The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions.

Bacterial RNP bodies (BR-bodies) are non-membrane-bound structures that facilitate mRNA decay by concentrating mRNA substrates with RNase E and the associated RNA degradosome machinery. However, the full complement of proteins enriched in BR-bodies has not been defined. Here we define the protein components of BR-bodies through enrichment of the bodies followed by mass spectrometry-based proteomic analysis. We found 111 BR-body enriched proteins, including several RNA binding proteins, many of which are also recruited directly to in vitro reconstituted RNase E droplets, showing BR-bodies are more complex than previously assumed. While most BR-body enriched proteins that were tested cannot phase separate, we identified five that undergo RNA-dependent phase separation in vitro, showing other RNP condensates interface with BR-bodies. RNA degradosome protein clients are recruited more strongly to RNase E droplets than droplets of other RNP condensates, implying that client specificity is largely achieved through direct protein-protein interactions. We observe that some RNP condensates assemble with preferred directionally, suggesting that RNA may be trafficked through RNP condensates in an ordered manner to facilitate mRNA processing/decay, and that some BR-body associated proteins have the capacity to dissolve the condensate. Finally, we find that RNA dramatically stimulates the rate of RNase E phase separation in vitro, explaining the dissolution of BR-bodies after cellular mRNA depletion observed previously. Altogether, these results suggest that a complex network of protein-protein and protein-RNA interactions controls BR-body phase separation and RNA processing.

Electroblotting through a tryptic membrane for LC-MS/MS analysis of proteins separated in electrophoretic gels.

Digestion of proteins separated via sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) remains a popular method for protein identification using mass-spectrometry based proteomics. Although robust and routine, the in-gel digestion procedure is laborious and time-consuming. Electroblotting to a capture membrane prior to digestion reduces preparation steps but requires on-membrane digestion that yields fewer peptides than in-gel digestion. This paper develops direct electroblotting through a trypsin-containing membrane to a capture membrane to simplify extraction and digestion of proteins separated by SDS-PAGE. Subsequent liquid chromatography-tandem mass spectrometry (LC-MS/MS) identifies the extracted peptides. Analysis of peptides from different capture membrane pieces shows that electrodigestion does not greatly disturb the spatial resolution of a standard protein mixture separated by SDS-PAGE. Electrodigestion of an Escherichia coli (E. coli) cell lysate requires four hours of total sample preparation and results in only 13% fewer protein identifications than in-gel digestion, which can take 24 h. Compared to simple electroblotting and protein digestion on a poly(vinylidene difluoride) (PVDF) capture membrane, adding a trypsin membrane to the electroblot increases the number of protein identifications by 22%. Additionally, electrodigestion experiments using capture membranes coated with polyelectrolyte layers identify a higher fraction of small proteolytic peptides than capture on PVDF or in-gel digestion.

Correction to: Spectrum of movement disorders and neurotransmitter abnormalities in paediatric POLG disease.

Due to a typesetting error the wrong Table 2 was used. The correct Table 2 is shown here.

Spectrum of movement disorders and neurotransmitter abnormalities in paediatric POLG disease.

OBJECTIVES: To describe the spectrum of movement disorders and cerebrospinal fluid (CSF) neurotransmitter profiles in paediatric patients with POLG disease. METHODS: We identified children with genetically confirmed POLG disease, in whom CSF neurotransmitter analysis had been undertaken. Clinical data were collected retrospectively. CSF neurotransmitter levels were compared to both standardised age-related reference ranges and to non-POLG patients presenting with status epilepticus. RESULTS: Forty-one patients with POLG disease were identified. Almost 50% of the patients had documented evidence of a movement disorder, including non-epileptic myoclonus, choreoathetosis and ataxia. CSF neurotransmitter analysis was undertaken in 15 cases and abnormalities were seen in the majority (87%) of cases tested. In many patients, distinctive patterns were evident, including raised neopterin, homovanillic acid and 5-hydroxyindoleacetic acid levels. CONCLUSIONS: Children with POLG mutations can manifest with a wide spectrum of abnormal movements, which are often prominent features of the clinical syndrome. Underlying pathophysiology is probably multifactorial, and aberrant monoamine metabolism is likely to play a role.

High-resolution profiling of histone h3 lysine 36 trimethylation in metastatic renal cell carcinoma.

Mutations in SETD2, a histone H3 lysine trimethyltransferase, have been identified in clear cell renal cell carcinoma (ccRCC); however it is unclear if loss of SETD2 function alters the genomic distribution of histone 3 lysine 36 trimethylation (H3K36me3) in ccRCC. Furthermore, published epigenomic profiles are not specific to H3K36me3 or metastatic tumors. To determine if progressive SETD2 and H3K36me3 dysregulation occurs in metastatic tumors, H3K36me3, SETD2 copy number (CN) or SETD2 mRNA abundance was assessed in two independent cohorts: metastatic ccRCC (n=71) and the Cancer Genome Atlas Kidney Renal Clear Cell Carcinoma data set (n=413). Although SETD2 CN loss occurs with high frequency (>90%), H3K36me3 is not significantly impacted by monoallelic loss of SETD2. H3K36me3-positive nuclei were reduced an average of ~20% in primary ccRCC (90% positive nuclei in uninvolved vs 70% positive nuclei in ccRCC) and reduced by ~60% in metastases (90% positive in uninvolved kidney vs 30% positive in metastases) (P<0.001). To define a kidney-specific H3K36me3 profile, we generated genome-wide H3K36me3 profiles from four cytoreductive nephrectomies and SETD2 isogenic renal cell carcinoma (RCC) cell lines using chromatin immunoprecipitation coupled with high-throughput DNA sequencing and RNA sequencing. SETD2 loss of methyltransferase activity leads to regional alterations of H3K36me3 associated with aberrant RNA splicing in a SETD2 mutant RCC and SETD2 knockout cell line. These data suggest that during progression of ccRCC, a decline in H3K36me3 is observed in distant metastases, and regional H3K36me3 alterations influence alternative splicing in ccRCC.

Response of 33 UK patients with infantile-onset Pompe disease to enzyme replacement therapy.

BACKGROUND: Enzyme replacement therapy (ERT) for infantile-onset Pompe disease has been commercially available for almost 10 years. We report the experience of its use in a cohort treated at three specialist lysosomal treatment centres in the UK. METHODS: A retrospective case-note review was performed, with additional data being gathered from two national audits on all such patients treated with ERT. The impact on the outcome of various characteristics, measured just prior to the initiation of ERT (baseline), was evaluated using logistic regression. RESULTS: Thirty-three patients were identified; 13/29 (45%) were cross-reactive immunological material (CRIM) negative, and nine were immunomodulated. At baseline assessment, 79% were in heart failure, 66% had failure to thrive and 70% had radiological signs of focal pulmonary collapse. The overall survival rate was 60%, ventilation-free survival was 40% and 30% of patients were ambulatory. Median follow-up of survivors was 4 years, 1.5 months (range 6 months to 13.5 years). As with previous studies, the CRIM status impacted on all outcome measures. However, in this cohort, baseline failure to thrive was related to death and lack of ambulation, and left ventricular dilatation was a risk factor for non-ventilator-free survival. CONCLUSION: The outcome of treated patients remains heterogeneous despite attempts at immunomodulation. Failure to thrive at baseline and left ventricular dilation appear to be associated with poorer outcomes.

Mitochondrial disorders and general anaesthesia: a case series and review.

Patients with mitochondrial disease are at risk of metabolic decompensation and often require general anaesthesia (GA) as part of their diagnostic work up and subsequent management. However, the evidence base for the use of GA is limited and inconclusive. We have documented the practice and outcome in the use of GA in paediatric patients with mitochondrial disease using a retrospective case review study of 38 mitochondrial patients who had undergone 58 anaesthetics within the regional metabolic service for the period 1989-2005. A variety of anaesthetic agents were used and the pattern of use reflects that seen in standard paediatric practice. There were no episodes of malignant hyperthermia and no documented intraoperative events attributable to the GA. Three postoperative adverse events were noted; one episode of hypovolaemia, one episode of acute on chronic renal failure, and one episode of metabolic decompensation 12 h post-muscle biopsy. Despite theoretical concern about this group of patients, adverse events after GA are rare and in most cases unrelated to the anaesthesia. Further prospective studies of GA in mitochondrial disease are required to create evidence-based clinical guidelines for safe practice.

The birth prevalence of PKU in populations of European, South Asian and sub-Saharan African ancestry living in South East England.

Phenylketonuria (PKU) is an autosomal recessive inborn error of metabolism (OMIM 261600). Treatment with a low-phenylalanine diet following early ascertainment by newborn screening prevents impaired cognitive development, the major disease phenotype in PKU. The overall birth prevalence of PKU in European, Chinese and Korean populations is approximately 1/10,000. Since the human PAH locus contains PKU-causing alleles and polymorphic core haplotypes that describe and corroborate an out-of-Africa range expansion in modern human populations, it is of interest to know the prevalence of PKU in different ethnic groups with diverse geographical origin. We estimated PKU prevalence in South East England, where a sizeable proportion of the population are of Sub-Saharan African or South Asian ancestry. Over the period 1994 to 2004 167 children were diagnosed with PKU. Using birth registration and census data to derive denominators, PKU birth prevalence per 10,000 live births (95% Bayesian credible intervals) was estimated to be 1.14 (0.96-1.33) among white, 0.11 (0.02-0.37) among black, and 0.29 (0.10-0.63) among Asian ethnic groups. This suggests that PKU is up to an order of magnitude less prevalent in populations with Sub-Saharan African and South Asian ancestry that have migrated to the UK.

Hepatocyte transplantation followed by auxiliary liver transplantation--a novel treatment for ornithine transcarbamylase deficiency.

We report the first successful use of hepatocyte transplantation as a bridge to subsequent auxiliary partial orthotopic liver transplantation (APOLT) in a child antenatally diagnosed with severe ornithine transcarbamylase (OTC) deficiency. A total of 1.74 x 10(9) fresh and cryopreserved hepatocytes were administered intraportally into the liver over a period of 6 months. Immunosuppression was with tacrolimus and prednisolone. A sustained decrease in ammonia levels and a gradual increase in serum urea were observed except during episodes of sepsis in the first 6 months of life. The patient was able to tolerate a normal protein intake and presented a normal growth and neurological development. APOLT was successfully performed at 7 months of age. We conclude that hepatocyte transplantation can be used in conjunction with APOLT as an effective treatment for severe OTC-deficient patients, improving neurodevelopmental outcomes.

High frequency of missense mutations in glycogen storage disease type VI.

Deficiency of liver glycogen phosphorylase in glycogen storage disease (GSD) type VI results in a reduced ability to mobilize glucose from glycogen. Six mutations of the PYGL gene, which encodes the liver isoform of the enzyme, have been identified in the literature. We have characterized eight patients from seven families with GSD type VI and identified 11 novel PYGL gene defects. The majority of the mutations were missense, resulting in the substitution of highly conserved residues. These could be grouped into those that were predicted to affect substrate binding (p.V456M, p.E673K, p.S675L, p.S675T), pyridoxal phosphate binding (p.R491C, p.K681T), or activation of glycogen phosphorylase (p.Q13P) or that had an unknown effect (p.N632I and p.D634H). Two mutations were predicted to result in null alleles, p.R399X and [c.1964_1969inv6;c.1969+1_+4delGTAC]. Only 7 of the 23 (30%) reported PYGL alleles carry nonsense, splice site or frameshift mutations compared to 68-80% of affected alleles of the highly homologous muscle glycogen phosphorylase gene, PYGM, that underlie McArdle disease. There was heterogeneity in the clinical symptoms observed in affected individuals. These varied from hepatomegaly and subclinical hypoglycaemia, to severe hepatomegaly with recurrent severe hypoglycaemia and postprandial lactic acidosis. We conclude that deficiency of liver glycogen phosphorylase is predominantly the result of missense mutations affecting enzyme activity. There are no common mutations and the severity of clinical symptoms varies significantly.

Auxiliary liver transplantation for propionic acidemia: a 10-year follow-up.

Orthotopic liver transplantation (OLT) is an established treatment for patients with liver-based metabolic disorders that produce structural and functional impairment. Auxiliary liver transplantation (ALT) has been proposed as an alternative approach due to the potential advantage of preserving the native liver that could be used for future gene therapy and also serves as a back-up should the graft fail. The aim of our study was to determine if ALT has the long-term potential to correct the underlying abnormality in propionic acidemia (PA). A retrospective analysis was performed on graft function, metabolic parameters and effects on development in a child who underwent ALT for PA at our institute. The clinical and biochemical parameters are near normal with no diet restrictions and with good graft survival. A normal growth and an acceptable neurological and psychomotor development were achieved in the child. ALT is feasible and provides adequate liver mass to prevent metabolic decompensation in PA.

A novel starch for the treatment of glycogen storage diseases.

OBJECTIVE: To determine whether a new starch offers better short-term metabolic control than uncooked cornstarch in patients with glycogen storage diseases (GSDs). STUDY DESIGN: A short-term double-blind cross-over pilot study comparing uncooked physically modified cornstarch (WMHM20) with uncooked cornstarch in patients with GSD types Ia, Ib and III. Twenty-one patients (ages 3-47, 9 female) were given 2 g/kg cornstarch or WMHM20 mixed in water. Blood glucose, lactate and insulin, and breath hydrogen and (13)CO2 enrichment were measured, at baseline and after each load. The hourly biochemical evaluations terminated when blood glucose was < or = 3.0 mmol/L, when the study period had lasted 10 h or when the patient wished to end the test. The alternative starch was administered under similar trial conditions a median of 10 days later. RESULTS: The median starch load duration was 9 h for WMHM20 versus 7 h for cornstarch. Glucose decreased more slowly (p = 0.05) and lactate was suppressed faster (p = 0.17) for WMHM20 compared with cornstarch. Peak hydrogen excretion was increased (p = 0.05) when cornstarch was taken. CONCLUSION: These data indicate longer duration of euglycaemia and better short-term metabolic control in the majority of GSD patients with WMHM20 compared to cornstarch.

Clinical, enzymatic and molecular characterization of nine new patients with malonyl-coenzyme A decarboxylase deficiency.

We report nine new patients with malonic aciduria associated with enzyme-confirmed malonyl-CoA decarboxylase (MCD) deficiency in eight. Clinical details were available on eight, and molecular genetic characterization was obtained for nine. As for 15 previously described patients, cardinal clinical manifestations included developmental delay and cardiomyopathy; metabolic perturbations (e.g. acidosis) and seizures, however, were infrequent or not observed in our patients. For all, detection of elevated malonic acid in urine (+/- increased C3DC acylcarnitine by analysis employing tandem mass spectrometry) led to pursuit of enzyme studies. MCD activities (nmol/h PER mg protein) revealed: control (n = 22), 16.2 +/- 1.8 (SEM; range 5.7-46.2); patients (n = 8, assayed in duplicate), 1.7 +/- 0.3 (10% of parallel control; range 0.6-2.8). Molecular characterization by DNA sequence analysis and multiplex ligation-dependent probe amplification revealed nine novel mutations (c.796C>T; p.Gln266X, c.481delC; p.Leu161CysfsX18, c.1367A>C; p.Tyr456Ser, c.1319G>T; p.Ser440Ile, c.1430C>T; p.Ser477Phe, c.899G>T; p.Gly300Val, c.799-1683_949-1293del3128, and two other large genomic deletions comprising exons 1 or the complete gene) and two known mutations in the MLYCD gene. Our findings increase the number of enzyme-confirmed MCD-deficient patients by >50%, and expand our understanding of the phenotypic and molecular heterogeneity of this rare disorder.

Refining the diagnosis of mitochondrial HMG-CoA synthase deficiency.

Mitochondrial HMG-CoA synthase deficiency is an inherited metabolic disorder caused by a defect in the enzyme that regulates the formation of ketone bodies. Patients present with hypoketotic hypoglycaemia, encephalopathy and hepatomegaly, usually precipitated by an intercurrent infection or prolonged fasting. The diagnosis may easily be missed as previously reported results of routine metabolic investigations, urinary organic acids and plasma acylcarnitines may be nonspecific or normal, and a high index of suspicion is required to proceed to further confirmatory tests. We describe a further acute case in which the combination of urinary organic acids, low free carnitine and changes in the plasma acylcarnitine profile on carnitine supplementation were very suggestive of a defect in ketone synthesis. The diagnosis of mitochondrial HMG-CoA synthase deficiency was confirmed on genotyping, revealing two novel mutations: c.614G > A (R188H) and c.971T > C (M307T). A further sibling, in whom the diagnosis had not been made acutely, was also found to be affected. The possible effects of these mutations on enzyme activity are discussed.

Adenylosuccinate lyase deficiency--first British case.

A deficiency of adenylosuccinate lyase (ASDL) is characterised by the accumulation of SAICAriboside (SAICAr) and succinyladenosine (S-Ado) in body fluids. The severity of the clinical presentation correlates with a low S-Ado/SAICAr ratio in body fluids. We report the first British case of ADSL deficiency. The patient presented at 14 days with a progressive neonatal encephalopathy and seizures. There was marked axial and peripheral hypotonia. Brain MRI showed widespread white matter changes. She died at 4 weeks of age. Concentrations of SAICAr and SAdo were markedly elevated in urine, plasma and CSF and the SAdo/SAICAr ratio was low, consistent with the severe phenotype. The patient was compound heterozygous for 2 novel ADSL mutations; c.9 G>C (A3P) and c.572 C>T (R190X).

Effect of corn hybrid and chop length of whole-plant corn silage on digestion and intake by dairy cows.

The objectives of this experiment were to study the effects of corn hybrid and chop length of whole-plant corn silage (WPCS) on intake, and to quantify ruminal digestive processes that could help to identify factors limiting dry matter intake (DMI). Eight lactating cows and 4 dry cows fitted with a ruminal cannula were randomly assigned to 4 treatments in a 4 x 4 Latin square design with replications for lactating cows and without for ruminally cannulated cows. Treatments were fed in a total mixed ration (TMR) containing 75% WPCS and 25% concentrate. The 4 WPCS differed in the characteristics of 2 conventional hybrids, less degradable vs. more degradable in the rumen and in the chop length, fine vs. coarse. The DMI was measured for all cows, and digestion measurements and chewing activities were recorded with the cannulated cows. With lactating cows, DMI and milk yield varied with corn hybrids but not with chop length. The less degradable hybrid in the rumen was the less ingested. Dry matter intake of dry ears followed the same trend, but the differences between hybrids were lower than that observed with the lactating cows and not significant. Dry matter digestibility in the total tract and rumen fill were not different between hybrids. Ruminal mean retention time was greater for the least degradable hybrid. The rumen fill capacity could explain intake differences between hybrids. Ingestive mastication strongly reduced particle size, and the efficiency of particle size reduction was more important with the coarsely chopped WPCS than the finely chopped ones. The small differences in particle size of material entering the rumen after mastication of WPCS during eating might explain the lack of response for decreasing chop length. Because the rumen fill decreased with the decrease in chop length, rumen fill could not be the only factor responsible for DMI control of WPCS.

Effect of corn particle size on site and extent of starch digestion in lactating dairy cows.

Two experiments were conducted to determine the effects of corn particle size (CPS) on site and extent of starch digestion in lactating dairy cows. Animals were fitted with ruminal, duodenal, and ileal cannulas. Dry corn grain accounted for 36% of dry matter intake. In experiment 1, 6 cows were used in a duplicate 3 x 3 Latin square design. Semiflint corn was used. Corn processing methods were grinding, medium rolling, and coarse rolling. The mean particle size of the processed corn was 730, 1807, and 3668 microm, respectively. Rumen digestibility of starch linearly decreased from 59% with ground corn to 36% with coarsely rolled corn. Similarly, small intestine digestibility linearly decreased with increased CPS, and consequently, the amount of starch digested in the small intestine was not affected by corn processing. In experiment 2, 4 cows were used in a 2 x 2 crossover design. Dent corn was used. Corn processing methods were grinding and coarse rolling. The mean particle size of the processed corn was 568 and 3458 microm, respectively. Rumen digestibility of starch decreased from 70% with ground corn to 54% with coarsely rolled corn. Small intestine digestibility of starch was not significantly affected by CPS, and the amount of starch digested in the small intestine tended to be greater for rolled than for ground corn. In both experiments, starch total tract digestibility decreased with increased CPS. In conclusion, CPS is an efficient tool to manipulate rumen degradability of cornstarch. In midlactation cows, the decrease in the amount of starch digested in the rumen between grinding and coarse rolling is partly compensated for by an increase in the amount of starch digested in the small intestine with dent genotype, but with semiflint genotype postruminal digestion is not increased and rumen escape starch is not utilized by the animal.

Biotinidase deficiency: a treatable leukoencephalopathy.

The clinical history and the neuroradiological findings have been reviewed for 5 patients with biotinidase deficiency. Patients were diagnosed in the UK, where neonatal screening for this disorder is not done. The age at presentation ranged from 4 weeks to 5 months and the median interval between presentation and diagnosis was 5.5 months. The main abnormalities on cerebral imaging were leukoencephalopathy and widening of the ventricles and extra-cerebral CSF spaces. White matter abnormalities included delayed myelination but, in some patients, the increased signal was too great to be explained just by failure of myelination. Subtle subcortical changes were the only abnormality in one patient. Follow-up studies after treatment with biotin showed improved myelination; in one case, this was accompanied by normalisation of the CSF spaces but another patient showed progressive atrophy and cystic degeneration. Most of these patients have neurological sequelae. Biotinidase deficiency should be excluded in all patients with unexplained neurological problems. Neonatal screening provides the best chance of a good outcome.