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Biomedical subjects

A W Johnson

Publications and source records attributed to A W Johnson.

At least 37 records · Page 2Linked to original sources

Inhibition of mRNA turnover in yeast by an xrn1 mutation enhances the requirement for eIF4E binding to eIF4G and for proper capping of transcripts by Ceg1p.

Null mutants of XRN1, encoding the major cytoplasmic exoribonuclease in yeast, are viable but accumulate decapped, deadenylated transcripts. A screen for mutations synthetic lethal with xrn1Delta identified a mutation in CDC33, encoding eIF4E. This mutation (glutamate to glycine at position 72) affected a highly conserved residue involved in interaction with eIF4G. Synthetic lethality between xrn1 and cdc33 was not relieved by high-copy expression of eIF4G or by disruption of the yeast eIF4E binding protein Caf20p. High-copy expression of a mutant eIF4G defective for eIF4E binding resulted in a dominant negative phenotype in an xrn1 mutant, indicating the importance of this interaction in an xrn1 mutant. Another allele of CDC33, cdc33-1, along with mutations in CEG1, encoding the nuclear guanylyltransferase, were also synthetic lethal with xrn1Delta, whereas mutations in PRT1, encoding a subunit of eIF3, were not. Mutations in CDC33, CEG1, PRT1, PAB1, and TIF4631, encoding eIF4G1, have been shown to lead to destabilization of mRNAs. Although such destabilization in cdc33, ceg1, and pab1 mutants can be partially suppressed by an xrn1 mutation, we observed synthetic lethality between xrn1 and either cdc33 or ceg1 and no suppression of the inviability of a pab1 null mutation by xrn1Delta. Thus, the inhibition of mRNA turnover by blocking Xrn1p function does not suppress the lethality of defects upstream in the turnover pathway but it does enhance the requirement for (7)mG caps and for proper formation of the eIF4E/eIF4G cap recognition complex.

Cell Nucleus↗

Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p.

The RAT1 gene of Saccharomyces cerevisiae encodes a 5'-->3' exoribonuclease which plays an essential role in yeast RNA degradation and/or processing in the nucleus. We have cloned a previously uncharacterized gene (YGL246c) that we refer to as RAI1 (Rat1p interacting protein 1). RAI1 is homologous to Caenorhabditis elegans DOM-3 and human DOM3Z. Deletion of RAI1 confers a growth defect which can be complemented by an additional copy of RAT1 on a centromeric vector or by directing Xrn1p, the cytoplasmic homolog of Rat1p, to the nucleus through the addition of a nuclear targeting sequence. Deletion of RAI1 is synthetically lethal with the rat1-1(ts) mutation and shows genetic interaction with a deletion of SKI2 but not XRN1. Polysome analysis of an rai1 deletion mutant indicated a defect in 60S biogenesis which was nearly fully reversed by high-copy RAT1. Northern blot analysis of rRNAs revealed that rai1 is required for normal 5.8S processing. In the absence of RAI1, 5.8S(L) was the predominant form of 5.8S and there was an accumulation of 3'-extended forms but not 5'-extended species of 5. 8S. In addition, a 27S pre-rRNA species accumulated in the rai1 mutant. Thus, deletion of RAI1 affects both 5' and 3' processing reactions of 5.8S rRNA. Consistent with the in vivo data suggesting that RAI1 enhances RAT1 function, purified Rai1p stabilized the in vitro exoribonuclease activity of Rat1p.

Amino Acid Sequence↗

Screening of newborn infants for cholestatic hepatobiliary disease with tandem mass spectrometry.

OBJECTIVE: To assess the feasibility of screening for cholestatic hepatobiliary disease and extrahepatic biliary atresia by using tandem mass spectrometry to measure conjugated bile acids in dried blood spots obtained from newborn infants at 7-10 days of age for the Guthrie test. SETTING: Three tertiary referral clinics and regional neonatal screening laboratories. DESIGN: Unused blood spots from the Guthrie test were retrieved for infants presenting with cholestatic hepatobiliary disease and from the two cards stored on either side of each card from an index child. Concentrations of conjugated bile acids measured by tandem mass spectrometry in the two groups were compared. MAIN OUTCOME MEASURES: Concentrations of glycodihydroxycholanoates, glycotrihydroxycholanoates, taurodihydroxycholanoates, and taurotrihydroxycholanoates. Receiver operator curves were plotted to determine which parameter (or combination of parameters) would best predict the cases of cholestatic hepatobiliary disease and extrahepatic biliary atresia. The sensitivity and specificity at a selection of cut off values for each bile acid species and for total bile acid concentrations for the detection of the two conditions were calculated. RESULTS: 218 children with cholestatic hepatobiliary disease were eligible for inclusion in the study. Two children without a final diagnosis and five who presented at <14 days of age were excluded. Usable blood spots were obtained from 177 index children and 708 comparison children. Mean concentrations of all four bile acid species were significantly raised in children with cholestatic hepatobiliary disease and extrahepatic biliary atresia compared with the unaffected children (P<0.0001). Of 177 children with cholestatic hepatobiliary disease, 104 (59%) had a total bile acid concentration >33 micromol/l (97.5th centile value for comparison group). Of the 61 with extrahepatic biliary atresia, 47 (77%) had total bile acid concentrations >33 micromol/l. Taurotrihydroxycholanoate and total bile acid concentrations were the best predictors of both conditions. For all cholestatic hepatobiliary disease, a cut off level of total bile acid concentration of 30 micromol/l gave a sensitivity of 62% and a specificity of 96%, while the corresponding values for extrahepatic biliary atresia were 79% and 96%. CONCLUSION: Most children who present with extrahepatic biliary atresia and other forms of cholestatic hepatobiliary disease have significantly raised concentrations of conjugated bile acids as measured by tandem mass spectrometry at the time when samples are taken for the Guthrie test. Unfortunately the separation between the concentrations in these infants and those in the general population is not sufficient to make mass screening for cholestatic hepatobiliary disease a feasible option with this method alone.

Age Factors↗

The identification of unusual bile acid metabolites by tandem mass spectrometry: use of low-energy collision-induced dissociation to produce informative spectra.

The use of collision-induced dissociation (CID) tandem mass spectrometry (MS/MS) has been shown to produce fragmentation that is useful for the structural analysis of bile acids and their conjugates. Low-energy CID using a triple quadrupole has been used to help characterise bile acid identity but the majority of work has been conducted using high-energy CID on specialised instrumentation. This paper describes the use of low-energy CID as a rapid method for identification of urinary bile acids and presents some examples of its use in the diagnosis of liver disease in infants. These include the differential diagnosis of peroxisomal disorders, identification of compounds (e.g. 3 beta,7 alpha-dihydroxy-5-cholenoic acid 3-sulphate) indicative of 3 beta-hydroxy-delta 5-C27-steroid dehydrogenase/isomerase deficiency and the confirmation of the identity of an unusual bile acid series consisting of different conjugates of lithocholic acid. The use of lithium cationisation and derivatisation with aminosulfonic acids for the analysis of unconjugated and glycine-conjugated bile acids has also been evaluated.

Bile Acids and Salts↗

NMD3 encodes an essential cytoplasmic protein required for stable 60S ribosomal subunits in Saccharomyces cerevisiae.

A mutation in NMD3 was found to be lethal in the absence of XRN1, which encodes the major cytoplasmic exoribonuclease responsible for mRNA turnover. Molecular genetic analysis of NMD3 revealed that it is an essential gene required for stable 60S ribosomal subunits. Cells bearing a temperature-sensitive allele of NMD3 had decreased levels of 60S subunits at the nonpermissive temperature which resulted in the formation of half-mer polysomes. Pulse-chase analysis of rRNA biogenesis indicated that 25S rRNA was made and processed with kinetics similar to wild-type kinetics. However, the mature RNA was rapidly degraded, with a half-life of 4 min. Nmd3p fractionated as a cytoplasmic protein and sedimented in the position of free 60S subunits in sucrose gradients. These results suggest that Nmd3p is a cytoplasmic factor required for a late cytoplasmic assembly step of the 60S subunit but is not a ribosomal protein. Putative orthologs of Nmd3p exist in Drosophila, in nematodes, and in archaebacteria but not in eubacteria. The Nmd3 protein sequence does not contain readily recognizable motifs of known function. However, these proteins all have an amino-terminal domain containing four repeats of Cx2C, reminiscent of zinc-binding proteins, implicated in nucleic acid binding or protein oligomerization.

Amino Acid Sequence↗

Application of magnetic chromatography to the isolation of lysosomes from fibroblasts of patients with lysosomal storage disorders.

A method for the purification of lysosomes from fibroblasts has been developed which uses endocytosis of superparamagnetic colloidal iron dextran particles followed by separation of the iron-containing lysosomes in a magnetic field. This permitted isolation of lysosomes from fibroblasts from patients with infantile sialic acid storage disorder and other lysosomal storage diseases in which a shift in lysosomal density induced by the storage material prevents purification by centrifugation in a Percoll gradient. The magnetic lysosomes isolated from these cells are very similar to those from normal cells as judged by lysosomal marker enzyme activity and 2D-PAGE analysis of the enriched proteins.

Cell Fractionation↗

Mutational analysis of exoribonuclease I from Saccharomyces cerevisiae.

Exoribonuclease I from yeast is a 175 kDa protein that is responsible for the majority of cytoplasmic mRNA degradation. Alignment of the Xrn1p sequence with homologs from yeast as well as from higher eukaryotes suggests that the protein is composed of several domains: two acidic N-terminal domains which likely contain the exonuclease, a basic middle domainand a basic C-terminal domain. Deletion analysisdemonstrated that the C-terminus is dispensable for most in vivo and in vitro functions but confers a dominant negative growth inhibition when expressed at high levels. This growth inhibition is not due to the exonuclease function of the protein. To identify specific residues responsible for in vivo function, a screen was carried out for non-complementing missense mutations. Fourteen single point mutations were identified that altered highly conserved amino acids within the first N-terminal domain of Xrn1p. All of the mutations reduced exonuclease activity measured in vivo and in vitro using affinity-purified proteins. The mutants fell into two phenotypic classes, those that reduced or abolished exonuclease activity without qualitatively changing the products of RNA degradation and those that gave rise to novel degradation intermediates on certain RNAs.

Amino Acid Sequence↗

Screening for medium chain acyl-CoA dehydrogenase deficiency using electrospray ionisation tandem mass spectrometry.

OBJECTIVE: To establish criteria for the diagnosis of medium chain acyl-CoA dehydrogenase (MCAD) deficiency in the UK population using a method in which carnitine species eluted from blood spots are butylated and analysed by electrospray ionisation tandem mass spectrometry (ESI-MS/MS). DESIGN: Four groups were studied: (1) 35 children, aged 4 days to 16.2 years, with proven MCAD deficiency (mostly homozygous for the A985G mutation, none receiving carnitine supplements); (2) 2168 control children; (3) 482 neonates; and (4) 15 MCAD heterozygotes. RESULTS: All patients with MCAD deficiency had an octanoylcarnitine concentration ([C8-Cn]) > 0.38 microM and no accumulation of carnitine species > C10 or < C6. Among the patients with MCAD deficiency, the [C8-Cn] was significantly lower in children > 10 weeks old and in children with carnitine depletion (free carnitine < 20 microM). Neonatal blood spots from patients with MCAD deficiency had a [C8-Cn] > 1.5 microM, whereas in heterozygotes and other normal neonates the [C8-Cn] was < 1.0 microM. In contrast, the blood spot [C8-Cn] in eight of 27 patients with MCAD deficiency > 10 weeks old fell within the same range as five of 15 MCAD heterozygotes (0.38-1.0 microM). However, the free carnitine concentrations were reduced (< 20 microM) in the patients with MCAD deficiency but normal in the heterozygotes. CONCLUSIONS: Criteria for the diagnosis of MCAD deficiency using ESI-MS/MS must take account of age and carnitine depletion. If screening is undertaken at 7-10 days, the number of false positive and negative results should be negligible. Because there have been no instances of death or neurological damage following diagnosis of MCAD deficiency in our patient group, a strong case can be made for neonatal screening for MCAD deficiency in the UK.

Acyl-CoA Dehydrogenase↗

A method for the quantitation of conjugated bile acids in dried blood spots using electrospray ionization-mass spectrometry.

Bile acid concentrations are elevated in the blood of neonates with cholestatic hepatobiliary disorders providing a possible means of screening for treatable conditions including biliary atresia. A method is described for the determination of concentrations of conjugated bile acids in dried blood spots using electrospray ionization mass spectrometry. Bile acids were eluted from the blood spots using methanol containing, as internal standards, the taurine and glycine conjugates of D4-chenodeoxycholic acid and D4-cholic acid. The samples were then reconstituted in acetonitrile/water and injected by autosampler into the electrospray source operating in negative ion mode. Optimal conditions were determined for both single quadrupole and tandem mass spectrometry analysis. Blood spot bile acid profiles were studied in two groups of infants (< 1 y), a cholestatic group (conjugated bilirubin > 25 mumol/L; n = 49), and a control group (n = 96). The best discrimination between the two groups was provided by measurements of taurodihydroxycholanoates (normal < 5 mumol/L; cholestatic group 18-94 mumol/L) and glycodihydroxycholanoates (normal < 5 mumol/L; cholestatic group 11-66 mumol/L). The method can also be adapted to detect unusual bile acids which are diagnostic of inborn errors of bile acid synthesis and peroxisomal disorders. The method is fast, reliable, reproducible, and relatively cheap; however, much more work is required to determine whether it can be used for mass screening for cholestasis. It will be necessary to show that measurement of bile acid concentrations in blood spots obtained at 7-10 d can be used to detect infants who currently present with jaundice, pale stools, and dark urine during the first 6 mo of life.

Bile Acids and Salts↗

Solitary adenocarcinoma metastasis mimicking sarcomatous degeneration in Paget's disease.

A rare case of mucinous adenocarcinoma presented as a solitary, metastatic deposit to a region of Paget's disease within the peripheral skeleton. Historical, physical, radiographic, and scintigraphic findings were indistinguishable from those of sarcomatous degeneration arising from pagetoid bone. This case supports the idea that when a painful, osteolytic lesion is discovered within a region of Paget's disease, bone scintigraphy has greater value of disclosing potential multifocal or multicentric disease than for providing etiologic specificity for the principal lesion.

Adenocarcinoma, Mucinous↗

Rat1p and Xrn1p are functionally interchangeable exoribonucleases that are restricted to and required in the nucleus and cytoplasm, respectively.

XRN1 encodes an abundant cytoplasmic exoribonuclease, Xrn1p, responsible for mRNA turnover in yeast. A screen for bypass suppressors of the inviability of xrn1 ski2 double mutants identified dominant alleles of RAT1, encoding an exoribonuclease homologous with Xrn1p. These RAT1 alleles restored XRN1-like functions, including cytoplasmic RNA turnover, wild-type sensitivity to the microtubule-destabilizing drug benomyl, and sporulation. The mutations were localized to a region of the RAT1 gene encoding a putative bipartite nuclear localization sequence (NLS). Fusions to green fluorescent protein were used to demonstrate that wild-type Rat1p is localized to the nucleus and that the mutant alleles result in mislocalization of Rat1p to the cytoplasm. Conversely, targeting Xrn1p to the nucleus by the addition of the simian virus 40 large-T-antigen NLS resulted in complementation of the temperature sensitivity of a rat1-1 strain. These results indicate that Xrn1p and Rat1p are functionally interchangeable exoribonucleases that function in and are restricted to the cytoplasm and nucleus, respectively. It is likely that the higher eukaryotic homologs of these proteins will function similarly in the cytoplasm and nucleus.

Amino Acid Sequence↗

Acute bronchiolitis in tropical Africa: a hospital-based perspective in Ibadan, Nigeria.

In a 30-month prospective study of severe acute lower respiratory infections in hospitalized pre-school Nigerian children, acute bronchiolitis was diagnosed in 67 cases; 19 (28.4%) and 2 (3.0%) of these had concomitant pneumonia or croup, respectively. The peak prevalence was in the wet (rainy) season (May-October). The male/female (M:F) ratio in infants < or = 6 months was 2.9:1, differing significantly from the 1.1:1 in older subjects (P = 0.04). None of the subjects had severe malnutrition. Neither a high fever (> or = 39 degrees C), nor tachypnea on admission was significantly correlated with co-existing pneumonia. Of the 29 subjects in whom it was possible to explore viral immunofluorescence studies and/or serodiagnosis, we identified 26 viral identifications in 18 (62.1%) cases; 6 (20.7%) had > or = 2 viruses. Respiratory syncytial virus was identified in 11 (38.0%) of the 29 cases, and parainfluenza virus (PIV) types 1, 2, and 3 in 10 (34.5%). PIV type 3 accounted for 7 cases, including 3 with bacteremia. Bacterial isolates were made in 9 (21.4%) of 42 blood cultures and in the only lung aspirate; Staphylococcus epidermidis and Staphylococcus aureus accounted for 4 and 3 cases, respectively. Although bacteremia was 2.9 times more common in cases with co-existing pneumonia or croup, the respective frequency of virus-positive cases and that of bacteremia was not significantly different between cases with bronchiolitis alone and those with associated pneumonia or croup. No deaths were recorded, but subjects aged > 6 months had a significantly shorter hospital stay than those < 6 months old (P = 0.02). Despite the limited sample size, our findings reflect the etiological importance of the paramyxoviruses and the seasonal pattern of bronchiolitis in tropical Africa.

Acute Disease↗

Ataxia associated with increased plasma concentrations of pristanic acid, phytanic acid and C27 bile acids but normal fibroblast branched-chain fatty acid oxidation.

Investigations of peroxisomal function were undertaken in an 8-year-old girl who developed motor difficulties at the age of 3.5 years and went on to develop a progressive ataxia and dysarthria. There were no other neurological abnormalities and she was of normal intelligence. Analysis of plasma very long-chain fatty acids revealed a normal C26 concentration and normal C24/C22 and C26/C22 ratios. Analysis of branched-chain fatty acids showed an elevated plasma phytanic acid concentration of 60 mumol/L (normal < 15) and a considerably elevated pristanic acid concentration of 50 mumol/L (normal < 2). Plasma concentrations of the C27 bile acids 3 alpha, 7 alpha-dihydroxycholestanoic acid (DHCA) and 3 alpha, 7 alpha, 12 alpha-trihydroxycholestanoic acid (THCA) and of the C29-dicarboxylic acid were also increased. We postulated that these results might be due to deficiency of the peroxisomal branched-chain acyl-CoA oxidase, but when oxidation of branched-chain fatty acids was studied in cultured skin fibroblasts it was found to be normal. Alternative explanations for the accumulation of branched-chain substrates for peroxisomal beta-oxidation are discussed. Treatment with a low-phytanic acid diet arrested the progression of the ataxia and led to a slight improvement.

Ataxia↗

Delta 4-3-oxosteroid 5 beta-reductase deficiency: failure of ursodeoxycholic acid treatment and response to chenodeoxycholic acid plus cholic acid.

BACKGROUND: In some infants with liver disease, 3-oxo-delta 4 bile acids are the major bile acids in urine, a phenomenon attributed to reduced activity of the delta 4-3-oxosteroid 5 beta-reductase required for synthesis of chenodeoxycholic acid and cholic acid. These patients form a heterogeneous group. Many have a known cause of hepatic dysfunction and plasma concentrations of chenodeoxycholic acid and cholic acid that are actually greater than those of the 3-oxo-delta 4 bile acids. It is unlikely that these patients have a primary genetic deficiency of the 5 beta-reductase enzyme. AIMS: To document the bile acid profile, clinical phenotype, and response to treatment of an infant with cholestasis, increased plasma concentrations of 3-oxo-delta 4 bile acids, low plasma concentrations of chenodeoxycholic acid and cholic acid, and no other identifiable cause of liver disease. PATIENTS: This infant was compared with normal infants and infants with cholestasis of known cause. METHODS: Analysis of bile acids by liquid secondary ionisation mass spectrometry and gas chromatography-mass spectrometry. RESULTS: The plasma bile acid profile of the patient was unique. She had chronic cholestatic liver disease associated with malabsorption of vitamins D and E and a normal gamma-glutamyltranspeptidase when the transaminases were increased. The liver disease failed to improve with ursodeoxycholic acid but responded to a combination of chenodeoxycholic acid and cholic acid. CONCLUSION: Treatment of primary 5 beta-reductase deficiency requires the use of bile acids that inhibit cholesterol 7 alpha-hydroxylase.

Bile Acids and Salts↗

Low doses of repetitive ultraviolet A induce morphologic changes in human skin.

Repetitive exposure of skin to sunlight is known to result in dermatoheliosis, characterized by photoaging and carcinogenesis. It has been demonstrated previously that relatively large amounts of ultraviolet (UV) A can produce photodamage and it is believed that UVB plays a major role in the induction of photodamage and photocarcinogenesis. The study reported here determines the cutaneous effects of minimal erythemal amounts of solar-simulated UV radiation as well as suberythemal and minimal erythemal doses of UVA. Previously non-sunexposed human skin was irradiated twice weekly for 24 weeks. Biopsies were obtained 12, 24 and 36 weeks after the initial irradiation and assessed for both epidermal and dermal alterations. Dermal elastic tissue content was measured via computerized image analysis. All UV treatment regimens produced observable epidermal and dermal changes. These alterations were observed after only 12 weeks of twice-weekly irradiation and were still evident 12 weeks after the final irradiation. Interestingly, UVA irradiation produced a decrease in elastic tissue content whereas solar-simulated UV produced a slight increase. Most notable were the changes produced by the suberythemal dose of UVA. Surprisingly, this relatively low UVA dose produced a reduction in elastic tissue content. The results of this investigation demonstrate that small amounts of UVA or solar-simulated UV are capable of producing cutaneous photodamage. These findings suggest that even suberythemal doses of repetitive UVA may lead to photoaging of the skin and that there is a need for daily broad spectrum UV protection.

Adult↗

Synthetic lethality of sep1 (xrn1) ski2 and sep1 (xrn1) ski3 mutants of Saccharomyces cerevisiae is independent of killer virus and suggests a general role for these genes in translation control.

Strand exchange protein 1 (Sep1) (also referred to as exoribonuclease I [Xrn1]) from Saccharomyces cerevisiae has been implicated in DNA recombination, RNA turnover, karyogamy, and G4 DNA pairing among other disparate cellular processes. Using a genetic approach to study the role of SEP1/XRN1 in mitotic yeast cells, we identified mutations in the genes superkiller 2 (SKI2) and superkiller 3 (SKI3) as synthetically lethal with an sep1 null mutation. The SKI genes are thought to comprise an intracellular antiviral system controlling the expression of killer toxin from double-stranded RNA virus found in many yeast strains. However, the lethality of sep1 ski2 and sep1 ski3 mutants was independent of the L-A and M viruses, suggesting that the SKI genes act in a general cellular process in addition to virus control. We propose that Sep1/Xrn1 and Ski2 both act to block translation on transcripts targeted for degradation. Using a temperature-sensitive allele of SEP1/XRN1, we show that double mutants display a synthetic cell cycle arrest in late G1 at Start.

Base Sequence↗