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Germ-line mutations in the von Hippel-Lindau tumor-suppressor gene are similar to somatic von Hippel-Lindau aberrations in sporadic renal cell carcinoma.

von Hippel-Lindau (VHL) disease is a hereditary tumor syndrome predisposing to multifocal bilateral renal cell carcinomas (RCCs), pheochromocytomas, and pancreatic tumors, as well as angiomas and hemangioblastomas of the CNS. A candidate gene for VHL was recently identified, which led to the isolation of a partial cDNA clone with extended open reading frame, without significant homology to known genes or obvious functional motifs, except for an acidic pentamer repeat domain. To further characterize the functional domains of the VHL gene and assess its involvement in hereditary and nonhereditary tumors, we performed mutation analyses and studied its expression in normal and tumor tissue. We identified germline mutations in 39% of VHL disease families. Moreover, 33% of sporadic RCCs and all (6/6) sporadic RCC cell lines analyzed showed mutations within the VHL gene. Both germ-line and somatic mutations included deletions, insertions, splice-site mutations, and missense and nonsense mutations, all of which clustered at the 3' end of the corresponding partial VHL cDNA open reading frame, including an alternatively spliced exon 123 nt in length, suggesting functionally important domains encoded by the VHL gene in this region. Over 180 sporadic tumors of other types have shown no detectable base changes within the presumed coding sequence of the VHL gene to date. We conclude that the gene causing VHL has an important and specific role in the etiology of sporadic RCCs, acts as a recessive tumor-suppressor gene, and appears to encode important functional domains within the 3' end of the known open reading frame.

Adult↗

Study of risk factors leading to coronary heart disease in urban Zulus.

Coronary heart disease (CHD) is still relatively uncommon in the black population of South Africa. We embarked on a study to determine the prevalence of risk factors leading to CHD in the black population of Durban. The study sample was selected from patients attending a dental clinic at a hospital. A total of 458 Zulus (age range 16-69 years) were studied. The prevalence of CHD was 2.4%. The prevalence percentage of selected risk factors were: hypertension (SBP > or = 140 mmHg and/or a DBP > or = 90 mmHg) was 28%, males 31.9%, females 25.4%; protective levels of high density lipoprotein cholesterol/total cholesterol (HDLC/TC) (> or = 20%) were 81.3%; diabetes, males 4.9%, females 2.9%; smoking > or = ten cigarettes per day, males 28.1%, females 3.4%; obesity, males 3.7%, females 22.6%. We have found the Minnesota Coding System for ECG changes of CHD and Rose questionnaire to be unreliable for eliciting CHD in Blacks. Hypercholesterolaemia is less common and this may explain the low incidence of CHD in Blacks. Epidemics of CHD as seen in the Indian, 'mixed' and white South Africans can still be prevented in the black population but preventive measures must be instituted rapidly.

Adult↗

[Analysis of p53 gene in gynecologic tumors].

The inactivation of the tumor suppressor gene p53 has been demonstrated in a variety of human tumors. Herein, we performed a p53 gene analysis of human gynecologic tumor cell lines and tumor tissues. In the SK-OV-3 cell line, Southern analysis suggested the presence of sequence deletions/rearrangements in at least one allele of p53 gene. Transcripts were not detectable by either Northern or PCR analysis. Sequencing analysis of the entire coding region revealed mutations changing the p53 amino acid composition in all six endometrial carcinoma cell lines tested (Ishikawa, Hec1-A, Hec1-B, KLE, RL95-2, and AN-3), and four cell lines in ovarian carcinoma cell lines (Caov-3, -4, OVCAR-3, and Kuramochi). Of the seven cervical carcinoma cell lines, two (HT-3 and C-33A) contained p53 codon changes. We were unable to detect the human papilloma virus (HPV) in these two cell lines. By contrast, five HPV-positive cervical carcinoma cell lines (HeLa S-3, Caski, SiHa, C-41, and ME-180) contained wild-type p53 gene sequences. Examination of loss of heterozygosity (LOH) by PCR revealed that about 30% of the human ovarian carcinoma tissues has LOH at the locus of p53 gene. We suggest that, in the HPV-positive cervical tumors, p53 inactivation occurred via the known mechanism of viral E6/cellular p53 protein association, whereas in all other tumors (ovarian carcinoma, endometrial carcinoma, HPV-negative cervical carcinoma) p53 function was compromised by changes in the amino acid sequence.

Base Sequence↗

Evaluation of an object-based data model implemented over a proprietary, legacy data model.

Most computerized medical information today is contained in legacy systems. As vendors slowly move to open systems, legacy systems remain in use and contain valuable information. This paper evaluates the use of an object model imposed on an existing database to improve the ease with which data can be accessed. This study demonstrates that data elements can be retrieved without specific programming knowledge of the underlying data structure. It also suggests that underlying data structures can be changed without updating application code. Programs written using the object model were easier to program but ran greater than one order of magnitude slower than traditionally coded programs. In this paper, the legacy information system is introduced, the methods used to implement and evaluate the object-based data model are explained, and the results and conclusions are presented.

Computer Systems↗

Erythrocyte pyruvate kinase deficiency. The influence of physiologically important metabolites on the function of normal and defective enzymes.

The dependence of the erythrocyte pyruvate kinase (PK)-catalyzed reaction on the glycolytic intermediates glucose-6-phosphate (Gluc-6-P), 2,3-diphosphoglycerate (2,3-DPG) and the nucleotides ADP and ATP was studied in normal individuals and 14 patients with PK deficiency. The Gluc-6-P concentrations in the erythrocytes are markedly elevated (4- to 6-fold) in 9 patients with severe hemolytic anemia compared to those 5 exhibiting a mild clinical course (up to 2-fold increased). 2,3-DPG is elevated up to 2 times compared to the controls whereas the measured ADP and ATP only slightly deviate from the normal range. Control experiments showed that these elevations of Gluc-6-P and 2,3-DPG do not depend on the number of reticulocytes. In enzyme kinetic terms, Gluc-6-P shifts the Hill coefficient to smaller values, i.e. suppresses the positive cooperativity (sigmoidal reaction kinetics), found in normal and some of the mutant enzymes and shift the noncooperative enzymes of some patients to an enzyme exhibiting negative cooperativity. The negative cooperativity already present in the enzymes of some of the patients suffering from severe hemolytic anemia becomes more pronounced upon addition of Gluc-6-P. Apparently 2,3-DPG acts as an antagonist to Gluc-6-P in increasing the Hill coefficient, i.e. enhancing the positive cooperativity of the normal enzyme. It shifts the hyperbolic patients' enzymes to a sigmoidal reaction type and the enzymes of those patients with negative cooperativity to a hyperbolic type. ADP and ATP show a similar behavior as 2,3-DPG, but additionally inhibit the enzyme at higher concentrations. The influence of all four phosphates on the Michaelis constant varies depending on the type of cooperativity, in some cases increasing and in some cases decreasing K0.5 PEP. With 7 of the patients, all of them with severe clinical course, a genetic analysis of their R-type PK gene was performed and genetic defects have been identified in the coding sequence. The found changes in the amino acid sequence and their corresponding location in the tertiary structure of the PK subunit can satisfactorily explain the alterations of the regulatory properties of the mutant enzymes thus allowing to establish a good correlation between altered structural and functional properties of the deficient enzyme and the severeness of the course of the disease.

2,3-Diphosphoglycerate↗

[Glutamate neurotransmission, stress and hormone secretion].

Glutamate neurotransmission has been investigated in relation to several physiological processes (learning, memory) as well as to neurodegenerative and other disorders. Little attention has been paid to its involvement in neuroendocrine response during stress. Penetration of excitatory amino acids from blood to the brain is limited by the blood-brain barrier. As a consequence, several toxic effects but also bioavailability for therapeutic purposes are reduced. A free access to circulating glutamate is possible only in brain structures lacking the blood-brain barrier or under conditions of its increased permeability. Excitatory amino acids were shown to stimulate the pituitary hormone release, though the mechanism of their action is still not fully understood. Stress exposure in experimental animals induced specific changes in mRNA levels coding the glutamate receptor subunits in the hippocampus and hypothalamus. The results obtained with the use of glutamate receptor antagonists indicate that a number of specific receptor subtypes contribute to the stimulation of ACTH release during stress. The authors provided also data on the role of NMDA receptors in the control of catecholamine release, particularly in stress-induced secretion of epinephrine. These results were the first piece of evidence on the involvement of endogenous excitatory amino acids in neuroendocrine activation during stress. Neurotoxic effects of glutamate in animals are well described, especially after its administration in the neonatal period. In men, glutamate toxicity and its use as a food additive are a continuous subject of discussions. The authors found an increase in plasma cortisol and norepinephrine, but not epinephrine and prolactin, in response to the administration of a high dose of glutamate. It cannot be excluded that these effects might be induced even by lower doses in situations with increased vulnerability to glutamate action (age, individual variability). (Tab. 1, Fig. 6, Ref. 44.).

Animals↗

Aldehyde dehydrogenase and acetaldehyde metabolism.

Ingested ethanol is first oxidized to acetaldehyde, primarily in the liver, then further oxidized to acetate. The oxidation of acetaldehyde is catalyzed by an NAD-dependent aldehyde dehydrogenase located in the liver mitochondrial matrix space. To date only one variant form of aldehyde dehydrogenase has been identified. Many Oriental people have an inactive mitochondrial form which possesses a lysine residue at position 487 rather than glutamate which is found in the active enzyme. We employed site directed mutagenesis to probe for active site residues in the enzyme and identified a number of residues which, if mutated, would produce an impaired or inactive enzyme. These mutations could be obtained by single base changes in the DNA coding for the enzyme. Though not identified in human populations, it is possible that these null mutants of the enzyme could exist in people deficient in active mitochondrial aldehyde dehydrogenase.

Acetaldehyde↗

Immune response associated with nonmelanoma skin cancer.

It is now clear that UV radiation causes nonmelanoma skin cancer in at least two ways: by causing permanent changes in the genetic code and by preventing immunologic recognition of mutant cells. These are interacting rather than separate mechanisms. Damage to DNA results in disregulation of cellular proliferation and initiates immune suppression by stimulating the production of suppressive cytokines. These cytokines contribute to the loss of immunosurveillance. Ultraviolet radiation has both local and systemic immunosuppressive effects. Locally, it depletes and alters antigen-presenting LC at the site of UV irradiation. Systemic suppression results when Ts cells are induced, by altered LC, by inflammatory macrophages that enter the skin following UV irradiation, or by the action of cytokines. Damage to DNA appears to be one of the triggering events in inducing systemic immunosuppression via the release of immunosuppressive cytokines and mediators. Immunologic approaches to treating skin cancers so far have concentrated on nonspecifically stimulating immune cells that infiltrate these tumors, but induction of specific immune responses against these tumors with antitumor vaccines has received little attention as yet. Preventive measures include sun avoidance and the use of sunscreens to prevent DNA damage by UV light. Future strategies may employ means to reverse UV-induced immunosuppression by using anti-inflammatory agents, biologicals that accelerate DNA repair or prevent the generation of immunosuppressive cytokines, and specific immunotherapy with tumor antigens. New approaches for studying the immunology of human skin cancers are needed to accelerate progress in this field.

Animals↗

Ventral pallidal representation of pavlovian cues and reward: population and rate codes.

We recorded neural activity in the ventral pallidum (VP) while rats learned a pavlovian reward association. Rats learned to distinguish a tone that predicted sucrose pellets (CS+) from a different tone that predicted nothing (CS-). Many VP units became responsive to CS+, but few units responded to CS-. When two CS+ were encountered sequentially, the earliest predictor of reward became most potent. Many VP units were also activated when the sucrose reward was received [unconditioned stimulus (UCS)]. These VP units for UCS remained responsive to sucrose reward after learning, even when sucrose was already predicted by CS+. Neural representation of reward learning and reward itself was characterized by population codes. The population of units that responded to CS+ increased with learning, whereas the population that responded to UCS did not change. A relative firing rate code also represented the identities of conditioned stimuli and UCS. Firing rate differences among stimuli were acquired early and remained stable during subsequent training, whereas population codes and behavioral conditioned responses continued to develop during subsequent training. Thus, the VP makes use of dynamic CS population and rate codes to encode pavlovian reward cues in reward learning and uses stable UCS population and firing codes to encode sucrose reward itself.

Acoustic Stimulation↗

Induction and characterization of mutations at the b locus of the medaka, Oryzias latipes.

The b locus is one of the most familiar pigmentation loci in the medaka, but its biochemical function is still unknown. Here we report induction of new mutations at the b locus by radiation and ENU. We also characterized all these mutations and previously isolated spontaneous ones on the phenotypic basis. Unexpectively, all the 18 induced mutations reduced melanin contents in both eyes and skin correlatively, although degree of reduction was varied from mutations to mutations. Moreover, presumed null mutants (bs8, bg8, bc2, bd3, bd6, bg13, bg19, bg24) had slightly melanized (dark red) eyes. These results suggest that the b-locus product plays an important but not a critical role in melanogenesis. The spontaneous mutants were divided into two types: one (bdl2, bdl3, and bp) had similarities with the induced mutants in that they had slightly colored eyes and skin, the other (bv, B', bd, bdl1, and b) exhibited normally black eyes but lightly colored skin. The present study supports our recent results (Fukamachi et al., 2001) that mutational changes were found in the coding region of the b gene in some of the mutants which reduced both eyes and skin melanogenesis, while the mutational change for the b allele could not be found there. We speculate that the bv, B', bd, bdl1, and b alleles might arise by the mutations in the regulatory region for skin melanogenesis.

Alleles↗

Benchmarking variation in coding accuracy across the United States.

The objective of this study was to measure the consistency of coded medical data through information managers' reports of the overall coding error level in patients' medical records. Using a cross-sectional design, we examined the reported percent of records containing coding errors significant enough to change a diagnostic related group (DRG). Results indicate about 87 percent, 9 percent, and 5 percent of respondents reported that significant coding errors existed in less than 5 percent, 6-10 percent, and greater than 10 percent of the medical records in their institutions, respectively. Significant variation was found in the accuracy and consistency of coding practice and associated data quality across key demographic and organizational variables. Significantly large error rates in coded data exist in some organizations. Given variations across key demographic characteristics, providers may tend to distrust all coded data, when aggregated. As the United States moves toward an evidence-based medicine environment, the use of current patient data classification methods may be of limited value without increased attention to coding practices.

Benchmarking↗

Increased MEN1 mRNA expression in sporadic pituitary tumours.

BACKGROUND: The MEN1 gene on chromosome 11q13 encodes a tumour suppressor gene, mutations in which cause multiple endocrine neoplasia (MEN) type 1 syndrome. Loss of heterozygosity (LOH) at this locus is a common finding amongst sporadic pituitary tumours. We have therefore screened the MEN1 gene for mutations in sporadic pituitary tumours and, as the gene is a putative tumour suppressor, have quantified mRNA expression in tumorous and normal pituitaries to assess the role of MEN1 in pituitary tumorigenesis. SUBJECTS AND DESIGN: Thirty-one nonfunctioning pituitary tumours, 8 GH secreting, 2 TSH-secreting tumours and 1 corticotrophinoma have been assessed for the presence of MEN1 mutations, to examine the hypothesis that MEN1 mutations may contribute to the pathogenesis of sporadic pituitary neoplasms. In addition, quantitative changes in the pretranslational expression of the tumour suppressor gene MEN1 have been determined in 42 pituitary tumours and 6 normal pituitaries using semiquantitative reverse transcriptase PCR. RESULTS: No novel or previously published mutations were apparent in the MEN1 coding regions of any tumours studied, although several polymorphisms were identified. Transcriptional changes of the gene, assessed by semiquantitative RT-PCR, indicated that nonfunctioning and GH-secreting pituitary tumours are associated with significantly increased pretranslational expression of the MEN1 gene. In addition, the single corticotrophinoma showed increased expression compared to normal, as did one of the two TSH-omas. CONCLUSION: Coding mutations of the putative tumour suppressor gene MEN1 are unlikely to contribute to pituitary tumorigenesis in sporadic nonfunctioning, GH-secreting and TSH-secreting adenomas. Changes in pretranslational expression of MEN1 were observed in pituitary tumours, suggesting that changes in the level of MEN1 expression, rather than coding changes, may be of functional importance in influencing sporadic pituitary tumorigenesis.

Adenoma↗

[Coding of diagnoses in chronic obstructive pulmonary disease--economic consequences].

BACKGROUND: We wanted to assess the quality of coding of diagnoses and procedures, the resulting DRG classification and the financial consequences of coding errors for the hospital owner in patients with chronic obstructive pulmonary disease. MATERIAL AND METHODS: We identified 330 hospitalizations in the Central Hospital of Akershus 1 January to 30 November 1999 in DRG 088 (chronic obstructive pulmonary diseases) after an initial DRG classification. The patients' discharge summaries were reviewed for errors in coding of diagnoses and procedures and, where applicable, recoded. DRG classification was then redone and the changes analysed. RESULTS: After review of 302 available discharge summaries (92%) and recoding, the most common primary diagnoses were chronic obstructive pulmonary disease (68%), respiratory failure (17%), and pneumonia (8%). The recoding led to change of the primary diagnosis in 16% of the patient stays, additional secondary diagnosis (18%) or both (18%). The coding was changed for 175 (58%) patients, of which 94 recodings (31%) led to changes in the resulting DRG. On average, the recoding led to an increase per hospitalization of 0.30 DRG points. Two of five coders frequently used respiratory failure as the primary diagnosis (37-43% for hospitalization). INTERPRETATION: The initial routine coding was incomplete. There was large variation in recoding between medically qualified coders; this may have considerable financial consequences for a hospital. There were several problems related to the interpretation of ICD-10 coding, creating opportunities for "upcoding".

Adult↗

Cloning, sequencing, and demonstration of polymorphism in trypanothione reductase from Crithidia fasciculata.

Trypanothione reductase (TR) is a target for drug design since it is unique to trypanosomatids, substituting for the otherwise ubiquitous enzyme, glutathione reductase. We report the cloning and sequencing of several cDNAs and genes encoding Crithidia fasciculata TR, the structure of which has recently been solved by crystallography. Single base polymorphisms are detected in cDNAs (containing 80% of the coding sequence) and two different genomic clones, including a glutamine to glutamate change in the C-terminal region of the TR coding region; other nucleotide changes are silent. Homology (from genomic clones, both of which contained signals appropriate for expression) to the Trypanosoma congolense gene was 63% at the nucleic acid level, with 68% amino acid identity; the significance of homologies to human and Escherichia coli glutathione reductase sequences is discussed. Polymorphic sites in the genomic clones included sites found in the cDNAs, indicating that differences existing in the genomic sequence are real, and propagated to RNA.

Amino Acid Sequence↗

Transformation from temporal to rate coding in a somatosensory thalamocortical pathway.

The anatomical connections from the whiskers to the rodent somatosensory (barrel) cortex form two parallel (lemniscal and paralemniscal) pathways. It is unclear whether the paralemniscal pathway is directly involved in tactile processing, because paralemniscal neuronal responses show poor spatial resolution, labile latencies and strong dependence on cortical feedback. Here we show that the paralemniscal system can transform temporally encoded vibrissal information into a rate code. We recorded the representations of the frequency of whisker movement along the two pathways in anaesthetized rats. In response to varying stimulus frequencies, the lemniscal neurons exhibited amplitude modulations and constant latencies. In contrast, paralemniscal neurons in both thalamus and cortex coded the input frequency as changes in latency. Because the onset latencies increased and the offset latencies remained constant, the latency increments were translated into a rate code: increasing onset latencies led to lower spike counts. A thalamocortical loop that includes cortical oscillations and thalamic gating can account for these results. Thus, variable latencies and effective cortical feedback in the paralemniscal system can serve the processing of temporal sensory cues, such as those that encode object location during whisking. In contrast, fixed time locking in the lemniscal system is crucial for reliable spatial processing.

Afferent Pathways↗

Training in Morse code enhances involuntary attentional switching to acoustic frequency: Evidence from ERPs.

This study examined the possibility that learning Morse code could result in cortical changes in processing of physical acoustic features, as indexed by the mismatch negativity (MMN) and P3a components of the auditory event-related potential (ERP). ERPs were recorded in 9 subjects who were learning Morse code. The subjects were presented with auditory stimuli at 3 different times relative to their training (before, during and after). These stimuli were presented within an auditory 'oddball' paradigm, with repetitive standard stimuli interspersed by one of three infrequent deviant stimuli (duration, frequency or SOA). The data showed that there was a significant increase in the P3a only for frequency deviants as a function of training, whereas the MMN response was not affected by the training. These data are interpreted in terms of an attentional switching to unfamiliar changes that participants would not expect among the signals that they would grow to anticipate while receiving Morse code.

Acoustic Stimulation↗

A noncoding motoric equivalent measures most of what the digit symbol does, including age changes.

The Digit Symbol test and a copying test with identical graphomotor requirements but not visual search, memory, or coding demands were given to 108 normal volunteers and neurologically screened physical rehabilitation patients age 20 to 90 yr. The ratio of coding to copying scores did not change over age, and the high correlations between them were similar across age groups. Little variance was unaccounted for; gross lapses in nonmotoric functions such as memory or attention may prevent Digit Symbol's use with some patients, but subtler decrements need not be invoked to explain age effects. Tentative norms provided here allow evaluation of individual deviations in coding/copying ratios or exploratory use of the copying test to monitor the course of disease or drug titration with patients whose linguistic or perceptual deficits invalidate Digit Symbol or Trail Making tests. If discrepant ratios characterize some groups of patients, the ratios may become useful diagnostic indices. If coding and copying are as closely related for patients with cerebral dysfunction as for normals, the copying test may become a useful alternative to Digit Symbol with patients unable to comply reliably with its requirements.

Adult↗

On combining protein sequences and nucleic acid sequences in phylogenetic analysis: the homeobox protein case.

Amino acid encoding genes contain character state information that may be useful for phylogenetic analysis on at least two levels. The nucleotide sequence and the translated amino acid sequences have both been employed separately as character states for cladistic studies of various taxa, including studies of the genealogy of genes in multigene families. In essence, amino acid sequences and nucleic acid sequences are two different ways of character coding the information in a gene. Silent positions in the nucleotide sequence (first or third positions in codons that can accrue change without changing the identity of the amino acid that the triplet codes for) may accrue change relatively rapidly and become saturated, losing the pattern of historical divergence. On the other hand, non-silent nucleotide alterations and their accompanying amino acid changes may evolve too slowly to reveal relationships among closely related taxa. In general, the dynamics of sequence change in silent and non-silent positions in protein coding genes result in homoplasy and lack of resolution, respectively. We suggest that the combination of nucleic acid and the translated amino acid coded character states into the same data matrix for phylogenetic analysis addresses some of the problems caused by the rapid change of silent nucleotide positions and overall slow rate of change of non-silent nucleotide positions and slowly changing amino acid positions. One major theoretical problem with this approach is the apparent non-independence of the two sources of characters. However, there are at least three possible outcomes when comparing protein coding nucleic acid sequences with their translated amino acids in a phylogenetic context on a codon by codon basis. First, the two character sets for a codon may be entirely congruent with respect to the information they convey about the relationships of a certain set of taxa. Second, one character set may display no information concerning a phylogenetic hypothesis while the other character set may impact information to a hypothesis. These two possibilities are cases of non-independence, however, we argue that congruence in such cases can be thought of as increasing the weight of the particular phylogenetic hypothesis that is supported by those characters. In the third case, the two sources of character information for a particular codon may be entirely incongruent with respect to phylogenetic hypotheses concerning the taxa examined. In this last case the two character sets are independent in that information from neither can predict the character states of the other. Examples of these possibilities are discussed and the general applicability of combining these two sources of information for protein coding genes is presented using sequences from the homeobox region of 46 homeobox genes from Drosophila melanogaster to develop a hypothesis of genealogical relationship of these genes in this large multigene family.

Algorithms↗