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At least 955 records · Page 53Linked to original sources

PubMed1998

Necessity of bevels for box only Class II composite restorations.

STATEMENT OF PROBLEM: The tooth preparation of a bevel is recommended to improve marginal quality of a composite restoration. However, in small Class II restorations, it is unclear if a bevel also contributed to a better marginal fit. PURPOSE: This study investigated the influence of tooth preparation design on microleakage of minimal posterior Class II composite restorations. MATERIAL AND METHODS: Box-shaped Class II tooth preparations for posterior composite restorations in maxillary premolars were restored with a total etch technique. The tooth preparations were beveled or non-beveled and the box prepared at a right angle cervically or additionally excavated. The facial and lingual box margins were also either beveled or unbeveled. The teeth were thermocycled and immersed in a dye solution. After sectioning specimens, dye penetration at the facial and palatal margins was recorded. RESULTS: A bevel-reduced microleakage both at the cervical and ascending walls. Enamel cracks were observed along certain unbeveled margins as recorded in this study. The additional excavation did not contribute to reduction of microleakage. CONCLUSIONS: Tooth preparation of a bevel is recommended for an optimal marginal seal in small box-type Class II composite restorations.

Analysis of Variance↗

PubMed2003

The molecular basis for phosphodependent substrate targeting and regulation of Plks by the Polo-box domain.

Polo-like kinases (Plks) perform crucial functions in cell-cycle progression and multiple stages of mitosis. Plks are characterized by a C-terminal noncatalytic region containing two tandem Polo boxes, termed the Polo-box domain (PBD), which has recently been implicated in phosphodependent substrate targeting. We show that the PBDs of human, Xenopus, and yeast Plks all recognize similar phosphoserine/threonine-containing motifs. The 1.9 A X-ray structure of a human Plk1 PBD-phosphopeptide complex shows that the Polo boxes each comprise beta6alpha structures that associate to form a 12-stranded beta sandwich domain. The phosphopeptide binds along a conserved, positively charged cleft located at the edge of the Polo-box interface. Mutations that specifically disrupt phosphodependent interactions abolish cell-cycle-dependent localization and provide compelling phenotypic evidence that PBD-phospholigand binding is necessary for proper mitotic progression. In addition, phosphopeptide binding to the PBD stimulates kinase activity in full-length Plk1, suggesting a conformational switching mechanism for Plk regulation and a dual functionality for the PBD.

Amino Acid Motifs↗

PubMed2002

Cloning and expression analysis of the chicken DEAD box gene DDX1.

DEAD box proteins are putative RNA unwinding proteins found in organisms ranging from mammals to bacteria. While some DEAD box genes expressed in higher eukaryotes are ubiquitous, others have distribution profiles that suggest a cell-, tissue-, or developmental-specific role. The DEAD box gene, DDX1, was identified by differential screening of a subtracted retinoblastoma cDNA library. A limited survey of human fetal tissues indicated that DDX1 mRNA has a widespread distribution but is not uniformly expressed in all tissues. To further document the spatial and temporal distribution of DDX1 during embryonic development, we cloned the chicken DDX1 cDNA. The predicted amino acid sequence of chicken DDX1 was 93% identical to that of human DDX1. All DEAD box motifs, as well as a SPRY domain, were present in chicken DDX1. Northern and Western blot analyses showed highest levels of DDX1 at early stages of development. Tissue maturation was generally accompanied by a decrease in expression, although DDX1 levels remained elevated in late embryonic retina and brain. In situ hybridization of retinal tissue sections revealed widespread distribution of DDX1 mRNA at early developmental stages with preferential expression in amacrine and ganglion cells of the differentiated tissue. Preferential expression of DDX1 was also observed in specific areas of the brain in older embryos, such as the external granule layer of the cerebellum. These results suggest a specific role for DDX1 in subsets of differentiated cells as well as a more general role in undifferentiated cells.

Amino Acid Sequence↗

PubMed2002

Characterization of the sequences encoding for Xenopus laevis box C/D snoRNP Nop56 protein.

Nop56p was initially identified in yeast as the third common component of the ribonucleoprotein particles (snoRNPs) assembled on box C/D small nucleolar RNAs (snoRNAs). Thereafter, the characterization of Nop56p homologs in Archaea and in several eukaryotes pointed to the highly conserved structure of this factor. Studies in yeast indicate that Nop56 is not required for the stability of box C/D snoRNAs. Through the isolation of a Xenopus laevis Nop56 cDNA clone, we have been able to characterize the X. laevis Nop56 protein (XNop56p). We showed that it is a common component of X. laevis box C/D snoRNPs and that it displays the same electrophoretic mobility of p62 protein that we previously characterized as a box C/D snoRNP component, not essential for snoRNA stability in X. laevis. Mapping the 5' end of X. laevis Nop56 transcript indicates that it starts with a pyrimidine tract and the analysis of genomic clones revealed a snoRNA encoded in one of NOP56 introns. Although these two characteristics could suggest that XNOP56 is a TOP gene, it is not translationally controlled in a growth-dependent manner.

Amino Acid Sequence↗

PubMed1998

Combinatorial control in ubiquitin-dependent proteolysis: don't Skp the F-box hypothesis.

The ubiquitin-dependent proteolytic pathway targets many key regulatory proteins for rapid intracellular degradation. Specificity in protein ubiquitination derives from E3 ubiquitin protein ligases, which recognize substrate proteins. Recently, analysis of the E3s that regulate cell division has revealed common themes in structure and function. One particularly versatile class of E3s, referred to as Skp1p-Cdc53p-F-box protein (SCF) complexes, utilizes substrate-specific adaptor subunits called F-box proteins to recruit various substrates to a core ubiquitination complex. A vast array of F-box proteins have been revealed by genome sequencing projects, and the early returns from genetic analysis in several organisms promise that F-box proteins will participate in the regulation of many processes, including cell division, transcription, signal transduction and development.

Animals↗

PubMed1998

CBF/NF-Y activates transcription of the human tryptophan hydroxylase gene through an inverted CCAAT box.

The human tryptophan hydroxylase gene (hTPH) encodes the rate-limiting enzyme in the biosynthesis of serotonin, a neurotransmitter which has been implicated in a number of psychiatric illnesses. This enzyme is expressed in a tissue-specific manner. We examined the transcriptional activity of a series of 5' deletion promoter-reporter constructs extending from nucleotide (nt) -1954 to +40 and found that the region between nt -163 and +40 contains a regulatory element important for efficient transcription of the gene, DNase I footprint analyses, using P815-HTR and HeLa nuclear protein extracts, revealed a single prominent footprint between nt -78 and -44. A cis-acting element in the footprint region was identified as an inverted CCAAT box (-67 ATTGG -63) by gel shift assays. Two base pair (bp) mutations in the core CCAAT sequence eliminated protein binding in gel shift assays and reduced transcriptional activity approximately 50% in transient transfection assays. Competitive gel shift assays showed that the protein binding to the hTPH CCAAT box was effectively competed by an oligonucleotide (oligo) harboring a binding site for CCAAT box binding factor (CBF)/nuclear factor-Y (NF-Y). A selective antibody against the B subunit of CBF/NF-Y supershifted the protein-DNA complex formed between the -90/-50 oligo probe and nuclear protein extracts. Our results indicate that the binding of CBF/NF-Y to the inverted CCAAT box is responsible for transcriptional activation of the nTPH gene.

Binding Sites↗

PubMed2001

Numerical analysis of biological clogging in two-dimensional sand box experiments.

Two-dimensional models for biological clogging and sorptive trace transport were used to study the progress of clogging in a sand box experiment. The sand box had been inoculated with a strip of bacteria and exposed to a continuous injection of nitrate and acetate. Brilliant Blue was regularly injected during the clogging experiment and digital images of the tracer movement had been converted to concentration maps using an image analysis. The calibration of the models to the Brilliant Blue observations shows that Brilliant Blue has a solid biomass dependent sorption that is not compliant with the assumed linear constant Kd behaviour. It is demonstrated that the dimensionality of sand box experiments in comparison to column experiments results in a much lower reduction in hydraulic conductivity (factor of 100) and that the bulk hydraulic conductivity of the sand box decreased only slightly. However, in the central parts of the clogged area, the observations and simulations clearly show a complex picture of flow diverting the injected nutrients around the clogged area as fingers. The calibration of the model demonstrates that the physical and microbiological processes (advection, dispersion, attachment-detachment, growth-decay) are all needed to capture the progress of clogging.

Acetates↗

PubMed2001

Ground performance of air conditioning and water recycle system for a Space Plant Box.

Researchers from 5 Japanese universities have developed a plant growth facility (Space Plant Box) for seed to seed experiments under microgravity. The breadboard model of the Space Plant Box was fabricated by assembling subsystems developed for microgravity. The subsystems include air conditioning and water recycle system, air circulation system, water and nutrient delivery system, lighting system and plant monitoring system. The air conditioning and water recycle system is simply composed of a single heat exchanger, two fans and hydrophilic fibrous strings. The strings allow water movement from the cooler fin in the Cooling Box to root supporting materials in the Plant Growth Chamber driven by water potential deficit. Relative humidity in the Plant Growth Chamber can be changed over a wide range by controlling the ratio of latent heat exchange to sensible heat exchange on the cooling fin of the heat exchanger. The transpiration rate was successfully measured by circulating air inside the Plant Growth Chamber only. Most water was recycled and a small amount of water needed to be added from the outside. The simple, air conditioning and water recycle system for the Space Plant Box showed good performance through a barley (Hordeum vulgare L.) growth experiment.

Air Conditioning↗

PubMed2002

U87 RNA, a novel C/D box small nucleolar RNA from mammalian cells.

A novel 72 nt small nucleolar RNA (snoRNA) called U87 was found in rat liver cells. This RNA possesses the features of C/D box snoRNA family: boxes C, D', C', D, and 11 nt antisense element complementary to 28S ribosomal RNA (rRNA). The vast majority of C/D box snoRNAs direct site-specific 2'-O-ribose methylation of rRNAs. U87 RNA is suggested to be involved in 2'-O-methylation of a G(3468) residue in 28S rRNA. U87 RNA was detected in different mammalian species with slight length variability. Rat and mouse U87 RNA gene was characterized. Unlike the majority of C/D box snoRNAs U87 RNA lacks the terminal stem required for snoRNA processing. However, U87 gene is flanked by 7 bp inverted repeats potentially able to form a terminal stem in U87 RNA precursor.

Animals↗

PubMed2002

Characterization of the SCAN box encoding RAZ1 gene: analysis of cDNA transcripts, expression, and cellular localization.

The SCAN box (SRE-ZBP; CT-fin51; AW-1; Number 18) is a highly-conserved 80-amino-acid domain identified in a subset of C(2)H(2) zinc finger proteins. We and others have recently demonstrated that the SCAN box is a protein association domain that mediates hetero- and homo-protein associations with SCAN box containing proteins. RAZ1 (SCAN-related protein associated with MZF1B) is a novel gene identified in a yeast two hybrid genetic screen for binding to the MZF1B SCAN box. RAZ1 maps to chromosome 20q11 at a region frequently disrupted in various leukemias. We characterized the RAZ1 gene by analysing cDNA transcripts, mRNA expression, and cellular localization of the expressed protein. RAZ1 mRNA expression was detected in various human tissues and cell lines by Northern blot analysis and multiple tissue expression arrays. Highest levels of expression are in prostate, testis, thyroid, liver, and kidney. The RAZ1 gene produces two transcripts with variant 5'-untranslated regions containing identical open reading frames that express a 28 kDa protein in vitro. RAZ1 transcription start sites were mapped by primer extension and confirmed by identification of the RAZ1 promoter in the 5' flanking genomic DNA. RAZ1 protein fused to the green fluorescent protein (GFP) localizes to the nucleus in a diffuse pattern and the carboxyl terminus containing the SCAN-related domain is sufficient for nuclear localization. These data suggest that RAZ1 is a widely expressed nuclear protein that may function as a key regulator of zinc finger transcription factor function.

5' Flanking Region↗

PubMed2003

Characterization of PTM5 in aspen trees: a MADS-box gene expressed during woody vascular development.

The vascular component of trees possesses some of the most specialized processes active in the formation of roots, stems, and branches, and its wood component continues to be of primary importance to our daily lives. The molecular mechanisms of wood development, however, remain poorly understood with few well-characterized regulatory genes. We have identified a vascular tissue-specific MADS-box gene, Populus tremuloides MADS-box 5 (PTM5) that is expressed in differentiating primary and secondary xylem and phloem. Phylogenetic analysis has shown that PTM5 is a member of the SOC1/TM3 class of MADS-box genes. Temporal expression analysis of PTM5 in staged vascular cambium and other tissues indicated that PTM5 expression is seasonal and is limited to spring wood formation and rapidly expanding floral catkins. Spatial expression analysis using in situ hybridization revealed that PTM5 expression is localized within a few layers of differentiating vascular cambium and xylem tissues as well as the vascular bundles of expanding catkins. Since many MADS-box genes are known to act as transcription factors, these results suggest that the coordinated expression of PTM5 with other vascular developmental genes may be a hallmark of the complex events that lead to the formation of the woody plant body.

Amino Acid Sequence↗

PubMed1998

Characterization of the maize prolamin box-binding factor-1 (PBF-1) and its role in the developmental regulation of the zein multigene family.

A maize prolamin box (P-box)-binding factor (PBF-1) has been purified and characterized from immature endosperm tissue. PBF-1 has a molecular weight of 38kDa. It is detected only in endosperm, but not in root or leaf tissues, consistent with its tissue-specific function. Site-directed mutagenesis experiments reveal that both the P-box and its flanking sequences are important for PBF-1 DNA binding. Developmental studies show that PBF-1 accumulates in the endosperm from 8 to at least 30days after pollination (DAP). From 16 to 24DAP, however, multiple shifted bands of protein(s)-DNA complexes can be observed, which correlate with an increase in zein gene expression. PBF-1 can also bind to the P-box from '22-kDa' and '19-kDa' zein promoters, but at a lower affinity than to the '27-kDa' zein promoter. The effects of protein dephosphorylation and zinc ion chelators on PBF-1 DNA binding activity are also shown. A model is proposed where PBF-1 serves as a 'recruiter' of class-specific transcription factors like Opaque2 (O2).

Chromatography, Affinity↗

PubMed1999

A GC-box is required for expression of the human vimentin gene.

Vimentin is an intermediate filament protein normally expressed in cells of mesenchymal origin. The promoter of the human vimentin gene (-1416 to +73) was shown to contain two positive-acting regions, separated by a negative region, and at least eight GC-boxes as determined by sequence homology (Rittling, S.R., Baserga, R., 1987. Mol. Cell. Biol. 7, 3908-3915). We have analyzed the region -900 to +41 for protein binding by in vivo footprinting experiments using ligation-mediated PCR. For the various GC-boxes, we detect protein binding only to that GC-box (at position -64 and -55) closest to the transcriptional start site. Transient transfection assays of various vimentin 5'-end fragments and mutations thereof fused to the reporter gene cat indicate that this sequence is indispensable for promoter function regardless of the inclusion of upstream DNA sequences. In vitro binding studies confirm that this region binds protein specifically. We suggest that this GC-box and its binding factor are required for regulated expression of the human vimentin gene.

Binding, Competitive↗

PubMed2002

The use of the Box-Behnken experimental design in the optimisation and robustness testing of a capillary electrophoresis method for the analysis of ethambutol hydrochloride in a pharmaceutical formulation.

Box-Behnken experimental designs do not appear to be extensively used in optimisation of analytical methods using capillary electrophoresis (CE). This paper describes the use of the Box-Behnken experimental design to optimise the factors affecting the separation of ethambutol hydrochloride (EB), its impurity 2-amino-1-butanol and the internal standard (phenylephrine hydrochloride) in a CE method for a pharmaceutical tablet assay. The three factors studied simultaneously were: buffer pH, buffer concentration and applied electric field, each at three levels. The method was optimised with respect to three responses: resolution between peaks, theoretical plate count and the migration time of the EB peak. A statistical programme, which applies a multiple response optimisation algorithm, was used to calculate and optimise the three responses simultaneously. The optimum conditions were established to be 58.0 mM sodium borate buffer at pH 9.50 and an applied electric field of 412 V/cm. The robustness of the method was also determined and confirmed using a second Box-Behnken design, as part of the validation exercise. System suitability values for the method were derived from the regression surface analysis. The CE method for a pharmaceutical tablet formulation was further validated according to current regulatory requirements, with respect to linearity and range, precision, specificity, accuracy and limit of quantitation. The optimised method gives a fast and efficient separation under 4 min, with complete resolution between the three peaks, and represents an improvement over the existing USP method. It can be concluded that the Box-Behnken experimental design provides a suitable means of optimising and testing the robustness of a CE pharmaceutical method.

Amino Alcohols↗

PubMed2001

How to be a gray box: dynamic semi-physical modeling.

A general methodology for gray-box, or semi-physical, modeling is presented. This technique is intended to combine the best of two worlds: knowledge-based modeling, whereby mathematical equations are derived in order to describe a process, based on a physical (or chemical, biological, etc.) analysis, and black-box modeling, whereby a parameterized model is designed, whose parameters are estimated solely from measurements made on the process. The gray-box modeling technique is very valuable whenever a knowledge-based model exists, but is not fully satisfactory and cannot be improved by further analysis (or can only be improved at a very large computational cost). We describe the design methodology of a gray-box model, and illustrate it on a didactic example. We emphasize the importance of the choice of the discretization scheme used for transforming the differential equations of the knowledge-based model into a set of discrete-time recurrent equations. Finally, an application to a real, complex industrial process is presented.

Algorithms↗

PubMed2001

The anaphase inhibitor Pds1 binds to the APC/C-associated protein Cdc20 in a destruction box-dependent manner.

An essential aspect of progression through mitosis is the sequential degradation of key mitotic regulators in a process that is mediated by the anaphase promoting complex/cyclosome (APC/C) ubiquitin ligase [1]. In mitotic cells, two forms of the APC/C exist, APC/C(Cdc20) and APC/C(Cdh1), which differ in their associated WD-repeat proteins (Cdc20 and Cdh1, respectively), time of activation, and substrate specificity [2, 3]. How the WD-repeat proteins contribute to APC/C's activation and substrate specificity is not clear. Many APC/C substrates contain a destruction box element that is necessary for their ubiquitination [4-6]. One such APC/C substrate, the budding yeast anaphase inhibitor Pds1 (securin), is degraded prior to anaphase initiation in a destruction box and APC/C(Cdc20)-dependent manner [3, 7]. Here we find that Pds1 interacts directly with Cdc20 and that this interaction requires Pds1's destruction box. Our results suggest that Cdc20 provides a link between the substrate and the core APC/C and that the destruction box is essential for efficient Cdc20-substrate interaction. We also find that Pds1 does not interact with Cdh1. Finally, the effect of spindle assembly checkpoint activation, known to inhibit APC/C function [8], on the Pds1-Cdc20 interaction is examined.

Anaphase↗

PubMed2002

Multiple Skp1-related proteins in Caenorhabditis elegans: diverse patterns of interaction with Cullins and F-box proteins.

BACKGROUND: The ubiquitin-proteasome pathway of proteolysis controls the abundance of specific regulatory proteins. The SCF complex is a type of ubiquitin-protein ligase (E3) that contributes to this pathway in many biological systems. In yeast and mammals, the SCF complex consists of common components, including Skp1, Cdc53/Cul1, and Rbx1, as well as variable components known as F-box proteins. Whereas only one functional Skp1 gene is present in the human genome, the genome of Caenorhabditis elegans has now been shown to contain at least 21 Skp1-related (skr) genes. The biochemical properties, expression, and function of the C. elegans SKR proteins were examined. RESULTS: Of the 17 SKR proteins examined, eight (SKR-1, -2, -3, -4, -7, -8, -9, and -10) were shown to interact with C. elegans CUL1 by yeast two-hybrid analysis or a coimmunoprecipitation assay in mammalian cells. Furthermore, SKR proteins exhibited diverse binding specificities for C. elegans F-box proteins. The tissue specificity of expression of the CUL1-interacting SKR proteins was also varied. Suppression of skr-1 or skr-2 genes by double-stranded RNA interference resulted in embryonic death, whereas that of skr-7, -8, -9, or -10 was associated with slow growth and morphological abnormalities. CONCLUSIONS: The multiple C. elegans SKR proteins exhibit marked differences in their association with Cullins and F-box proteins, in tissue specificity of expression, and in phenotypes associated with functional suppression by RNAi. At least eight of the SKR proteins may, like F-box proteins, act as variable components of the SCF complex in C. elegans.

Amino Acid Motifs↗

PubMed1999

View box luminance measurements and their effect on reader performance.

RATIONALE AND OBJECTIVES: The purpose of this study was to investigate the importance of view box luminance and viewing conditions on low-contrast detection by readers. MATERIALS AND METHODS: Radiographs of a mammographic contrast-detail phantom were examined on 632 view box panels. The luminance of these panels was obtained by using a calibrated meter and ranged from 860 to 3,300 nit. Twelve radiologists reported the number of contrast-detail disks for each size (diameter, 0.3-7.0 mm) deemed to be visible on films with optical densities of 1.00-2.60. Radiologist performance in reading low-contrast phantom images was also studied as a function of room illuminance and image masking. RESULTS: Median luminance was 1,700 nit, with 25- and 75-percentile values of 1,450 and 2,150 nit, respectively. Low-contrast visibility generally was independent of view box luminance, regardless of film density or disk diameter. Low-contrast visibility deteriorated when masking around the image was removed and at normal room illuminance. The greatest deterioration in performance occurred at the highest film densities and with the smallest size disks. CONCLUSION: Detection of low-contrast features on radiographs is relatively independent of view box luminance, but it is degraded by the presence of stray light and by increased room illuminance.

Adult↗