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Biomedical subjects

S Forrest

Publications and source records attributed to S Forrest.

At least 37 records · Page 2Linked to original sources
PubMed1997

Human flavin-containing monooxygenase form 3: cDNA expression of the enzymes containing amino acid substitutions observed in individuals with trimethylaminuria.

Trimethylaminuria is an autosomal recessive human disorder affecting a small part of the population as an inherited polymorphism. Individuals diagnosed with trimethylaminuria excrete relatively large amounts of trimethylamine in their urine, sweat, and breath, and this results in a fishy odor characteristic of trimethylamine. Activity of the human flavin-containing monooxygenase (FMO) has been proposed to be deficient in trimethylaminuria patients causing a decrease in the metabolism of trimethylamine that results in a fishy body odor. Cohorts of Australian, American, and British individuals suffering from trimethylaminuria have been identified. The human FMO3 cDNA was amplified from lymphocytes of affected patients. We report preliminary evidence of substitutions detected by screening of the cDNA and genomic DNA. The variant human FMO3 cDNA was constructed from wild type human FMO3 cDNA by site-directed mutagenesis as maltose-binding protein fusions. Five distinct human FMO3 mutants were expressed as fusion proteins in Escherichia coli and compared with wild type human FMO3 maltose-binding proteins (FMO3-MBP) for the N-oxygenation of 10-[(N,N-dimethylamino)pentyl]-2-(trifluoromethyl)phenothiazine, tyramine, and trimethylamine. Human Lys158 FMO3-MBP and, to a greater extent, human Glu158 FMO3-MBP efficiently N-oxygenated the three amine substrates. Human Lys158 Ile66 FMO3-MBP, Glu158 Ile66 FMO3-MBP, Lys158 Leu153 FMO3-MBP, and Glu158 Leu153 FMO3-MBP were all constructed as mutants identified as possible FMO3 variants responsible for trimethylaminuria and were found to be inactive as N-oxygenases. The results suggest that mutations at codons 66 and 153 of FMO3 can cause trimethylaminuria in humans. We observed a common polymorphism of Lys to Glu at codon 158 of FMO3 that segregated with almost equal allele frequencies in a number of control Australian and North American samples studied. The Lys158 to Glu158 human FMO3 polymorphism does not decrease trimethylamine N-oxygenation for the cDNA-expressed enzyme and thus does not appear to be causative of trimethyaminuria. The data show that the functional activity of human FMO3 can be significantly altered by amino acid changes that have been observed in individuals with clinically diagnosed trimethylaminuria.

DNA, Complementary↗
PubMed1997

Modified Method for the Detection of the CAG Repeat Expansion in Huntington's Disease and Application to a Predictive Testing Protocol.

Background: The identification of the CAG trinucleotide repeat expansion as the cause of Huntington's disease (HD) has dramatically altered the ease and uptake of testing. The direct test for the mutation allows testing of many more consultands, particularly those individuals whose family structure is not suitable for linkage analysis. Therefore, protocols that can rapidly handle a number of samples and give accurate reliable results are essential. Methods and Results: The HD1/HD2 set of primers, which amplify the variable CAG and polymorphic CCG repeats, and the HD1/HD3 set of primers, which amplify only the variable CAG repeat, were used. Comparison of internally labeled with end-labeled polymerase chain reaction product was made. "Lysates" made from blood were investigated as suitable material for the HD polymerase chain reaction. Conclusions: The conditions used for detection of the CAG repeat in the huntingtin gene by end labeling of one of the primers that amplifies only the CAG repeat were improved, and an efficient protocol that reduces sample preparation and storage by using lysates from blood rather than extracted purified genomic DNA was developed.

Journal Article↗
PubMed1997

Spinal Muscular Atrophies: An Ongoing Diagnostic Dilemma?

Background: Spinal muscular atrophies (SMAs) are a group of autosomal recessive disorders of anterior horn cell degeneration. Three genes-survival motor neuron (SMN), neuronal apoptosis inhibitory protein (NAIP), and, more recently, p44 (subunit of basal transcription factor II)-have been considered as candidate genes. The region spanning these genes has a complex organization, which makes molecular analysis difficult. Methods and Results: Molecular genetic testing of deletions of exons 7 and 8 of the SMN(T) (telomeric copy) gene and exon 5 of the NAIP(T) (telomeric copy) gene was performed in 39 diagnosed SMA patients, 31 cases referred as possible SMA, and 24 cases of prenatal diagnosis of SMA. Linkage analysis using markers flanking the SMA region was also performed. In general, the findings of involvement of SMN and NAIP gene deletions in patients diagnosed with SMA are in agreement with those previously published. One possible SMA case was found to be homozygously deleted only for exon 7 of SMN(T) and one deleted only for exon 5 of the NAIP(T) gene. Conclusions: SMAs exemplify human inherited disorders in which application of a variety of different techniques and a search for mutations in multiple genes are involved. Deletion testing of candidate genes (SMN, NAIP) is a powerful approach in patients affected or suspected of being affected with SMA. It is proposed that the direct SMN gene deletion test can be offered as the only test for prenatal diagnosis of SMA in families in which the clinically affected sibling has also been shown to have the homozygous deletion.

Journal Article↗
PubMed1997

The ecology of echo.

Echo is a generic ecosystem model in which evolving agents are situated in a resource-limited environment. The Echo model is described, and the behavior of Echo is evaluated on two well-studied measures of ecological diversity: relative species abundance and the species-area scaling relation. In simulation experiments, these measures are used to compare the behavior of Echo with that of a neutral model, in which selection on agent genotypes is random. These simulations show that the evolutionary component of Echo makes a significant contribution to its behavior and that Echo shows good qualitative agreement with naturally occurring species abundance distributions and species-area scaling relations.

Biological Evolution↗
PubMed1996

The clinical role of the nurse teacher: an exploratory study of the nurse teacher's present and ideal role in the clinical area.

This paper describes a study which aimed to explore the present and ideal role of the nurse teacher in the clinical area from the perspective of: nurse teachers; ward sisters/charge nurses; staff nurses and students nurses undertaking the 'traditional' and Project 2000 programmes of training. The study adopted a qualitative design. Findings from this study demonstrate that the clinical role of the nurse teacher lacks clarity, however, clear criteria emerged as to how trained nurses and student nurses perceived the ideal role. Nurse teachers' role in assuring the quality of the clinical learning environment emerged as a major area of criticism. It was suggested that, if nurse teachers adopted a clinical role that was primarily concerned with supporting clinically based nurses in their teaching role, this served to assure the quality of students' clinical learning experience. In conclusion, it is suggested that for nurse teachers to meet the needs of trained nurses and student nurses in the clinical area, the role must be diverse and flexible. Attempts to prescribe a unimodel approach to deliver the service should be avoided. Rather, the role must be negotiated between teachers, clinical nurses and students, and constructed in a way that best meets the needs of all parties concerned.

Faculty, Nursing↗
PubMed1995

The impact of newborn screening on cystic fibrosis testing in Victoria, Australia.

Newborn screening for cystic fibrosis (CF) by examining the levels of immunoreactive trypsinogen was introduced in Victoria in 1989. This was modified by the addition of testing for the common CF gene mutation, delta F508, in 1990. Problems with the first newborn screening protocol were overcome with the addition of the DNA test as there was no need to contact the majority of families, there was a reduced number of sweat tests, and less anxiety was experienced by parents. The mode of diagnosis changed from failure to thrive, steatorrhoea, rectal prolapse, and family history to diagnosis through newborn screening. Newborn screening dramatically reduced the time of diagnosis of CF to approximately six weeks or less in the majority of cases. Since the introduction of newborn screening, the uptake of prenatal diagnosis in CF families has increased two and a quarter fold.

Algorithms↗
PubMed1994

Whose quality of care is it anyway? Methodological issues in evaluating residential care for the mentally ill.

The paper reports on issues of methodology regarding the evaluation of residential care for mentally ill people. A literature review examines the development of research approaches to studying residential care practices, from qualitative descriptive studies to quantitative comparative studies. The difficulty of definition and measurement in high-quality residential care is discussed. Findings are presented from an ethnographic study of care structure and process, and the experience of staff and clients, conducted in two residential care settings. Anomalies are reported in the use of quantitative and qualitative research methods. There is a discussion of methodological issues that arise from anomalous findings.

Adult↗
PubMed1993

Genetic algorithms: principles of natural selection applied to computation.

A genetic algorithm is a form of evolution that occurs on a computer. Genetic algorithms are a search method that can be used for both solving problems and modeling evolutionary systems. With various mapping techniques and an appropriate measure of fitness, a genetic algorithm can be tailored to evolve a solution for many types of problems, including optimization of a function of determination of the proper order of a sequence. Mathematical analysis has begun to explain how genetic algorithms work and how best to use them. Recently, genetic algorithms have been used to model several natural evolutionary systems, including immune systems.

Algorithms↗
PubMed1993

A new codon 15 rhodopsin gene mutation in autosomal dominant retinitis pigmentosa is associated with sectorial disease.

OBJECTIVE: To ascertain and characterize rhodopsin gene mutations in autosomal dominant retinitis pigmentosa and to correlate these mutations with the clinical phenotypes. METHODS: DNA was extracted from leukocytes, and the rhodopsin gene was amplified and analyzed using molecular-biological methods. Clinical and electrophysiological data were collected from patient charts. RESULTS: We found a disease-causing mutation that was previously undescribed, to our knowledge, for autosomal dominant retinitis pigmentosa within codon 15 of exon 1 of the rhodopsin gene. It was a single base-pair transversion (AAT to AGT) leading to a serine-for-asparagine substitution. This altered a glycosylation site in the intradiscal portion of the rhodopsin molecule. The pedigree examined demonstrated an inferior distribution of retinal pigmentary changes and predominantly superior visual field loss with relative preservation of electroretinographic amplitudes and good vision, which is consistent with sectorial or sectorial-like retinitis pigmentosa. CONCLUSIONS: A codon 15 rhodopsin gene mutation caused retinitis pigmentosa in the pedigree studied. There may be an association between intradiscal rhodopsin gene mutations and sectorial forms of retinitis pigmentosa.

Adult↗
PubMed1993

Analysis of sequence contexts flanking T.G mismatches leads to predictions about reactivity of the mismatched T to osmium tetroxide.

Osmium tetroxide and hydroxylamine are used to detect mutations in DNA and RNA after hybridization of mutant and wild-type DNA. Mismatched T and C bases, respectively, are modified by these reagents and the DNA strand cleaved at the mismatched bases by subsequent treatment with piperidine. This allows detection and location of the mutation. Although most T.G mismatches have been reported to be reactive to osmium tetroxide, some have been reported to be unreactive. The aim of this study was to collect and analyze the reactive and unreactive T.G mismatches. We have collected sequence contexts of all reactive and unreactive T.G mismatches for analysis. This involves 10 unreactive T.G mismatches (plus one T.C) and 19 reactive T.G mismatches. Sequence effects of bases surrounding these mismatches must influence this reactivity. There must be many types of such sequence effects. We postulate that because of the dominance of 5' G bases near the T of unreactive T.G mismatches and the absence of 5' G bases in reactive T.G mismatches that the stacking of the 5' G on the mismatched T is the reason for this lack of reactivity in the majority of the cases studied here.

Base Sequence↗
PubMed1993

Finger prick blood testing in Leber hereditary optic neuropathy.

Individuals from 33 unrelated Australian families with optic atrophy were screened for 10 different single base alterations in mitochondrial DNA (mtDNA) associated with Leber hereditary optic neuropathy (LHON) using direct polymerase chain reaction amplification of blood spots collected on Guthrie cards. This method using blood spots allows easily accessible screening for LHON mtDNA mutations with minimal biohazard risk and reduced expense in the storage and transport of specimens.

Base Sequence↗
PubMed1993

Genetic algorithms for DNA sequence assembly.

This paper describes a genetic algorithm application to the DNA sequence assembly problem. The genetic algorithm uses a sorted order representation for representing the orderings of fragments. Two different fitness functions, both based on pairwise overlap strengths between fragments, are tested. The paper concludes that the genetic algorithm is a promising method for fragment assembly problems, achieving usable solutions quickly, but that the current fitness functions are flawed and that other representations might be more appropriate.

Algorithms↗
PubMed1990

Methods of detection of single base substitutions in clinical genetic practice.

The ability to diagnose human diseases at the DNA level has become possible because of a rapid development in DNA technology, particularly in the area of detection of single base substitutions. Mutations in the genomic DNA of a particular gene may be inferred indirectly using linkage analysis and restriction fragment length polymorphisms. However, direct detection of the mutation is the more favourable approach. The advent of the polymerase chain reaction to amplify specific regions of genomic DNA or mRNA has enhanced the speed and sensitivity of many of the screening and diagnostic procedures. Screening methods have been developed that will detect at least 70% and, with some methods, close to 100% of all mutations. The methods include ribonuclease A cleavage, denaturing gradient gel electrophoresis, chemical cleavage of mismatch and direct sequencing. Choice of method is based on a number of factors and will depend on the structure of the gene to be analysed. Following identification of a mutation using one of the screening procedures, prenatal diagnosis and carrier testing can be offered. The overall aim is to develop a method that has the potential to determine the mutation present in an index case of a previously untested family in a few days, thus allowing any other relevant family member to be tested.

Base Composition↗
PubMed1989

Possibilities and limitation of prenatal diagnosis and carrier determination for Duchenne and Becker muscular dystrophy using cDNA probes.

Two cDNA probes, cf23a and cf56a, identify deletions of selected exons in about 50% of our DMD/BMD patients. We have estimated the most likely order of the 11 exons detectable with both probes with respect to the different extensions of the deletions. In one of our BMD pedigrees, the observed deletion could be traced in the affected males through three generations. This result shows that with the use of cDNA probes detecting deletions, the only risk of error in genomic prenatal diagnosis is the general high frequency of new mutations for DMD/BMD. This is important progress in diagnosis compared to the 2 to 5% risk of misdiagnosis because of crossing over events using conventional linkage analysis with bridging or intragenic probes. The first prenatal diagnosis of an unaffected fetus of a woman who is a DMD carrier according to ultrasound examination is described. In one of our DMD males, the cDNA probe cf56a detects a deletion breakpoint. His sister also shows the altered band and is therefore a DMD carrier, while his mother has a totally normal band pattern. The interpretation of this observation could be either germline mosaicism or two identical new mutations. The identification of deletion breakpoints is a new diagnostic strategy, especially for carrier determination, which excludes misdiagnosis owing to crossing over events and the problems of dosage estimation. It is, however, limited by the low frequency of breakpoints detectable with cDNA probes. Therefore, the generation of new intron probes in this region is an important goal.

Chromosome Deletion↗