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PubMed2005

Differentiation of developmental and post-orthodontic white lesions using image analysis.

The aim of this study was to investigate differences in shape and size characteristics between developmental opacities and post-orthodontic white enamel lesions using computerized image analysis. Material, in the form of 35 mm slides, was obtained from the archive of photographic patient records in the orthodontic clinic at the Charles Clifford Dental Hospital. Images of 30 teeth with developmental white lesions and 30 teeth with post-orthodontic white lesions were selected using strict inclusion and exclusion criteria. The slides were converted to a digital format, coded, placed in a random order and analysed blindly using a computerized image analysis system by one clinician. After a 2 week interval, the images were recorded, placed in a new random order and the measurements repeated. The outcome measures were: area and luminance proportionality, and the shape of the perimeter line (expressed as the mathematical factor, roundness). Reproducibility was assessed by a paired samples t-test for systematic error and the intra-class correlation coefficient (ICC) for random error. Differences between groups were tested using the Mann-Whitney U-test for non-parametric data. Reproducibility was substantial for all measurements except for developmental white lesion roundness, which was moderate. There was a statistically significant difference between developmental white opacities and post-orthodontic white lesions for measurements of luminance intensity, proportionality (P = 0.002) and roundness (P = 0.001). Developmental white opacities had a higher luminance (i.e. were whiter) and the boundaries were more circular in shape than the post-orthodontic lesions. Roundness is a useful measure when distinguishing developmental and post-orthodontic demineralization.

Dental Enamel↗
PubMed1989

Biosynthesis of winter flounder antifreeze proprotein in E.coli.

A semisynthetic winter flounder antifreeze proprotein (proAFP) coding region was constructed and inserted into a lacZ expression vector. ProAFP was produced from the vector in Escherichia coli as a C-terminal fusion to the first 289 amino acids of beta-galactosidase (beta-gal). The proAFP and beta-gal domains of the beta-gal-proAFP fusion protein were separated by the recognition signal for the blood coagulation protease, factor Xa. Upon induction with isopropylthio-beta-D-galactoside the fusion protein accumulated to levels of 15% of the total protein. The beta-gal-proAFP fusion protein was partially purified by differential centrifugation, but required solubilization prior to factor Xa digestion. The solubilized fusion protein was efficiently and correctly cleaved by factor Xa, after which the proAFP was purified by gel permeation. Bacterial proAFP was indistinguishable from natural proAFP by the criteria of antifreeze activity, amino-terminal sequence (15 cycles), reverse-phase HPLC and SDS-polyacrylamide gel electrophoresis. Circular dichroism measurements showed that proAFP is a composite of random coil and alpha-helical secondary structure, with an alpha-helix content of 44% at 0 degrees C. It seems probable that the C-terminal region of proAFP, which corresponds to the mature AFP protein, is mainly alpha-helical, and that the N-terminal pro-segment is random coiled.

Amino Acid Sequence↗
PubMed1992

Characterization of sequence changes in kinetoplast DNA maxicircles of drug-resistant Leishmania.

We have compared kinetoplast DNA maxicircles of tunicamycin- and arsenite-resistant variants of repeatedly cloned Leishmania mexicana amazonensis showing DNA amplification with wild-type and arsenite-resistant variants of the same lineage that do not show DNA amplification. DNA restriction patterns and the degree of cross-hybridization between maxicircle DNA fragments of parasites displaying DNA amplification and those of parasites without amplification were examined. In addition, the nucleotide sequence of the cytochrome b (Cyb) gene from the coding region was compared between these two groups of parasites. Extensive changes were found in the nucleotide sequences and the amino acid sequences of the cytochrome gene of the maxicircles of variants with DNA amplification. The Cyb genes from both groups had much shorter open reading frames than the same gene from Leishmania tarentolae and Trypanosoma brucei. The simultaneous changes in maxicircles and minicircles of these variants suggest that they may confer the advantage of maintaining viable mitochondrial function under selective pressure.

Amino Acid Sequence↗
PubMed2005

Dual DNA recognition codes of a short peptide derived from the basic leucine zipper protein EmBP1.

Sequence-specific DNA binding of short peptide dimers derived from a plant basic leucine zipper protein EmBP1 was studied. A homodimer of the EmBP1 basic region peptide recognized a palindromic DNA sequence, and a heterodimer of EmBP1 and GCN4 basic region peptides targets a non-palindromic DNA sequence when a beta-cyclodextrin/adamantane complex is utilized as a dimerization domain. A homodimer of the EmBP1 basic region peptide binds the native EmBP1 binding 5'-GCCACGTGGC-3' and the native GCN4 binding 5'-ATGACGTCAT-3' sequences with almost equal affinity in the alpha-helical conformation, indicating that the basic region of EmBP1 by itself has a dual recognition codes for the DNA sequences. The GCN4 basic region peptide binds 5'-ATGAC-3' in the alpha-helical conformation, but it neither shows affinity nor helix formation with 5'-GCCAC-3'. Because native EmBP1 forms 100 times more stable complex with 5'-GCCACGTGGC-3' over 5'-ATGACGTCAT-3', our results suggest that the sequence-selectivity of native EmBP1 is dictated by the structure of leucine zipper dimerization domain including the hinge region spanning between the basic region and the leucine zipper.

Amino Acid Sequence↗
PubMed1992

Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of plant mitochondrial genome.

Analysis of the mitochondrial DNA of a liverwort Marchantia polymorpha by electron microscopy and restriction endonuclease mapping indicated that the liverwort mitochondrial genome was a single circular molecule of about 184,400 base-pairs. We have determined the complete sequence of the liverwort mitochondrial DNA and detected 94 possible genes in the sequence of 186,608 base-pairs. These included genes for three species of ribosomal RNA, 29 genes for 27 species of transfer RNA and 30 open reading frames (ORFs) for functionally known proteins (16 ribosomal proteins, 3 subunits of H(+)-ATPase, 3 subunits of cytochrome c oxidase, apocytochrome b protein and 7 subunits of NADH ubiquinone oxidoreductase). Three ORFs showed similarity to ORFs of unknown function in the mitochondrial genomes of other organisms. Furthermore, 29 ORFs were predicted as possible genes by using the index of G + C content in first, second and third letters of codons (42.0 +/- 10.9%, 37.0 +/- 13.2% and 26.4 +/- 9.4%, respectively) obtained from the codon usages of identified liverwort genes. To date, 32 introns belonging to either group I or group II intron have been found in the coding regions of 17 genes including ribosomal RNA genes (rrn18 and rrn26), a transfer RNA gene (trnS) and a pseudogene (psi nad7). RNA editing was apparently lacking in liverwort mitochondria since the nucleotide sequences of the liverwort mitochondrial DNA were well-conserved at the DNA level.

Base Sequence↗
PubMed1978

Expression of bacteriophage M13 DNA in vivo. Localization of the transcription initiation and termination signal of the mRNA coding for the major capsid protein.

During the infection cycle of the filamentous bacteriophage M13 a phage specific RNA species is made which selectively directs in vitro the synthesis of the precursor of the major capsid protein encoded by gene VIII. This RNA is unstable (its mean half-life is 11 min) and is made in amounts representing at least 2% of the newly synthesized RN. Nucleotide sequence analysis have indicated that the synthesis of this RNA species is initiated and terminated at the same promoter (G0.18) and termination signal (T0.25) of the M13 genome as the 8S RNA species made in vitro under the direction of M13 replicative form DNA.

Base Sequence↗
PubMed1989

Nitrite reductase from Pseudomonas aeruginosa: sequence of the gene and the protein.

The gene coding for nitrite reductase of Pseudomonas aeruginosa has been cloned and its sequence determined. The coding region is 1707 bp long and contains information for a polypeptide chain of 568 amino acids. The sequence of the mature protein has been confirmed independently by extensive amino acid sequencing. The amino-terminus of the mature protein is located at Lys-26; the preceding 25 residue long extension shows the features typical of signal peptides. Therefore the enzyme is probably secreted into the periplasmic space. The mature protein is made of 543 amino acid residues and has a molecular mass of 60,204 Da. The c-heme-binding domain, which contains the only two Cys of the molecule, is located at the amino-terminal region. Analysis of the protein sequence in terms of hydrophobicity profile gives results consistent with the fact that the enzyme is fully water soluble and not membrane bound; the most hydrophilic region appears to correspond to the c-heme domain. Secondary structure predictions are in general agreement with previous analysis of circular dichroic data.

Amino Acid Sequence↗
PubMed1990

Heterogeneity among the 2 microns plasmids in Saccharomyces cerevisiae: a new sequence for the REP1 gene.

Some species of yeasts contain naturally-occurring circular DNA plasmids. The most studied of these plasmids is the 2 microns circle of Saccharomyces cerevisiae. Three variants of this plasmid, Scp1, Scp2 and Scp3, have been described according to their restriction maps [Cameron et al., Nucleic Acids Res. 4 (1977) 1429-1448; Livingston, Genetics 86 (1977) 73-84]. The entire nucleotide (nt) sequence of the Scp1 variant from strain A364A has been published [Hartley and Donelson, Nature 286 (1980) 860-864]. We report here the nt sequence of the 2 microns plasmid REP1 gene from S. cerevisiae strain SKQ2n. According to the restriction analysis, this plasmid is the Scp3 variant previously described. The only observed differences between the Scp1 and Scp3 variants were the loss of one EcoRI restriction site and an apparent deletion in Scp3. The nt sequence we report differs significantly from the previously published one for Scp1. The differences correspond to 128 (about 8.5%) substituted, deleted or additional nt of 1510 nt compared. These differences affect the coding region (8%) as well as the noncoding regions (9.7%). Regarding the putative encoded proteins, 38 (about 10%) amino acids (aa) are modified or deleted in our sequence and 11 are added. Most of these aa modifications are not randomly distributed but are concentrated in certain regions. These observations are indicative of important intraspecific evolution between the two 2 microns plasmid variants considered, as well as of conservative selection pressure on some domains of the REP1 protein.

Amino Acid Sequence↗
PubMed1988

Expression in Escherichia coli and characterization of human growth-hormone-releasing factor.

A chemically synthesized DNA sequence, coding for the 44 amino acid residues of human growth-hormone-releasing factor (GRF) preceded by a tryptophan codon, was cloned in frame with Escherichia coli trpE gene within a pBR322-derived plasmid. GRF was expressed in E. coli as a fused polypeptide chain (TrpE-GRF) and then the GRF amino acid sequence was released from the fused protein by specific chemical cleavage at the tryptophan residue using o-iodosobenzoic acid. The thioether group of the methionine residue of GRF was converted in the sulfonium salt derivative, in order to prevent irreversible oxidation of methionine to the sulfone derivative by the o-iodosobenzoic acid reagent. GRF was purified by HPLC and characterized in terms of amino acid composition after acid hydrolysis, protein sequencing and gel electrophoretic behaviour. These data clearly established that the biosynthetic GRF was identical to the natural one, except for the lack of amidation at the carboxyl-terminal amino acid. Far-ultraviolet circular dichroism measurements established that both biosynthetic and natural GRF are devoid of secondary structure in aqueous solution at neutral pH, whereas both peptide samples achieve a high percentage of helical structure in the presence of trifluoroethanol.

Chromatography, High Pressure Liquid↗
PubMed1988

Instruction No. 3/1988, 1 June 1988.

This Instruction contains provisions relating to the injury and maltreatment of children and women and the enforcement of support payments to women and children. With respect to the maltreatment of children, it provides that the Spanish Office of the Public Prosecutor shall a) curb child abuse; b) take decisive action to protect minors who have been abused or are helpless and to execute the new responsibilities imposed by Law 21/1987 of November 11, which modifies the Civil Code with respect to adoption; and c) collect the necessary data with regard to felonies or misdemeanors that involve child abuse so as to allow for the compilation of annual statistics which may identify the magnitude of this problem; With respect to the maltreatment of women, the prosecutor shall a) curb the abuse of women, investigating those cases where a lack of evidence exists because women are afraid; and b) collect the necessary data with regard to felonies or misdemeanors that involve the abuse of women so as to allow for the compilation of annual statistics which may identify the social reality of this problem. With respect to support payments, the Instruction urges all prosecutors to monitor the execution of support payments using all judicial means authorized, including penal actions when applicable, or enforcement mechanisms which have been mentioned in this memo, that is, conditioning visitation rights on timely payment of the support established for food and education of the children. In Circular No. 32 of 15 April 1988, the National Directorate of Police is called on to provide all necessary police assistance to women who have been the object of illegitimate acts of force so that they can report such acts and to inform women of laws designed to help them and the means of availing themselves of these laws. See Anuario de Derecho Penal y Ciencias Penales, Vol. 41, No. 3, September-December 1988, p. 978.

Behavior↗
PubMed1992

Peptidyl antithrombogenic agents for extracorporeal blood circulation.

The reduction of platelet aggregation and adhesion is essential for preventing thrombus formation during extracorporeal circulation. This report addresses some performances of peptidyl antithrombogenic agents which bind to the adhesive site of fibrinogen. This was based on the recent finding that the sequence of the binding domain of the platelet membrane receptor to fibrinogen was identified as TDVNGDGRHDL (one-letter amino acid code; Thr-Asp-Val-Asn-Gly-Asp-Gly-Arg-His-Asp-Leu), entitled B12. The addition of B12 and shorter-chain analogue peptides dose-dependently suppressed platelet aggregation and adhesion onto a fibrinogen-coated surface. The shorter the amino acid sequence, the less effective was inhibition. The inhibitory effect on platelet adhesion in vivo was significant under continuous infusion of B12. These inhibitory effects were compared with those by a receptor-binding RGD (Arg-Gly-Asp) peptide, which is the common active site to adhesive proteins.

Amino Acid Sequence↗
PubMed2007

Accessory proteins assist exonuclease-deficient bacteriophage T4 DNA polymerase in replicating past an abasic site.

Replicative DNA polymerases, such as T4 polymerase, possess both elongation and 3'-5' exonuclease proofreading catalytic activities. They arrest at the base preceding DNA damage on the coding DNA strand and specialized DNA polymerases have evolved to replicate across the lesion by a process known as TLS (translesion DNA synthesis). TLS is considered to take place in two steps that often require different enzymes, insertion of a nucleotide opposite the damaged template base followed by extension from the inserted nucleotide. We and others have observed that inactivation of the 3'-5' exonuclease function of T4 polymerase enables TLS across a single site-specific abasic [AP (apurinic/apyrimidinic)] lesion. In the present study we report a role for auxiliary replicative factors in this reaction. When replication is performed with a large excess of DNA template over DNA polymerase in the absence of auxiliary factors, the exo- polymerase (T4 DNA polymerase deficient in the 3'-5' exonuclease activity) inserts one nucleotide opposite the AP site but does not extend past the lesion. Addition of the clamp processivity factor and the clamp loader complex restores primer extension across an AP lesion on a circular AP-containing DNA substrate by the exo- polymerase, but has no effect on the wild-type enzyme. Hence T4 DNA polymerase exhibits a variety of responses to DNA damage. It can behave as a replicative polymerase or (in the absence of proofreading activity) as a specialized DNA polymerase and carry out TLS. As a specialized polymerase it can function either as an inserter or (with the help of accessory proteins) as an extender. The capacity to separate these distinct functions in a single DNA polymerase provides insight into the biochemical requirements for translesion DNA synthesis.

Bacteriophage T4↗
PubMed1991

Evidence that the entire length of a kinetoplast DNA minicircle is transcribed in Trypanosoma cruzi.

A 1.3 kb cDNA (cDNA52) was derived from Trypanosoma cruzi trypomastigote mRNA. Using single stranded probes in Northern blots, we identified the putative coding strand of cDNA52. In addition, a minor band was detected in RNA from epimastigotes that was absent in RNA from trypomastigotes. Nucleotide sequence analysis revealed that cDNA52 was highly homologous to T. cruzi kinetoplast DNA minicircle sequences. All four conserved regions of T. cruzi minicircles were identified in cDNA52. Using several criteria, we demonstrated that the hybridization signals were not caused by contaminating minicircle DNA in the RNA preparations. The data provide direct evidence for the unprecedented finding that the entire length of a kDNA minicircle is transcribed in T. cruzi.

Amino Acid Sequence↗
PubMed1982

Transformation of hamster kidney cells by fragments of BK virus DNA.

Hamster kidney cells were transformed, with comparable efficiency, by circular or linear molecules of complete BK virus (BKV) genome and by agarose gel-purified fragments of BKV DNA obtained by single or double digestions with various restriction endonucleases. Only fragments containing the complete early region of BKV DNA displayed transforming activity. Analysis by blot hybridization of the arrangement of viral DNA sequences in a cloned cell line transformed by a 3.8-kilobase fragment, obtained after sequential digestion of BKV DNA with HhaI and BamHI, showed the presence of seven viral integrations into the cellular DNA. Apparently all of the integrated viral molecules contained the entire early region of BKV DNA. Large T antigen, small t antigen, and the 56,000-dalton nonviral Tau antigen were detected in transformed cells by immunoprecipitation. The pattern of integration of viral sequences in transformed cells was constant over many generations. Likewise, large T antigen was always detected in transformed cells at various passage levels. These results may suggest that all of the sequences of the early region coding for large T antigen are required for transformation by BKV. Alternatively, subgenomic segments of the BKV DNA early region may be unable to transform because the appropriate polyadenylation site, necessary to obtain a complete functional transcriptional unit, is removed by the restriction enzyme cleavage.

Animals↗
PubMed1994

Production and characterization of recombinant rat brain-derived neurotrophic factor and neurotrophin-3 from insect cells.

Rat brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3) were engineered for expression in a baculovirus-infected Spodoptera frugiperda insect cell system. The BDNF and NT-3 from the culture supernatants were purified by ion-exchange and reverse-phase chromatography to apparent homogeneity. The purification procedure yielded approximately 2 mg of pure rat BDNF or NT-3 per liter of culture supernatant. A single N-terminus only was found for either secreted molecule and was analogous to that predicted from the corresponding cDNA sequence. The recombinant neurotrophins obtained were also homogeneous with regard to molecular weight and amino acid sequence. In their native conformation, the insect cell-produced rat BDNF and NT-3 molecules were homodimers consisting of 119 amino acid polypeptide chains. Thus, although the genes transfected into the S. frugiperda cells coded for proBDNF or proNT-3, the BDNF and NT-3 recovered after purification were > 95% fully processed, mature protein. Mature recombinant rat BDNF and NT-3 were found not to be significantly glycosylated. Pure, recombinant rat BDNF and NT-3 promoted the survival of embryonic dorsal root ganglion neurons in the low picomolar range. Because recombinant rat BDNF and NT-3 can be obtained in large quantities, purified to near homogeneity, and are identical in amino acid sequence to the corresponding human proteins, they are suitable for evaluation in animal models.

Amino Acid Sequence↗
PubMed1991

Pax-6, a murine paired box gene, is expressed in the developing CNS.

A multigene family of paired-box-containing genes (Pax genes) has been identified in the mouse. In this report, we describe the expression pattern of Pax-6 during embryogenesis and the isolation of cDNA clones spanning the entire coding region. The Pax-6 protein consists of 422 amino acids as deduced from the longest open reading frame and contains, in addition to the paired domain, a paired-type homeodomain. Beginning with day 8 of gestation, Pax-6 is expressed in discrete regions of the forebrain and the hindbrain. In the neural tube, expression is mainly confined to mitotic active cells in the ventral ventricular zone along the entire anteroposterior axis starting at day 8.5 of development. Pax-6 is also expressed in the developing eye, the pituitary and the nasal epithelium.

Amino Acid Sequence↗
PubMed1999

Mutations of human topoisomerase II alpha affecting multidrug resistance and sensitivity.

Two mutations, R450Q and P803S, in the coding region of the human topoisomerase II alpha gene have been identified in the atypical multidrug resistant (at-MDR) cell line, CEM/VM-1, which exhibits resistance to many structurally diverse topoisomerase II-targeting antitumor drugs such as VM-26, doxorubicin, m-AMSA, and mitoxantrone. The R450Q mutation mapped in the ATP utilization domain, while the P803S mutation mapped in the vicinity of the active site tyrosine of human topoisomerase II alpha. However, the roles of these two mutations in conferring multidrug resistance are unclear. To study the roles of these two mutations in conferring multidrug resistance, we have characterized the recombinant human DNA topoisomerase II alpha containing either single or double mutations. We show that both R450Q and P803S mutations confer resistance in the absence of ATP. However, in the presence of ATP, the R450Q, but not the P803S, mutation can confer multidrug resistance. The R450Q enzyme was shown to exhibit impaired ATP utilization both for enzyme catalysis and for its ability to form the circular protein clamp. Interestingly, an unrelated mutation, G437E, which is also located in the same domain as the R450Q mutation, exhibited multidrug hypersensitivity in the absence of ATP. However, in the presence of ATP, the G437E enzyme is only minimally hypersensitive to various topoisomerase II drugs. In contrast to the R450Q enzyme, the G437E enzyme exhibited enhanced ATP utilization for enzyme catalysis. In the aggregate, these results support the notion that the multidrug resistance and sensitivity of these mutant enzymes are due to a specific defect in ATP utilization during enzyme catalysis.

Adenosine Triphosphate↗
PubMed1985

Major acute-phase alpha(1)protein in the rat: structure, molecular cloning, and regulation of mRNA levels.

Rat major acute-phase alpha(1)protein (MAP) was characterized by determining its secondary structure, ligand binding and partial amino acid sequence. A cDNA clone expressing MAP and coding for the entire mature protein was isolated from a cDNA library in E. coli prepared from rat liver mRNA. By hybridization to nick translated cDNA, mRNA for MAP was found only in liver, where it increased 17-fold during acute inflammation. Constant proportions of rates of leucine incorporation into MAP over mRNA levels in liver indicated that the regulation of the synthesis of MAP is due to a change in the rate of synthesis and/or the stability of mRNA for MAP, but not the rate of its translation.

Acute-Phase Proteins↗