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At least 1,621 records · Page 90Linked to original sources
PubMed1987

Structure of the yeast isoleucyl-tRNA synthetase gene (ILS1). DNA-sequence, amino-acid sequence of proteolytic peptides of the enzyme and comparison of the structure to those of other known aminoacyl-tRNA synthetases.

The ILS1 gene encoding for cytoplasmic isoleucyl-tRNA synthetase from Saccharomyces cerevisiae was subcloned from a 5.4-kb insert of the shuttle vector YEp13 to M13mp8 and M13mp9. Nucleotide sequence analysis of a 4.3-kb BamHI-HpaI fragment revealed a single open reading frame from which we deduced the amino-acid sequence of the enzyme. Independently obtained amino-acid sequence information from ten tryptic peptides of the purified enzyme confirmed the gene-derived structure. The enzyme is comprised of 1073 amino-acids consistent with earlier determinations of its molecular mass. The codon usage of ILS1 is typical of abundant yeast proteins. A significant homology to E. coli isoleucyl- and valyl-tRNA synthetases as well as to yeast valyl-tRNA synthetase was detected. The characteristic amino-acid residues of the aminoacyl-adenylate site and of the potential binding site of the 3'-end of tRNA found in other synthetases are present in the structure.

Amino Acid Sequence↗
PubMed1992

Fast quantitative assay of sequence-specific endonuclease activity based on DNA sequencer technology.

A quantitative assay of the sequence-specific endonuclease activity of Vsr DNA mismatch endonuclease is described. The procedure rests on fluorescently labelled oligonucleotide substrates and an automated DNA sequencer to determine amounts of both educt and product of the reaction; thus each individual measurement is internally standardized. The assay achieves high sample throughput by parallel measurement of multiple samples. Because of its capacity to produce and process large sets of experimental data, the system is particularly well suited for the determination of reaction kinetics. The procedure lends itself to further simplification by implementing software additions for direct peak integration. Obviously, the principle of the assay can be extended to the study of other enzymes, such as restriction endonucleases or sequence-specific proteases.

Base Sequence↗
PubMed2005

A novel Markov pairwise protein sequence alignment method for sequence comparison.

The Smith-Waterman (SW) algorithm is a typical technique for local sequence alignment in computational biology. However, the SW algorithm does not consider the local behaviours of the amino acids, which may result in loss of some useful information. Inspired by the success of Markov Edit Distance (MED) method, this paper therefore proposes a novel Markov pairwise protein sequence alignment (MPPSA) method that takes the local context dependencies into consideration. The numerical results have shown its superiority to the SW for pairwise protein sequence comparison.

Amino Acid Sequence↗
PubMed1995

IgH and L chain variable region gene sequence analyses of twelve synovial tissue-derived B cell lines producing IgA, IgG, and IgM rheumatoid factors structure/function comparisons of antigenic specificity, V gene sequence, and Ig isotype.

In the present study, the complete sequences of the Ig H and L chain variable region genes of twelve RF+ B cell lines from two patients with RA were analyzed. Seven of the RF-producing B cells used VH3 family genes, four used VH4 genes, and one a VH1 gene. All but two of the cell lines expressing VH3 genes utilized different family members; among the VH4-expressing cells, a more restricted pattern was noted. V kappa gene use was restricted to the V kappa I and III families; V lambda gene use was more diverse, involving five different families. Computer comparisons of the expressed VH genes with their presumed germline progenitors indicated significant differences in every instance; eight of the corresponding VL genes also were significantly different. In many cases, assignment of the germline D segment(s) incorporated into the rearranged VH genes was impossible. These differences from the germline gene segments indicated the extensive changes induced by rearrangement, enzymatic activities, and somatic mutation. In hopes of defining a structural reason for the disparate antigen specificities of these cells, the CDR3 amino acid sequences of the multi- vs. the mono-reactive RF-producers were compared. Although CDR3 length was not appreciably different between these two sets of mAb, a greater than two-fold increase in charged amino acids was found in the H chain CDR3 of the multireactive RF. This relationship did not exist for the L chain CDR3. Thus, these sequence data indicate the use of a broad base of Ig V gene segments that have undergone extensive diversification. Based on the localization of R substitutions in the CDR of most of the V genes studied, the diversification appears to be antigen driven and selected. The significance of these findings for the evolution of these B cell clones into isotype-switched producers that are heterogeneous for antigen specificity (mono- vs. multi-reactivity) is discussed.

Aged↗
PubMed1994

Computer search of transcription control sequences in small plant virus DNA reveals a sequence highly homologous to the enhancer element of histone promoters.

The positions of nucleotide sequences which can act as binding sites for plant transcriptional trans-acting protein factors have been mapped in DNA of plant circovirus--coconut foliar decay virus (CFDV). It was found that CFDV promoter region contains sequence motif homologous to the regulatory type I element of plant histone genes. We have also found the presence of the element I motifs in DNAs of other small plant viruses. Taking into account the mechanism of regulation of histone gene expression it appears that these sequences may play a role in a cell cycle-dependent regulation of plant virus DNA transcription and replication.

Base Sequence↗
PubMed2003

Complete sequence of the genome of the human isolate of Andes virus CHI-7913: comparative sequence and protein structure analysis.

We report here the complete genomic sequence of the Chilean human isolate of Andes virus CHI-7913. The S, M, and L genome segment sequences of this isolate are 1,802, 3,641 and 6,466 bases in length, with an overall GC content of 38.7%. These genome segments code for a nucleocapsid protein of 428 amino acids, a glycoprotein precursor protein of 1,138 amino acids and a RNA-dependent RNA polymerase of 2,152 amino acids. In addition, the genome also has other ORFs coding for putative proteins of 34 to 103 amino acids. The encoded proteins have greater than 98% overall similarity with the proteins of Andes virus isolates AH-1 and Chile R123. Among other sequenced Hantavirus, CHI-7913 is more closely related to Sin Nombre virus, with an overall protein similarity of 92%. The characteristics of the encoded proteins of this isolate, such as hydrophobic domains, glycosylation sites, and conserved amino acid motifs shared with other Hantavirus and other members of the Bunyaviridae family, are identified and discussed.

Amino Acid Sequence↗
PubMed1991

Sequence analysis of firefly luciferase family reveals a conservative sequence motif.

A conservative sequence motif was extracted from an alignment of the firefly luciferase family. AngR derived from a pathogenic bacterium and acetyl-CoA synthetases derived from two ascomycete fungi were identified as members of the firefly luciferase family by a homology search with the motif and other sequence comparison analyses. The motif sequence shares several characteristics with the phosphate-binding sites of phosphoproteins and nucleotide-binding proteins. A multiple alignment and an unrooted phylogenetic tree were constructed for the investigation of evolutionary relationships within the firefly luciferase family.

Amino Acid Sequence↗
PubMed1988

Human carbonyl reductase. Nucleotide sequence analysis of a cDNA and amino acid sequence of the encoded protein.

Carbonyl reductase (EC 1.1.1.184) is one of several monomeric, NADPH-dependent oxidoreductases having wide specificity for carbonyl compounds that are generally referred to as the aldoketoreductases. The grouping of the enzyme into the family has been proposed on the basis of functional similarities and in the absence of structural data. Here, we describe the isolation and characterization of a cDNA clone complementary to human carbonyl reductase mRNA from a human placenta cDNA library constructed in phage lambda gt11. The cDNA consists of 1199 base pairs and contains an open reading frame encoding a protein comprised of 277 amino acids with a Mr of 30,375. The predicted amino acid sequence was confirmed by partial sequence analysis of the carbonyl reductase protein. Comparison of the protein sequence with the primary structures of other aldoketoreductases revealed no significant homologies. A possible homology, on the other hand, exists between carbonyl reductase and "short" subunit alcohol/polyol dehydrogenases.

Alcohol Oxidoreductases↗
PubMed1986

cDNA and deduced protein sequence for the beta B1-crystallin polypeptide of the chicken lens. Conservation of the PAPA sequence.

The nucleotide sequence of two cDNA clones corresponding to the beta B1-crystallin mRNA (formerly beta 35) of the chicken eye lens has been determined. The derived amino acid sequence of the chicken beta B1 polypeptide fits well with the two-domain, four "Greek Key" motif structure common to the beta gamma-crystallin superfamily of proteins. The calculated molecular weight of the encoded chicken beta B1 protein is 27,267. The beta B1 polypeptide has both an N- and C-terminal extension and is highly homologous to the mammalian beta B1-crystallin polypeptide. There is a 72% homology between the core regions of the chicken and bovine beta B1 polypeptides; by contrast, there is only 27% homology between the N-terminal extensions of these polypeptides. The N-terminal extension of chicken beta B1 contains a short alternating proline-alanine (PAPA) sequence, like that in the mammalian beta B1, and has some homology with the N-terminal region of histone H1.4, myosin light chain, prokaryotic outer membrane protein A, and adenovirus 24/28-kDa early protein. At the nucleic acid level, the chicken beta B1 crystallin gene has an atypical polyadenylation signal, AATTAAA. This appears to be associated with microheterogeneity of the polyadenylation site by comparison of two cDNA clones, suggesting an additional level at which diversity in crystallin gene expression may arise.

Amino Acid Sequence↗
PubMed1984

The nucleotide sequence of the gene for malF protein, an inner membrane component of the maltose transport system of Escherichia coli. Repeated DNA sequences are found in the malE-malF intercistronic region.

The malF gene product is an inner membrane component of the maltose transport system in Escherichia coli. Some gene fusions between malF and lacZ (encoding the normally cytoplasmic enzyme beta-galactosidase) produce hybrid proteins which are membrane-bound while other fusions produce hybrid proteins which are cytoplasmic (Silhavy, T. J., Casadaban, M. J., Shuman, H. A., and Beckwith, J. R. (1976) Proc. Natl. Acad. Sci. U. S. A. 73, 3423-3427). To further analyze the localization properties of the different classes of fusion proteins and of the intact MalF protein, we have obtained the DNA sequence of 5 malF-lacZ fusions and the wild type malF gene. From the predicted amino acid sequence, MalF protein contains 514 amino acids and has a molecular weight of 56,947. Analysis of the hydropathic character of MalF using the Kyte-Doolittle assignments (Kyte, J., and Doolittle, R. F. (1982) J. Mol. Biol. 157, 105-132), indicates that the protein may have 2 or 3 amino-terminal membrane-spanning segments and 4 or 5 carboxy-terminal membrane-spanning segments separated by a region of 181 hydrophilic residues. Localization properties of the different fusion proteins correspond with degree of hydrophobicity. By sequencing upstream from malF, the malE-malF intercistronic region was found to be 153 base pairs in length and to contain inverted repeats, homologous to intercistronic repeats of many other operons. Further analysis of this region may help in understanding the observed step-down in synthesis of the MalF protein.

ATP-Binding Cassette Transporters↗
PubMed1994

[Primary structure of the intracellular serine proteinase from Bacillus amyloliquefaciens. III. Amino acid sequence of peptides obtained by hydrolysis with a Glu,Asp-specific proteinase. Reconstruction of the entire amino acid sequence of the proteinase].

Glu,Asp-specified protease hydrolysate of intracellular serine proteinase (ISP) was separated by ion-exchange chromatography on a sulphocationite resin followed by HPLC to yield 30 individual peptides. Their sequences, spanning to 243 amino acid residues, were determined by the manual Edman procedure. Four overlapping fragments were reconstructed by comparing their sequences with those of tryptic and chymotryptic peptides. To arrange these fragments in the proteinase polypeptide chain and to reconstruct the enzyme's total sequence, additional peptides were isolated from the tryptic hydrolysate and analysed. Primary structure of ISP, corresponding to 297 amino acid residues, was reconstructed. Its comparison with related serine proteinases revealed the following levels of homology: with Bacillus subtilis intracellular serine proteinase, 88%; with secretory subtilisin BPN' produced by B. amyloliquefaciens, 46%.

Amino Acid Sequence↗
PubMed1993

A common sequence motif near nonhomologous recombination breakpoints involving Ig sequences.

Analysis of nonhomologous recombination events at the Ig loci revealed that a four base sequence, 5'-CCAG-3', or its complement, 5'-CTGG-3', is present within seven nucleotides in 12 of the 13 examined recombination breakpoints. Statistical analysis of the data indicates that this occurrence has a probability of less than 10(-5) of occurring by chance. This sequence is infrequently found at nonhomologous recombination breakpoints in non-Ig sequences, suggesting that its contribution may be either Ig- or B cell-specific. Intriguingly, this tetranucleotide is also found to be associated with the breakpoints of VH gene replacement and isotype switching, suggesting that common pathways may be involved in all three B cell processes.

B-Lymphocytes↗
PubMed1995

The SRY protein, like HMG 1, recognizes (CA)n sequences, an abundant repeat sequence in vertebrates.

The sex-determining region of the Y chromosome gene, sry is expressed in the foetal mouse for a brief period, just before testis differentiation, which could be consistent with negative autoregulation. SRY is a DNA binding protein which can bind to cruciform DNA and to linear DNA with a sequence specificity. We have examined if the Sry gene contain DNA binding sites for the SRY protein itself. We have found that in an in vitro assay, the SRY protein binds to several sites of the Sry gene and especially to a (CA)25 sequence and to a (CAG)30 repeat. These binding suggest that the function of SRY and in a general way HMG-box proteins may be mediated by an interaction with repeat sequences.

Animals↗
PubMed2001

MRI of spinal hardware: comparison of conventional T1-weighted sequence with a new metal artifact reduction sequence.

OBJECTIVE: This study was designed to compare diagnostic quality of MR images of patients with spinal hardware acquired using a conventional T1-weighted spin-echo sequence and a new metal artifact reduction sequence (MARS). CONCLUSION: The new MARS sequence effectively reduces the degree of tissue-obscuring artifact produced by spinal fixation hardware and subjectively improves image quality compared with the conventional T1-weighted spin-echo sequence.

Adult↗
PubMed2005

Sequence effect of docetaxel and carboplatin on toxicity, tumor response and pharmacokinetics in non-small-cell lung cancer patients: a phase I study of two sequences.

PURPOSE: To investigate sequence effects on toxicity, tumor response and pharmacokinetics of docetaxel and carboplatin, together with a determination of the maximum-tolerated dose (MTD) and recommended dose for each schedule. PATIENTS AND METHODS: A total of 46 chemotherapy-naive patients with advanced non-small-cell lung cancer were randomized to receive docetaxel before (schedule A) or after (schedule B) carboplatin. The dose levels studied were [docetaxel (mg/m(2))/carboplatin (mg x min/ml)] 50/5, 60/5, 60/6, 60/7, and 70/6. Treatment cycles were repeated every 3 or 4 weeks unless disease progression or undue toxicity occurred. RESULTS: Of the 46 patients, 44 were assessable for toxicity and received a total of 84 cycles. The major dose-limiting toxicity was neutropenia. When the docetaxel dose was 60 mg/m(2), the carboplatin MTD was deemed to be AUC 7 in both schedules. When the docetaxel dose was escalated to 70 mg/m(2), the carboplatin MTD was reached in schedule A, and the dose-limiting toxicity was not observed in schedule B. Tumor response was observed in 4 of 22 patients (18%) with schedule A and 8 of 19 (42%) with schedule B. Clearances of both drugs were not affected by sequence: 111.2+/-26.8 ml/min and 107.8+/-29.0 ml/min for carboplatin (P=0.69), and 26.7+/-8.3 l/h and 22.8+/-7.0 l/h for docetaxel (P=0.19) in schedules A and B, respectively. CONCLUSIONS: Carboplatin AUC 6 followed by docetaxel 70 mg/m(2) was a favorable regimen for phase II study because of likely lower toxicity and a potentially higher response rate than the reverse sequence schedule. The mechanism of the sequence effects on toxicity and tumor response could not be explained by the pharmacokinetic interactions.

Adult↗
PubMed2006

Enhancement of brain tumors in 0.23-T low-field MRI: comparison of edema attenuated inversion recovery (EDAIR) sequences with T1-weighted sequence.

RATIONALE AND OBJECTIVES: The aim of this study is to explore whether edema attenuated inversion recovery (EDAIR) sequences could be used to improve tumor contrast in contrast-enhanced low-field 0.23-Tesla magnetic resonance imaging (MRI) using 0.1 mmol/kg of gadolinium-based contrast agent. MATERIALS AND METHODS: Ten patients with brain tumors were examined by using the following contrast-enhanced sequences: T1-weighted spin echo, EDAIR with inversion time (TI) of 600 milliseconds, and EDAIR with TI of 800 milliseconds. Images were assessed both quantitatively and qualitatively. RESULTS: Results suggest that tumor contrast enhancement in low-field MRI can be improved without increasing contrast agent dose. EDAIR 600 appears to be optimal in most cases. CONCLUSIONS: This inversion recovery sequence could be applicable as an additional sequence in the imaging of metastases in low-field MRI, as well as imaging of any other enhancing brain tumors or lesions in low-field MRI.

Adolescent↗
PubMed2003

Determination of water self-diffusion coefficient in complex food products by low field 1H PFG-NMR: comparison between the standard spin-echo sequence and the T1-weighted spin-echo sequence.

In 1990, Van Den Enden et al. proposed a method for the determination of water droplet size distributions in emulsions using a pulsed-field-gradient nuclear magnetic resonance (PFG-NMR) T1-weighted stimulated-echo technique. This paper describes both the T1-weighted spin-echo sequence, an improved method based on this earlier work, and, the standard PFG spin-echo sequence. These two methods were compared for water self-diffusion coefficient measurement in the fatty protein concentrate sample used as a 'cheese model.' The transversal and longitudinal relaxation parameters T1 and T2 were determined according to the temperature and investigated for each sample; fat-free protein concentrate sample, pure anhydrous milk fat, and fatty protein concentrate sample. The water self-diffusion in fat-free protein concentrate samples followed a linear behavior. Consequently, the water self-diffusion coefficient could be easily characterized for fat-free protein concentrate samples. However, it seemed more complicated to obtain accurate water self-diffusion in fatty protein concentrate samples since the diffusion-attenuation data were fitted by a bi-exponential function. This paper demonstrates that the implementation of the T1-weighted spin-echo sequence, using the different T1 properties of water and fat phases, allows the accurate determination of water self-diffusion coefficient in a food product. To minimize the contribution of the 1H nuclei in the fat phase on the NMR echo signal, the fat protons were selectively eliminated by an additional 180 degrees pulse. This new method reduces the standard errors of diffusion data obtained with a basic spin-echo technique, by a factor of 10. The effectiveness of the use of the T1-weighted spin-echo sequence to perform accurate water self-diffusion coefficients measurement in fatty products is thus demonstrated.

Animals↗
PubMed2003

Motor sequence learning and reading ability: is poor reading associated with sequencing deficits?

Although it is widely assumed that children with learning disabilities have "sequencing problems," these have not been well specified. A non-verbal serial reaction time (SRT) paradigm was used to evaluate motor sequence learning in 422 children between ages 7 and 11 in relation to reading, cognitive ability level, and attention problems. The children demonstrated the response profile typically associated with motor sequence learning, but the component of the profile indicative of implicit sequence learning was not reliably associated with any of the predictors. Cognitive ability predicted overall response time; cognitive ability, reading, and attention problems each predicted overall accuracy. Explicit learning was predicted by cognitive ability, but not by reading or attention problems. Thus, we found no evidence that poor reading is preferentially associated with a domain general deficit in sequential learning.

Aptitude↗