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PubMed2002

Microalbuminuria modifies the mortality risk associated with electrocardiographic ST-T segment changes.

OBJECTIVES: We sought to investigate whether microalbuminuria, a proposed marker of generalized vascular damage, enhances the prognostic value of ST-T segment changes for all-cause and cardiovascular mortality in the general population. BACKGROUND: ST-T segment changes on the rest electrocardiogram (ECG) predict mortality in the general population. However, the excess risk seems to be low, particularly in nonhospitalized populations with a low cardiovascular risk profile. METHODS: In a population of 7,330 male and female subjects, a total of 89 deaths (1.2%) occurred during a median three-year follow-up. In 69 of these, the cause of death was obtained from the Central Bureau of Statistics: 25 subjects died of cardiovascular causes (36%). Using computerized Minnesota coding, ST-T segment changes were coded as 4.1-4 and 5.1-4. Microalbuminuria was defined as a urinary albumin excretion of 30 to 300 mg per 24 h. RESULTS: The combination of ST-T segment changes and microalbuminuria showed a higher hazard ratio (HR) for all-cause mortality (HR 8.6 [95% confidence interval [CI] 4.8 to 15.2, p < 0.0001), as compared with ST-T segment changes in the absence of microalbuminuria (HR 1.3 [95% CI 0.7 to 2.5]), which was independent of other cardiovascular risk factors (HR 3.3 [95% CI 1.5 to 7.1], p = 0.002). The combination showed a higher HR when only cardiovascular deaths were taken into account, as compared with all-cause mortality (HR 24.5 [95% CI 7.9 to 76.0], p < 0.0001), which also counted for ST-T segment changes alone (HR 4.4 [95% CI 1.4 to 14.5], p = 0.02). After controlling for other risk factors, the HRs were 10.4 (95% CI 2.5 to 43.6, p = 0.001) for the combination and 2.7 (95% CI 0.6 to 12.3) for ST-T segment changes alone. CONCLUSIONS: This study suggests that, in subjects with ST-T segment changes on their rest ECG, microalbuminuria could identify those at increased risk of all-cause and cardiovascular mortality.

Adult↗
PubMed1986

Sequence, evolution and differential expression of the two genes encoding variant small subunits of ribulose bisphosphate carboxylase/oxygenase in Chlamydomonas reinhardtii.

We have sequenced the two genes for the small subunit of ribulose bisphosphate carboxylase/oxygenase (Rubisco) in Chlamydomonas reinhardtii and analyzed their expression. The two genes encode variant small subunits that differ by four amino acid residues. Both genes are expressed and each is transcribed into an RNA of distinct size. The accumulation of the two RNAs changes depending on the growth conditions, so the small subunit composition of Rubisco may be expected to differ in response to the environment. The C. reinhardtii small subunit sequence is homologous to those of vascular plants or cyanobacteria, but is longer at the amino terminus and in internal positions. The number and location of the intervening sequences in the genes from C. reinhardtii and from other plants differ. In several cases, internal length differences in the polypeptide coincide with the positions of introns in the coding sequence. Thus, changes in the exon structure of the genes during evolution may have been accompanied by substantial changes in the encoded protein. The translation and splicing signals in C. reinhardtii are similar to those of other eukaryotes, but the transcription signals are less conserved and the highly biased codon usage is very unusual.

Amino Acid Sequence↗
PubMed1994

The CDR1 sequences of a major proportion of human germline Ig VH genes are inherently susceptible to amino acid replacement.

The variable (V) genes of antigen-selected antibodies are known to exhibit a higher frequency of amino acid replacement mutations in the sequences encoding the antigen-contacting complementarity-determining regions (CDRs) than in those encoding the 'structural' framework regions (FRs). Here, Bernard Chang and Paolo Casali analyse the impact of regional differences in the codon composition of human germline Ig VH and VL genes on regional differences in the frequency of replacement mutations in the gene products (i.e. the antigen-binding sites of antibody molecules). This analysis reveals that CDR and FR sequences can differ significantly in their inherent susceptibility to amino acid replacement given any single nucleotide change. Thus, the CDR sequences of all the Ig VH genes analysed comprise a higher frequency of codons susceptible to replacement mutations than would be expected for a random sequence. Conversely, the FR sequences comprise codons less susceptible to replacement mutations than expected. Random accumulation of nucleotide changes throughout the coding sequence of an Ig V-gene segment containing CDRs inherently more prone to replacement mutations than the respective FRs would inevitably yield a higher rate of amino acid replacements in the CDRs than in the FRs. This would provide a fertile structural substrate of hypervariability for antigen selection while still maintaining the structural integrity of the FRs.

Amino Acid Sequence↗
PubMed2004

Electrochemical coding of single-nucleotide polymorphisms by monobase-modified gold nanoparticles.

Rapidly increasing information about the human genome requires a fast and simple method for the detection of single-nucleotide polymorphisms (SNPs). To date, the conventional SNP detection technologies have been unable to identify all possible SNPs and needed further development in cost, speed, and sensitivity. Here we describe a novel method to discriminate and code all possible combinations. SNPs were coded by monitoring the changes in the electrochemical signal of the monobase-modified colloidal gold (Au) nanoparticles. First, a chitosan layer was formed on the alkanethiol self-assembled monolayer-modified Au nanoparticle. The monobases were then attached onto the chitosan-coated Au nanoparticles through their 5' phosphate group via the formation of a phosphoramidate bond with the free amino groups of chitosan. The size of the surface-modified Au nanoparticle was found to be 8.46 +/- 1.53 nm by using atomic force microscopy. If there is a SNP in DNA and the mismatched bases are complementary to the monobase, Au nanoparticles accumulate on the electrode surface in the presence of DNA polymerase I (Klenow fragment), thus resulting in a significant change in the Au oxide wave. In this report, monobase-modified Au nanoparticles show not only the presence of a SNP, but also identify which bases are involved within the pair. Especially, the identification of a transversion SNP, which contains a couple of the same pyrimidine or purine bases, is greatly simplified. A model study was performed by using a synthetic 21-base DNA probe related to tumor necrosis factor (TNF-alpha) along with its all possible mutant combinations. This versatile nanoparticle-based electrochemical protocol is a promising candidate for coding all mutational changes.

Base Sequence↗
PubMed2004

Different thresholds for detection and discrimination of odors in the honey bee (Apis mellifera).

Naturally occurring odors used by animals for mate recognition, food identification and other purposes must be detected at concentrations that vary across several orders of magnitude. Olfactory systems must therefore have the capacity to represent odors over a large range of concentrations regardless of dramatic changes in the salience, or perceived intensity, of a stimulus. The stability of the representation of an odor relative to other odors across concentration has not been extensively evaluated. We tested the ability of honey bees to discriminate pure odorants across a range of concentrations at and above their detection threshold. Our study showed that pure odorant compounds became progressively easier for honey bees to discriminate with increasing concentration. Discrimination is, therefore, a function of odorant concentration. We hypothesize that the recruitment of sensory cell populations across a range of concentrations may be important for odor coding, perhaps by changing its perceptual qualities or by increasing its salience against background stimuli, and that this mechanism is a general property of olfactory systems.

Animals↗
PubMed1985

Homoeotic transformations in man: implications for the mechanism of embryonic development and for the organization of epithelia.

Homoeotic transformations are substitutions of one body part for another which arise during embryogenesis or regeneration. They are well known among the Arthropoda but are not generally thought to occur in Man or other vertebrates. In this paper the occurrence and characteristics of 21 types of epithelial heterotopia and metaplasia are reviewed and it is concluded that they are fully comparable with the homoeotic transformations of the arthropods.. The transformations are concentrated in the gastrointestinal, urinary and female reproductive systems and typically appear as foci of ectopic epithelium with a sharp discontinuity of cell type at the edges of the patches. Most of the transformations occur in renewal tissues and must therefore be interpreted as changes in the states of determination (epigenetic codings) of the stem cells rather than changes between already differentiated cells. Most, but not all, of the transformations are between tissues whose precursors are neighbouring regions of a common cell sheet during early embryogenesis and which are therefore likely to have neighbouring epigenetic codings. Following the Cairns hypothesis for epithelial organization it is proposed that stem cells themselves are protected against changes in epigenetic coding but their daughter cells, normally destined to differentiate and die, are not. Homoeotic transformations may thus occur in situations in which daughter cells become promoted to stem cells which happens either during the growth phase of the organism or during tissue regeneration in the adult.

Animals↗
PubMed1993

Mutations in the RET proto-oncogene are associated with MEN 2A and FMTC.

Multiple endocrine neoplasia type 2A (MEN 2A) and familial medullary thyroid carcinoma (FMTC) are dominantly inherited conditions which predispose to the development of endocrine neoplasia. Evidence is presented that sequence changes within the coding region of the RET proto-oncogene, a putative transmembrane tyrosine kinase, may be responsible for the development of neoplasia in these inherited disorders. Single strand conformational variants (SSCVs) in exons 7 and 8 of the RET proto-oncogene were identified in eight MEN 2A and four FMTC families. The variants were observed only in the DNA of individuals who were either affected or who had inherited the MEN2A or FMTC allele as determined by haplotyping experiments. The seven variants identified were sequenced directly. All involved point mutations within codons specifying cysteine residues, resulting in nonconservative amino acid changes. Six of the seven mutations are located in exon 7. A single mutation was found in exon 8. Variants were not detected in four MEN 2B families studied for all exon assays available, nor were they detectable in 16 cases of well documented sporadic medullary thyroid carcinoma or pheochromocytoma that were tested for exon 7 variants. Coinheritance of the mutations with disease and the physical and genetic proximity of the RET proto-oncogene provide evidence that RET is responsible for at least two of the three inherited forms of MEN 2. Neither the normal function, nor the ligand of RET are yet known. However, its apparent involvement in the development of these inherited forms of neoplasia as well as in papillary thyroid carcinoma suggest an important developmental or cell regulatory role for the protein.

Amino Acid Sequence↗
PubMed2001

High-throughput sequence identification of gene coding variants within alcohol-related QTLs.

Low initial response to alcohol has been shown to be among the best predictors of development of alcoholism. A similar phenotypic measure, difference in initial sensitivity to ethanol, has been used for the genetic selection of two mouse strains, the Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS) mice, and for the subsequent identification of four quantitative trait loci (QTLs) for alcohol sensitivity. We now report the application of high throughput comparative gene sequencing in the search for genes underlying these four QTLs. To carry out this search, over 1.7 million bases of comparative DNA sequence were generated from 68 candidate genes within the QTL intervals, corresponding to a survey of over 36,000 amino acids. Eight central nervous system genes, located within these QTLs, were identified that contain a total of 36 changes in protein coding sequence. Some of these coding variants are likely to contribute to the phenotypic variation between ILS/ISS animals, including sensitivity to alcohol, providing specific new genetic targets potentially important to the neuronal actions of alcohol.

Alcoholism↗
PubMed2002

Automatic and controlled processing of melodic contour and interval information measured by electrical brain activity.

Most work on how pitch is encoded in the auditory cortex has focused on tonotopic (absolute) pitch maps. However, melodic information is thought to be encoded in the brain in two different "relative pitch" forms, a domain-general contour code (up/down pattern of pitch changes) and a music-specific interval code (exact pitch distances between notes). Event-related potentials were analyzed in nonmusicians from both passive and active oddball tasks where either the contour or the interval of melody-final notes was occasionally altered. The occasional deviant notes generated a right frontal positivity peaking around 350 msec and a central parietal P3b peaking around 580 msec that were present only when participants focused their attention on the auditory stimuli. Both types of melodic information were encoded automatically in the absence of absolute pitch cues, as indexed by a mismatch negativity wave recorded during the passive conditions. The results indicate that even in the absence of musical training, the brain is set up to automatically encode music-specific melodic information, even when absolute pitch information is not available.

Adult↗
PubMed1977

Functional development of mechanoreceptive neurons innervating the glabrous skin in postnatal kittens.

We studied single units innervating the glabrous forepaw skin of 35 domestic kittens ranging in age from 1 to 52 postnatal days. There aspects of coding were emphasized: (a) size and force thresholds of receptive fields, (b) time course of recovery between stimulus presentations, and (c) electrical conduction properties of the afferent nerve fibers. Receptive field (RF) size and force thresholds were (a) positively correlated with age for palmar but not digital RFs, and (b) were significantly larger on palm than on digits. Unit responsiveness was highly dependent on intertrial interval, complete recovery requiring at least 30 sec. Conduction velocity increased more rapidly than nerve fiber length, thus conduction time decreased with age. Refractory period decreased with age, but the conduction velocities of sequential spikes were proportional, regardless of age. These changes which we observed can more readily be ascribed to alterations of the mechanical properties of skin and conduction properties of nerve fibers than to changes in the coding mechanisms themselves.

Action Potentials↗
PubMed2006

A DGGE system for comprehensive mutation screening of BRCA1 and BRCA2: application in a Dutch cancer clinic setting.

Rapid and reliable identification of deleterious changes in the breast cancer genes BRCA1 and BRCA2 has become one of the major issues in most DNA services laboratories. To rapidly detect all possible changes within the coding and splice site determining sequences of the breast cancer genes, we established a semiautomated denaturing gradient gel electrophoresis (DGGE) mutation scanning system. All exons of both genes are covered by the DGGE scan, comprising 120 amplicons. We use a semiautomated approach, amplifying all individual amplicons with the same PCR program, after which the amplicons are pooled. DGGE is performed using three slightly different gel conditions. Validation was performed using DNA samples with known sequence variants in 107 of the 120 amplicons; all variants were detected. This DGGE mutation scanning, in combination with a PCR test for two Dutch founder deletions in BRCA1 was then applied in 431 families in which 52 deleterious changes and 70 unclassified variants were found. Fifteen unclassified variants were not reported before. The system was easily adopted by five other laboratories, where in another 3,593 families both exons 11 were analyzed by the protein truncation test (PTT) and the remaining exons by DGGE. In total, a deleterious change (nonsense, frameshift, splice-site mutation, or large deletion) was found in 661 families (16.4%), 462 in BRCA1 (11.5%), 197 in BRCA2 (4.9%), and in two index cases a deleterious change in both BRCA1 and BRCA2 was identified. Eleven deleterious changes in BRCA1 and 36 in BRCA2 had not been reported before. In conclusion, this DGGE mutation screening method for BRCA1 and BRCA2 is proven to be highly sensitive and is easy to adopt, which makes screening of large numbers of patients feasible. The results of screening of BRCA1 and BRCA2 in more than 4,000 families present a valuable overview of mutations in the Dutch population.

Ambulatory Care Facilities↗
PubMedDate not supplied

The revised burn diagram and its effect on diagnosis-related group coding.

Diagnosis-related group (DRG) codes for burn injuries are defined by thresholds of the percentage of total body surface area and depth of burns, and by whether surgery, debridement, or grafting or both occurred. This prospective study was designed to determine whether periodic revisions of the burn diagram resulted in more accurate assignment of the International Classification of Diseases and DRG codes. The admission burn diagrams were revised after admission and after each surgical procedure. All areas grafted (deep second-and third-degree burns) were diagrammed as "third-degree," after the current convention that both are biologically the same and require grafting. The multiple diagrams from 82 charts were analyzed to determine the disparities in the percentage of total body surface area burn and the percentage of body surface area third-degree burn. The revised diagrams differed from the admission diagrams in 96.5% of the cases. In 77% of the cases, the revised diagram correctly depicted the percentage of body surface area third-degree burn as confirmed intraoperatively. In 7.3% of the cases, diagram revision changed the DRG code. Documenting wound evolution in this manner allows more accurate assignment of the International Classification of Diseases and DRG codes, assuring optimal reimbursement under the prospective payment system.

Burn Units↗
PubMed2001

Temporary inactivation of the retrosplenial cortex causes a transient reorganization of spatial coding in the hippocampus.

The ability to navigate accurately is dependent on the integration of visual and movement-related cues. Navigation based on metrics derived from movement is referred to as path integration. Recent theories of navigation have suggested that posterior cortical areas, the retrosplenial and posterior parietal cortex, are involved in path integration during navigation. In support of this hypothesis, we have found previously that temporary inactivation of retrosplenial cortex results in dark-selective impairments on the radial maze (Cooper and Mizumori, 1999). To understand further the role of the retrosplenial cortex in navigation, we combined temporary inactivation of retrosplenial cortex with recording of complex spike cells in the hippocampus. Thus, behavioral performance during spatial memory testing could be compared with place-field responses before, and during, inactivation of retrosplenial cortex. In the first experiment, behavioral results confirmed that inactivation of retrosplenial cortex only impairs radial maze performance in darkness when animals are at asymptote levels of performance. A second experiment revealed that retrosplenial cortex inactivation impaired spatial learning during initial light training. In both experiments, the normal location of hippocampal "place fields" was changed by temporary inactivation of retrosplenial cortex, whereas other electrophysiological properties of the cells were not affected. The changes in place coding occurred in the presence, and absence, of behavioral impairments. We suggest that the retrosplenial cortex provides mnemonic spatial information for updating location codes in the hippocampus, thereby facilitating accurate path integration. In this way, the retrosplenial cortex and hippocampus may be part of an interactive neural system that mediates navigation.

Action Potentials↗
PubMedDate not supplied

Information limits on neural identification of colored surfaces in natural scenes.

If surfaces in a scene are to be distinguished by their color, their neural representation at some level should ideally vary little with the color of the illumination. Four possible neural codes were considered: von-Kries-scaled cone responses from single points in a scene, spatial ratios of cone responses produced by light reflected from pairs of points, and these quantities obtained with sharpened (opponent-cone) responses. The effectiveness of these codes in identifying surfaces was quantified by information-theoretic measures. Data were drawn from a sample of 25 rural and urban scenes imaged with a hyperspectral camera, which provided estimates of surface reflectance at 10-nm intervals at each of 1344 x 1024 pixels for each scene. In computer simulations, scenes were illuminated separately by daylights of correlated color temperatures 4000 K, 6500 K, and 25,000 K. Points were sampled randomly in each scene and identified according to each of the codes. It was found that the maximum information preserved under illuminant changes varied with the code, but for a particular code it was remarkably stable across the different scenes. The standard deviation over the 25 scenes was, on average, approximately 1 bit, suggesting that the neural coding of surface color can be optimized independent of location for any particular range of illuminants.

Color Perception↗
PubMedDate not supplied

Mutagenic assessment of 1,N6-ethenodeoxyadenosine in DNA.

The mutagenic role of 1-N6-Ethenodeoxydenosine (epsilon A) was assessed by a genetic assay of mutations in the 5' coding region of the lacl gene of Escherichia coli. 1-N6-Etheno-2-deoxydadenosine 5'-triphosphate (epsilon dATP) was substituted for dATP during in vitro DNA synthesis on M13 recombinant uracil single stranded DNA bearing the lacl gene, catalyzed by the large fragment of E. coli DNA polymerase I. DNA products were transfected into a strain of E. coli lacking a chromosomal copy of the lacl gene, and i- phenotypic mutants were seen as blue plaques in the absence of inducer. Mutant progeny were characterized by dideoxy sequencing in the N-terminal region of the lacl gene where epsilon A had originally replaced A, and were found to have T-->C transitions. The frequency of base substitution mutation was different in each of three target sites tested. Taking into account the sequence changes and the coding properties at target sites, we conclude that in general, epsilon A increases the mutation frequency when compared with the control (transfection with unsubstituted DNA). This increase was similar to that produced by in vitro primer elongation in absence of dATP. The combined results of the electrophoretic assay of primer elongation, measurements of mutation frequency, and sequence analysis of mutant phage progeny support the proposal that epsilon A in template DNA can be mutagenic through epsilon AC mispairing during in vivo replication.

Base Composition↗
PubMed1992

Periodical changes of amino acid reactivity within the genetic code.

Enthalpies (delta H++) and entropies (delta S++) of activation for the reaction of 18 N'-hydroxysuccinimide esters of N-protected proteinaceous amino acids with p-anisidine were measured and free enthalpies of activation (delta G++) at 25 degrees C were calculated on this basis. A regular correlation between delta G++s and the corresponding amino acid codons was found. To obtain this correlation all the codons had to be arranged in a closed ring in which the consecutive codons were connected by one-step mutational changes. One-step mutations appeared as a regular series: 2,3,3,3,1,3,3,3,1,3,3,3,1,3,3,3,2,3,3,3. (the numbers denote a codon position in which a change took place). There were three such 'one-step mutation periods' in the ring, each containing 20 codons (in each block of 16 codons with A, U and C, in the central position and 4 codons containing G in the central position). The end of the third period (UG) and the beginning of the first period were bridged by the four codons of glycine with G in the second position. The values of delta G++ change similarly in each period, increasing upon approaching Lys, Pro, and Ile. The periodical relation between the chemical reactivities of the coded amino acids (reflected by delta G++s) and the structure of their codons could be of importance for the origin of the genetic code i.e. for selection of proper codons for the definite amino acids.

Amino Acid Sequence↗
PubMed2001

Functional conservation of the promoter regions of vertebrate tyrosinase genes.

Tyrosinase is the key enzyme for synthesizing melanin pigments, which primarily determine mammalian skin coloration. Considering the important roles of pigments in the evolution and the adaptation of vertebrates, phylogenetic changes in the coding and flanking regulatory sequences of the tyrosinase gene are particularly intriguing. We have now cloned cDNA encoding tyrosinase from Japanese quail and snapping turtle. These nonmammalian cDNA are highly homologous to those of the mouse and human tyrosinases, whereas the 5' flanking sequences are far less conserved except for a few short sequence motifs. Nevertheless, we demonstrate that the 5' flanking sequences from the quail or turtle tyrosinase genes are capable of directing the expression of a fused mouse tyrosinase cDNA when introduced into cultured mouse albino melanocytes. This experimental method, which reveals the functional conservation of regulatory sequences in one cell type (the melanocyte), may be utilized to evaluate phylogenetic differences in mechanisms controlling specific gene expression in many other types of cells. We also provide evidence that the 5' flanking sequences from these nonmammalian genes are functional in vivo by producing transgenic mice. Phylogenetic changes of vertebrate tyrosinase promoters and the possible involvement of conserved sequence motifs in melanocyte-specific expression of tyrosinase are discussed.

5' Flanking Region↗
PubMed2004

DGGE-based whole-gene mutation scanning of the dystrophin gene in Duchenne and Becker muscular dystrophy patients.

Duchenne and Becker muscular dystrophy (DMD and BMD) are caused by mutations in the dystrophin gene. Large rearrangements in the gene are found in about two-thirds of DMD patients, with approximately 60% carrying deletions and 5-10% carrying duplications. Most of the remaining 30-35% of patients are expected to have small nucleotide substitutions, insertions, or deletions. To detect these subtle changes within the coding and splice site determining sequences of the dystrophin gene, we established a semiautomated denaturing gradient gel electrophoresis (DGGE) mutation scanning system. The DGGE scan covers the dystrophin gene with 95 amplicons, PCRed either individually or in a multiplex setup. PCR and pooling were performed semiautomatically, using a pipetting robot and 384-well plates, enabling concurrent amplification of DNA of four patients in one run. Amplification of individual fragments was performed using one PCR program. The products were pooled just before gel loading; DGGE requires only a single gel condition. Validation was performed using DNA samples harboring 39 known DMD variants, all of which could be readily detected. DGGE mutation scanning was applied to analyze 135 DMD/BMD patients and potential DMD carriers without large deletions or duplications. In DNA from 25 out of 44 DMD patients (57%) and from 5 out of 39 BMD patients (13%), we identified clear pathogenic changes. All mutations were different, with the exception of one DMD mutation, which occurred twice. In DNA from 10 out of 44 potential DMD carriers, including four obligate carriers, we detected causative changes, including one pathogenic change in every obligate carrier. In addition to these pathogenic changes, we detected 15 unique unclassified variants, i.e., changes for which a pathogenic nature is uncertain.

DNA Mutational Analysis↗