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PubMed1985

Analysis of several bovine lutropin beta subunit cDNAs reveals heterogeneity in nucleotide sequence.

Several, independent lutropin beta subunit cDNA clones have been isolated from a lambda gt-11 pituitary cDNA library. The complete nucleotide sequence of four clones was determined. A number of single nucleotide differences were detected including three changes within the coding sequence. One of these nucleotide changes resulted in a change in the predicted amino acid sequence, while two did not. These changes may reflect heterogeneity in the animals from which pituitaries were obtained, or they may reflect errors which occurred during the construction or cloning of the cDNA. Two other differences in nucleotide sequence suggest differences in the processing of precursor mRNAs. One difference involves the deletion of three nucleotides from the coding sequence of one of the clones. This probably reflects the use of alternate splicing sites at intron-exon boundaries. The other likely processing difference is reflected by the fact that one of the clones contains a much longer 3' untranslated region than the other clones. This difference probably arose due to a single nucleotide difference leading to selection of an alternate polyadenylation site.

Amino Acid Sequence↗

PubMed2005

A particle track-repeating algorithm for proton beam dose calculation.

A particle track-repeating algorithm has been developed for proton beam dose calculation for radiotherapy. Monoenergetic protons with 250 MeV kinetic energy were simulated in an infinite water phantom using the GEANT3 Monte Carlo code. The changes in location, angle and energy for every transport step and the energy deposition along the track were recorded for the primary protons and all secondary particles. When calculating dose for a patient with a realistic proton beam, the pre-generated particle tracks were repeated in the patient geometry consisting of air, soft tissue and bone. The medium and density for each dose scoring voxel in the patient geometry were derived from patient CT data. The starting point, at which a proton track was repeated, was determined according to the incident proton energy. Thus, any protons with kinetic energy less than 250 MeV can be simulated. Based on the direction of the incident proton, the tracks were first rotated and for the subsequent steps, the scattering angles were simply repeated for air and soft tissue but adjusted properly based on the scattering power for bone. The particle step lengths were adjusted based on the density for air and soft tissue and also on the stopping powers for bone while keeping the energy deposition unchanged in each step. The difference in nuclear interactions and secondary particle generation between water and these materials was ignored. The algorithm has been validated by comparing the dose distributions in uniform water and layered heterogeneous phantoms with those calculated using the GEANT3 code for 120, 150, 180 and 250 MeV proton beams. The differences between them were within 2%. The new algorithm was about 13 times faster than the GEANT3 Monte Carlo code for a uniform phantom geometry and over 700 times faster for a heterogeneous phantom geometry.

Algorithms↗

PubMed2002

Should therapeutic abortion be legal in Nicaragua: the response of Nicaraguan obstetrician-gynaecologists.

Abortion is legal in Nicaragua only to save the life of the woman. In 2002, amendments to the Penal Code to change the penalties for obtaining and providing illegal abortions and regulations on the authorization of legal abortions are due to be debated in the legislature. In a context of extensive media coverage and debate between women's health and rights groups and a powerful movement to make all abortions illegal, medical professionals have also been effective in influencing law and policy. In May 2001, the Nicaraguan Society of Obstetrics and Gynecology presented the results of a study of the views of 198 obstetrician-gynaecologists on pending legislation regulating therapeutic abortion and the medical and ethical implications of providing therapeutic abortion services. All but nine of the 198 participants in the study, who comprised 76% of all registered obstetrician-gynaecologists in Nicaragua, believed that therapeutic abortion should not be criminalized and over 90% believed that there were cases in which therapeutic abortion was necessary to save women's lives. Some also supported legislative reform to allow abortion in cases of rape and fetal malformation. These results countered claims by the Nicaraguan Medical Association (AMN), taken up by the Church and anti-abortion legislators and groups, that therapeutic abortion was no longer necessary due to modern medicine. The election of anti-abortion politicians to powerful positions in early 2002 has created a formidable challenge when the proposed revisions to the Penal Code are debated.

Abortion, Therapeutic↗

PubMed2006

Contrast gain control is drift-rate dependent: an informational analysis.

Neurons in the visual cortex code relative changes in illumination (contrast) and adapt their sensitivities to the visual scene by centering the steepest regions of their sigmoidal contrast response functions (CRFs: spike rate as a function of contrast) on the prevailing contrast. The influence of this contrast gain control has not been reported at nonoptimal drift rates. We calculated the Fisher information contained in the CRFs of halothane-anesthetized cats. Fisher information gives a measure of the accuracy of contrast representations based on the ratio of the square of the steepness of the CRF and the spike-rate dependency of the spiking variance. Variance increases with spike rate, so Fisher information is maximal where the CRF is steep and spike rates are low. Here, we show that the contrast at which the maximal Fisher information (C(MFI)) occurs for each adapting drift rate is at a fixed level above the adapting contrast. For adapting contrasts of 0 to 0.32 the relationship between C(MFI) and adapting contrast is well described by a straight line with a slope close to 1. The intercept of this line on the C(MFI)-axis is drift-rate dependent, although the slope is not. At high drift rates relative to each cell's peak the C(MFI) offset is higher than that for low drift rates. The results show that the contrast coding strategy in visual cortex maximizes accuracy for contrasts above the prevailing contrast in the environment for all drift rates. We argue that tuning the system for accuracy at contrasts above the prevailing value is optimal for viewing natural scenes.

Animals↗

PubMed2006

Loss of heterozygosity and microsatellite instability at the Xq28 and the A/G heterozygosity of the QM gene are associated with ovarian cancer.

The QM gene is located at Xq28 of the X chromosome. QM may act as a tumor suppressor and may also participate in the 60S ribosomal subunit assembly. We studied loss of heterozygosity (LOH) and microsatellite instability (MSI) of microsatellite markers DXS15A, DXS1107, WI12360 and WI9327 for the Xq28 region in 29 ovarian cancer biopsies. The results showed that the LOH frequencies were 18.2%, 30%, 26.3% and 20.8% for WI12360, WI9327, DXS1107 and DXS15A, respectively, whereas the MSI rates were 18.2%, 50.0%, 31.6% and 12.5%, respectively. All tumors showed LOH or MSI for at least one of these markers. Sequencing the QM cDNA did not identify any mutation other than the adenine (A)/guanine (G) replacement at the 605th nucleotide which changes the coding from serine to asparagine. In 17 (58.6%) of the 29 tumors, both A and G types of QM mRNA were detected, indicating that the QM was A/G heterozygous and escaped X-inactivation. However, cDNA and genomic DNA sequencing revealed that the adjacent normal tissues showed the A/G heterozygosity in only 3 of the 17 cases, while in the remaining 14 cases, four had no more adjacent tissue available and ten revealed either G or A at the 605th nt, indicating an A/G point mutation in these tumors. The allele distribution was 32.8% for the A and 67.2% for the G type QM gene. The frequencies of A/A, G/G and A/G homo- or hetero-zygosity were 3.5%, 37.9% and 58.6%, respectively in cancer tissues but they were 26.1%, 52.2% and 21.7%, respectively in the adjacent tissues, indicating a higher heterozygous rate in cancer (58.6% vs 21.7%, p < 0.01). These results suggest that high frequencies of LOH and MSI at the Xq28 and of the A/G heterozygosity at the 605th nt of the QM gene may be associated with ovarian cancer.

Breast Neoplasms↗

PubMed2000

Mutation analysis of the inwardly rectifying K(+) channels KCNJ6 (GIRK2) and KCNJ3 (GIRK1) in juvenile myoclonic epilepsy.

Genetic factors play a major role in the etiology of idiopathic generalized epilepsy. However, in most syndromes, especially the common ones, multiple genetic factors seem to be involved. Mutations in K(+) channel genes have previously found to be associated with epilepsy both in humans and in mice. The weaver mice phenotype, characterized by ataxia, tremor, male infertility, and tonic-clonic seizures, is caused by a point mutation in the inwardly rectifier K(+) channel gene KCNJ6 (GIRK2). A knockout mouse model deprived of functional KCNJ6 protein is susceptible to spontaneous and provoked seizures without showing the histological signs of neuronal cell death found in the weaver mouse. Thus, the KCNJ6 gene seems to play an important role in seizure control. We therefore performed a mutation analysis of KCNJ6 and the related KCNJ3 gene in 38 patients with juvenile myoclonic epilepsy (JME). Two novel same-sense nucleotide exchanges were identified, but none of these changed the coding sequence. These results do not support a major role for the KCNJ6/KCNJ3 heteromeric receptor in the etiology of JME. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 96:8-11, 2000

Animals↗

PubMed1998

A de novo missense mutation (R1623Q) of the SCN5A gene in a Japanese girl with sporadic long QT sydrome. Mutations in brief no. 140. Online.

Two missense mutations and a nine-nucleotide deletion of the cardiac sodium channel (SCN5A) gene have been shown to cause long QT syndrome (LQTS) in several familial cases. We identified a novel missense mutation (R1623Q) of the SCN5A gene in a Japanese girl with sporadic LQTS. We used polymerase chain reaction, single-strand conformation polymorphism analysis and DNA sequence analysis to identify a mutation of the SCN5A gene in the patient. A single nucleotide substitution of guanine to adenine, in codon 1612, changed the coding sense of the SCN5A from arginine to glutamine (R1623Q) in the S4 segment of domain IV which is a highly conserved region of the SCN5A. This mutation was not identified in the unaffected biological parents and brother of the patient, and 100 normal, unrelated individuals. This finding is the first evidence of a de nova mutation in SCN5A associated with LQTS.

Amino Acid Substitution↗

PubMed1992

International trends in the incidence of bone cancer are not related to drinking water fluoridation.

BACKGROUND: Because osteosarcomas may develop in rats exposed to fluoridated water, water fluoridation might pose a cancer risk to humans. METHODS: A time trend analysis of the cumulative risk (CR) of bone cancer for the period 1958-1987 for 40 cancer registry areas showed an increased risk for young males in Canada, Europe, and the United States, and a decreased lifetime risk for either sex in Europe. RESULTS: This was unrelated to water fluoridation and may have resulted from changes in coding practices. Bone cancer risk was inversely related to the incidence of cancers of unknown origin, suggesting that bone metastases were erroneously coded as primary bone cancer. In 1968-1972, most areas recorded more bone cancer deaths than new cases of the disease. CONCLUSIONS: The mortality/incidence ratio, but not the incidence rate (IR), has dropped sharply since then, which erodes the basis of past inferences relating cancer mortality to fluoridation.

Animals↗

PubMed2002

Evaluation of FOXP2 as an autism susceptibility gene.

A mutation in the gene FOXP2 was recently identified as being responsible for a complicated speech and language phenotype in a single large extended pedigree. This gene is of interest to autism because it lies in one of the most consistently linked autism chromosomal regions of interest. We therefore tested this gene for its involvement in autism in a large sample of autism families. We completely sequenced the exon containing the mutation, screened the remaining coding sequence using SSCP technology, and identified and genotyped two novel intronic tetranucleotide repeat polymorphisms that were then analyzed for evidence of linkage and linkage disequilibrium (LD). We identified two families in which heterozygous deletions of a small number of glutamines in a long poly-glutamine stretch were found in one parent and the autistic probands; no other non-conservative coding sequence changes were identified. Linkage and LD analyses were performed in 75 affected sibling pair families and in two subgroups of this sample defined by the presence/absence of severe language impairment. One allele appeared to have an opposite pattern of transmission in the language based subgroups, but otherwise the linkage and LD analyses were negative. We conclude that FOXP2 is unlikely to contribute significantly to autism susceptibility.

Alleles↗

PubMed2003

Evolution of a pigmentation gene, the melanocortin-1 receptor, in primates.

The melanocortin-1 receptor (MC1R) forms a critical switch in the production of orange/red pheomelanin and black/brown eumelanin pigments during hair development in mammals. The molecular evolution of the melanocortin-1 receptor gene was investigated in a broad range of primate species, including several groups with large differences in distribution of orange/red and black hairs. Primate MC1R has been subject to purifying selection throughout most of its evolution, with small changes in selective constraint being detected early in primate evolution. In contrast to the situation in humans and domestic mammals, many intraspecific and intrageneric differences in primate coat color cannot be attributed to changes in the MC1R coding sequence. Nevertheless, important changes in the biochemical function of MC1R are suggested by mutations in sites of known functional importance, particularly in New World monkeys and lemurs. The evolution of the MC1R in lion tamarins is anomalous, with a combination of a high nonsynonymous to synonymous substitution rate (dN/dS) ratio, deletions, and substitutions.

Adaptation, Physiological↗

PubMed2005

International Classification of Childhood Cancer, third edition.

BACKGROUND: The third edition of the International Classification of Diseases for Oncology (ICD-O-3), which was published in 2000, introduced major changes in coding and classification of neoplasms, notably for leukemias and lymphomas, which are important groups of cancer types that occur in childhood. This necessitated a third revision of the 1996 International Classification of Childhood Cancer (ICCC-3). METHODS: The tumor categories for the ICCC-3 were designed to respect several principles: agreement with current international standards, integration of the entities defined by newly developed diagnostic techniques, continuity with previous childhood classifications, and exhaustiveness. RESULTS: The ICCC-3 classifies tumors coded according to the ICD-O-3 into 12 main groups, which are split further into 47 subgroups. These 2 levels of the ICCC-3 allow standardized comparisons of the broad categories of childhood neoplasms in continuity with the previous classifications. The 16 most heterogeneous subgroups are broken down further into 2-11 divisions to allow study of important entities or homogeneous collections of tumors characterized at the cytogenetic or molecular level. Some divisions may be combined across the higher-level categories, such as the B-cell neoplasms within leukemias and lymphomas. CONCLUSIONS: The ICCC-3 respects currently existing international standards and was designed for use in international, population-based, epidemiological studies and cancer registries. The use of an international classification system is especially important in the field of pediatric oncology, in which the low frequency of cases requires rigorous procedures to ensure data comparability.

Brain Neoplasms↗

PubMed2008

Mosaic tetraploidy and transient GFI1 mutation in a patient with severe chronic neutropenia.

This report presents the case of a 15-year-old male with severe chronic neutropenia, leukopenia, and persistent tetraploid mosaicism in the bone marrow and peripheral blood. His father had mild neutropenia and bone marrow tetraploidy. Flow cytometric analysis of DNA content peripheral blood showed tetraploidy in 20% of granulocytes and 15% of monocytes. Sequence analysis of the ELA2 gene was normal, but the GFI1 gene exhibited transient appearance of single base changes the coding region and promoter. We speculate that an underlying genetic defect, inherited in an autosomal dominant pattern, leads to both disordered mitosis and neutropenia in this kindred.

Adolescent↗

PubMed1997

Induction and repair of cyclobutane pyrimidine dimers in the Escherichia coli tRNA gene tyrT: Fis protein affects dimer induction in the control region and suppresses preferential repair in the coding region of the transcribed strand, except in a short region near the transcription start site.

We analysed induction and repair of UV induced pyrimidine dimers in the Escherichia coli tRNA gene tyrT. In wild-type (WT) log or stationary phase different patterns of induction occurred in the three Fis binding sites and the core promoter -35 sequence of the control region: this was absent in fis- cells. In stationary WT cells, slow, similar rates of repair occurred throughout the non-transcribed strand (NTS). Faster repair occurred in the NTS control region in WT log phase. NTS repair in fis- cells was similar, except the control region differed less between phases. Heterogeneous repair occurred along the transcribed strand (TS). In the control region repair was faster than in the NTS. Repair in the TS coding region changed between growth phases or if repair took place in different media. When irradiated log phase WT cells were in rich medium, two TS domains were evident: a fast-repaired domain within 31 nucleotides from the transcription start site; and a more slowly repaired domain composed of the rest of the TS. A sharp gradient existed in the small domain with very fast repair at the beginning and diminished repair towards the end. Fast transcription coupled repair (TCR) in the small domain was absent in the TS large domain, where repair was similar to the NTS and to the entire TS in mfd- cells. In similarly treated stationary phase WT cells, TCR occurred in the large domain. Depletion of Fis reinstates TCR to a lesser extent, whilst a substitution of five nucleotides at the Fis binding sites in the upstream activating sequence reinstates TCR. Reinstatement of TCR was also achieved by incubating irradiated WT cells in minimal salt medium without the required amino acid. Our results suggest that Fis indirectly suppresses preferential repair in the TS large domain by stimulating transcription.

Base Sequence↗

PubMed1996

Identification of seven novel mutations in LH beta-subunit gene by SSCP.

Seven new point mutations have been identified from LH beta-subunit gene by PCR-mediated SSCP, and sequencing. One mutation was found changing amino acid from Gln102 to Ser102. The remaining six mutations, which did not change the codings, were in complete linkage disequilibrium. SSCP can be used in the diagnosis of LH-related disorders.

DNA Mutational Analysis↗

PubMed1989

Evolution of chromosome bands: molecular ecology of noncoding DNA.

Giemsa dark bands, G-bands, are a derived chromatin character that evolved along the chromosomes of early chordates. They are facultative heterochromatin reflecting acquisition of a late replication mechanism to repress tissue-specific genes. Subsequently, R-bands, the primitive chromatin state, became directionally GC rich as evidenced by Q-banding of mammalian and avian chromosomes. Contrary to predictions from the neutral mutation theory, noncoding DNA is positionally constrained along the banding pattern with short interspersed repeats in R-bands and long interspersed repeats in G-bands. Chromosomes seem dynamically stable: the banding pattern and gene arrangement along several human and murine autosomes has remained constant for 100 million years, whereas much of the noncoding DNA, especially retroposons, has changed. Several coding sequence attributes and probably mutation rates are determined more by where a gene lives than by what it does. R-band exons in homeotherms but not G-band exons have directionally acquired GC-rich wobble bases and the corresponding codon usage: CpG islands in mammals are specific to R-band exons, exons not facultatively heterochromatinized, and are independent of the tissue expression pattern of the gene. The dynamic organization of noncoding DNA suggests a feedback loop that could influence codon usage and stabilize the chromosome's chromatin pattern: DNA sequences determine affinities of----proteins that together form----a chromatin that modulates----rate constants for DNA modification that determine----DNA sequences. Theories of hierarchical selection and molecular ecology show how selection can act on Darwinian units of noncoding DNA at the genome level thus creating positionally constrained DNA and contributing minimal genetic load at the individual level.

Base Sequence↗

PubMed2006

Psychiatric disorders certified on death certificates in an English population.

BACKGROUND: Psychiatric disorders are sometimes certified on death certificates, but seldom selected as the underlying cause of death. The majority of deaths with a certified psychiatric cause are usually omitted from official mortality statistics, which are typically based on the underlying cause alone. AIM: To report on death rates for psychiatric disorders, as certified on death certificates, including all mentioned causes as well as the underlying cause of death. METHOD: Analysis of database including all certified causes of death in 1979-1999, in three time periods defined by coding rule changes. RESULTS: Statistics on the underlying cause of death grossly under-estimated certified psychiatric disorders. For example, in the first period of our study they missed 88% of deaths in which schizophrenia was a certified cause, 98% of affective psychosis, and 96% of depression. Over time, considering all certified causes, age-standardised death rates for schizophrenia declined, those for affective psychosis showed no change, and those for depression and dementia increased. CONCLUSION: The decline in mortality rates for schizophrenia, and the increase for depression and dementia, may reflect real changes over time in disease prevalence at death, although other explanations are possible and are discussed.

Age Distribution↗

PubMed2003

Molecular phylogeny and evolution of the plant-specific seven-transmembrane MLO family.

Homologues of barley Mlo encode the only family of seven-transmembrane (TM) proteins in plants. Their topology, subcellular localization, and sequence diversification are reminiscent of those of G-protein coupled receptors (GPCRs) from animals and fungi. We present a computational analysis of MLO family members based on 31 full-size and 3 partial sequences, which originate from several monocot species, the dicot Arabidopsis thaliana, and the moss Ceratodon purpureus. This enabled us to date the origin of the Mlo gene family back at least to the early stages of land plant evolution. The genomic organization of the corresponding genes supports a monophyletic origin of the Mlo gene family. Phylogenetic analysis revealed five clades, of which three contain both monocot and dicot members, while two indicate class-specific diversification. Analysis of the ratio of nonsynonymous-to-synonymous changes in coding sequences provided evidence for functional constraint on the evolution of the DNA sequences and purifying selection, which appears to be reduced in the first extracellular loop of 12 closely related orthologues. The 31 full-size sequences were examined for potential domain-specific intramolecular coevolution. This revealed evidence for concerted evolution of all three cytoplasmic domains with each other and the C-terminal cytoplasmic tail, suggesting interplay of all intracellular domains for MLO function.

Amino Acid Sequence↗

PubMed2004

Genetic analysis of the cardiac sodium channel gene SCN5A in Koreans with Brugada syndrome.

The SCN5A gene encodes the alpha subunit of the human cardiac voltage-gated sodium channel. Mutations in SCN5A are responsible for Brugada syndrome, an inherited cardiac disease that leads to idiopathic ventricular fibrillation (IVF) and sudden death. In this study, we screened nine individuals from a single family and 12 sporadic patients who were clinically diagnosed with Brugada syndrome. Using PCR-SSCP, DHPLC, and DNA sequencing analysis, we identified a novel single missense mutation associated with Brugada syndrome in the family and detected a C5607T polymorphism in Korean subjects. A single nucleotide substitution of G to A at nucleotide position 3934 changed the coding sense of exon 21 of the SCN5A from glycine to serine (G1262S) in segment 2 of domain III (DIII-S2). Four individuals in the family carried the identical mutation in the SCN5A gene, but none of the 12 sporadic patients did. This mutation was not found in 150 unrelated normal individuals. This finding is the first report of a novel mutation in SCN5A associated with Brugada syndrome in Koreans.

Base Sequence↗