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PubMed1980

Nomina dubia and available names.

The availability or non-availability of a name is a question of historical fact. A name once made available under the International Code of Zoological Nomenclature can be rendered unavailable only by use of the plenary powers of the Commission. The question whether a name is a nomen dubium or not is a matter of taxonomic judgement. The difficulty with the Sarcocystinae discussed by Frenkel et al. (1979) stems from the fact that, under the present provisions of the Code, it is not possible to designate for the species concerned types that will serve any useful function. The Commission is now considering changes to the Code proposed to remedy this defect in a general, legislative way. It will not, as a matter of general practice, entertain proposals for the suppression of names merely because they are considered to be nomina dubia. The application submitted by Professor Frenkel and his collegaues will nevertheless be published in the Bulletin of Zoological Nomenclature so that the Commission can, if necessary, deliver a ruling on it before the new edition of the Code has appeared.

Animals↗
PubMed1989

Characterisation of the dihydrofolate reductase-thymidylate synthetase gene from human malaria parasites highly resistant to pyrimethamine.

To investigate the genetic basis of drug resistance in human malaria parasites, we have sequenced the entire dihydrofolate reductase thymidylate synthetase DHFR-TS bifunctional gene from the highly pyrimethamine-resistant K1 isolate of Plasmodium falciparum. The protein is predicted to consist of 607 amino acids (aa), (71,685 Da), with an N-terminal methionine encoded by the second start codon of the open reading frame. Compared to the sequence from drug-sensitive parasites, there are two nucleotide changes in the coding region which bring about a substitution of Arg for Cys at aa position 59 and Asn for Thr at aa position 108. Both changes occur in regions of the DHFR domain involved in inhibitor and cofactor binding and are hence strongly implicated in drug resistance. The gene is present as a single copy in both K1 and drug-sensitive FCR3 isolates, and is assigned to chromosome 4. Codon usage follows the pattern observed in that of malarial surface antigen genes, with the exception fo codons corresponding to Val and Pro. The Asn and Lys contents of the predicted protein are exceptionally high, these residues being particularly concentrated in the DHFR and junction domains.

Amino Acid Sequence↗
PubMed2001

Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis.

Comparative sequence analysis has facilitated the discovery of protein coding genes and important functional sequences within proteins, but has been less useful for identifying functional sequence elements in nonprotein-coding DNA because the relatively rapid rate of change of nonprotein-coding sequences and the relative simplicity of non-coding regulatory sequence elements necessitates the comparison of sequences of relatively closely related species. We tested the use of comparative DNA sequence analysis to aid identification of promoter regulatory elements, nonprotein-coding RNA genes, and small protein-coding genes by surveying random DNA sequences of several Saccharomyces yeast species, with the goal of learning which species are best suited for comparisons with S. cerevisiae. We also determined the DNA sequence of a few specific promoters and RNA genes of several Saccharomyces species to determine the degree of conservation of known functional elements within the genome. Our results lead us to conclude that comparative DNA sequence analysis will enable identification of functionally conserved elements within the yeast genome, and suggest a path for obtaining this information.

Base Sequence↗
PubMed1997

The composition of coding joints formed in V(D)J recombination is strongly affected by the nucleotide sequence of the coding ends and their relationship to the recombination signal sequences.

V(D)J recombination proceeds in two stages. Precise cleavage at the border of the conserved recombination signal sequences (RSSs) and the coding ends results in flush double-stranded signal ends and coding ends terminating in hairpins. In the second stage, the signal and coding ends are processed into signal and coding joints. Coding ends containing certain nucleotide homopolymers affect the efficiency of V(D)J recombination. In this study, we have tested the effect of small changes in coding-end nucleotide composition on the frequency of coding- and signal joint formation. Furthermore, we have determined the sequences of coding joints resulting from recombination of coding ends with different compositions. We found that the presence of two T nucleotides 5' of both RSSs, but not a single T, reduces the frequency of signal joint formation, i.e., interferes with the cleavage stage of V(D)J recombination. However, coding-joint processing is sensitive even to a single T. Both the sequence of the coding ends and the particular RSS (12-mer or 23-mer) with which the coding end is associated affect the final composition of the coding joints. Thus, the presence of P nucleotides, the conservation of one undeleted coding end, the formation of joints without any deletions, and the template-dependent insertion of nucleotides are strongly influenced by the coding-end nucleotide composition and/or RSS association. The implications of these results with respect to the processing of coding ends are discussed.

Animals↗
PubMed1978

Increase in hospitalisation for childhood asthma.

Asthma admissions among children under 15 years of age have increased nearly three-fold over the period 1959-73. The possible reasons for this increase have been examined using available data supplemented by the results of a special study of hospital disease indexes and case notes. Changes in diagnostic coding and trends in diagnostic fashion do not appear to be important. Part of the increase may be due to an increase in readmission rates. Changes in admission criteria resulting from changes in therapy, organisation of care, and illness behaviour have been considered. However, on present evidence an increase in morbidity cannot be excluded, and this could be investigated by repeat prevalence surveys of schoolchildren. If morbidity remains unchanged, admission policies for children with asthma should be reviewed.

Adolescent↗
PubMed1993

Asthma mortality: another opinion--is it a matter of life and ... bread?

There is a general consensus that the mortality rates for asthma in much of the developed world have been increasing for the past 10-15 years. This has occurred despite an improved information base regarding diagnosis and management as well as the development of novel and more effective therapeutic modalities. Several explanations have been proposed for this increase, including a statistical artifact based on a change in the coding criteria for asthma from the International Classification of Diseases Version 8 (ICD-8) to ICD-9, worsened pollution, delays in seeking medical help, behavioral changes, deficits in asthma education of both patients and primary care providers, toxicity of beta agonists, and noncompliance with medications. We suggest that although all of these are potential etiological factors, there may exist still another major etiological risk. There have been dramatic changes in our eating habits and food preparation. In general, we eat less total calories, more meals outside the home, and more refined or prepared foods. With the emphasis on reducing the intake of saturated fats and cholesterol, we eat more polyunsaturated fats both by choice and secondary to manufacturers' attempts to improve the appeal of foods to health-conscious government and the public. The drive to remove animal fats and cholesterol from our diet has resulted in the replacement of animal fats with vegetable oil in food manufacture, fast-food frying, and even home preparation. One result of these dietary habits has been a doubling from 8 to 15% of the percentage of the polyunsaturated linoleic acid in body fat. We postulate that this, and other nutritional changes, will render asthma a more difficult syndrome to manage and will contribute adversely to the inflammatory abnormalities in airways.

Adrenergic beta-Agonists↗
PubMed1995

Heterogeneous expression of glycoprotein Ib, IX and V in platelets from two patients with Bernard-Soulier syndrome caused by different genetic abnormalities.

Bernard-Soulier syndrome (BSS) is a rare inherited bleeding disorder, which is caused by deficiency or decrease of the platelet GPIb/IX/V complex. Analysis of two patients with BSS by flow cytometry of the blood revealed different expression patterns of the components of the GPIb/IX/V complex. In case 1, GPIX was completely absent but residual amounts of GPIb alpha and GPV were detectable; in case 2, GPIb alpha was completely absent. We amplified the coding regions of GPIb alpha, GPIb beta, GPV, and GPIX from the patients' genomic DNA with the polymerase chain reaction (PCR) and sequenced the PCR products. in case 1, we identified a point mutation in the GPIX coding region that changes the codon for tryptophan-126 (TGG) to a nonsense codon (TGA). In case 2, we found a deletion of nucleotide within seven adenine repeats at the position of 1932 to 1938 in the coding region of GPIb alpha, which causes a frame shift that results in 58 altered amino acids and a premature stop codon. These genetic changes alter the transmembrane domain of GPIX or GPIb alpha and, therefore, would prevent proper insertion of the proteins in the plasma membrane. Thus, abnormality of a single component protein (GPIX or GPIb alpha) alters the assembly of the GPIb/IX/V complex and causes heterogeneous surface expression of GPIb alpha, GPV and GPIX.

Adult↗
PubMed1990

Changes in steady-state levels of mRNAs coding for type IV collagen, laminin and fibronectin following capillary basement membrane thickening in human adult onset diabetes.

The development of capillary basement membrane thickening has been linked to microvascular changes known to occur in tissues of patients with type II diabetes. Previous evidence has suggested that capillary basement membrane thickening is due to increased basement membrane synthesis. In this study, skin samples from 8 diabetic patients with confirmed capillary basement membrane thickening and 7 non-diabetic controls were used to assess steady state levels of mRNAs coding for several basement components including pro alpha 1(IV) collagen, laminin and fibronectin. Total RNA was extracted from abdominal skin samples and levels of mRNAs coding for the basement membrane components laminin, fibronectin and pro alpha 1(IV) collagen, a fibrillar collagenous protein, pro alpha 1(I) collagen and an intracellular polypeptide, gamma-actin, were determined by dot blot hybridization analysis. While there were no changes of steady state levels of pro alpha 1(I) collagen mRNA and laminin mRNA, a significant reduction was noted in the quantitative recovery of mRNA levels for pro alpha 1(IV) collagen, gamma-actin and fibronectin in total RNA isolated from the skin of diabetic patients. This reduction in levels of mRNAs coding for basement membrane components contrasts with pathological confirmation of an accumulation of endothelial capillary basement membrane in skin from diabetic patients and suggests that basement membrane thickening arises more as a consequence of reduced basement membrane degradation than elevated synthesis of basement membrane components.

Aged↗
PubMed1996

A proposed revision of current ICD-9-CM malnutrition code definitions.

Protein-energy malnutrition (PEM) is as common today in adult medical and surgical patients as it was when it was first identified more than 25 years ago. Under the current diagnosis-related group (DRG) payment system, malnutrition is considered a comorbidity or complicating condition. Thus, the identification and coding of malnutrition through the use of the International Classification of Diseases, ninth edition, Clinical Modification (ICD-9-CM) malnutrition codes can potentially change a patient's DRG and subsequently increase the amount of reimbursement a hospital receives. Unfortunately, the definitions for the current ICD-9-CM malnutrition diagnosis codes were developed principally in relation to clinical syndromes of primary PEM seen in pediatric age groups in less developed countries, rather than in relation to syndromes seen in hospitalized adult patients in industrialized societies. This discrepancy often leads to confusion and inconsistency when institutions attempt to code adult patients for malnutrition. Furthermore, inaccurate coding can result in inadequate reimbursement or rejection of a claim. Clearly, a separate description of the different forms of PEM seen in adults is needed not only for optimal application of nutrition support therapies but also for accurate medical records, quality assurance procedures, and reimbursement purposes. On the basis of 20 years of experience providing nutrition support to hospitalized adult patients, this article presents a schema developed at the Deaconess Hospital (Boston,Mass) that attempts to better define adult PEM using the ICD-9-CM malnutrition codes. The purpose of this article is to foster discussion and ultimately promote general agreement about a definition of adult PEM.

Aged↗
PubMed1996

Genes involved in cell cycle G1 checkpoint control are frequently mutated in human melanoma metastases.

A common characteristic of cancer cells is unrestrained cell division. This may be caused by mutational changes in genes coding for components of cell cycle-controlling networks. Alterations in genes involved in G1 checkpoint control have been registered in many human tumours, and investigations from several laboratories show that such alterations, taken together, are the most frequent changes detected in cancer cells. The present paper describes mutational analysis by polymerase chain reaction-single-strand conformation polymorphism (PCR/SSCP) and nucleotide sequence analysis of the genes coding for the p15, p53 and N-ras proteins in 26 metastases from 25 melanoma patients. The registered mutation frequencies add together with previously registered mutations in p16 in the same patient samples to a substantial total frequency of 44% of patients with mutation in at least one of the investigated genes. These results show the occurrence of heterogeneous defects among components of the cell cycle controlling machinery in a human melanoma tumour sample collection and demonstrate that the total frequency of detected alterations increases with the number of cell cycle controlling genes included in the screening panel.

Carrier Proteins↗
PubMed1990

Genetic code 1990. Outlook.

The genetic code is evolving as shown by 9 departures from the universal code: 6 of them are in mitochondria and 3 are in nuclear codes. We propose that these changes are preceded by disappearance of a codon from coding sequences in mRNA of an organism or organelle. The function of the codon that disappears is taken by other, synonymous codons, so that there is no change in amino acid sequences of proteins. The deleted codon then reappears with a new function. Wobble pairing between anticodons and codons has evolved, starting with a single UNN anticodon pairing with 4 codons. Directional mutation pressure affects codon usage and may produce codon reassignments, especially of stop codons. Selenocysteine is coded by UGA, which is also a stop codon, and this anomaly is discussed. The outlook for discovery of more changes in the code is favorable, and open reading frames should be compared with actual sequential analyses of protein molecules in this search.

Anaerobiosis↗
PubMed2000

Dolichol phosphate mannose synthase (DPM1) mutations define congenital disorder of glycosylation Ie (CDG-Ie)

Congenital disorders of glycosylation (CDGs) are metabolic deficiencies in glycoprotein biosynthesis that usually cause severe mental and psychomotor retardation. Different forms of CDGs can be recognized by altered isoelectric focusing (IEF) patterns of serum transferrin (Tf). Two patients with these symptoms and similar abnormal Tf IEF patterns were analyzed by metabolic labeling of fibroblasts with ¿2-(3)Hmannose. The patients produced a truncated dolichol-linked precursor oligosaccharide with 5 mannose residues, instead of the normal precursor with 9 mannose residues. Addition of 250 microM mannose to the culture medium corrected the size of the truncated oligosaccharide. Microsomes from fibroblasts of these patients were approximately 95% deficient in dolichol-phosphate-mannose (Dol-P-Man) synthase activity, with an apparent K(m) for GDP-Man approximately 6-fold higher than normal. DPM1, the gene coding for the catalytic subunit of Dol-P-Man synthase, was altered in both patients. One patient had a point mutation, C(274)G, causing an R(92)G change in the coding sequence. The other patient also had the C(274)G mutation and a 13-bp deletion that presumably resulted in an unstable transcript. Defects in DPM1 define a new glycosylation disorder, CDG-Ie.

Brain Diseases, Metabolic, Inborn↗
PubMed2003

Adaptation to display rotation and display gain distortions during drawing.

The relationship between movement extent and movement direction coding mechanisms was investigated using a visuomotor adaptation paradigm. To determine if these mechanisms are either modular or interdependent, young healthy college students were tested while they performed a visually guided drawing task that incorporated varying combinations of movement distance and direction distortions. Analysis of participants' standardized movement duration, initial directional error, and movement length over the course of the adaptation process revealed a certain degree of interdependence between direction and extent coding mechanisms. Specifically, changes in final adaptation levels and after-effects depended on the order of introduction of the visual distortions. This interaction can be characterized as unidirectional, where alterations in rotational feedback interfere with subsequent adaptation to gain changes, whereas alterations in "display gain" do not significantly impede the adaptation to "display rotation". Moreover, simultaneous exposure to gain and rotational distortions resulted in better learning. The results argue against an independent coding of movement direction and extent during adaptation by the central nervous system.

Adaptation, Physiological↗
PubMed1986

Nucleotide and derived amino acid sequences of a cDNA coding for pre-uteroglobin from the lung of the hare (Lepus capensis).

An almost full-length cDNA coding for pre-uteroglobin from hare lung was cloned and sequenced. The derived amino acid sequence indicated that hare pre-uteroglobin contained 91 amino acids, including a signal peptide of 21 residues. Comparison of the nucleotide sequence of hare pre-uteroglobin cDNA with that previously reported for the rabbit gene indicated five silent point substitutions and six others leading to amino acid changes in the coding region. The untranslated regions of both pre-uteroglobin mRNAs were very similar. The amino acid changes observed are discussed in relation to the different progesterone-binding abilities of both homologous proteins.

Amino Acid Sequence↗
PubMed1999

Elucidating sequence codes: three codes for evolution.

The sequences are related to evolution in several ways. First, they carry traces of a distant past. Two sequence features point to the earliest sequence organization. The universal hidden GCU-periodical pattern in mRNA suggests the earliest codons: GCU and its nine-point-change derivatives. They code for seven amino acids that by several criteria are also the oldest. Together it makes the earliest form of the triplet code, still recognizable in the extant sequences. Another feature present in the sequences, apparently, since separation of prokaryotes and eukaryotes, is hidden genome segmentation. Both protein-coding and noncoding sequences appear to have been formed by fusion of standard size units, about 360 bp (120 aa) in eukaryotes and 450 bp (150 aa) in prokaryotes. Presumably, the units have been functioning at some stage of evolution as autonomous single-gene size elements. There are sequence designs that promote evolution. One such design suitable for fast adaptation is the tandem repetition of identical sequences, so that their copy numbers in the repeat arrays would modulate (tune) the expression of nearby genes. The tandem repeat expansion diseases illustrate this mechanism in a dramatic way: overtuning of the respective gene expression leads to the disease.

Adaptation, Biological↗
PubMed2002

Temporal pitch in electric hearing.

Both place and temporal codes in the peripheral auditory system contain pitch information, however, their actual use by the brain is unclear. Here pitch data are reported from users of the cochlear implant, which provides the ability to change the temporal code independently from the place code. With fixed electrode stimulation, both frequency discrimination and pitch estimate data show that the cochlear implant users can only discern differences in pitch for frequencies up to about 300 Hz. An integration model can predict pitch estimation from frequency discrimination, reinforcing Fechner's hypothesis relating sensation magnitude to stimulus discriminability. The present results suggest that 300 Hz is the upper boundary of the temporal code and that the absolute place information should be included in the present pitch models. They further suggest that future cochlear implants need to increase the number of independent electrodes to restore normal pitch range and resolution.

Adult↗
PubMed2000

[History of medical ethics in Korea: focused on analysis of medical codes and covenants].

This article deals with the emergence of the codes of medical ethics and their change in Korean history. The modernized medical codes or covenants by the group of medical doctors has been made from the mid-twentieth century, although Korea has a long tradition of medical ethics, so called the Confucian medical ethics, Insul or Uido which were taken on very strong paternalistic characters. The history of the codes of medical ethics in contemporary Korea showed several revisions in 1961, 1965, 1979, and 1997 since the first establishment in 1955. Changes of political circumstances, the cultural level of the people, medical care system, and medical power leaded to the revisions. Throughout the revisions the codes or covenants of medical ethics in Korea has changed from simple translations of the codes by the World Medical Association and the American Medical Association to the reflexes of domestic medical situations; from the ones based on paternalistic doctor-patient relationship to more democratic ones; from the ones that only medical ethics were expressed to the ones that bioethics was expressed too.

Ethics, Medical↗
PubMed2000

Representation of waveform periodicity in the auditory midbrain of the bullfrog, Rana catesbeiana.

The period of complex signals is encoded in the bullfrog's eighth nerve by a synchrony code based on phase-locked responding. We examined how these arrays of phase-locked activity are represented in different subnuclei of the auditory midbrain, the torus semicircularis (TS). Recording sites in different areas of the TS differ in their ability to synchronize to the envelope of complex stimuli, and these differences in synchronous activity are related to response latency. Cells in the caudal principal nucleus (cell sparse zone) have longer latencies, and show little or no phase-locked activity, even in response to low modulation rates, while some cells in lateral areas of the TS (magnocellular nucleus, lateral part of principal nucleus) synchronize to rates as high as 90-100 Hz. At midlevels of the TS, there is a lateral-to-medial gradient of synchronization ability: cells located more laterally show better phaselocking than those located more medially. Pooled all-order interval histograms from short latency cells located in the lateral TS represent the waveform periodicity of a biologically relevant complex harmonic signal at different stimulus levels, and in a manner consistent with behavioral data from vocalizing male frogs. Long latency cells in the caudal parts of the TS (cell sparse zone, caudal magnocellular nucleus) code stimulus period by changes in spike rate, rather than by changes in synchronized activity. These data suggest that neural codes based on rate processing and time domain processing are represented in anatomically different areas of the TS. They further show that a populationbased analysis can increase the precision with which temporal features are represented in the central auditory system.

Acoustic Stimulation↗