating conservative interventions for urinary continence after prostatectomy. DATA COLLECTION AND ANALYSIS: At least two reviewers assessed the methodological quality of trials and abstracted data. MAIN RESULTS: Ten trials met the inclusion criteria, eight trials amongst men after radical prostatectomy, one trial after transurethral resection of prostate and one after either operation. There was considerable variation in the interventions, populations and outcome measures. The trials were of moderate quality and data were not available for many of the pre-stated outcomes. Confidence intervals were wide: it was not possible to reliably identify or rule out a useful effect. There was some support from five trials for pelvic floor muscle training with biofeedback being better than no treatment or sham treatment in the short term for men after radical prostatectomy: relative risk for incontinence with pelvic floor muscle training and biofeedback versus no treatment: 0.74 (95% confidence interval 0.60 to 0.93). Analysis of other conservative interventions such as pelvic floor muscle training alone, transcutaneous electrical nerve stimulation and rectal electrical stimulation, or combinations of these interventions were inconclusive. There were too few data to determine effects on incontinence after transurethral resection of the prostate. The findings should be treated with caution as there were few studies, all of moderate quality. Men in one trial reported a preference for one type of external compression device compared to two others or no treatment. The effect of other conservative interventions such as lifestyle changes remains undetermined as no trials involving these interventions were identified. Men's symptoms tended to improve over time, irrespective of management. REVIEWERS' CONCLUSIONS: The value of the various approaches to conservative management of postprostatectomy incontinence remains uncertain. There may be some benefit of offering pelvic floor muscle training with biofeedback early in the postoperative period immediately following removal of the catheter as it may promote an earlier return to continence. Long-term incontinence may be managed by external penile clamp, but there are safety problems.

Biofeedback, Psychology↗
PubMed1994

Structure and localization of the IGFBP-1 gene and its expression during liver regeneration.

Insulin-like growth factor-binding protein-1s are important modulators of the insulin-like growth factors that may have both positive and negative effects on the ability of insulin-like growth factors to stimulate cell growth. The IGFBP-1 gene is one of the most highly induced immediate-early genes after partial hepatectomy. The IGFBP-1 gene is also expressed at a high level during fetal liver development and in response to nutritional changes and diabetes. Therefore it may have important roles in liver growth and metabolism. To begin to examine the regulation of this gene, we cloned and sequenced the entire mouse IGFBP-1 gene. Its structure is highly similar to that of the human gene, and, in addition to the exonic regions, the two genes are highly conserved in specific regions in the promoter and first intron. Analysis of this conservation allows us to predict important regulatory sites that define the tissue specific and insulin-mediated regulation of the gene and identify potential sites that might be important for the transcriptional induction during liver regeneration. The mouse gene is located on mouse chromosome 11; it is found at the boundary between regions in the mouse genome homologous to human chromosomes 22 and 7. We found IGFBP-1 mRNA in both parenchymal and nonparenchymal RNA after partial hepatectomy. Using in situ hybridization of IGFBP-1 mRNA in regenerating rat liver tissue, we demonstrated IGFBP-1 transcripts in several cell types. We found that IGFBP-1 gene induction after partial hepatectomy is paralleled by protein expression.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed2001

[Construction of mucosal vaccine derived from HBV surface antigen epitope A and the assay of its immunogenicity].

The fusion gene of HBV(adr) surface antigen epitope and B subunit of Cholera toxin was constructed and expressed successfully in E. coli at high yield. After denaturation-renaturation process, SDS-PAGE analysis showed that most of the renatured product reassociated in a pentameric form which was the same as natural CTB. Western blot analysis indicated that the immunogenicity of HBsAg antigen epitope was conserved. Moreover, ELISA analysis of the sera of orally, intranasally and intraperitoneally immunized mice showed that the circulating IgG antibodies to HBsAg were developed. The results may be helpful for constructing the novel mucosal vaccine with high efficacy.

Animals↗
PubMed1998

Clonal analysis of cmp44E, which encodes a conserved putative transmembrane protein, indicates a requirement for cell viability in Drosophila.

We have identified the cmp44E gene which encodes a putative multi-pass transmembrane protein that is conserved from yeast to humans. The expression of cmp44E during embryogenesis is ubiquitous with notably higher levels in the CNS and brain. It is also expressed in the germline during the germarial stages as well as several later stages of oogenesis. Utilizing a P-element insertion at the 5' end of cmp44E we have isolated several deletions, created by imprecise excision events which eliminate most or all of its coding region. Analysis of these deficiencies has revealed that cmp44E is an essential gene required for embryogenesis. Results obtained from germline clone analysis indicate that cmp44E is not only required in the germline slem cells early in oogenesis, but is also required in other tissues probably due to it being required for cell viability. Finally, using germline transformation, we have identified a minimal genomic fragment capable of fully rescuing a null allele of cmp44E.

Amino Acid Sequence↗
PubMed1992

Amino acid substitution analysis of E. coli thymidylate synthase: the study of a highly conserved region at the N-terminus.

Amino acid substitution analysis within a highly conserved region of Escherichia coli thymidylate synthase (TS), using suppression of amber mutations by tRNA suppressors, has yielded a bank of 124 new mutationally altered TS proteins. These mutant proteins have been used to study the structure-function relationship of the Escherichia coli TS protein at the N-terminus corresponding to residues 20 through 35. This region contains a block of amino acids whose sequence has been well conserved among other known TS proteins from various organisms. Positions 20 through 25 contain a surface loop structure and positions 26 through 35 encompass a beta-strand. We find that residues surrounding a beta-bulge structure within the beta-strand are particularly sensitive to amino acid substitution, suggesting that this structure is maintained by a highly ordered packing arrangement. Three residues in the surface loop that are present at the base of the substrate binding pocket are also sensitive to amino acid substitution. The remainder of the conserved sites, including those at the dimer interface, are tolerant to most, if not all, of the substitutions tested.

Amino Acid Sequence↗
PubMed2005

Characterization of Spodoptera litura multicapsid nucleopolyhedrovirus 38.7 k protein, which contains a conserved BRO domain.

Homology analysis revealed that Spodoptera litura multicapsid nucleopolyhedrovirus (SpltMNPV) 38.7 k protein has 22-83% amino acid identities with Ecotropis obliqua NPV, Mamestra configurata MNPV, Helicoverpa armigera SNPV, H. zea SNPV, S. exigua MNPV and S. littoralis MNPV 38.7 k proteins. Analysis of the relationship of these 38.7 k proteins indicated that they contain a conserved BRO-N domain, and SpltMNPV and SpliMNPV 38.7 k proteins also contain a motif found in all known viral and prokaryotic single-strand DNA binding proteins. RT-PCR results showed that SpltMNPV 38.7 k gene is transcribed actively at the late stage of infection and the mRNA start site was mapped within a consensus baculovirus late promoter motif (ATAAG). Western blot analysis revealed that the 38.7 k was expressed in infected S. litura cells as a 41 kDa form and this protein distributed in the nucleus of infected cells. Using a histone extraction protocol, SpltMNPV 38.7 k could be detected in the histone H1 fraction. Micrococcal nuclease treatment released SpltMNPV 38.7 k protein from the chromatin fraction, suggesting that its involvement in nucleosome structures. Furthermore, column chromatography using DNA-cellulose showed that SpltMNPV 38.7 k protein interacted with nucleic acids. It was proposed that SpltMNPV 38.7 k might function as a DNA-binding protein.

Amino Acid Motifs↗
PubMedDate not supplied

[Conservative management of infected and/or exterior pacemakers. Analysis of 35 cases].

Thirty-five cases of infected pacemakers were revised comparing the results obtained through the conservative attitude in comparison to the traditional attitude. It was pointed out a way to better even further the results obtained through the conservative attitude. Some surgical and medical problems were analized and the way to came through them with respect to this complication, the literature that is in favor of this conduct was also analyzed.

Electrodes, Implanted↗
PubMed1998

A highly conserved genomic region in baculoviruses: sequence analysis of an 11.3 kbp DNA fragment (46.5-55.1 m.u.) of the Spodoptera exigua multicapsid nucleopolyhedrovirus.

A DNA fragment of 11.3 kilobase pairs (kbp) in size of the baculovirus Spodoptera exigua multicapsid nucleopolyhedrovirus (SeMNPV) genome (46.5 to 55.1 m.u.) was completely sequenced. Analysis of the sequence revealed eleven potential open reading frames (ORF). Ten of these ORFs showed significant amino acid identity to Autographa californica MNPV (AcMNPV) and Orgyia pseudotsugata MNPV (OpMNPV) genes p6.9, lef5, 38K, p19, p143, p25, p18, vp33, lef4, and vp39. One ORF (XC12) has no homolog in other baculoviruses and may be unique to SeMNPV. All but three of these putative genes are preceded by the consensus baculovirus late promoter element (5'-ATAAG-3'). The genetic organization and the putative map of transcripts of this fragment suggested that this region is highly similar to a region in AcMNPV fragment EcoRI-D. Comparison of the genetic organization of this 11.3 kbp fragment with the genomes of AcMNPV, OpMNPV, Bombyx mori NPV (BmNPV) and SeMNPV revealed that this region is highly conserved among baculovirus genomes. This is in contrast to the genetic organization of the polyhedrin-p10 region, which is much more diverged, but has been taken as point of reference to orient baculovirus physical maps. Through its diversity the latter region, however, would be an excellent candidate to determine baculovirus relatedness and phylogeny. The presence of conserved and diverged regions in baculovirus genomes with respect to gene order is reminiscent to the situation in other large DNA viruses, such as herpes- and poxviruses, where conserved central and diverged terminal parts are common characteristics. The role of this feature in the genomic organization of large DNA viruses is discussed with particular emphasis on virus replication and evolution.

Animals↗