Efficient discovery of single-nucleotide polymorphisms in coding regions of human genes

Single nucleotide polymorphisms in protein coding regions (cSNPs) are of great interest for their effects on phenotype and potential for mapping disease genes. We have identified 5,400 novel exonic SNPs from alignments of public EST data to the draft human genome sequence, and approximately 12,000 more novel exonic SNPs from EST cluster alignments. We found 82% of the genomic-aligned SNPs and 63% of the EST-only SNPs to be detectably polymorphic in 20 Finnish DNA samples. 37% of the SNPs mapped to known protein coding regions, yielding 6,500 distinct, novel cSNPs from the two datasets. These data reveal selection against mutations that alter protein structure, and distinct classes of genes under strongly positive vs. negative pressure from natural selection for amino acid replacement (detected by K(A)/K(S)ratio). We have searched these cSNPs for compatibility with the amino acid profile at each site and structural impact on protein core stability.

Reversible sensorineural hearing loss

We present an unusual case of temporary sensorineural hearing loss in a 6-year-old child due to carbon monoxide. This was shown on both the audiograms and confirmed with objective testing using otoacoustic emissions. Carbon monoxide poisoning is one of the few recognised causes of reversible sensorineural hearing loss, though it may also lead to a permanent deficit. This is discussed along with other potential causes of reversible sensorineural hearing loss.

The founder mutation MSH2*1906G-->C is an important cause of hereditary nonpolyposis colorectal cancer in the Ashkenazi Jewish population

Hereditary nonpolyposis colorectal cancer (HNPCC) is caused by mutations in the mismatch-repair genes. We report here the identification and characterization of a founder mutation in MSH2 in the Ashkenazi Jewish population. We identified a nucleotide substitution, MSH2*1906G-->C, which results in a substitution of proline for alanine at codon 636 in the MSH2 protein. This allele was identified in 15 unrelated Ashkenazi Jewish families with HNPCC, most of which meet the Amsterdam criteria. Genotype analysis of 18 polymorphic loci within and flanking MSH2 suggested a single origin for the mutation. All colorectal cancers tested showed microsatellite instability and absence of MSH2 protein, by immunohistochemical analysis. In an analysis of a population-based incident series of 686 Ashkenazi Jews from Israel who have colorectal cancer, we identified 3 (0.44%) mutation carriers. Persons with a family history of colorectal or endometrial cancer were more likely to carry the mutation than were those without such a family history (P=.042), and those with colorectal cancer who carried the mutation were, on average, younger than affected individuals who did not carry it (P=.033). The mutation was not detected in either 566 unaffected Ashkenazi Jews from Israel or 1,022 control individuals from New York. In hospital-based series, the 1906C allele was identified in 5/463 Ashkenazi Jews with colorectal cancer, in 2/197 with endometrial cancer, and in 0/83 with ovarian cancer. When families identified by family history and in case series are included, 25 apparently unrelated Ashkenazi Jewish families have been found to harbor this mutation. Although this pathogenic mutation is not frequent in the Ashkenazi Jewish population (accounting for 2%-3% of colorectal cancer in those whose age at diagnosis is <60 years), it is highly penetrant and accounts for approximately one-third of HNPCC in Ashkenazi Jewish families that fulfill the Amsterdam criteria.

Regional cerebral blood flow changes in patients with intractable obsessive compulsive disorders treated by limbic leukotomy

The object of this study is to assess the changes in regional cerebral blood flow (rCBF) following stereotactic limbic leukotomy in patients with medically intractable Obsessive-Compulsive Disorder (OCD). Technetium-99-Hexa Methyl Propylene Amine Oxime (99mTc-HMPAO) Single Photon Emission Computed Tomography (SPECT) data obtained before and after limbic leukotomy were subjected to image fusion with MRI images. Eight samples were obtained from healthy voluteers. After localization of the ROI (Region Of Interest) in anatomical area, rCBF measurements were obtained by METLAB. The results of this study show a change of rCBF following limbic leukotomy in intractable OCD. Postoperative 99mTc-HMPAO SPECT findings implicate the medial frontal cortex, cingulate and striatum, which culd be linked to limbic leukotomy that blocks the functional connection of corticolimbic loop.

Application of multi-parameter flow cytometry using fluorescent probes to study substrate toxicity in the indene bioconversion

The bioconversion of indene to cis-(1S,2R) indandiol, a potential key intermediate in the synthesis of Merck's HIV protease inhibitor, CRIXIVAN trade mark, can be achieved using a Rhodococcus strain. This study using Rhodococcus I24 reports on the application of multiparameter flow cytometry for the measurement of cell physiological properties based on cytoplasmic membrane (CM) integrity and membrane depolarization as indicators of toxic effects of the substrate, indene. Quantification of intact polarized CM, intact depolarized CM and permeabilized CM of a large population of bacterial cells has been conducted using specific intracellular and membrane-binding fluorescent stains. Measurements of oxygen uptake rate (OUR) and optical density (OD) as indicators of metabolic activity and biomass growth, respectively, were also made. Indene concentrations of up to 0.25 g/L (0.037 g indene/g dry cell weight) did not significantly (<5% compared to control) affect cell light-scattering properties, intact CM, membrane polarization, respiratory activity, or biomass growth. Between this value and 1.5 g/L (0.221 g indene/g dry cell weight), the changes in intact CM, respiratory activity and biomass growth were relatively insignificant (<5% compared to control), although dissipation of the membrane potential of a significant proportion of the cell population occurred at 0.50 g/L (0.074 g indene/g dry cell weight). At 2.5 g/L (0.368 g indene/g dry cell weight) there was a significant increase in the dead cell population, accompanied by changes in the extracellular cationic concentrations and substantial decrease in respiratory activity. The primary effect of indene toxicity was the disruption of the proton motive force across the cytoplasmic membrane which drives the formation of ATP. The disruption of the proton motive force may have been due to the measured changes in proton permeability across the membrane. In addition, indene may have directly inhibited the membrane-bound enzymes related to respiratory activity. The overall consequence of this was reduced respiratory activity and biomass growth. The cell physiological properties measured via flow cytometry are important for understanding the effects of toxicity at the cellular level which neither measurements of biomass growth or indandiol formation rates can provide since both are cell averaged measurements. The technique described here can also be used as a generic tool for measuring cell membrane properties in response to toxicity of other indene-resistant strains that may be possible to use as recombinant hosts to perform the biotransformation of indene. This study has demonstrated that flow cytometry is a powerful tool for the measurement of cell physiological properties to assess solvent toxicity on whole cell biocatalysts.

Alteration of PTEN expression in endometrial carcinoma is associated with down-regulation of cyclin-dependent kinase inhibitor, p27

AIMS

PTEN is a recently identified tumour suppressor inactivated in a wide variety of human cancers, including endometrial cancers. Mutation of the PTEN tumour suppressor gene has been reported in approximately 50-83% of endometrial adenocarcinoma. Despite this fact, study of the expression of PTEN protein in human tumours is limited. PTEN protein functions as a tumour suppressor by regulating the cell cycle and survival through signal transduction pathway. PTEN protein was considered to have a dual-specificity phosphatase activity, but it is now known that its principal physiological activity is mainly derived from its lipid phosphatase activity. The cyclin-dependent kinase inhibitor, p27, has been suggested as a downstream target of cell cycle arrest of PTEN in various in vitro studies. In this study, we evaluated the alteration of PTEN protein expression in endometrial carcinoma and assessed its relationship to the expression of p27, the presumed downstream target of PTEN.

METHODS AND RESULTS

Immunohistochemical staining was performed on 66 cases of endometrial carcinoma including 61 endometrioid type and five serous type, using antibodies to PTEN and p27. Loss or decrease of PTEN expression was observed in 66% (40/61 cases) of uterine endometrioid carcinoma, whereas most uterine serous carcinoma (4/5 cases) showed intense PTEN expression. Four (30%) of 13 endometrial hyperplasia synchronous with endometrioid carcinoma demonstrated complete loss of PTEN expression. All endometrioid carcinoma synchronous with PTEN-negative endometrial hyperplasia showed loss of PTEN expression. Alteration of PTEN expression was not correlated with histological grade or stage. Decreased immunoreactivity of p27 was found in 48 cases (79%) of 61 endometrioid carcinoma, and 76% (36 cases) of them also showed loss or decrease of PTEN expression. Four of five uterine serous carcinoma revealed strong p27 immunoreactivity, all of which showed intense PTEN expression. A positive correlation between PTEN and p27 expression was statistically significant (Mantel-Haenszel chi2 test, P=0.001). Immunoreactivity of p27 was not related to histological grade and clinical stage.

CONCLUSION

These results show that PTEN and p27 are differentially expressed in endometrioid type carcinoma compared with those of the serous type, and suggest that the cyclin-dependent kinase inhibitor, p27, is a downstream target of PTEN-dependent cell cycle arrest in endometrial carcinoma.

Isolation and identification of a novel satellite DNA family highly conserved in several Cervidae species

In an attempt to amplify cervid satellite II DNA from the genomes of Indian muntjac and Chinese muntjac, a pair of primers derived from the white tailed deer satellite II DNA clone (OvDII) yielded a prominent approximately 1 kb polymerase chain reaction (PCR) product (in addition to the expected 0.7 kb satellite II DNA fragments) in both species. The approximately 1 kb products were cloned, sequenced, and analyzed by Southern blotting and fluorescence in situ hybridization (FISH). This revealed that the approximately 1 kb cloned sequences indeed represent a previously unknown cervid satellite DNA family, which is now designated as cervid satellite IV DNA. Approximately 1 kb PCR clones were also obtained from the genomes of the black tailed deer and Canadian woodland caribou with similar primer pairs. Extremely high sequence conservation (over 90% homology) was observed among the clones generated from all four deer species and PCR-Southern hybridization experiments further verified the co-amplification of two kinds of satellite DNA sequences with the same pair of primers. This satellite DNA was found to co-localize with centromeric proteins at the kinetochore by a simultaneous FISH and immunofluorescence study. Due to its high sequence conservation and close association with kinetochores, the newly identified satellite DNA may have a functional centromeric role.

Psychopathology in children from families with blood disorders: a cross-national study

BACKGROUND

This study examines the prevalence of psychiatric disorders in affected and in unaffected siblings from families with haemophilia or beta-thalassaemia.

METHOD

Based on data derived from a cross-sectional and multi-centre study into the resilience of 115 families with blood disorders. Sociodemographic and developmental data were collected from the parent using a standardised and semi-structured interview, and medical data were elicited from the attending clinician. The children's psychopathology was assessed with the Schedule for Affective Disorders and Schizophrenia (K-SADS).

RESULTS

Children with beta-thalassaemia were twice as likely to receive a diagnosis of psychiatric disorder and more likely to show a higher degree of impairment of general functioning than haemophilic boys or unaffected children from families with blood disorders. Clinical severity of haemophilia or beta-thalassaemia was not associated with significant differences in prevalence of child psychiatric disorders or impairment. Mothers' evaluation of their relationship with their child as 'less than easy' predicted psychopathology.

CONCLUSIONS

The high prevalence of psychopathology in children with beta-thalassaemia reported in this study suggests that specific blood disorders have differential impact on affected children. This difference may be related to medical therapy advances in haemophilia so that haemophilic boys can lead an almost normal life.

The natural history and antiviral treatment of hepatitis C in haemophilia

People with haemophilia who received non-virucidally treated large-pool clotting factor before 1986 were infected with hepatitis C virus (HCV), previously referred to as non-A, non-B hepatitis. Approximately one-tenth of patients have been shown to clear infection naturally and shown persistently negative HCV PCR. Patients have been infected with genotypes 1, 2 and 3 reflecting the plasma donors in Northern Europe and the United States. Several studies have shown that HCV mono-infection has a very slow progression. Co-infection with human immunodeficiency virus (HIV), however, can hasten the progression to cirrhosis and liver failure. Genotype 1 and older age at first infection also increase the progression rate. Candidates with detectable HCV RNA are candidates for therapy. The combination of standard interferon-alpha and ribavirin doubles the effectiveness of interferon-alpha alone and is the current standard of care for the treatment of chronic hepatitis C. The duration of therapy depends on the genotype and level of viraemia. Patients with genotypes 2 or 3 should have 6 months' therapy while those with genotype 1 and > 2 million copies mL-1 should have 1 year of therapy. Pegylated interferon is an emerging therapy. Patients co-infected with HIV, in whom treatment has stabilized the HIV infection, may be able to tolerate therapy for HCV infection. Liver transplantation is indicated for patients with haemophilia who have decompensated hepatitis C infection.

Molecular conformation-activity relationship of decamethonium congeners

BACKGROUND

Of the polymethylene bismethonium congeners (C5-C12 and C18), decamethonium (C10) is the most potent neuromuscular blocking agent. We tested the hypothesis that these congeners act as straight molecules and will not bend easily in spite of the flexible connecting chain between the methonium heads. For congeners higher than C10, we also hypothesized that the relative difficulty with which the molecules to bend to conform to the interonium distance of C10 proportionately reduces their neuromuscular blocking potency.

METHODS

Each congener was modelled and subjected to computer searches for representative low-energy molecular conformers. The conformation-potency relationship of the congeners was examined.

RESULTS

For all congeners, we found that the lowest energy conformer (the 'global minimum') has a straight-chain conformation. Reduction of the interonium distance (by bending) incurs a steep energy penalty linearly related to the distance reduced. The global minimum of C10 has an interonium distance of 14.03 A and a total molecular length of 20.10 A. For other congeners, the interonium distance differential from that of C10 and the energy penalty required to conform to the interonium distance of C10 (where applicable) correlate with the reported logarithmic (mmol kg(-1)) dose requirement for neuromuscular block.

CONCLUSIONS

The C10 congeners strongly prefer a straight conformation. Their molecular length and resistance to bending is key to their neuromuscular blocking potency. A molecular length of approximately 20 A should best fit the space available to neuromuscular blocking agents between the two receptive sites of the endplate acetylcholine receptor.

Protein glycation: creation of catalytic sites for free radical generation

In a glycation reaction, alpha-dicarbonyl compounds such as deoxyglucosone, methylglyoxal, and glyoxal are more reactive than the parent sugars with respect to their ability to react with amino groups of proteins to form inter- and intramolecular cross-links of proteins, stable end products called advanced Maillard products or advanced end products (AGEs). The AGEs, which are irreversibly formed, accumulate with aging, atherosclerosis, and diabetes mellitus, and are especially associated with long-lived proteins such as collagens, lens crystallins, and nerve proteins. It was suggested that the formation of AGEs not only modifies protein properites but also induces biological damage in vivo. In this report, we summerize results obtained from our studies for (1) identifying the structure of the cross-linked radical species formed in the model system-the reaction between alpha-dicarbonyl methylglyoxal with amino acids, and (2) the reactivity of the radical center of the protein created by the similar reaction. These results indicate that glycation of protein generates active centers for catalyzing one-electron oxidation-reduction reactions. This active center, which exhibits enzyme-like character, is suggested to be the cross-linked Schiff-based radical cation of the protein. It mimics the characteristics of the metal-catalyzed oxidation system. These results together indicate that glycated proteins accumulated in vivo provide stable active sites for catalyzing the formation of free redicals.

Genetic antagonism between body weight and milk production in beef cattle

Korean cattle have an unusually short suckling period (4 mo) due to poor milking ability, and this is a hindrance to growth of calves. Therefore, Korean cattle breeders have shown interest in genetic improvement of milking ability. In this study, body weight (birth weight, weaning weight, and yearling weight) and five daily milk yields by period in Korean cattle (Hanwoo) were analyzed using a two-trait sire and maternal grandsire mixed model. The milk yields used were actually measured at sequential intervals from 1 to 4 mo after calving. Posterior means of the parameters were estimated using Gibbs sampling. Heritability estimates (0.25 to 0.26) for daily milk yield at weaning were larger than those with other periods. Genetic impact on daily milk yield, especially at weaning, was emphasized in order to lengthen the suckling period of Korean cattle. Genetic correlation estimates between BW and daily milk yield were all negative (-0.08 to -0.16 for birth weight, -0.04 to -0.21 for weaning weight, and -0.12 to -0.19 for yearling weight), whereas environmental correlation estimates were all positive (0.20 to 0.39 for birth weight, 0.34 to 0.51 for weaning weight, and 0.30 to 0.45 for yearling weight). The negative estimates of genetic correlation between weight and milk yield implied genetic antagonism between direct and maternal effects for weaning weight of beef cattle.

Non-bronchoscopic bronchoalveolar lavage in the microbiological diagnosis of pneumonia in mechanically ventilated patients

A prospective study comparing standardized non-bronchoscopic bronchoalveolar lavage (sNB-BAL) and non-specific endotracheal aspirate (NsETA) in the microbiological diagnosis of pneumonia in mechanically ventilated patients is described. One hundred episodes in 82 mechanically ventilated patients with or without radiological and clinical diagnostic criteria of pneumonia were studied. NsETA and sNB-BAL was performed on the day of study. Fifty-one patients had pneumonia (21 ventilator-associated, 12 hospital-acquired, 18 community-acquired) and 49 had no pneumonia as defined by widely accepted clinico-radiological criteria. The sNB-BAL was found to be significantly more specific (0. 73) compared to NsETA (0.35) for the microbiological diagnosis of pneumonia. Colonization rates with NsETA were significantly higher compared to sNB-BAL (P value <0.0001). No patient had complications attributable to the sNB-BAL procedure. We conlude that sNB-BAL is a safe, effective, sensitive, specific and inexpensive procedure for the serial evaluation of pneumonia in mechanically ventilated patients.