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PubMed1994

Complete nucleotide sequence of a beta-cell tropic variant of coxsackievirus B4.

A mouse pancreas-adapted variant of coxsackievirus B4 (P-CB4) has been shown to replicate in, and cause an excessive release of insulin from, pancreatic beta cells cultured in vitro. The prototype CB4 strain (JVB Benschoten), from which the adapted variant was derived, although able to replicate in cultured islets does not cause a similar release of insulin from the beta cells. The pancreas-adapted virus has also been shown to cause host cell protein synthesis shut-off in beta cells and to inhibit (pro)insulin biosynthesis. These metabolic changes occur in the absence of cytolytic damage [Szopa et al.: Bioscience Reports 5:63-69, 1985 and Cell Biochemistry and Function 4:181-187, 1986]. To investigate the genetic basis for this beta cell tropism, the complete nucleotide sequence of P-CB4 has been determined and compared to that of the previously published sequence of the prototype CB4 strain (JVB Benschoten) [Jenkins et al.: Journal of General Virology 68:1835-1848, 1987]. Twenty-five nucleotide sequence differences were observed. Of these, six occur in the 5' noncoding region of the genome and 19 in the coding region (resulting in seven amino acid changes). The possible significance of these changes in relation to the beta cell tropism of the pancreas-adapted virus is discussed.

Base Sequence↗
PubMed2003

Fine structural evaluation of the iris after unilateral treatment with latanoprost in patients undergoing bilateral trabeculectomy (the Mainz II study).

OBJECTIVE: To investigate by masked electron microscopy whether 6 months of topical latanoprost caused pathological changes in the peripheral iris of patients with glaucoma. METHODS: Seventeen patients with bilateral primary open-angle glaucoma requiring trabeculectomy were recruited for this study. The iridectomy taken during surgery on the first eye served as a control. The second test eye was treated topically with latanoprost for 6 months before its trabeculectomy. Fourteen patients completed the treatment arm of the study, and 1 of these underwent marked color change. As a result, 31 iridectomy specimens were fixed, coded, and evaluated. RESULTS: The specimens were evaluated for evidence of stromal inflammation, vascular alterations, and stromal and posterior epithelial degeneration. None of these features was evident in any of the 31 iridectomy specimens. There was evidence of the incidence of free melanin granules in the stroma, melanin turnover, abundance of stromal clump cells, atypical cellular features in melanocytes, and prominence of the anterior border. After code breaking, it was evident that none of these features distinguished the test from the fellow irises in our group. The patient with color change in the test iris did not stand out from the others in this analysis. Qualitative reexamination of further sections after unmasking gave the impression of increased melanin granule numbers in the melanocytes of the anterior border region. CONCLUSIONS: The ultrastructure of the iridectomies from the latanoprost-treated eyes and the fellow eyes conformed to published standards for normal iris. There was no evidence of early ultrastructural changes, which might have been the harbingers of latanoprost-induced iris abnormality.

Administration, Topical↗
PubMed1997

Identification of mutations in a Sindbis virus variant able to establish persistent infection in BHK cells: the importance of a mutation in the nsP2 gene.

Sindbis virus is a positive strand RNA virus that has provided a valuable model for studying virus structure and replication. It is also being developed as a vector for the expression of heterologous proteins. Many studies with this virus are carried out in cultured BHK cells where infection is usually highly cytopathic and within 1 or 2 days after infection all of the cells are dead. Weiss et al. had established a persistently infected culture of BHK cells by infecting the cells with a virus preparation highly enriched in defective interfering (DI) particles and had isolated an attenuated virus, SIN-1 virus, from the culture [Weiss et al. (1980) J. Virol. 33, 463-474]. SIN-1 virus, free of DI particles, was able to establish a persistent infection in BHK cells. We initiated studies to determine what changes in the genome of the virus were responsible for this phenotype. We describe here the cDNA cloning and sequencing of the 5' terminus and the four nonstructural protein genes from SIN-1 virus. A single coding mutation in the nsP2 gene (a predicted change of Pro-726 --> Ser) produced a virus that was able to establish persistent infection in BHK cells. Additional mutations in the other genes were required to decrease the synthesis of viral RNA to a level similar to that found in cells infected with SIN-1 virus. Incorporation of the nsP2 mutation into a Sindbis virus expression vector led to a higher level of synthesis of the reporter protein, beta-galactosidase, than that obtained with the original Sindbis virus replicon.

Animals↗
PubMed2000

Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription.

The activities of several mRNA processing factors are coupled to transcription through binding to RNA polymerase II (Pol II). The largest subunit of Pol II contains a repetitive carboxy-terminal domain (CTD) that becomes highly phosphorylated during transcription. mRNA-capping enzyme binds only to phosphorylated CTD, whereas other processing factors may bind to both phosphorylated and unphosphorylated forms. Capping occurs soon after transcription initiation and before other processing events, raising the question of whether capping components remain associated with the transcription complex after they have modified the 5' end of the mRNA. Chromatin immunoprecipitation in Saccharomyces cerevisiae shows that capping enzyme cross-links to promoters but not coding regions. In contrast, the mRNA cap methyltransferase and the Hrp1/CFIB polyadenylation factor cross-link to both promoter and coding regions. Remarkably, the phosphorylation pattern of the CTD changes during transcription. Ser 5 phosphorylation is detected primarily at promoter regions dependent on TFIIH. In contrast, Ser 2 phosphorylation is seen only in coding regions. These results suggest a dynamic association of mRNA processing factors with differently modified forms of the polymerase throughout the transcription cycle.

Models, Genetic↗
PubMed2006

[Changes in emotional experience during the course of psychoanalytic therapy].

OBJECTIVES: Does the subjective emotional experience of patients change in the course of psychoanalytic treatment? METHODS: Ten patients were interviewed four times during their first two years in psychoanalytic therapy. Interviews were coded with regard to the patients' subjective emotional experience. Changes in individual emotion profiles were then tested for associations with therapy outcome using a hierarchical linear model. RESULTS: Better therapy outcome was associated with an increase in emotional variability and a decrease in the proportion of negative emotions. In contrast, neither the number of emotions verbalized by the patients nor the frequencies of specific emotion categories were associated with therapy outcome. CONCLUSIONS: Remarkable changes of emotional experience during the course of psychoanalytic treatment could be demonstrated. Particularly, a more variable emotional experience proved to be closely associated with improvement in mental health.

Adult↗
PubMed1989

The Computer-Assisted Postmortem Identification (CAPMI) system: sorting algorithm improvements.

Refinements to the original Computer-Assisted Postmortem Identification (CAPMI) software algorithms and general data handling were suggested as a result of observations made following the Gander plane crash of 1985. The presence of highly fragmented and scattered remains following most plane crashes suggested that changes to procedure might improve CAPMI performance for use in these types of disasters. A total of 162 ante- and postmortem dental records which had been used successfully to identify victims of the Gander disaster were coded for anonymity and used for this investigation. Changes in data construction and management were made to CAPMI, according to concepts which were thought might improve system performance, and tested. Although most tested techniques improved CAPMI performance, the data suggested that replacement of "virgin" chartings with "data unknown" results in improved performance of CAPMI largely independent of other factors. Of 162 possible record matches, the original algorithm successfully listed the true record match in the top 20 possibilities 74% of the time; the tested variations on the original algorithm yielded results across a range of 38 to 83% successes, with most techniques performing better than the original algorithm. Results of this investigation have been incorporated into improved CAPMI procedures and software.

Accidents, Aviation↗
PubMed1990

False-positive coding for acute myocardial infarction on hospital discharge records: chart audit results from a tertiary centre.

Hospital medical records staff enter diagnostic codes on charts using the International Classification of Diseases (Clinically Modified), Ninth Revision (ICD-9-CM). In a downtown Toronto tertiary hospital, 209 consecutive charts coded for acute myocardial infarction as the primary diagnosis in 1987-88 were reviewed. Criteria for documentation of acute myocardial infarction included symptomatic, electrocardiographic and enzymatic elements. Forty-three (21%) false-positives, ie, charts coded acute myocardial infarction where criteria were not fulfilled, were found (95% confidence interval 15 to 26%). Physician diagnosis of acute myocardial infarction appeared on the face sheet of 30 of the false-positive cases. Common reasons for false-positive face sheet entries and chart coding were acute myocardial infarction within the previous eight weeks with transfer or readmission for coronary angiography and other procedures; and presumed acute myocardial infarction on admission subsequently unproven or disproved. The false-positive proportion was similar to a Canadian study drawing on charts from hospitals of various sizes in 1977, lower than in recent reports from various American tertiary teaching hospitals (P less than 0.0001), and higher than in five Boston area community hospitals (P = 0.0005) where procedure-related transfers or readmissions of previous acute myocardial infarction patients were less likely. This audit lends credence to arguments that changes are needed in ICD-9-CM codes for acute myocardial infarction and in the assignation of reasons for hospitalization.

Canada↗
PubMed2004

Positive selection in MAOA gene is human exclusive: determination of the putative amino acid change selected in the human lineage.

Monoamine oxidase A (MAOA) is the X-linked gene responsible for deamination and subsequent degradation of several neurotransmitters and other amines. Among other activities, the gene has been shown to play a role in locomotion, circadian rhythm, and pain sensitivity and to have a critical influence on behavior and cognition. Previous studies have reported a non-neutral evolution of the gene attributable to positive selection in the human lineage. To determine whether this selection was human-exclusive or shared with other species, we performed a population genetic analysis of the pattern of nucleotide variation in non-human species, including bonobo, chimpanzee, gorilla, and orangutan. Footprints of positive selection were absent in all analyzed species, suggesting that positive selection has been recent and unique to humans. To determine which human-unique genetic changes could have been responsible for this differential evolution, the coding region of the gene was compared between human, chimpanzee, and gorilla. Only one human exclusive non-conservative change is present in the gene: Glu151Lys. This human substitution affects protein dimerization according to a three-dimensional structural model that predicts a non-negligible functional shift. This is the only candidate position at present to have been selected to fixation in humans during an episode of positive selection. Divergence analysis among species has shown that, even under positive selection in the human lineage, the MAOA gene did not experience accelerated evolution in any of the analyzed lineages, and that tools such as K(a)/ K(s) would not have detected the selective history of the gene.

Amino Acid Sequence↗
PubMed2004

CyDAS: a cytogenetic data analysis system.

For statistical analyses in cancer cytogenetics, the genomic changes encoded by the karyotype must be translated into numerical codes. We developed a program, which extracts chromosomal gains and losses as well as breakpoints from the karyotype. The changes are compiled in tables according to the chromosome bands involved and/or depicted in projection to the respective chromosome ideogram. The data are ready to be integrated into further statistical analyses. The program may be run as desktop or Internet application.

Chromosome Aberrations↗
PubMed2005

A compound heterozygous change found in Peters' anomaly.

PURPOSE: To determine whether sequence variations in the congenital glaucoma gene, CYP1B1, are present in individuals with Peters' anomaly, a developmental eye anomaly frequently associated with glaucoma. METHODS: The CYP1B1 coding region was screened in 26 individuals with Peters' anomaly (9 familial and 17 simplex cases) by heteroduplex analysis using the Transgenomic Wave nucleic acid fragment analysis system. Deviations from the wild type pattern were determined by sequencing. RESULTS: Six nucleotide positions varied from the wild type. Four of these have previously been observed in clinically normal individuals: -13 in intervening sequence 1 (IVS1), codons 48, 432, and 449. We found a novel sequence variation at -16 in IVS1 in one affected individual. A novel compound heterozygote pattern was observed at codon 432 in 6 of our 26 unrelated cases with Peters' anomaly. CONCLUSIONS: This is the first report of 2 novel CYP1B1 sequence variations seen in Peters' anomaly. The -16 IVS1 change is outside the coding region and likely to be a rare polymorphism. The compound heterozygous change at codon 432 is within a conserved part of the coding region and substitutes valine with either leucine or arginine. This change has not been observed in 100 normal controls. Furthermore, we propose how this finding may affect protein function.

Aryl Hydrocarbon Hydroxylases↗
PubMed1978

[Desire for therapeutic abortion in the dependents of foreign workers. Outpatients psychiatric evaluation (author's transl)].

The change in paragraph 218 of the criminal code regarding abortion was responsible for new guidelines for the psychiatric evaluation regarding a therapeutic abortion is reported. The commonest indications were medical reasons such as exhaustion, and reactive depression. There was one case of schizophrenia, one case of affective psychosis, two attempted suicides, twenty reactive depressions, one character disorder, and one case of cerebral seizures. Five applications were approved. The follow-up evaluation of the women with the approved and dismissed applications for therapeutic abortions showed no physical or psychic abnormalities. A comparison with 88 German applicants showed similar results. The stringent evaluation of applications for therapeutic abortion is still necessary even after the change of the law.

Abortion, Legal↗
PubMed1985

Attention to television: intrastimulus effects of movement and scene changes on alpha variation over time.

Central and occipital EEG alpha were used as an on-line measure of momentary changes in covert attention during television viewing. Alpha was recorded during nine 30-second commercials shown embedded in a half-hour situation comedy. Two time series were constructed for data analysis. A stimulus series consisted of codes representing the presence or absence of scene changes or person and object movement for each half-second interval of the commercials. The alpha series consisted of median alpha scores for each half-second interval, aggregated across 26 subjects. The alpha series was regressed on the movement and scene change series, both of which produced significant increments in R, even after autocorrelational effects inherent in the alpha series were removed. As a validity check on the attentional interpretation of alpha, it was shown that mean alpha for each commercial was significantly (negatively) correlated with recall and recognition of commercial contents. The results are discussed in terms of their implications for further use of continuously-recorded alpha in research on factors that influence attention to television.

Adult↗
PubMed2001

Amino acid repetitions in the dihydropteroate synthase of Streptococcus pneumoniae lead to sulfonamide resistance with limited effects on substrate K(m).

Sulfonamide resistance in Streptococcus pneumoniae is due to changes in the chromosomal folP (sulA) gene coding for dihydropteroate synthase (DHPS). The first reported laboratory-selected sulfonamide-resistant S. pneumoniae isolate had a 6-bp repetition, the sul-d mutation, leading to a repetition of the amino acids Ile(66) and Glu(67) in the gene product DHPS. More recently, clinical isolates showing this and other repetitions have been reported. WA-5, a clinical isolate from Washington State, contains a 6-bp repetition in the folP gene, identical to the sul-d mutation. The repetition was deleted by site-directed mutagenesis. Enzyme kinetic measurements showed that the deletion was associated with a 35-fold difference in K(i) for sulfathiazole but changed the K(m) for p-aminobenzoic acid only 2.5-fold and did not significantly change the K(m) for 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine pyrophosphate. The enzyme characteristics of the deletion variant were identical to those of DHPS from a sulfonamide-susceptible strain. DHPS from clinical isolates with repetitions of Ser(61) had very similar enzyme characteristics to the DHPS from WA-5. The results confirm that the repetitions are sufficient for development of a resistant enzyme and suggest that the fitness cost to the organism of developing resistance may be very low.

Adolescent↗
PubMed1978

Effects of picrotoxin and strychnine on rabbit retinal ganglion cells: changes in centre surround receptive fields.

1. The effects of picrotoxin and strychnine on the centre surround types of ganglion cell (X, Y, sluggish sustained and sluggish transient with on or off centres, and colour coded) were studied in the rabbit retina. 2. Picrotoxin changed the centre surround balance in favour of the centre for Y cells and sluggish transient cells but not for X cells or sluggish sustained cells. 3. Inhibition by a moving radial grating was abolished by picrotoxin for off centre Y cells, but not for on centre Y cells. 4. Picrotoxin abolished the surround response for six on centre sustained cells. These were hybrid cells with conduction velocities and receptive field properties characteristic of more than one of the X, Y and sluggish categories. The surround was not abolished by picrotoxin for any of the cells which fell in the standard X, Y and sluggish categories. 5. Strychnine did not affect the centre surround balance substantially in any of the cells tested. Strychnine did effect the transients: in general strychnine shortened or abolished them, while picrotoxin made them larger.

Action Potentials↗
PubMed1989

Nucleotide sequence of high-passage hepatitis A virus strain HM175: comparison with wild-type and cell culture-adapted strains.

The nucleotide sequence of cDNA from a high-passage, cell culture-adapted variant of hepatitis A virus strain HM175 was compared with the previously determined sequences of wild-type virus and two other cell culture-adapted variants. A total of 42 nucleotide changes were detected when the sequence was compared with wild-type virus. Five of these changes were common to all cell culture-adapted strains and a further two changes were shared by the strains that had experienced the greatest number of cell culture passages. The mutations were distributed throughout the genome coding for amino acid substitutions in regions 2B, 2C and 3D with silent changes in 1C and the 5' non-coding region. The possible relevance of these mutations to cell culture adaptation and attenuation is discussed.

Animals↗
PubMed1997

Correction of hypermutability, N-methyl-N'-nitro-N-nitrosoguanidine resistance, and defective DNA mismatch repair by introducing chromosome 2 into human tumor cells with mutations in MSH2 and MSH6.

The human DNA mismatch repair genes hMSH2 and hMSH6 encode the proteins that, together, bind to mismatches to initiate repair of replication errors. Human tumor cells containing mutations in these genes have strongly elevated mutation rates in selectable genes and at microsatellite loci, although mutations in these genes cause somewhat different mutator phenotypes. These cells are also resistant to killing by certain drugs and are defective in mismatch repair. Because the elevated mutation rates in these cells may lead to mutations in additional genes that are causally related to the other defects, here we attempt to establish a cause-effect relationship between the hMSH2 and hMSH6 gene mutations and the observed phenotypes. The endometrial tumor cell line HEC59 contains mutations in both alleles of hMSH2. The colon tumor cell line HCT15 contains mutations in hMSH6 and also has a sequence change in a conserved region of the coding sequence for DNA polymerase delta, a replicative DNA polymerase. We introduced human chromosome 2 containing the wild-type hMSH2 and hMSH6 genes into HEC59 and HCT15 cells. Introduction of chromosome 2 to HEC59 cells restored microsatellite stability, sensitivity to N-methyl-N'-nitro-N-nitrosoguanidine treatment, and mismatch repair activity. Transfer of chromosome 2 to HCT15 cells also reduced the mutation rate at the HPRT locus and restored sensitivity to N-methyl-N'-nitro-N-nitrosoguanidine treatment and mismatch repair activity. The results demonstrate that the observed defects are causally related to mutations in genes on chromosome 2, probably hMSH2 or hMSH6, but are not related to sequence changes in other genes, including the gene encoding DNA polymerase delta.

Cell Fusion↗
PubMed1993

What's lost in inverted faces?

Disproportionate inversion decrements for recognizing faces and other homogeneous stimuli are often interpreted as evidence that experts use relational features to recognize stimuli that share a configuration. However, it has never directly been shown that inversion disrupts the coding of relational features more than isolated features. Here we report three studies that compare inversion decrements for detecting changes that span the isolated-relational features continuum. Relatively large inversion decrements occurred for relational features (Thatcher illusion changes, internal feature spacing), with smaller decrements for isolated features (presence/absence of facial hair or glasses). The one discrepancy was a relatively large inversion decrement for detecting changes to the eyes and mouth, which we had classified as an isolated feature change. However, this decrement disappeared when the features were presented out of the face context (Experiments 2 and 3), suggesting that it occurs because subjects spontaneously code relations between the features and the rest of the face. Although the results support the interpretation of disproportionate inversion effects as evidence of relational coding, the difficulty of classifying changes as isolated or relational highlights an undesirable ambiguity in the isolated-relational feature distinction. We therefore consider alternative construals of the configural coding notion.

Facial Expression↗
PubMed2006

Rules for modeling signal-transduction systems.

Formalized rules for protein-protein interactions have recently been introduced to represent the binding and enzymatic activities of proteins in cellular signaling. Rules encode an understanding of how a system works in terms of the biomolecules in the system and their possible states and interactions. A set of rules can be as easy to read as a diagrammatic interaction map, but unlike most such maps, rules have precise interpretations. Rules can be processed to automatically generate a mathematical or computational model for a system, which enables explanatory and predictive insights into the system's behavior. Rules are independent units of a model specification that facilitate model revision. Instead of changing a large number of equations or lines of code, as may be required in the case of a conventional mathematical model, a protein interaction can be introduced or modified simply by adding or changing a single rule that represents the interaction of interest. Rules can be defined and visualized by using graphs, so no specialized training in mathematics or computer science is necessary to create models or to take advantage of the representational precision of rules. Rules can be encoded in a machine-readable format to enable electronic storage and exchange of models, as well as basic knowledge about protein-protein interactions. Here, we review the motivation for rule-based modeling; applications of the approach; and issues that arise in model specification, simulation, and testing. We also discuss rule visualization and exchange and the software available for rule-based modeling.

Computer Simulation↗

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