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J R Yates

Publications and source records attributed to J R Yates.

At least 109 records · Page 6Linked to original sources
PubMed1997

Direct analysis of protein mixtures by tandem mass spectrometry.

Methods to identify proteins contained in mixtures are described. The approach uses microcolumn liquid chromatography and automated tandem mass spectrometry in conjunction with protein and nucleotide database searching algorithms. This approach is applied to the identification of proteins obtained by immunoprecipitation reactions, interaction with a GST protein fusion products and interaction with a macromolecular complex.

Chromatography, Liquid↗
PubMed1997

Female germline mosaicism in tuberous sclerosis confirmed by molecular genetic analysis.

We have investigated a family in which three siblings with the autosomal dominant disorder tuberous sclerosis had unaffected parents. The family were typed for polymorphic markers spanning the two genes known to cause tuberous sclerosis located at 9q34 (TSC1) and 16p13.3 (TSC2). TSC1 markers showed different maternal and paternal haplotypes in affected children, excluding a mutation in TSC1 as the cause of the disease. For the TSC2 markers all the affected children had the same maternal and paternal haplotypes, as did three of their unaffected siblings. Mutation screening by RT-PCR and direct sequencing of the TSC2 gene identified a 4 bp insertion TACT following nucleotide 2077 in exon 18 which was present in the three affected children but not in five unaffected siblings or the parents. This mutation would cause a frameshift and premature termination at codon 703. Absence of the mutation in lymphocyte DNA from the parents was consistent with germline mosaicism and this was confirmed by our finding of identical chromosome 16 haplotypes in affected and unaffected siblings, providing unequivocal evidence of two different cell lines in the gametes. Molecular analysis of the TSC2 alleles present in the affected subjects showed that the mutation had been inherited from the mother. This is the first case of germline mosaicism in tuberous sclerosis proven by molecular genetic analysis and also the first example of female germline mosaicism for a characterized autosomal dominant gene mutation apparently not associated with somatic mosaicism.

Adult↗
PubMed1997

Mutations in the TSC2 gene: analysis of the complete coding sequence using the protein truncation test (PTT).

Mutations in the TSC2 gene on chromosome 16p13.3 are responsible for approximately 50% of familial tuberous sclerosis (TSC). The gene has 41 small exons spanning 45 kb of genomic DNA and encoding a 5.5 kb mRNA. Large germline deletions of TSC2 occur in <5% of cases, and a number of small intragenic mutations have been described. We analysed mRNA from 18 unrelated cases of TSC for TSC2 mutations using the protein truncation test (PTT). Three cases were predicted to be TSC2 mutations on the basis of linkage analysis or because a hamartoma from the patient showed loss of heterozygosity for 16p13.3 markers. Three overlapping PCR products, covering the complete coding sequence of mRNA, were generated from lymphoblastoid cell lines, translated into 35S-methionine labelled protein, and analysed by SDS-PAGE. PCR products showing PTT shifts were directly sequenced, and mutations confirmed by restriction enzyme digestion where possible. Six PTT shifts were identified. Five of these were caused by mutations predicted to produce a truncated protein: (i) a sporadic case showed a 32 bp deletion in exon 11, and a mutant mRNA without exon 11 was produced; the normal exon 10 was also spliced out; (ii) a sporadic case had a 1 bp deletion in exon 12 (1634delT); (iii) a TSC2-linked mother and daughter pair had a G-->T transversion in exon 23 (G2715T) introducing a cryptic splice site causing a 29 bp truncation of mRNA from exon 23; (iv) a sporadic case showed a 2 bp deletion in exon 36; (v) a sporadic case showed a 1 bp insertion disrupting the donor splice site of exon 37 (5007+2insA), resulting in the use of an upstream exonic cryptic splice site to cause a 29 bp truncation of mRNA from exon 37. In one case, the PTT shift was explained by in-frame splicing out of exon 10, in the presence of a normal exon 10 genomic sequence. Alternative splicing of exon 10 of the TSC2 gene may be a normal variant. Three 3rd base substitution polymorphisms were also detected during direct sequencing of PCR products. Confirmed mutations were identified in 28% of the families studied and on the assumption that half of the sporadic cases should have TSC2 mutations, a crude estimate of the detection rate would be 60%. This compares favourably with other screening methods used for TSC2, notably SSCP, and since PTT involves much less work it may be the method of choice.

Alternative Splicing↗
PubMed1997

Instability of normal (CTG)n alleles in the DM kinase gene.

We report on a myotonic dystrophy (DM) family exhibiting instability of normal sized (CTG)n alleles in the DM kinase gene on the non-DM chromosome. At least two mutational events involving normal DM alleles must have occurred in this family; one was characterised as a 34-35 (CTG)n repeat mutation. These findings represent a dissociation between (CTG)n repeat instability and myotonic dystrophy. Furthermore, this family highlights genetic counselling issues relating to the pathogenicity of alleles at the upper end of the normal size range and the risk of further expansion into the disease range.

Adult↗
PubMed1997

Genetic linkage to the collagen alpha 1 (V) gene (COL5A1) in two British Ehlers-Danlos syndrome families with variable type I and II phenotypes.

To investigate the role of COL5A1 as a candidate gene for Ehlers-Danlos syndrome (EDS), we have carried out linkage studies in two large British families with EDS type I/II and type II, respectively. Fourteen living, affected individuals were identified by family history, clinical examination and ultrastructural analysis. A polymorphic intragenic simple sequence repeat at the COL5A1 locus showed linkage to EDS without recombination to give a combined lod score of 5.7. We have previously reported linkage to COL5A1 in an EDS type I/II family which brings the total lod score to 9.8 at zero recombination. Taken together, these data implicate COL5A1 as an important cause of EDS and confirm that types I and II are allelic.

Collagen↗
PubMed1996

Analysis of naturally processed peptides eluted from HLA DRB1*0402 and *0404.

Understanding the structural features of naturally processed peptides found within the major histocompatibility complex (MHC) class II peptide binding groove from disease-associated MHC molecules may provide insights into the nature of potential disease-related antigens. Class II MHC/peptide complexes were purified by immunoaffinity from transformed B cell lines homozygous for DRB1*0404 (an allele associated with rheumatoid arthritis) and *0402 (a closely related allele not associated with this disease). Peptides were eluted at acidic pH, fractionated by reversed phase HPLC, and analyzed by capillary electrophoresis. Those fractions containing a single dominant peptide were sequenced by automated Edman degradation and tandem mass spectrometry. The predominant peptide species identified came from non-polymorphic regions of the HLA class I molecules expressed by each cell line. Peptides from DRB1*0404 were found to be nested clusters derived from positions 26-43 of the HLA-B and -C alpha-chain. DRB1*0402 contained as the predominant peptide species a nested cluster from positions 129-145 of the HLA-B alpha-chain. The primary structure of the class I derived peptides was consistent with that seen by peptides exhibiting promiscuous DR binding behavior. Processing of MHC-derived peptides by MHC class II molecules is a common occurrence in the transformed B cell lines analyzed.

B-Lymphocytes↗
PubMed1996

Identification of phosphorylation sites of human 85-kDa cytosolic phospholipase A2 expressed in insect cells and present in human monocytes.

The phosphorylation sites on the human, 85-kDa cytosolic phospholipase A2 (cPLA2) were identified using recombinant cPLA2 expressed in Spodoptera frugiperda (Sf9) cells. Analysis by high performance liquid chromatography of tryptic digests of 32P-labeled recombinant cPLA2 showed four major peaks of radiolabeled phosphopeptides. The phosphorylated residues were identified as Ser-437, Ser-454, Ser-505, and Ser-727 using mass spectrometry and automated Edman sequencing. Sf9 cells infected with recombinant virus expressing cPLA2 exhibited a time-dependent release of arachidonic acid in response to the calcium ionophore A23187 or the protein phosphatase inhibitor okadaic acid, which was not observed in Sf9 cells infected with wild-type virus. Stimulation of Sf9 cells with A23187 and okadaic acid also increased the level of phosphorylation of cPLA2. Okadaic acid, but not A23187, induced a gel shift of cPLA2 and increased the level of phosphorylation of Ser-727 by 4.5-fold, whereas the level of phosphorylation of the other sites increased by 60% or less in response to both agonists. To determine whether the same sites on cPLA2 were phosphorylated in mammalian cells, human monocytes were studied. Okadaic acid stimulation of monocytes induced a gel shift of cPLA2, increased the release of arachidonic acid, and increased the level of phosphorylation of cPLA2 on serine residues. Comparison of two-dimensional peptide maps of tryptic digests of 32P-labeled recombinant cPLA2 and human monocyte cPLA2 demonstrated that the same peptides on cPLA2 were phosphorylated in mammalian cells as in insect cells. These results show that the Sf9-baculovirus expression system is useful for investigation of the phosphorylation sites on cPLA2. The results also suggest that phosphorylation of the cPLA2 by protein kinases other than mitogen-activated protein kinase may be important for the regulation of arachidonic acid release.

Amino Acid Sequence↗
PubMed1996

Mixture analysis using a quadrupole mass filter/quadrupole ion trap mass spectrometer.

A hybrid tandem mass spectrometer is constructed by interfacing a quadrupole mass filter (Q) to a quadrupole ion trap mass spectrometer (QITMS) and is evaluated for the analysis of mixtures. The mass filter is set to selectively inject ions of a particular m/z or, in scanning mode, to sequentially inject ions into the QITMS for subsequent manipulation and detection. Performance of the instrument is demonstrated using a mixture of ions created by electron impact ionization of perfluorotributylamine (FC-43) and peptide ions generated by pulsed Cs+ bombardment. Resulting data are compared to those obtained by utilizing only the ion trap. Molecular weight, fragmentation, and high-resolution analyses for the sequentially injected mass-filtered peptides show improved performance over similar measurements employing only the ion trap mass spectrometer. Performance is optimized when ions are not rf-isolated in the QITMS. Using the hybrid, a resolution of 33,200 is achieved for angiotensin I. Dramatic reduction of space charge-induced signal suppression is demonstrated for LSIMS of Glu-fibrinopeptide B. 'On-the-fly' collision-induced dissociation is performed for m/z 502 from FC-43, where fragmentation is induced by increasing the ion injection energy. Collision-induced dissociation efficiencies for fragmentation of angiotensin I by resonance excitation are investigated as a function of cooling time for different modes of operation of the hybrid. A current limitation of the instrument is the time required to port the data for acquisition.

Amino Acid Sequence↗
PubMed1996

Clinical features in affected males with X-linked retinoschisis.

OBJECTIVES: To assess the phenotypic variation and visual prognosis of affected males with X-linked retinoschisis. DESIGN: Patients were ascertained from clinical geneticists and ophthalmologists in the United Kingdom. Genetic linkage analysis was carried out using polymorphic microsatellite markers from the Xp22 region of the X chromosome. PATIENTS: Fifty-six males from 16 British families with X-linked retinoschisis. RESULTS: Best-corrected visual acuity ranged from 20/20 to 20/600; 14 (25%) of the patients saw 20/40 or better, and 27 (55%) read N6 or better. Visual acuity was poorer in older patients (chi 2 =30.4, df=4, P<.001). Macular abnormalities were seen in all eyes. Foveal schisis was the most common abnormality seen in patients younger than 40 years (73 eyes [83%]), but in older patients a blunted foveal reflex or pigmentary atrophy was more common (17 eyes [85%]). Peripheral retinoschisis was seen in 40 (71%) of the patients. Vitreous hemorrhage occurred in 12 (21%) and retinal detachment in nine (16%) of the patients. Four eyes were blind as a result of retinal detachment. CONCLUSIONS: Although no evidence exists for genetic heterogeneity in X- linked retinoschisis, there is wide phenotypic variation. The most serious sight-threatening complications are vitreous hemorrhage and retinal detachment. In uncomplicated cases, the prognosis for vision is good, although deterioration of vision occurs in the fourth and fifth decades of life because of macular atrophy.

Adolescent↗
PubMed1996

Clonality of tuberous sclerosis harmatomas shown by non-random X-chromosome inactivation.

Tuberous sclerosis (TSC) is an autosomal dominant condition characterised by tumour-like malformations (hamartomas) in the brain and other organs. A proportion of hamartomas from patients with TSC show loss of heterozygosity (LOH) for DNA markers in the region of either the TSC1 gene on chromosome 9q34 or the TSC2 gene on 16p13.3. This implies that these lesions are clonal. We have studied X-chromosome inactivation, as a marker of clonality, in 13 hamartomas from females with TSC. The hamartomas comprised five renal angiomyolipomas, three fibromas and seven other lesions. In previous studies, four of the lesions showed LOH. A polymerase chain reaction assay was used to analyse differential methylation of an HpaII restriction site adjacent to the androgen-receptor triplet-repeat polymorphism on Xq11-12. In 12 of the lesions, there was a skewed inactivation pattern with one X chromosome being fully methylated and the other unmethylated. Normal tissue showed a random pattern of inactivation. These data confirm that most TSC hamartomas are clonal in origin. This is an intriguing finding, since these lesions are composed of more than one cell type.

Angiomyolipoma↗
PubMed1996

Protein identification by solid phase microextraction-capillary zone electrophoresis-microelectrospray-tandem mass spectrometry.

We describe an analytical system for the rapid identification of proteins by correlation of tandem mass spectra with protein sequence databases. The system consists of an integrated solid phase microextraction/capillary zone electrophoresis peptide separation device that is connected through a microelectrospray ion source to a tandem mass spectrometer. The limits of detection are 660 amol of sample at a concentration limit of < 33 amol/microliters for peptide mass measurement, and < 10 fmol of sample, at a concentration limit of < 300 amol/microliters for peptide analysis by collision-induced dissociation. Using this system, we have identified low nanogram amounts of yeast proteins separated by high-resolution two-dimensional gel electrophoresis.

Databases, Factual↗
PubMed1996

Future prospects for the analysis of complex biological systems using micro-column liquid chromatography-electrospray tandem mass spectrometry.

An overview is provided of methods for the study of complex biological processes by using micro-column liquid chromatography-electrospray ionization tandem mass spectrometry. Procedures discussed include electrospray ionization, micro-column liquid chromatography, tandem mass spectrometry, tandem mass spectra data interpretation for peptides, and database searching with mass spectral data. Several problems in immunology are discussed to illustrate this approach.

Amino Acid Sequence↗
PubMed1996

A family with Stickler syndrome type 2 has a mutation in the COL11A1 gene resulting in the substitution of glycine 97 by valine in alpha 1 (XI) collagen.

Stickler syndrome (hereditary arthro-ophthalmopathy) is the commonest inherited cause of retinal detachment and one of the commonest autosomal dominant connective tissue dysplasias. There is clinical and locus heterogeneity with about two thirds of families linked to the gene encoding type II procollagen (COL2A1). Families with Sticklers syndrome type 1 have a characteristic congenital vitreous anomaly and are linked without recombination to markers at the COL2A1 locus. In contrast families with the type 2 variety have a different vitreo-retinal phenotype and are not linked to the COL2A1 gene. Type XI collagen is a quantitatively minor fibrillar collagen related to type V collagen and associated with the more abundant type II collagen fibrils. A mutation in COL11A2, the gene for alpha 2 (XI) procollagen, has recently been found in a family described as having Stickler syndrome, although there was no ocular involvement. Here we show for the first time that a family with the full Type 2 Stickler syndrome including vitreous and retinal abnormalities is linked to the COL11A1 gene and characterise the mutation as a Glycine to Valine substitution at position 97 of the triple helical domain caused by a single base G-->T mutation. These results are the first to provide confirmation that type XI collagen is an important structural component of human vitreous. They also support previous work suggesting that mutations in the genes encoding collagen XI can give rise to some manifestations of Stickler syndrome, but of these, only mutations in COL11A1 will give the full syndrome including the vitreo-retinal features.

Collagen↗
PubMed1996

The gene encoding collagen alpha1(V)(COL5A1) is linked to mixed Ehlers-Danlos syndrome type I/II.

The Ehlers-Danlos syndrome (EDS) is a heterogeneous group of inherited connective tissue disorders in which cutaneous fragility and ligamentous laxity often combine with vascular, gastrointestinal, and skeletal deformities. There is considerable phenotypic overlap between the more common forms of EDS (types I and II), in which specific molecular defects have not yet been identified. Recently, genetic linkage has been demonstrated between the COL5A1 gene, which encodes the alphal chain of type V collagen, and EDS type II in a large British kindred. Using a polymorphic intragenic simple sequence repeat at the COL5A1 locus, we now demonstrate tight linkage to EDS type I/II in a three-generation family, giving a LOD score (log10 of the odds for linkage) of 4.07 at zero recombination. The variation in expression in this family suggests that EDS types I and II are allelic, and the linkage data support the hypothesis that mutation in COL5A1 can cause both phenotypes.

Aged↗