Laboratory-evolved Vanillyl-alcohol Oxidase Produces Natural Vanillin

The flavoenzyme vanillyl-alcohol oxidase was subjected to random mutagenesis to generate mutants with enhanced reactivity to creosol (2-methoxy-4-methylphenol). The vanillyl-alcohol oxidase-mediated conversion of creosol proceeds via a two-step process in which the initially formed vanillyl alcohol (4-hydroxy-3-methoxybenzyl alcohol) is oxidized to the widely used flavor compound vanillin (4-hydroxy-3-methoxybenzaldehyde). The first step of this reaction is extremely slow due to the formation of a covalent FAD N-5-creosol adduct. After a single round of error-prone PCR, seven mutants were generated with increased reactivity to creosol. The single-point mutants I238T, F454Y, E502G, and T505S showed an up to 40-fold increase in catalytic efficiency (k(cat)/K-m) with creosol compared with the wild-type enzyme. This enhanced reactivity was due to a lower stability of the covalent flavin-substrate adduct, thereby promoting vanillin formation. The catalytic efficiencies of the mutants were also enhanced for other ortho-substituted 4-methylphenols, but not for p-cresol (4-methylphenol). The replaced amino acid residues are not located within a distance of direct interaction with the substrate, and the determined three-dimensional structures of the mutant enzymes are highly similar to that of the wild-type enzyme. These results clearly show the importance of remote residues, not readily predicted by rational design, for the substrate specificity of enzymes

Structural Studies on Flavin Reductase PheA2 Reveal Binding of NAD in an Unusual Folded Conformation and Support Novel Mechanism of Action

The catabolism of toxic phenols in the thermophilic organism Bacillus thermoglucosidasius A7 is initiated by a two-component enzyme system. The smaller flavin reductase PheA2 component catalyzes the NADH-dependent reduction of free FAD according to a ping-pong bisubstrate-biproduct mechanism. The reduced FAD is then used by the larger oxygenase component PheA1 to hydroxylate phenols to the corresponding catechols. We have determined the x-ray structure of PheA2 containing a bound FAD cofactor (2.2 Angstrom), which is the first structure of a member of this flavin reductase family. We have also determined the x-ray structure of reduced holo-PheA2 in complex with oxidized NAD (2.1 Angstrom). PheA2 is a single domain homodimeric protein with each FAD-containing subunit being organized around a six-stranded beta-sheet and a capping alpha-helix. The tightly bound FAD prosthetic group (K-d=10 nM) binds near the dimer interface, and the re face of the FAD isoalloxazine ring is fully exposed to solvent. The addition of NADH to crystalline PheA2 reduced the flavin cofactor, and the NAD product was bound in a wide solvent-accessible groove adopting an unusual folded conformation with ring stacking. This is the first observation of an enzyme that is very likely to react with a folded compact pyridine nucleotide. The PheA2 crystallographic models strongly suggest that reactive exogenous FAD substrate binds in the NADH cleft after release of NAD product. Nanoflow electrospray mass spectrometry data indeed showed that PheA2 is able to bind one FAD cofactor and one FAD substrate. In conclusion, the structural data provide evidence that PheA2 contains a dual binding cleft for NADH and FAD substrate, which alternate during catalysis

Real-time monitoring of enzymatic DNA hydrolysis by electrospray ionization mass spectrometry

A fast and direct method for the monitoring of enzymatic DNA hydrolysis was developed using electrospray ionization mass spectrometry. We incorporated the use of a robotic chip-based electrospray ionization source for increased reproducibility and throughput. The mass spectrometry method allows the detection of DNA fragments and intact non-covalent protein–DNA complexes in a single experiment. We used the method to monitor in real-time single-stranded (ss) DNA hydrolysis by colicin E9 DNase and to characterize transient non-covalent E9 DNase–DNA complexes present during the hydrolysis reaction. The mass spectra showed that E9 DNase interacts with ssDNA in the absence of a divalent metal ion, but is strictly dependent on Ni(2+) or Co(2+) for ssDNA hydrolysis. We demonstrated that the sequence selectivity of E9 DNase is dependent on the ratio protein:ssDNA or the ssDNA concentration and that only 3′-hydroxy and 5′-phosphate termini are produced. It was also shown that the homologous E7 DNase is reactive with Zn(2+) as transition metal ion and that this DNase displays a different sequence selectivity. The method described is of general use to analyze the reactivity and specificity of nucleases

Fixed priority scheduling with pre-emption thresholds and cache-related pre-emption delays: integrated analysis and evaluation

Commercial off-the-shelf programmable platforms for real-time systems typically contain a cache to bridge the gap between the processor speed and main memory speed. Because cache-related pre-emption delays (CRPD) can have a significant influence on the computation times of tasks, CRPD have been integrated in the response time analysis for fixed-priority pre-emptive scheduling (FPPS). This paper presents CRPD aware response-time analysis of sporadic tasks with arbitrary deadlines for fixed-priority pre-emption threshold scheduling (FPTS), generalizing earlier work. The analysis is complemented by an optimal (pre-emption) threshold assignment algorithm, assuming the priorities of tasks are given. We further improve upon these results by presenting an algorithm that searches for a layout of tasks in memory that makes a task set schedulable. The paper includes an extensive comparative evaluation of the schedulability ratios of FPPS and FPTS, taking CRPD into account. The practical relevance of our work stems from FPTS support in AUTOSAR, a standardized development model for the automotive industry

Evidence for Recipient-Derived Cells in Peribiliary Glands and Biliary Epithelium of the Large Donor Bile Ducts After Liver Transplantation

Introduction Chimerism after orthotopic liver transplantation (OLT) has largely been investigated in intrahepatic cellular constituents. However, little is known about chimerism in the extrahepatic and large intrahepatic bile ducts. Our aim was to evaluate the presence and extent of chimerism after OLT in the peribiliary glands (PBG) and the luminal epithelium of the large donor bile ducts. Methods For this study, we examined six extrahepatic and large intrahepatic bile ducts from livers that were re-transplanted. In all cases there was a sex-mismatch between donor and recipient (female donor organ and male recipient), which allowed to discriminate between donor- and recipient-derived cells. Specimens from female to female transplants were used as negative controls and male to male transplants as positive controls. Fluorescencein situhybridization (FISH) for Y and X chromosomes was performed and the percentage of XY positive cells was determined among biliary epithelial cells. Immunohistochemistry was used to correlate chimerism with histological features. Results Cholangiocellular chimerism in all studied specimens ranged from 14 to 52%. The degree of chimerism was not associated with biliary damage. Marked chimerism was present at 5 days post-OLT. Ki-67-positivity was detected in 1-8% of the epithelial cells at the time of liver re-transplantation, and this correlated inversely with the degree of chimerism. Conclusion Recipient-derived cholangiocytes are present in the large bile ducts of the donor liver after OLT. The presence of chimerism in the large bile ducts suggests that recipient-derived cells may play a role in biliary regeneration following ischemia-induced injury during OLT

Native mass spectrometry provides direct evidence for DNA mismatch-induced regulation of asymmetric nucleotide binding in mismatch repair protein MutS

The DNA mismatch repair protein MutS recognizes mispaired bases in DNA and initiates repair in an ATP-dependent manner. Understanding of the allosteric coupling between DNA mismatch recognition and two asymmetric nucleotide binding sites at opposing sides of the MutS dimer requires identification of the relevant MutS.mmDNA.nucleotide species. Here, we use native mass spectrometry to detect simultaneous DNA mismatch binding and asymmetric nucleotide binding to Escherichia coli MutS. To resolve the small differences between macromolecular species bound to different nucleotides, we developed a likelihood based algorithm capable to deconvolute the observed spectra into individual peaks. The obtained mass resolution resolves simultaneous binding of ADP and AMP.PNP to this ABC ATPase in the absence of DNA. Mismatched DNA regulates the asymmetry in the ATPase sites; we observe a stable DNA-bound state containing a single AMP.PNP cofactor. This is the first direct evidence for such a postulated mismatch repair intermediate, and showcases the potential of native MS analysis in detecting mechanistically relevant reaction intermediates

Global methylation in relation to methotrexate-induced oral mucositis in children with acute lymphoblastic leukemia

Background Children with acute lymphoblastic leukemia (ALL) often suffer from toxicity of chemotherapeutic drugs such as Methotrexate (MTX). Previously, we reported that 20% of patients receiving high-dose MTX developed oral mucositis. MTX inhibits folate metabolism, which is essential for DNA methylation. We hypothesize that MTX inhibits DNA methylation, which results into adverse effects. We studied DNA methylation markers during high-dose methotrexate treatment in pediatric acute lymphoblastic leukemia (ALL) in relation to developing oral mucositis. Materials & methods S-Adenosyl-Methionine (SAM) and S-Adenosyl-Homocysteine (SAH) levels and LINE1 DNA methylation were measured prospectively before and after high-dose methotrexate (HD-MTX 4 x 5g/m2) therapy in 82 children with ALL. Methotrexate-induced oral mucositis was registered prospectively. Oral mucositis (grade 3 National Cancer Institute Criteria) was used as clinical endpoint. Results SAM levels decreased significantly during methotrexate therapy (-16.1 nmol/L (-144.0 – +46.0), p<0.001), while SAH levels and the SAM:SAH ratio did not change significantly. LINE1 DNA methylation (+1.4% (-1.1 –+6.5), p<0.001) increased during therapy. SAM and SAH levels were not correlated to LINE1 DNA methylation status. No association was found between DNA methylation markers and developing oral mucositis. Conclusions This was the first study that assessed DNA methylation in relation to MTX-induced oral mucositis in children with ALL. Although global methylation markers did change during methotrexate therapy, methylation status was not associated with developing oral mucositis

Hypothermic oxygenated machine perfusion reduces bile duct reperfusion injury after transplantation of donation after circulatory death livers

INTRODUCTION: Dual hypothermic oxygenated machine perfusion (DHOPE) of the liver has been advocated as a method to reduce ischemia-reperfusion injury. This study aimed to determine whether DHOPE reduces IR injury of the bile ducts in DCD liver transplantation. MATERIALS AND METHODS: In a recently performed phase 1-trial, ten DCD livers were preserved with DHOPE after static cold storage (SCS) (www.trialregister.nl NTR4493). Bile duct biopsies were obtained at the end of SCS (before DHOPE; baseline) and after graft reperfusion in the recipient. Histological severity of biliary injury was graded according to an established semi-quantitative grading system. Twenty liver transplantations using DCD livers not preserved with DHOPE served as control. RESULTS: Baseline characteristics and the degree of bile duct injury at baseline (end of SCS) were similar between both groups. In controls, degree of stroma necrosis (P=0.002) and injury of the deep peribiliary glands (P=0.02) increased after reperfusion, compared to baseline. In contrast, in DHOPE preserved livers the degree of bile duct injury did not increase after reperfusion. Moreover, there was less injury of deep peribiliary glands (P=0.04) after reperfusion in the DHOPE group, compared to controls. CONCLUSION: This study suggests that DHOPE reduces ischemia-reperfusion injury of bile ducts after DCD liver transplantation. This article is protected by copyright. All rights reserved

SN 2003du: Signatures of the Circumstellar Environment in a Normal Type Ia Supernova?

We present observations of the Type Ia supernova 2003du and report the detectionof an unusual, high-velocity component in the Ca II infrared triplet, similar tofeatures previously observed in SN 2000cx and SN 2001el. This feature exhibits a large expansion velocity (~18,000 km/s) which is nearly constant between -7 and +2 days relative to maximum light, and disappears shortly thereafter. Otherthan this feature, the spectral evolution and light curve resemble those of a normal SN Ia. We find that the Ca II feature can plausibly be caused by a dense shell formed when circumstellar material of solar abundance is overrun by the rapidly expanding outermost layers of the SN ejecta. Model calculations show that the optical and infrared spectra are remarkably unaffected by the circumstellar interaction. In particular, no hydrogen lines are detectable in either absorption or emission. The only qualitatively different features are the strong, high-velocity feature in the Ca II IR-triplet, and a somewhat weaker O I feature near 7,300 AA. The morphology and time evolution of these features provide an estimate for the amount of accumulated matter and an indication of the mixing in the dense shell. We apply these diagnostic tools to SN 2003du and infer that about 2 x 10^{-2} M_sun of solar abundance material may have accumulated in a circumstellar shell prior to the observations. Furthermore, the early light curve data imply that the circumstellar material was originally very close to the progenitor system, perhaps from an accretion disk, Roche lobe or common envelope.Comment: 35 Pages, 11 Figures, to appear in ApJ. Resubmission includes expanded discussion & new figures to match with accepted journal versio