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At least 1,621 records · Page 90Linked to original sources
PubMed1993

Molecular cloning and characterization of the mouse RB1 promoter.

We report the isolation and characterization of the mouse RB1 promoter and surrounding DNA sequences, and the identification of elements required for basal transcriptional activity. The mouse RB1 promoter, like the human homologue, has a high G + C content, constitutes a CpG island and is devoid of typical TATA and CAAT boxes. The first 235 base-pairs upstream of the translation initiation codon in the mouse promoter exhibit 80% sequence homology with the human sequence. This homology includes a region which contains putative binding sites for the transcription factors Sp1, ATF and E2F/DRTF1. Four major transcription initiation sites were identified downstream of this conserved region. Mutational analysis revealed that the Sp1 and ATF binding sites, but not the putative E2F/DRTF1 binding site, are critical for promoter activity. Complete disruption of the putative Sp1 and ATF sites abrogated transcription, whereas the introduction of point mutations, previously identified in the Sp1 and ATF sites in two low penetrance retinoblastoma families, reduced promoter activity in a cell type specific manner. Less reduction in activity occurred in retinoic acid induced differentiated P19 cells and NIH3T3 mouse fibroblasts than in undifferentiated embryonal carcinoma P19 cells. Activity of the RB1 promoter was found to be stimulated in retinoic-acid induced differentiated P19 cells compared to undifferentiated P19; this stimulation required intact Sp1 and ATF sites but not the putative E2F/DRTF1 binding site. Our results indicate that basal level of RB1 expression is governed by Sp1 and ATF.

Animals↗
PubMed1996

The var genes of Plasmodium falciparum are located in the subtelomeric region of most chromosomes.

PfEMP1, a Plasmodium falciparum-encoded protein on the surface of infected erythrocytes is a ligand that mediates binding to receptors on endothelial cells. The PfEMP1 protein, which is encoded by the large var gene family, shows antigenic variation and changes in binding phenotype associated with alterations in antigenicity. We have constructed a yeast artificial chromosome contig of chromosome 12 from P. falciparum and show that var genes are arranged in four clusters; two lie amongst repetitive subtelomeric sequences and two occur in the more conserved central region. Analysis of parasite chromosomes by pulsed field gel electrophoresis (PFGE) demonstrates that most contain var genes and two-dimensional PFGE has shown that var genes are located at chromosome ends interspersed amongst repetitive sequences present in the subtelomeric complex. Analysis of a var gene located in the subtelomeric region of chromosome 12 has shown that it has close homologues at the opposite end of the chromosome and in the subtelomeric region of two other chromosomes. This suggests that recombination between heterologous chromosomes has occurred in the subtelomeric regions of these chromosomes. The subtelomeric location of var genes dispersed amongst repetitive sequences has important implications for generation of antigenic variants and novel cytoadherent specificities of this protein.

Animals↗
PubMed1996

[Asymptomatic pneumoperitoneum after fiber gastroscopy].

A case of asymptomatic pneumoperitoneum after fiber gastroscopic sclerosis of bleeding gastric erosions is presented. Air bubbles in gastric curvatures without evidence of macroscopic perforation were found at laparotomy. We comment the etiologies of pneumoperitoneum without macroscopic perforation and suggest that the management of patients with asymptomatic pneumoperitoneum with normal clinical examination and blood analysis might be conservative to avoid needless laparotomies.

Aged↗
PubMed1996

Cloning of the mouse fusin gene, homologue to a human HIV-1 co-factor.

Previous studies have demonstrated that mouse cells do not become infected with HIV-1 despite transfection with human CD4. Recently, a human protein termed "fusin" with characteristics of a seven-transmembrane-spanning receptor was found to be a co-factor required for the entry and fusion of HIV-1 with human CD4-bearing lymphocytes. Thus, cloning of the murine homologue of the human fusin (also termed CXCR-4) gene could provide an important comparative tool for identification of the structures crucial for fusin function. Using degenerate PCR, the mouse homologue of human fusin was cloned from a peritoneal exudate cell cDNA library. The predicted amino acid sequence is 91% identical to human fusin. Twenty-eight of the 37 amino acid differences between mouse and human fusin are located in the ectodomains, suggesting that the intracytoplasmic components that mediate G protein binding and signaling are highly conserved. Northern blot analysis showed a message of 2.2 kb in thymus, spleen, neutrophils, and primary astrocyte cultures. Lymphoid and monocyte cell lines also expressed message for fusin. The coding regions of most chemokine receptors lack introns. In contrast, cloning of genomic DNA for mouse fusin revealed the presence of a 2.3-Kb intron separating the first seven amino acids from the remaining 352 residues. Therefore, the mouse fusin gene has a unique genomic organization compared with other chemokine receptors.

Amino Acid Sequence↗
PubMed1997

T cell receptor of Fas-sensitive T cells in rheumatoid synovium.

Apoptosis is found in synoviocytes and CD3+ T cells in the synovium of patients with rheumatoid arthritis (RA). To analyze the pathogenesis of apoptosis in rheumatoid synovium, we examined the expression of Fas Ag, Fas ligand (Fas-L), and TCR on T cells susceptible to anti-Fas mAbs. Fas Ag is expressed on 40 to 60% of CD3+ T cells in the synovium as measured by immunohistochemical and flow cytometry methods. It was observed by the reverse transcription-PCR method that Fas-L is overexpressed on T cells infiltrating the rheumatoid synovium. These results suggest that apoptosis in RA synovium is mediated by the Fas/Fas-L pathway. PCR-single-strand conformation polymorphism clearly demonstrated that more than 50% of T cells that accumulate in synovium are removed by incubation with anti-Fas mAbs for 24 h in vitro, indicating that these cells are Fas sensitive. Junctional sequence analysis revealed several conserved amino acids motifs (ERxxxSMNTE, IAAEGLLG, QxEGxD, VPD, TLAGxYNEQ, EPSE, LTNxGEL, QGK, NIP, GLL, and KWT) in the CDR3 region of accumulated Fas-sensitive T cell clones, whereas these motifs were not detected in Fas-resistant clones. In conclusion, our findings support the notion that Fas-sensitive T cells in rheumatoid synovium are generated by Ag stimulation and recognize relatively limited T cell epitopes on autoantigens, suggesting that susceptibility to anti-Fas mAbs might be a selection marker for activated autoreactive T cells in RA.

Aged↗
PubMed1997

Biocultural approaches to health and mortality in an Old Order Amish community.

The assumption that Amish cultural value of cooperation leads to greater longevity, prosperity and well-being among elders was examined using historical demographic and ethnographic analysis in a conservative Old Order Amish community. Migration, fertility, mortality and morbidity data since 1948 were used to identify population structure. The population pyramid in the Amish community (3% of the population over age 60, compared to 18% of the neighboring non-Amish rural area) is largely determined by natural fertility with low infant mortality. Household ethnography explored health beliefs, access to health care, caregiving patterns, and economic strategies. The perception that community cooperation and altruistic behavior were of benefit to Amish health is supported by mortality rates. Amish age standardized death rates were 19% below the US death rate in 1960. Migrating to form new communities and selectively utilizing acute (but not preventive or public) health care services, emerged as strong cultural patterns that facilitate reproductive success among the Amish.

Anthropology, Cultural↗
PubMed1997

Characterization and expression of c-type lysozyme cDNA from Japanese flounder (Paralichthys olivaceus).

Lysozyme is a widely distributed enzyme located in the serum, skin mucus, and other organs of fish, which is responsible for catalyzing the hydrolysis of the cell walls of most bacteria. A c-type of lysozyme cDNA was cloned from a kidney cDNA library of the Japanese flounder (Paralichthys olivaceus). The cDNAs consisted of 612 bp, which coded for 143 amino acid residues. The deduced amino acid sequence of Japanese flounder c-type lysozyme possessed 72.9%, 57.4%, and 65.4% identities with rainbow trout, chicken, and human c-type lysozymes, respectively. Comparison of the c-type lysozymes showed that the catalytic residues, the residues binding to sugar chains, and cysteine residues were completely conserved. Northern blot analysis indicated that the c-type lysozyme gene is apparently transcribed in the head kidney, posterior kidney, spleen, brain, and ovary of healthy flounder. When flounder were experimentally infected with Edwardsiella tarda, quantities of the c-type lysozyme mRNA increased in the head kidney, spleen, and ovary of the flounder.

Amino Acid Sequence↗
PubMedDate not supplied

[Conservative treatment of benign esophageal strictures using dilation. Analysis of 500 cases].

UNLABELLED: The benign esophageal stenoses (BES) are common complications owing to many etiologies: gastroesophageal reflux, ingestion of corrosive agents, esophageal surgery, radiotherapy, postendoscopic variceal sclerotherapy, drug ingestion, prolonged nasogastric intubation, extrinsic compression and esophageal webs. Esophageal dilatations are worldwide recommended to treat this complication, employing dilators of many types and diameters and facilitating the food ingestion. PURPOSE: Evaluation of the results and advantages of the conservative treatment of the BES using esophageal dilatations, in outpatient service of upper digestive endoscopy. METHODS: During the period from 1981 to 1999, 500 patients with BES were treated and followed up at the Gastrocenter - UNICAMP, in an individually Program of Esophageal Dilatation for each case. The highest number of cases was under ages from 31 to 60 years old (52,8%), and males (59,2%). The most predominant etiologies were: peptic stenosis (30,4%), caustic ingestion (23,6%), anastomosis (23,2%), megaesophagus (8,0%) and prolonged nasogastric ingestion entubation (6,4%), totalizing 91,6% of the BES. Most of patients (94,2%) were submitted to the maximum of 25 dilations. Dilators from 10,5 to 16 mm were employed in 95,6% of the cases. The duration of the treatment was 24 months in 76,2% of the BES. Esophageal perforations occurred in 6 patients (1,2%), without mortality. RESULTS: Were considered excellent, good and bad results, respectively in 76,2%, 18,2% and 5,6% of the cases. On the other hand, excellent results were recorded in 81,0% of the peptic stenosis, 66,1% of the caustic stenosis and 82,7% of the anastomotic stenosis. The conservative treatment failed in 9,3% of the caustic stenosis, 4,3% of the anastomotic stenosis and 3,9% of the peptic stenosis. Thus, the caustic stenosis were unsuccessfull in the highest percentage of unsuccessful. CONCLUSION: The conservative treatment using guidewire dilators (Savary-Gilliard and Eder-Puestow) is the first choice in the BES, is effective for long time, with short complications and the surgical treatment is indicated only when the dilatations failed.

Adolescent↗
PubMed2005

Variation in structural location and amino acid conservation of functional sites in protein domain families.

BACKGROUND: The functional sites of a protein present important information for determining its cellular function and are fundamental in drug design. Accordingly, accurate methods for the prediction of functional sites are of immense value. Most available methods are based on a set of homologous sequences and structural or evolutionary information, and assume that functional sites are more conserved than the average. In the analysis presented here, we have investigated the conservation of location and type of amino acids at functional sites, and compared the behaviour of functional sites between different protein domains. RESULTS: Functional sites were extracted from experimentally determined structural complexes from the Protein Data Bank harbouring a conserved protein domain from the SMART database. In general, functional (i.e. interacting) sites whose location is more highly conserved are also more conserved in their type of amino acid. However, even highly conserved functional sites can present a wide spectrum of amino acids. The degree of conservation strongly depends on the function of the protein domain and ranges from highly conserved in location and amino acid to very variable. Differentiation by binding partner shows that ion binding sites tend to be more conserved than functional sites binding peptides or nucleotides. CONCLUSION: The results gained by this analysis will help improve the accuracy of functional site prediction and facilitate the characterization of unknown protein sequences.

Amino Acid Sequence↗
PubMed2005

Randomized trials of breast-conserving therapy versus mastectomy for primary breast cancer: a pooled analysis of updated results.

We have undertaken a pooled analysis of the 6 major randomized trials comparing mastectomy (MT) and breast-conserving therapy (BCT) in the treatment of primary breast cancer. Specifically, these trials compared the 2 most widely used options in local treatment: mastectomy and axillary dissection (MT) versus breast-conserving surgery, axillary dissection, and breast radiotherapy (BCT). The early results of these 6 trials formed the basis for a 1990 National Institutes of Health Consensus statement. However, most of these trials have recently published long-term follow-up results, and this pooled analysis incorporates the updated results of these 6 trials. For each of these trials, the observed number of treatment events was compared with that expected under the null hypothesis, given the number of patients per arm and the total number of events. Approximate odds ratios were computed using the observed and expected number of events, and the variance of the observed number of events. These were then pooled across trials to give overall odds ratios for the risk of locoregional recurrence, total recurrence, and death. Four of the 6 trials show that MT significantly reduces the risk of locoregional recurrence when compared with BCT, and the pooled odds ratio also shows a significant benefit for MT (odds ratio [OR], 1.561; 95% confidence interval [CI], 1.289-1.890; P < 0.001). However, only 1 trial shows a statistically significant benefit for MT in reducing mortality, and the pooled odds ratio shows no significant difference between MT and BCT (OR, 1.070; 95% CI, 0.935-1.224; P = 0.33). This pooled analysis confirms that MT and BCT have comparable effects on mortality, even after long-term follow up. However, BCT is associated with a significantly greater risk of locoregional recurrence.

Adult↗
PubMed2000

Comparative sequence analysis of 634 kb of the mouse chromosome 16 region of conserved synteny with the human velocardiofacial syndrome region on chromosome 22q11.2.

Mouse genomic DNA sequence extending 634 kb on proximal mouse chromosome 16 was compared to the corresponding human sequence from chromosome 22q11.2. Haploinsufficiency for this region results in velocardiofacial syndrome (VCFS) in humans. The mouse region is rearranged into three conserved blocks relative to human, but gene content and position are highly conserved within these blocks. Examination of the boundaries of one of these blocks suggested that the evolutionary chromosomal rearrangement occurred in the mouse lineage, resulting in inactivation of the mouse orthologue of ZNF74. Sequence analysis identified 21 genes and 15 ESTs. These include 2 novel genes, Srec2 and Cals2, and previously undescribed splice variants of several other genes. Exon discovery was carried out using GRAIL2, MZEF, or comparative analysis across 491 kb of conserved mouse and human sequence. Sequence comparison was highly effective, identifying every gene and nearly every exon without the high frequency of false-positive predictions seen when algorithmic methods were used alone. In combination, these procedures identified every gene with no false-positive predictions. Comparative sequence analysis also revealed regions of extensive conservation among noncoding sequences, accounting for 6% of the sequence. A library of such sequences has been established to form a resource for generalized studies of regulatory and structural elements.

Abnormalities, Multiple↗
PubMedDate not supplied

[The surgery of the endolymphatic sac: a conservative or destructive procedure?].

A detailed analysis of different aspects relative to endolymphatic sac surgery employed as conservative surgical treatment in Menière's disease is presented. The presumed basic principles for this type of surgery, which have led several otologists to adopt this procedure in the therapeutical protocol followed in Menière's disease, are discussed along with the good symptomatological results obtained. Particular emphasis is put on the multiple functions which have been attributed to the endolymphatic sac in the functional dynamics of the entire inner ear environment. Among these functions, relevance is given to the secretory activity, which is presumed to be triggered by endolymphatic dysbarisms, which implies that macromolecules that are able to interact with fluid metabolism (glycosaminoglycans) might flow into the luminal endolymphatic space, a phenomenon which may well open new perspectives for the pathogenesis and treatment of Menière's disease. On the grounds of these premises, the conservative aspect of endolymphatic sac surgery, along with its mechanism of action, is reassessed.

Ear, Inner↗
PubMed1994

Structural similarities between chaperone molecules of the HSP60 and HSP70 families deduced from hydrophobic cluster analysis.

In this study, the conservation of strong structural landmarks between all the members of two chaperone families (HSP60 and HSP70) was deduced from their sequences by hydrophobic cluster analysis. On this basis, we propose that the ATP-binding environment is maintained by a similar fold in both protein families. The observed similarities extend throughout the proteins, including both the ATPase domain and the C-terminal substrate-binding domain.

Adenosine Triphosphatases↗
PubMed2001

[Conservative treatment of choroidal melanoma using iodine-125 brachytherapy, technique and preliminary analysis of 78 patients].

PURPOSE: Iodine 125 curietherapy is one of the conservative treatments of uveal melanoma. The technique used to achieve these results was simplified through the physical characteristics of the radioelement and the optimized-dosimetry program employed. PATIENTS AND METHODS: 78 patients with choroidal melanoma were treated with iodine 125. About 100 Gy were delivered to the superior pole of the tumour. The minimal length of follow-up was 17 months and the average, 67 months. RESULTS: There was 88% local control, leading to lowered visual acuity in 76% of the cases. Radiation retinopathy, directly related to proximity to the macula, is the principle etiology. Seven patients died of hepatic metastasis, five patients were enucleated. Four patients were further treated with protontherapy to make up for noncontrol locally. CONCLUSION: One dose of 100 Gy to the superior pole of the tumor seemed to lead to good local control, with the exception of complications related to proximity to the macula and the optic nerve. In this attempt to optimize irradiation, the time lapse between any benefit in local control derived from irradiation and posttherapeutic complications observed remains insufficient to evaluate any relationship.

Adult↗
PubMed1999

Genomic analysis of male germ cell-specific actin capping protein alpha.

The Gsg3 gene which expresses specifically in haploid germ cells is a mouse testicular homolog of somatic cell type actin capping protein alpha (ACP alpha). We have obtained a mouse Gsg3 genomic clone using cDNA as a probe. Sequencing data showed that the Gsg3 gene was not interrupted by introns. The transcription initiation site of the gene was preceded not by a TATA box or GC rich promoter motifs, but by two consensus cAMP-response element (CRE) motifs at the putative position. Southern blotting analysis showed that Gsg3 is a single copy gene in the mouse, and conserved in mammals. Phylogenetic analysis showed that Gsg3 is a novel ACP alpha specific for haploid germ cells.

Amino Acid Sequence↗
PubMed1991

Sequence, function, and regulation of the Vmw65 gene of herpes simplex virus type 2.

We determined the sequence of the gene for the virion transactivator protein Vmw65 of herpes simplex virus type 2 (HSV-2), strain 333. An analysis of the coding sequence revealed an overall high degree of primary sequence conservation (86%) relative to the HSV-1 protein, although the carboxy-terminal region which encompasses the powerful acidic transactivation domain of the HSV-1 protein was slightly less well conserved (70%). One important change in this region was the presence of a proline residue in a region of the HSV-2 protein which is thought to form an amphipathic alpha-helix in the HSV-1 homolog. Despite the occurrence of this helix-disrupting residue, the HSV-2 protein exhibited powerful transactivation properties for immediate-early target promoters. We also demonstrated that the HSV-2 protein forms a transcriptional complex (TRF.C) with the cellular Oct-1 protein and target TAATGARAT elements from immediate-early promoters. A comparison of upstream sequences from the two Vmw65 genes revealed good conservation of proximal promoter elements but considerable divergence elsewhere. Specifically, the HSV-2 promoter alone carries 9.5 copies of a 9-bp direct repeat (GGGGCGGGA) ending 85 bp upstream of the conserved TTAAAT element. An analysis of transcription factor binding sites in vitro revealed that cellular factor Sp1 bound to the direct repeat sequence of the HSV-2 promoter and that cellular factor USF bound to a proximal element present in both HSV-1 and HSV-2 promoters. Mutational analysis of the HSV-2 promoter demonstrated that the integrity of both of these binding sites was important for the full activity of the promoter.

Amino Acid Sequence↗
PubMed1992

cDNA cloning and molecular characterization of MSE55, a novel human serum constituent protein that displays bone marrow stromal/endothelial cell-specific expression.

Hemonectin is a lineage-specific cytoadhesive protein that may be involved in the developmentally regulated adhesion of granulocytic cells to bone marrow stroma. Immunoblot analysis using an anti-hemonectin antibody recognizes two distinct immunoreactive species in endothelial cell lysates (approximately M(r) 65,000) and human serum (approximately M(r) 55,000). Initial characterization of the 55-kDa protein has now been completed by isolating the cDNA from a human endothelial cell expression library. Sequence analysis of overlapping clones identifies a composite sequence spanning 2030 nucleotides with an open reading frame of 1173 base pairs. No significant sequence similarity was observed on analysis of current GenBank databases. The open reading frame was expressed as a recombinant protein in Escherichia coli and used as an immunogen for the production of a specific polyclonal antibody. Immunoblotting with this antibody identifies a single immunoreactive species of apparent M(r) 55,000 in HUVEC lysates and human serum, confirming that a secreted form normally circulates as a serum constituent protein. This antibody fails to recognize purified hemonectin, suggesting that the M(r) 55,000 protein is not hemonectin. Cross-species Southern blot analysis reveals persistent hybridizing fragments in all species tested, suggestive of a developmentally conserved function. Northern blot analysis demonstrates expression limited to endothelial and bone marrow stromal cells, but not poly(A) RNA from monkey liver, spleen, brain, lung, and kidney. On this basis, we have designated this novel protein MSE55, for marrow stromal/endothelial cell protein with a molecular mass of 55,000 daltons. Its tissue-specific expression may suggest a functional role in hematopoiesis.

Adaptor Proteins, Signal Transducing↗
PubMed2001

Long-range comparison of human and mouse SCL loci: localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences.

Long-range comparative sequence analysis provides a powerful strategy for identifying conserved regulatory elements. The stem cell leukemia (SCL) gene encodes a bHLH transcription factor with a pivotal role in hemopoiesis and vasculogenesis, and it displays a highly conserved expression pattern. We present here a detailed sequence comparison of 193 kb of the human SCL locus to 234 kb of the mouse SCL locus. Four new genes have been identified together with an ancient mitochondrial insertion in the human locus. The SCL gene is flanked upstream by the SIL gene and downstream by the MAP17 gene in both species, but the gene order is not collinear downstream from MAP17. To facilitate rapid identification of candidate regulatory elements, we have developed a new sequence analysis tool (SynPlot) that automates the graphical display of large-scale sequence alignments. Unlike existing programs, SynPlot can display the locus features of more than one sequence, thereby indicating the position of homology peaks relative to the structure of all sequences in the alignment. In addition, high-resolution analysis of the chromatin structure of the mouse SCL gene permitted the accurate positioning of localized zones accessible to restriction endonucleases. Zones known to be associated with functional regulatory regions were found to correspond precisely with peaks of human/mouse homology, thus demonstrating that long-range human/mouse sequence comparisons allow accurate prediction of the extent of accessible DNA associated with active regulatory regions.

Animals↗