[A classification of crackles by the linear predictive coding method].
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Adult↗
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Results for “recognition code”
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Specificity of AAG codon recognition by lysyl transfer ribonucleic acid from yeast.
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Adenine Nucleotides↗
Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity.
The specificity with which the genetic code is read in protein synthesis, and with which other highly specific biosynthetic reactions take place, can be increased above the level available from free energy differences in intermediates or kinetic barriers by a process defined here as kinetic proofreading. A simple kinetic pathway is described which results in this proofreading when the reaction is strongly but nonspecifically driven, e.g., by phosphate hydrolysis. Protein synthesis, amino acid recognition, and DNA replication, all exhibit the features of this model. In each case, known reactions which otherwise appear to be useless or deleterious complications are seen to be essential to the proofreading function.
Amino Acid Sequence↗
Early recognition of regional cardiac ischemia using a 3-axis accelerometer sensor.
Perioperative mortality in coronary artery bypass grafting is usually caused by reduced left ventricular function due to regional myocardial ischemia or infarction. Post-operative graft occlusion is a well-known problem in coronary surgery. A sensitive tool to detect graft occlusion and monitor myocardial function may give the opportunity to revise malfunctioning grafts before departure from the hospital. This paper describes how a new method can detect cardiac ischemia using a 3-axis piezoelectric accelerometer. In three anesthetized pigs, a 3-axis piezoelectric accelerometer was sutured on the lateral free wall of the left ventricle. The left anterior descending (LAD) was occluded for different time periods and the accelerometer data were sampled with a PC. Short-time Fourier transform was calculated based on the accelerometer time series. The results were visualized using a 2D color-coded time-frequency plot. In the area of occlusion, a change to stronger power of higher harmonics was observed. Consequently, a difference value between the instant frequency pattern and a reference frequency pattern showed a rise in absolute value during the occlusion period. The preliminary results indicate that early recognition of regional cardiac ischemia is possible by analyzing accelerometer data acquired from the three animal trials using the prototype 3-axis accelerometer sensor.
Acceleration↗
Nucleotide sequence of the glnA control region of Escherichia coli.
The RNA polymerase binding sites present along a DNA segment encompassing the glnA, glnL, and glnG genes have been identified in a hybrid plasmid carrying this chromosomal region of Escherichia coli. The DNA sequence was determined of an 817 base pair segment that contains the region coding for the first 42 amino acids of the NH2-terminal and of the glnA structural gene, as well as its regulatory region. Analysis of this nucleotide sequence revealed three probable RNA polymerase recognition sites, imperfect palindromes, inverted repeats, and direct repeated sequences.
Base Sequence↗
Polymorphism of the IGHA gene in sheep.
Genetic variation in immunoglobulin A, the most abundant immunoglobulin in mammalian cells, has not been reported in ruminants. In this study, variation in the immunoglobulin heavy alpha chain constant gene (IGHA) of sheep was investigated by amplification of a fragment that included the hinge coding sequence, followed by single-strand conformational polymorphism (SSCP) analysis and DNA sequencing. Three novel sequences, each characterized by unique SSCP banding patterns, were identified. One or two sequences were detected in individual sheep and all the sequences identified shared high homology to the published ovine and bovine IGHA sequences, suggesting that these sequences represent allelic variants of the IGHA gene in sheep. Sequence alignment showed that these sequences differed mainly in the 3' end of exon 1 and in the coding sequence of the hinge region. There was either a deletion or an insertion of two codons in the hinge coding region in these allelic variants. Codon usage in the hinge coding region was quite different from that in the non-hinge coding regions of the gene, suggesting different evolution of the IGHA hinge sequence. Three novel amino acid sequences of ovine IGHA were also predicted, and variation in these sequences might not only affect antigen recognition but also susceptibility to cleavage by bacterial or parasitic proteases.
Alleles↗
Synthesis of chicken major histocompatibility complex class II oligomers using a baculovirus expression system.
Chicken major histocompatibility complex (MHC) B21 and B19 haplotypes are associated with resistance and susceptibility to Marek's disease (MD), respectively. T-cell-mediated immune response is crucial in coordinating protection against Marek's disease virus (MDV) infection, but it has been difficult to identify and characterize antigen-specific T-cells. MHC class II tetramers and oligomers have been widely used for characterization of antigen-specific T-cells in the context of infectious and autoimmune diseases. Thus, the objective of this study was to synthesize chicken MHC class II oligomers of B21 and B19 haplotypes for the future identification of antigen-specific T-cells. To achieve this objective, full-length coding sequences of chicken MHC class II B21 and B19 molecules were amplified and the molecules were expressed as fusion proteins, carrying Fos and Jun leucine zipper (LZ), histidine-tag and biotin ligase recognition site sequences, using a baculovirus expression system. Recombinant MHC-II were loaded with self-peptides, which stabilized the heterodimer in SDS-PAGE and allowed the detection of these molecules in Western blots with a conformation-specific anti-chicken MHC class II antibody. Biotinylated MHC molecules were conjugated to streptavidin to form oligomers, which were resolved under the transmission electron microscope through immuno-gold labelling, thus confirming success of oligomerization. In conclusion, chicken MHC class II oligomers may be used in the future to study the antigen-specific CD4+ T-cell compartment.
Animals↗
RS cyclophilins: identification of an NK-TR1-related cyclophilin.
We report the isolation of a large cyclophilin protein containing RS (arginine-serine) repeats from a yeast two-hybrid screen using ClK (CDC28/cdc2-like kinase) as a probe. This Clk associating RS-cyclophilin (CARS-Cyp) possesses 39% homology to the NK-TR1 (natural killer tumor recognition protein-1) we have previously characterized (Anderson et al. (1993) Proc. Natl. Acad. Sci. USA 90 (1993) 542-546). CARS-Cyp is expressed in a variety of tissues and cell types, and codes for a protein with a predicted mass of 89 kDa containing a cyclophilin-related domain, two Nopp140 (nucleolar phosphoprotein of 140 kDa)-related domains, and a large RS domain. The RS-cyclophilins, a novel class of proteins, may play an important role in the regulation of pre-mRNA splicing.
Amino Acid Isomerases↗
The alpha-helical neck region of human lung surfactant protein D is essential for the binding of the carbohydrate recognition domains to lipopolysaccharides and phospholipids.
We have expressed the carbohydrate recognition domains (CRDs) of human lung surfactant protein D (SP-D) in Escherichia coli as a trimeric structure held together by the alpha-helical neck region of the molecule. The DNA sequence coding for the neck-region peptide and the CRD of SP-D was subcloned and expressed as a fusion protein containing the E. coli maltose binding protein (MBP). After removal of the MBP, the recombinant structure, containing three CRDs of SP-D, was found to be comparable to native SP-D in terms of carbohydrate binding specificity, the binding to lipopolysaccharides (LPSs) of Gram-negative bacteria, and interaction with phospholipids. The CRD of SP-D, without the neck region peptide, was also expressed and shown to behave as a monomer that showed a very weak affinity for maltose-agarose, LPSs and phospholipids. The alpha-helical neck region on its own showed affinity for phospholipids and thus might contribute to the binding of SP-D to these structures. However, the possibility that hydrophobic patches, which are exposed only in the isolated neck region and not in the intact SP-D, plays a role in neck region-phospholipid interaction, cannot be excluded. The results confirm the importance of the neck region as a trimerizing agent in bringing together three CRDs and suggest that multivalency is important in the strong binding of SP-D to carbohydrate targets.
Binding Sites↗
Electrostatic potentials of DNA. Comparative analysis of promoter and nonpromoter nucleotide sequences.
Distribution of electrostatic potential of DNA fragments was evaluated. A method for calculation of electrostatic potential distribution based on Coulomb's law is proposed for long DNA fragments (approximately 1000 nucleotide pairs). For short DNA sequences, this technique provides a good correlation with the results obtained using Poisson-Boltzmann equation thus justifying its application in comparative studies for long DNA fragments. Calculation was performed for several DNA fragments from E. coli and bacteriophage T7 genomes containing promoter and nonpromoter regions. The results obtained indicate that coding regions are characterized by more homogeneous distribution of electrostatic potential whereas local inhomogeneity of DNA electrostatic profile is typical for promoter regions. The possible role of electrostatic interactions in RNA polymerase-promoter recognition is discussed.
Anion Transport Proteins↗
Construction and in vitro testing of a novel fab-hirudin-based fusion protein that targets fibrin and inhibits thrombin in a factor xa-dependent manner.
Fibrin targeting of the thrombin inhibitor hirudin via chemical coupling is effective in vitro and in vivo. However, since chemical coupling has limitations, a recombinant approach was taken to improve the fibrin-targeting ability of hirudin. Additionally, to activate hirudin selectively at the target area and thereby limit side effects in an in vivo setting, the authors aimed to construct an inactive precursor molecule that is converted into an active thrombin inhibitor only upon cleavage by factor Xa. Using PCR, the coding region for hirudin was fused to parts of the genomic DNA of the IgG heavy chain that was cloned from the antifibrin antibody-producing hybridoma cell line 59D8. Additionally, a factor Xa recognition site was introduced between the antibody and the hirudin sequence. The fusion construct was then transfected into a heavy-chain loss variant of the hybridoma cell line 59D8. After selection of stable hybridoma clones, the expressed fusion protein was evaluated for its molecular size (57 kd) and its binding ability to the fibrin-specific peptide Bbeta 15-22. The cleavage of the fusion protein by factor Xa was demonstrated by HPLC. The recombinant anticoagulant revealed antithrombin activity only after cleavage by factor Xa. Thus, the newly designed hirudin fusion protein revealed the anticipated functions in vitro. Further experiments are needed to prove whether this precursor anticoagulant allows a highly clot-specific and efficient thrombin inhibition in vivo.
Antibodies, Monoclonal↗
Two genes for carbohydrate catabolism are divergently transcribed from a region of DNA containing the hexC locus in Pseudomonas aeruginosa PAO1.
The hexC locus of Pseudomonas aeruginosa PAO1 was localized to a 247-bp segment of chromosomal DNA on the multicopy broad-host-range vector pRO1614. The presence of this plasmid (pPZ196) in strain PAO1 produced the so-called "hexC effect," a two- to ninefold increase in the activities of four carbohydrate catabolism enzymes, glucokinase, glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydratase, and 2-keto-3-deoxy-6-phosphogluconate aldolase. The extent of the hexC effect was restricted, since three independently regulated metabolic enzymes were not affected by the presence of the hexC plasmid. Furthermore, the hexC-containing plasmid did not suppress catabolite repression control. Nucleotide sequence analysis of the segment of DNA encompassing hexC revealed a 128-bp region rich in adenosine-plus-thymine (AT) content separating two divergent open reading frames (ORFs). Transcriptional start sites for these two genes were mapped to the intergenic region, demonstrating that this sequence contained overlapping divergent promoters. The intergenic region contained potential regulatory sequences such as dyad symmetry motifs, polydeoxyadenosine tracts, and a sequence matching the integration host factor recognition site in Escherichia coli. One of the ORFs encoded a 610-amino-acid protein with 55 to 60% identity to 6-phosphogluconate dehydratase from E. coli and Zymomonas mobilis. The second ORF coded for a protein of 335 amino acids that displayed 45 to 60% identity to the NAD-dependent glyceraldehyde-3-phosphate dehydrogenase (GAP) family of enzymes. The NAD-dependent GAP gene on the P. aeruginosa chromosome was previously unmapped. GAP was found to exhibit the hexC-dependent increase in its basal activity, establishing it as a fifth catabolic enzyme in the multioperonic hex regulon.
Amino Acid Sequence↗
Potential impacts of patient access to their electronic care records.
This paper examines the interest and expectations of patients having access to their electronic care records. Semi-structured prospective interviews were performed with 109 patients in a community setting in London where all records are stored digitally either as coded data, free text or scanned in from the paper original. A booth had recently been set up for patients to access their electronic records in the waiting room with secure access through fingerprint recognition technology. The interviews detailed history and levels of interest in access, impact on relationship with clinician, familiarity with digital media and issues of security and accuracy. Patients were more interested in seeing their electronic than their paper record; they felt it would improve their relationship with their clinician; they generally trusted in the security of their records; they anticipated that there would be some mistakes; they were enthusiastic about the idea of adding to the record themselves, but were divided about having access over the internet. Patients are confident in and anticipate the value of having access to their electronic records.
Adolescent↗
[Analysis of the nucleotide sequence of a fragment (92-100%) of the CELO avian adenovirus genome].
The nucleotide sequence of 92-100% of the adenovirus CELO (FAV1), strain Phelps, genome has been determined. The computer analysis of the sequences revealed a ClaI site methylated by m*Ecodam. A recognition site for XbaI and two sites for PstI, not found in the corresponding genome of CELO, strain Ote, have been determined. Three extensive (more than 100 amino acid residues) open reading frames exist, coding for the polypeptides with molecular weights of 31.5, 19.3 and 14.5 kD (276, 178 and 128 amino acids, respectively). Some shorter open reading frames have been detected as well within the sequences studied.
Amino Acid Sequence↗
Concurrent care coverage by Medicare.
Medicare is a Federal Health Insurance Program administered by the Health Care Financing Administration for the elderly and certain disabled persons. The Texas Medicare carrier disseminates information and develops educational programs for improved understanding. "Concurrent care" exists when services are performed by more than one physician during a period of time for the same patient. Since Medicare does not have specialty designations for endocrinology, oncology, rheumatology, hematology, and infectious disease physicians, an X6 modifier is used for recognition. Services by two physicians of the same specialty or subspecialty rarely warrant coverage, but services by one physician and later care by another physician for an acute episode do warrant coverage. Emergency department codes should be used when care is given in that department and appropriate modifiers should be used by second- and third-opinion consultants in order to avoid the appearance of concurrent care. Diagnosis related to specialty and documentation of acute situations help avoid denial for "not reasonable or necessary" services. Physicians should use the "Waiver of Liability" when concurrent care seems necessary but is not likely to be covered by Medicare.
Aged↗
Surfactant protein A-binding proteins. Characterization and structures.
An alveolar cell membrane protein acts as a surfactant protein A (SP-A) receptor; it binds SP-A and regulates surfactant secretion. We identified such alveolar cell membrane SP-A-binding proteins using anti-idiotype antibodies directed against the surfactant protein binding region of anti-surfactant antibodies. These monoclonal anti-idiotype antibodies, A2C and A2R, also recognize an alveolar cell membrane protein of approximately 30 kDa. A pulmonary protein of approximately 30 kDa binds SP-A. Unique cDNAs encoding this protein were identified in human (4.1-kilobase) and porcine (1.8-kilobase) lung expression libraries. Coding regions of these cDNAs cross-hybridize with each other under stringent conditions. Both cDNAs encode similar approximately 32-kDa proteins that bind SP-A. The human and porcine SP-A recognition (SPAR) proteins resemble each other, as well as other cell membrane receptors. Their projected structures are consistent with cell membrane receptors. Recombinant human and porcine SPAR proteins bind SP-A as well as the two anti-idiotype antibodies just as do native lung proteins of approximately 30 kDa. SPAR transcripts are expressed primarily in lung. The cellular distribution of these transcripts, as determined by in situ hybridization, is similar to that of SPAR protein, as determined by immunohistochemistry; both are found in cells consistent with type II pneumocytes. SPAR-producing cells resemble the alveolar cells expressing SP-B and SP-C transcripts in appearance, location, and distribution. Therefore, cDNAs for pulmonary SP-A-binding proteins from two disparate species have been isolated and sequenced, and the recombinant proteins they encode bind the same ligand. Further structural, functional, and genetic studies of these proteins may help explain how pulmonary surfactant secretion is regulated.
Amino Acid Sequence↗
What parameters can be used for individual acoustic recognition by the greater flamingo?
The greater flamingo Phoenicopterus ruber is a colonial bird for which acoustic communication plays a great role, in particular during the mating period. The study of contact calls emitted by the adults allow enables identification of some acoustic parameters which may be used for individual recognition. It appears that the frequential values of the harmonics, the distribution of energy in the spectrum as well as beats (mimicking amplitude modulations) are susceptible to represent individual markers. On the contrary, the coding of the individual identity does not depend on frequency modulation since this latter is practically lacking. These results are remarkably similar to those obtained from another colonial bird species, the emperor penguin Aptenodytes forsteri, and may correspond to signal adaptations to special acoustic constraints of the colonial way of life.
Animal Communication↗
The relationship between phonological codes on memory and spelling tasks for students with and without learning disabilities.
The purpose of the study was to determine the degree to which 31 (23 boys and 8 girls) 13-year-old children with learning disabilities from Grades 7, 8, and 9 were comparable to younger (9-year-old) reading- and spelling-matched controls in (a) phonological similarity effects, (b) phonetically based misspellings, and (c) relationships between memory and spelling performance. Children with reading disabilities and reading-recognition-matched controls, subgrouped by spelling ability, were compared on their memory for phonetically similar and dissimilar word lists and types of spelling errors. The results indicate that children with reading disabilities who are matched to younger children on both reading recognition and spelling ability exhibit normal phonological effects on memory and spelling measures. Within each reading group, low spellers produced more semiphonetic errors than high spellers, and high spellers produced more phonetic errors than low spellers. Significant correlations between memory and spelling error measures were more frequent for children with reading disabilities when compared to controls matched on reading and spelling ability. It was concluded that the phonological performance of reading/spelling-matched children with reading disabilities is characterized by an overreliance on phonological codes, whereas their counterparts' performance reflects independent and less generalizable use of phonological substrates across tasks.
Adolescent↗