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Functional analysis of the 5' flanking sequence in the ovine beta 1-adrenergic receptor gene.

Functional data for the promoter of the beta 1-adrenergic receptor (beta 1AR) gene are lacking. We previously cloned the ovine beta 1AR gene and mapped the transcription start sites. We now report data on ovine beta 1AR gene expression obtained by transient transfection. Progressive deletion of upstream 5' flanking region moderately increased transcription activity in three cell lines compared to the full-length promoter. Deletion of sequences between -1530 and -953 produced the greatest increase in transcriptional activity. This region encompassed a putative GRE and an AP1 site. Deletion of the transcription start sites eliminated nearly all of the activity. Dexamethasone significantly increased activity of each of the promoter constructs tested in C6 glioma cells and an embryonic myocardial cell line, W1 cells. T3 alone had no effect and cotreatment with T3 did not augment the effects of dexamethasone. We conclude, basal transcription activity is repressed by a mechanism which operates through element(s) in the proximal promoter. Glucocorticoids increase transcription through mechanism(s) within the same region. We speculate that this region in the ovine beta 1AR promoter may be responsible for its unique transcription regulation.

Animals↗

Functional analysis of the heterologous NSP1 genes in the genetic background of simian rotavirus SA11.

Function of rotavirus NSP1 was analyzed by using single-NSP1 gene-substitution reassortants, SKF, SDF, and SNF which have the NSP1 gene derived from human rotaviruses KU, DS-1, and canine rotavirus K9, respectively, in the genetic background of simian rotavirus SA11. The NSP1 genes from KU, DS-1, K9, and SA11 exhibited 58-76% nucleotide sequence identity to one another. No substantial difference in viral growth was observed among the reassortants and SA11. However, production of NSP1 was not detected in SNF when viral proteins were labelled with 35S-methionine during replication in MA104 cells, in contrast to SA11, SKF and SDF which exhibited evident expression of NSP1. Difference in reassortant formation was examined among the reassortant clones generated between human rotavirus strain 69M and either of SA11, SKF or SNF. Although reassortant formation rate was significantly lower in the cross 69M x SNF than the other crosses, selection rates of RNA segments from parent strain 69M in the resultant reassortants was similar among the crosses. Selectivity of homologous and heterologous NSP1 genes in SA11 background was also analyzed by mixed infection and multiple passages among the single-NSP1 gene-reassortants and/or SA11, KU NSP1 gene was selected most frequently, whereas homologous (SA11) NSP1 gene was least efficiently segregated. These results indicated that viral growth and genome segment reassortment with other viruses may not be influenced by the presence of heterologous NSP1 and its expression level, while genomic diversity of NSP1 genes might have been associated with the relative adaptability to the genetic background of SA11.

Animals↗

Nucleotide sequence comparisons and functional analysis of yeast centromere DNAs.

We determined the nucleotide sequence of DNA segments containing functional centromeres (CEN3 and CEN11) isolated from yeast chromosomes III and XI. The two centromere regions differ in primary nucleotide sequence, but contain structural features in common. Both centromere regions contain an extremely A + T-rich core segment 87-88 bp in length, flanked by two short sequences (14 bp and 11 bp) that are identical in both DNAs. These elements plus one additional 10 bp region of perfect homology are positioned in an almost identical spatial arrangement within the two centromere regions. Significant homologies are also observed among the sequences flanking the high A + T region and various satellite DNA sequences from higher eucaryotes, although no repeated sequences occur near the yeast centromeres. Centromere activity in vivo is maintained on relatively small DNA fragments (627 bp for CEN3 and 858 bp for CEN11), as assayed by mitotic stabilization of autonomously replicating ars plasmids in yeast.

Base Sequence↗

Structural and functional analysis of bovine herpesvirus 1 minor glycoproteins.

This paper focuses on the structure and functions of bovine herpesvirus 1 minor glycoproteins gH, gE, gG and gp42. It reviews the progress which has been made in their identification and characterization, in the study of their temporal expression and processing in infected cells, and finally in the understanding of their biological activities. In addition, aspects discussed include a comparison with two other alphaherpesviruses, namely herpes simplex virus and pseudorabies virus.

Animals↗

The role of UV-B radiation in aquatic and terrestrial ecosystems--an experimental and functional analysis of the evolution of UV-absorbing compounds.

We analysed and compared the functioning of UV-B screening pigments in plants from marine, fresh water and terrestrial ecosystems, along the evolutionary line of cyanobacteria, unicellular algae, primitive multicellular algae, charophycean algae, lichens, mosses and higher plants, including amphibious macrophytes. Lichens were also included in the study. We were interested in the following key aspects: (a) does the water column function effectively as an 'external UV-B filter'?; (b) do aquatic plants need less 'internal UV-B screening' than terrestrial plants?; (c) what role does UV screening play in protecting the various plant groups from UV-B damage, such as the formation of thymine dimers?; and (d) since early land 'plants' (such as the predecessors of present-day cyanobacteria, lichens and mosses) experienced higher UV-B fluxes than higher plants, which evolved later, are primitive aquatic and land organisms (cyanobacteria, algae, lichens, mosses) better adapted to present-day levels of UV-B than higher plants? Furthermore, polychromatic action spectra for the induction of UV screening pigments of aquatic organisms have been determined. This is relevant for translating 'physical' radiation measurements of solar UV-B into 'biological' and 'ecological' effects. From the action spectra, radiation amplification factors (RAFs) have been calculated. These action spectra allow us to determine any mitigating or antagonistic effects in the ecosystems and therefore qualify the damage prediction for the ecosystems under study. We summarize and discuss the main results based on three years of research of four European research groups. The central theme of the work was the investigation of the effectiveness of the various screening compounds from the different species studied in order to gain some perspective of the evolutionary adaptations from lower to higher plant forms. The induction of mycosporine-like amino acids (MAAs) was studied in the marine dinoflagellate Gyrodinium dorsum, the green algal species Prasiola stipitata and in the cyanobacterium Anabaena sp. While visible (400-700 nm) and long wavelength UV-A (315-400 nm) showed only a slight effect, MAAs were effectively induced by UV-B (280-315 nm). The growth of the lower land organisms studied, i.e. the lichens Cladina portentosa, Cladina foliacaea and Cladonia arbuscula, and the club moss Lycopodiumannotinum, was not significantly reduced when grown under elevated UV-B radiation (simulating 15% ozone depletion). The growth in length of the moss Tortula ruralis was reduced under elevated UV-B. Of the aquatic plants investigated the charophytes Chara aspera showed decreased longitudinal growth under elevated UV-B. In the 'aquatic higher plants' studied, Ceratophyllum demersum, Batrachium trichophyllum and Potamogeton alpinus, there was no such depressed growth with enhanced UV-B. In Chara aspera, neither MAAs nor flavonoids could be detected. Of the terrestrial higher plants studied, Fagopyrum esculentum, Deschampsia antarctica, Vicia faba, Calamagrostis epigejos and Carex arenaria, the growth of the first species was depressed with enhanced UV-B, in the second species length growth was decreased, but the shoot number was increased, and in the latter two species of a dune grassland there was no reduced growth with enhanced UV-B. In the dune grassland species studied outdoors, at least five different flavonoids appeared in shoot tissue. Some of the flavonoids in the monocot species, which were identified and quantified with HPLC, included orientin, luteolin, tricin and apigenin. A greenhouse study with Vicia faba showed that two flavonoids (aglycones) respond particularly to enhanced UV-B. Of these, quercetin is UV-B inducible and mainly located in epidermal cells, while kaempferol occurs constitutively. In addition to its UV-screening function, quercetin may also act as an antioxidant. Polychromatic action spectra were determined for induction of the UV-absorbing pigments in three photosynthetic organisms, representing very different taxonomic groups and different habitats. In ultraviolet photobiology, action spectra mainly serve two purposes: (1) identification of the molecular species involved in light absorption; and (2) calculation of radiation amplification factors for assessing the effect of ozone depletion. Radiation amplification factors (RAFs) were calculated from the action spectra. In a somewhat simplified way, RAF can be defined as the percent increase of radiation damage for a 1% depletion of the ozone layer. Central European summer conditions were used in the calculations, but it has been shown that RAF values are not critically dependent on latitude or season. If only the ultraviolet spectral region is considered, the RAF values obtained are 0.7 for the green alga Prasiola stipitata, 0.4 for the dinoflagellate Gyrodinium dorsum, and 1.0 for the cyanobacterium Anabaena sp. In the case of P. stipitata, however, the effect of visible light (PAR, photosynthetically active radiation, 400-700 nm) is sufficient to lower the RAF to about 0.4, while the PAR effect for G. dorsum is negligible. RAFs for some damage processes, such as for DNA damage (RAF=2.1 if protective effects or photorepair are not considered [1]), are higher than those above. Our interpretation of this is that if the ozone layer is depleted, increased damaging radiation could overrule increased synthesis of protective pigments. In addition to investigating the functional effectiveness of the different screening compounds, direct UV effects on a number of key processes were also studied in order to gain further insight into the ability of the organisms to withstand enhanced UV-B radiation. To this end, the temperature-dependent repair of cyclobutane dimers (CPD) and (6-4) photoproducts induced by enhanced UV-B was studied in Nicotiana tabacum, and the UV-B induction of CPD was studied in the lichen Cladonia arbuscula. Also, photosynthesis and motility were monitored and the response related to the potential function of the screening compounds of the specific organism.

Biological Evolution↗

Large-scale functional analysis using peptide or protein arrays.

The array format for analyzing peptide and protein function offers an attractive experimental alternative to traditional library screens. Powerful new approaches have recently been described, ranging from synthetic peptide arrays to whole proteins expressed in living cells. Comprehensive sets of purified peptides and proteins permit high-throughput screening for discrete biochemical properties, whereas formats involving living cells facilitate large-scale genetic screening for novel biological activities. In the past year, three major genome-scale studies using yeast as a model organism have investigated different aspects of protein function, including biochemical activities, gene disruption phenotypes, and protein-protein interactions. Such studies show that protein arrays can be used to examine in parallel the functions of thousands of proteins previously known only by their DNA sequence.

Peptide Library↗

A large-scale, gene-driven mutagenesis approach for the functional analysis of the mouse genome.

A major challenge of the postgenomic era is the functional characterization of every single gene within the mammalian genome. In an effort to address this challenge, we assembled a collection of mutations in mouse embryonic stem (ES) cells, which is the largest publicly accessible collection of such mutations to date. Using four different gene-trap vectors, we generated 5,142 sequences adjacent to the gene-trap integration sites (gene-trap sequence tags; http://genetrap.de) from >11,000 ES cell clones. Although most of the gene-trap vector insertions occurred randomly throughout the genome, we found both vector-independent and vector-specific integration "hot spots." Because >50% of the hot spots were vector-specific, we conclude that the most effective way to saturate the mouse genome with gene-trap insertions is by using a combination of gene-trap vectors. When a random sample of gene-trap integrations was passaged to the germ line, 59% (17 of 29) produced an observable phenotype in transgenic mice, a frequency similar to that achieved by conventional gene targeting. Thus, gene trapping allows a large-scale and cost-effective production of ES cell clones with mutations distributed throughout the genome, a resource likely to accelerate genome annotation and the in vivo modeling of human disease.

Animals↗

Functional analysis after supracricoid partial laryngectomy with cricohyoidoepiglottopexy.

OBJECTIVES: To assess prospectively speech and swallowing function in a series of 17 patients after supracricoid partial laryngectomy with cricohyoidoepiglottopexy. STUDY DESIGN: Retrospective study. METHODS: From 1983 to 1996, 69 patients at Department of Otolaryngology-Head and Neck Surgery, CHUV (Lausanne, Switzerland) underwent a supracricoid partial laryngectomy with cricohyoidoepiglottopexy. Seventeen of them (25%) could be contacted and accepted participation in a functional evaluation that included a questionnaire to document their present nutritional status and diet. A formal voice evaluation was also performed, which included psychoacoustic evaluation of vocal qualities, fundamental frequency parameters, phonation intensity range, phonatory quotient (vital capacity divided by maximum phonation time), and a laryngeal video laryngoscopy performed with a rigid endoscope. RESULTS: Median postoperative follow-up was 66 months (range, 12-152 mo). Nine of 17 patients (53%) recovered a normal diet with no increased incidence of aspirations. Seven of 17 had minor limitations such as no peanuts, dry bread, or rice. Two of 17 patients were restricted to pureed food. Assessment of voice showed a clearly decreased mean fundamental frequency at 70.1 Hz (normal range, 121-211 Hz) and a narrowed frequency range of phonation with a mean value of 8.8 semitones (normal value, 27). Forty-two percent of the patients went back to their normal professional life after the operation. Among the 10 who did not, 3 (16%) retired and 7 actually had to give up their profession, because of the modification of their voice or general asthenia and age close to retirement. CONCLUSION: Restoration of laryngeal function after supracricoid partial laryngectomy with cricohyoidoepiglottopexy is satisfactory. Although most of the patients seem to recover normal swallowing function, severe voice alterations appear to be inevitable.

Adult↗

Functional analysis of HLA-DR-expressing keratinocytes from tuberculin reactive skin.

We examined the functional roles of HLA-DR+ keratinocytes which were induced in vivo from tuberculin reactive skin. At 4 days after intradermal PPD injection, about 80% of keratinocytes obtained from the tuberculin reactive area expressed DR antigens. In 14 of 18 individuals examined, PPD-pulsed DR+ keratinocyte fraction induced autologous T-cell proliferation. The proliferative response was PPD-dependent, antigen specific; it depended upon DR expression by the keratinocyte fraction, because it did not occur in the presence of the PPD-nonpulsed DR+ keratinocyte fraction and was completely blocked by mouse monoclonal antibody to HLA-DR. However, the antigen-presenting capacity of the DR+ keratinocyte fraction appeared to be less than that of monocytes or the DR+ epidermal cell fraction. The DR+ keratinocyte fraction was also able to stimulate allogeneic T-cell DNA synthesis, but the DR- keratinocyte fraction could not. The possible influences of contaminant Langerhans cells and mononuclear cells in the DR+ keratinocyte fraction were considered to be unlikely. These results suggest that DR+ keratinocytes, which are induced in vivo, can both present the antigen to autologous T cells and stimulate allogeneic T cells.

Cell Division↗

Construction of an in vivo nonsense readthrough assay system and functional analysis of ribosomal proteins S12, S4, and S5 in Bacillus subtilis.

To investigate the function of ribosomal proteins and translational factors in Bacillus subtilis, we developed an in vivo assay system to measure the level of nonsense readthrough by utilizing the LacZ-LacI system. Using the in vivo nonsense readthrough assay system which we developed, together with an in vitro poly(U)-directed cell-free translation assay system, we compared the processibility and translational accuracy of mutant ribosomes with those of the wild-type ribosome. Like Escherichia coli mutants, most S12 mutants exhibited lower frequencies of both UGA readthrough and missense error; the only exception was a mutant (in which Lys-56 was changed to Arg) which exhibited a threefold-higher frequency of readthrough than the wild-type strain. We also isolated several ribosomal ambiguity (ram) mutants from an S12 mutant. These ram mutants and the S12 mutant mentioned above (in which Lys-56 was changed to Arg) exhibited higher UGA readthrough levels. Thus, the mutation which altered Lys-56 to Arg resulted in a ram phenotype in B. subtilis. The efficacy of our in vivo nonsense readthrough assay system was demonstrated in our investigation of the function of ribosomal proteins and translational factors.

Amino Acid Substitution↗

A novel interferon-inducible domain: structural and functional analysis of the human interferon regulatory factor 1 gene promoter.

We have cloned and functionally characterized the human interferon regulatory factor 1 (IRF-1) gene promoter. The promoter contains a CpG island, with several GC boxes, a CAAT box, but no TATA box. IRF-1 mRNA is strongly induced by gamma interferon (IFN-gamma) but more weakly and transiently by IFN-alpha. There are several putative kappa B motifs and numerous AA(G/A)G(G/T)A and GAAANN motifs throughout the promoter. The IRF-1 promoter is not autoregulated by the IRF-1 gene product. IFN inducibility of the promoter was studied with 5' deletion mutants linked to a heterologous reporter gene. Gel mobility shift assays were used to show IFN-inducible factor binding to the IRF-1 promoter. These studies showed that IFN inducibility is conferred by a novel imperfect inverted-repeat arrangement of two GAAANN motifs within a domain, 130 nucleotides upstream of transcription initiation. This inverted repeat binds a factor upon induction with IFN and can confer IFN inducibility on a heterologous promoter. Conversely, point mutations of the inverted repeat are not IFN inducible when linked to the same heterologous promoter.

Base Sequence↗

Molecular cloning, functional analysis, and RNA expression analysis of connexin45.6: a zebrafish cardiovascular connexin.

In the vertebrate cardiovascular system, gap junctions function in intercellular communication essential for both the coordinated propagation of the heartbeat and the control of vasomotor responses in the vascular system. Connexins, the protein subunits of gap junctions, are coded by a multigene family. In this study, a connexin gene (zfCx45.6), which exhibits 53% amino acid identity to chick Cx42, was cloned from zebrafish genomic DNA. With the use of the LN54 radiation hybrid panel, zfCx45.6 was mapped to zebrafish linkage group 9. Northern blots and RT-PCR revealed the presence of zfCx45.6 mRNA in the embryo before 2 h postfertilization (hpf) and then again beginning at about 12 hpf, after which time no major changes in relative expression levels were detected. In the adult, zfCx45.6 mRNA continued to be detected in the heart, as well as the brain, liver, and ovary, but not the lens. Whole mount in situ hybridization revealed zfCx45.6 mRNA was expressed at high levels in the major vessels of the entire embryo and in both the atrium and ventricle of the adult heart. Expression of zfCx45.6 channels in paired Xenopus oocytes produced high levels of intercellular coupling that was voltage sensitive. With the previous isolation of zebrafish Cx43 and Cx43.4, zebrafish orthologues have now been isolated for three of the four connexins expressed in the mammalian cardiovascular system.

Amino Acid Sequence↗

Technical note. Modulation transfer function analysis of a newly revised rotational panoramic machine.

OBJECTIVES: To determine the modulation transfer function (MTF) and noise equivalent passband (NE) values for a newly revised rotational panoramic X-ray machine, the PC-1000 (Panoramic Corp., Fort Wayne, Indiana, USA). METHODS: Images of a 10 microns test slit were taken at various locations along the X-ray beam projection path using a Lanex Regular/T-Mat G image receptor. Line spread functions were obtained at specific beam paths by scanning slit images with a microdensitometer. RESULTS: MTF values were highest around the central plane of the image layer, with a maximum near the centre of 0.25 at 4 cycles/mm. The NE values near the central plane of image layer were 1.4 cycles/mm. MTF and NE values in the anterior region were low, 0.2 and 1.2, respectively. The width of the image layer was narrower in the anterior and wider in the posterior segments. Rapid decreases in MTF and NE values were found on the X-ray tube side compared with the receptor side of the central plane. Using a spatial frequency of 0.25 MTF the shape of the image layer was coincident with that determined visually. CONCLUSION: On the basis of the MTF and NE values the image resolution produced by this machine is considered acceptable for panoramic dental radiography.

Mathematics↗

Surgical treatment of partial atrioventricular septal defect: functional analysis of the mitral valve in the postoperative period.

OBJECTIVE: To study mitral valve function in the postoperative period after correction of the partial form of atrioventricular septal defect. METHODS: Fifty patients underwent surgical correction of the partial form of atrioventricular septal defect. Their mean age was 11.8 years and 62% of the patients were males. Preoperative echocardiography showed moderate and severe mitral insufficiency in 44% of the patients. The mitral valve cleft was sutured in 45 (90%) patients (group II - GII). Echocardiographies were performed in the early postoperative period, and 6 and 12 months after hospital discharge. RESULTS: The patients who had some type of arrhythmia in the postoperative period had ostium primum atrial septal defect of a larger size (2.74 x 2.08 cm). All 5 patients in group I (GI), who did not undergo closure of the cleft, had a competent mitral valve or mild mitral insufficiency in the preoperative period. One of these patients began to have moderate mitral insufficiency in the postoperative period. On the other hand, in GII, 88.8% and 82.2% of the patients had competent mitral valve or mild mitral insufficiency in the early and late postoperative periods, respectively. CONCLUSION: The mitral valve cleft was repaired in 90% of cases. Echocardiography revealed competent mitral valve or mild mitral insufficiency in 88.8% and 82.2% of GII patients in the early and late postoperative periods, respectively.

Adolescent↗

An evaluation of a brief functional analysis format within a vocational setting.

We conducted and compared both brief and extended functional analyses of disruptive behaviors for 3 individuals with developmental disabilities who attended a vocational training program. Results demonstrated that the brief assessment identified the function of 2 of the 3 participants' disruptive behavior compared to the extended assessment.

Adult↗

Streamlined approach to functional analysis of promoter-region polymorphisms.

We have developed a rapid method for identifying functional promoter-region polymorphisms. Using a modified pGL3 luciferase expression T-vector, we can amplify by PCR, clone, identify allelic pairs of a polymorphic gene promoter region, and prepare plasmids for cell culture 10 promoters (20 allele pairs) per week per researcher. By utilizing 96-well plate technology and an internal control plasmid expressing secreted alkaline phosphatase, each of these allele pairs can be tested for relative promoter activity in each of three cell lines (HEK293t, TE671, and JEG3) with similar resources.

Alleles↗

[Functional analysis of the single nucleotide polymorphisms in the PRKCZ gene].

OBJECTIVE: To study the function of 5 single nucleotide polymorphisms (SNPs) of the PRKCZ gene, a susceptibility gene for type 2 diabetes in Han population of North China, in the pathogenesis of the disease. METHODS: Bioinformatic methods and reporter gene activity determination were used to analyze the function of the 5 SNPs. RESULTS: The reporter gene activities of different alleles of 2 SNPs, rs427811 and rs809912, were obviously different, which implies that these 2 SNPs might be susceptibility loci of the disease. CONCLUSION: The PRKCZ gene is further confirmed to be a susceptibility gene for type 2 diabetes in Han population of North China. Two SNPs in the gene play a role in the pathogenesis of the disease by affecting the expression level of PRKCZ gene.

Alleles↗

Expression-based discovery of variation in the human glutathione S-transferase M3 promoter and functional analysis in a glioma cell line using allele-specific chromatin immunoprecipitation.

Discovery and functional evaluation of biologically significant regulatory single nucleotide polymorphisms (SNP) in carcinogen metabolism genes is a difficult challenge because the phenotypic consequences may be both transient and subtle. We have used a gene expression screening approach to identify a functional regulatory SNP in glutathione S-transferase M3 (GSTM3). Anttila et al. proposed that variation in GSTM3 expression was affected by exposure to cigarette smoke and inheritance of the GSTM1-null genotype. To investigate the mechanism of GSTM3 expression was affected by exposure to cigarette smoke and inheritance of the GSTM1-null genotype. To investigate the mechanism of GSTM3 expression variation, we measured GSTM3 expression in lymphoblast cells from a human Centre d'Etude du Polymorphisme Humain family and observed a low expression phenotype. Promoter sequencing revealed two novel GSTM3 promoter SNPs: A/C and A/G SNPs, 63 and 783 bp upstream of the codon 1 start site, respectively. In this pedigree, the two children homozygous for the -63C/C genotype had 8-fold lower GSTM3 expression relative to the two children with the -63A/A genotype, with no association between A-783G SNP and GSTM3 expression. Further evaluation using genotyped glioma cell lines and with luciferase reporter constructs showed that the -63C allele was associated with lower GSTM3 expression (P < 0.0001 and P < 0.003). RNA pol II chromatin immunoprecipitation was combined with quantitative probed-based allelic discrimination genotyping to provide direct evidence of a 9-fold reduced RNA pol II binding capacity for the -63C allele. These results show that the GSTM3 -63C allele strongly affects gene expression in human cell lines and suggests that individuals who carry the low expression allele may be deficient in glutathione transferase catalyzed biological functions.

Base Sequence↗