Selective base excision repair of DNA damage by the non‐base‐flipping DNA glycosylase AlkC

DNA glycosylases preserve genome integrity and define the specificity of the base excision repair pathway for discreet, detrimental modifications, and thus, the mechanisms by which glycosylases locate DNA damage are of particular interest. Bacterial AlkC and AlkD are specific for cationic alkylated nucleobases and have a distinctive HEAT‐like repeat (HLR) fold. AlkD uses a unique non‐base‐flipping mechanism that enables excision of bulky lesions more commonly associated with nucleotide excision repair. In contrast, AlkC has a much narrower specificity for small lesions, principally N3‐methyladenine (3mA). Here, we describe how AlkC selects for and excises 3mA using a non‐base‐flipping strategy distinct from that of AlkD. A crystal structure resembling a catalytic intermediate complex shows how AlkC uses unique HLR and immunoglobulin‐like domains to induce a sharp kink in the DNA, exposing the damaged nucleobase to active site residues that project into the DNA. This active site can accommodate and excise N3‐methylcytosine (3mC) and N1‐methyladenine (1mA), which are also repaired by AlkB‐catalyzed oxidative demethylation, providing a potential alternative mechanism for repair of these lesions in bacteria.     

A Micromethod for the Isolation of Large and Small Microvessels from Frozen Autopsied Human Brain

Microvessels were isolated from autopsied human brain using a simple procedure involving disruption, sieving, and centrifugation on a sucrose density gradient. The present procedure is characterized by isolation, from frozen autopsied brain, of materials either from the cerebral cortex or white matter, and subsequent separation of the capillary fraction from the large vessel fraction. The preparation appears highly purified under phase-contrast microscopic examination. The purity was also established by the enrichment of gamma-glutamyl transpeptidase activity and by the nearly negligible cerebroside content in the vessel fractions as compared to the brain homogenate.     

Regional and Subcellular Distribution in Mammalian Brain of the Enzymes Producing Adenosine

The activities of 5'-nucleotidase, 2'-nucleotidase, alkaline phosphatase, and acid phosphatase were measured in rat and autopsied human brains. The four phosphatases in the rat brain showed little change in activity after death. The activities of adenosine-producing enzymes were compared in various parts of rat and human brains. When phosphatase activity was measured at pH 7.5, 5'-nucleotidase showed the highest activity in the most parts of the brain. The activity of 2'-nucleotidase and that of nonspecific phosphatase were almost the same at pH 7.5. However, higher phosphatase activity was observed in all parts of the brain when nonspecific phosphatase activity was measured at pH 10.0 or 5.5. High specific activity of 5'-nucleotidase in the brain was detected in the membranous components, especially in the synaptic membranes. The activity of 2'-nucleotidase was distributed in the soluble and synaptosomal fractions. The highest activity of both alkaline and acid phosphatases was recovered in the crude mitochondrial fraction, with the highest specific activity in the microsomal fraction. Phosphatase activity was distributed widely in the rat brain. The activity of 5'-nucleotidase was high in the medulla oblongata, thalamus, and hippocampus, but low in the peripheral nerve, spinal cord, and occipital lobe. The activity of 2'-nucleotidase was high in the vermis and frontal lobe. The highest acid and alkaline phosphatase activities were detected in the frontal lobe and in the olfactory bulb, respectively. The distribution of the four phosphatases in the autopsied human brain was similar to that in the rat brain. The highest 5'-nucleotidase activity was observed in the temporal lobe and thalamus.(ABSTRACT TRUNCATED AT 250 WORDS)     

Changes in nucleotide pools during conidia formation of Penicillium chrysogenum in solid culture

Abstract Using Cellophane-sheet techniques, changes in nucleotide pool size during conidia formation of Penicillium chrysogenum on agar plates were studied. On conidia-forming medium (nutritionally poor medium), the pool size of nucleoside triphosphates, especially GTP, decreased dramatically at mid-growth phase, concomitantly with the exhaustion of extracellular phosphate. Onset of conidia formation was observed just after the GTP pool decrease.     

Decrease of rat liver cysteine dioxygenase (cysteine oxidase) activity mediated by glucagon.

The hepatic cysteine dioxygenase activity of rats was markedly decreased by the intraperitoneal administration of glucagon. The enzyme activity was also decreased by either dibutyryl cyclic AMP or theophylline. The prior administration of actinomycin D completely blocked the glucagon-mediated decrease of enzyme activity, while administrations of this inhibitor of protein synthesis after glucagon injection did not block the decrease of enzyme activity. A single administration of actinomycin D resulted in a slight increase of cysteine dioxygenase activity in the rat liver. On the other hand, the injection of cycloheximide resulted in a rapid decrease of the hepatic cysteine dioxygenase with a half-life of 2.5 h. The half-life of the enzyme in rat liver after glucagon administration was one hour. The administration of hydrocortisone or insulin had no effect on the glucagon-mediated decrease of cysteine dioxygenase of rat liver. The enzyme activity of alloxan diabetic rat liver was almost the same as that of the intact rat liver. The evidence obtained here suggests that enhancement of degradation or inactivation of cysteine dioxygenase is responsible for the glucagon-mediated decrease of the enzyme activity in rat liver.     

Traveling and Pinned Fronts in Bistable Reaction-Diffusion Systems on Networks

Traveling fronts and stationary localized patterns in bistable reaction-diffusion systems have been broadly studied for classical continuous media and regular lattices. Analogs of such non-equilibrium patterns are also possible in networks. Here, we consider traveling and stationary patterns in bistable one-component systems on random Erdös-Rényi, scale-free and hierarchical tree networks. As revealed through numerical simulations, traveling fronts exist in network-organized systems. They represent waves of transition from one stable state into another, spreading over the entire network. The fronts can furthermore be pinned, thus forming stationary structures. While pinning of fronts has previously been considered for chains of diffusively coupled bistable elements, the network architecture brings about significant differences. An important role is played by the degree (the number of connections) of a node. For regular trees with a fixed branching factor, the pinning conditions are analytically determined. For large Erdös-Rényi and scale-free networks, the mean-field theory for stationary patterns is constructed.     

Determinants of variations in coronary revascularization practices

Background:

The ratio of percutaneous coronary interventions to coronary artery bypass graft surgeries (PCI:CABG ratio) varies considerably across hospitals. We conducted a comprehensive study to identify clinical and nonclinical factors associated with variations in the ratio across 17 cardiac centres in the province of Ontario.

Methods:

In this retrospective cohort study, we selected a population-based sample of 8972 patients who underwent an index cardiac catheterization between April 2006 and March 2007 at any of 17 hospitals that perform invasive cardiac procedures in the province. We classified the hospitals into four groups by PCI:CABG ratio (low [< 2.0], low–medium [2.0–2.7], medium–high [2.8–3.2] and high [> 3.2]). We explored the relative contribution of patient, physician and hospital factors to variations in the likelihood of patients receiving PCI or CABG surgery within 90 days after the index catheterization.

Results:

The mean PCI:CABG ratio was 2.7 overall. We observed a threefold variation in the ratios across the four hospital ratio groups, from a mean of 1.6 in the lowest ratio group to a mean of 4.6 in the highest ratio group. Patients with single-vessel disease usually received PCI (88.4%–99.0%) and those with left main artery disease usually underwent CABG (80.8%–94.2%), regardless of the hospital’s procedure ratio. Variation in the management of patients with non-emergent multivessel disease accounted for most of the variation in the ratios across hospitals. The mode of revascularization largely reflected the recommendation of the physician performing the diagnostic catheterization and was also influenced by the revascularization “culture” at the treating hospital.

Interpretation:

The physician performing the diagnostic catheterization and the treating hospital were strong independent predictors of the mode of revascularization. Opportunities exist to improve transparency and consistency around the decision-making process for coronary revascularization, most notably among patients with non-emergent multivessel disease.Large inter-regional and inter-hospital variations exist in the ratio of percutaneous coronary intervention (PCI) procedures to coronary artery bypass graft (CABG) surgeries performed in many countries, but the reasons for these variations are uncertain.^1–3 Bypass surgery was the first method of coronary revascularization to be developed.⁴ The less-invasive alternative of PCI was developed initially to treat single-vessel disease. However, advances in PCI technology (e.g., bare-metal stents and, later, drug-eluting stents) combined with increased operator experience have led to its use for a broader list of indications, including multivessel disease and acute coronary syndromes.^5–7In Ontario, Canada’s most populous province, the overall PCI:CABG ratio has steadily increased, from 1.6 in 2001 to 2.7 in 2006 (unpublished data available from the authors upon request); similar increases have been observed in other jurisdictions.^1,2,8 Although the change in ratio has been driven in part by expanded use of urgent PCI for acute myocardial infarction (MI), increased use of PCI in patients with multivessel disease has likely also been a contributing factor. This application of PCI is more controversial, because several studies, including the recent randomized SYNTAX (Synergy Between Percutaneous Coronary Intervention with TAXUS and Cardiac Surgery) trial, have shown that long-term outcomes of certain patients with multivessel disease were better with CABG surgery than with PCI.^9–13In addition to an overall increase in the PCI:CABG ratio, the amount of variation in the ratio across cardiac centres in Ontario has also steadily increased over time, with more than a threefold regional variation observed in 2006 (unpublished data available from the authors upon request). This degree of variation has raised concerns among some policy-makers and clinicians as to why such striking variations exist in Ontario’s universal health care system. To address this issue, we conducted a comprehensive study to identify clinical and nonclinical factors associated with variations in the PCI:CABG ratio across the province’s 17 cardiac centres.     

2-({6-[(3R)-3-amino-3-methylpiperidine-1-yl]-1,3-dimethyl-2,4-dioxo-1,2,3,4-tetrahydro-5H-pyrrolo[3,2-d]pyrimidine-5-yl}methyl)-4-fluorobenzonitrile (DSR-12727): a potent, orally active dipeptidyl peptidase IV inhibitor without mechanism-based inactivation of CYP3A

We report on the identification of 2-({6-[(3R)-3-amino-3-methylpiperidine-1-yl]-1,3-dimethyl-2,4-dioxo-1,2,3,4-tetrahydro-5H-pyrrolo[3,2-d]pyrimidine-5-yl}methyl)-4-fluorobenzonitrile (DSR-12727) (7a) as a potent and orally active DPP-4 inhibitor without mechanism-based inactivation of CYP3A. Compound 7a showed good DPP-4 inhibitory activity (IC(50)=1.1 nM), excellent selectivity against related peptidases and other off-targets, good pharmacokinetic and pharmacodynamic profile, great in vivo efficacy in Zucker-fatty rat, and no safety concerns both in vitro and in vivo.     

Expression of a xylose-specific transporter improves ethanol production by metabolically engineered Zymomonas mobilis

Zymomonas mobilis is a promising organism for biofuel production as it can produce ethanol from glucose at high rates. However, Z. mobilis does not natively ferment C5 sugars such as xylose. While it has been engineered to do so, the engineered strains do not metabolize these sugars at high rates. Previous research has identified some of the bottlenecks associated with xylose metabolism in Z. mobilis. In this work, we investigated transport as a possible bottleneck. In particular, we hypothesized that the slow uptake of xylose through the promiscuous Glf transporter may limit the efficiency of xylose metabolism in Z. mobilis. To test this hypothesis, we expressed XylE, the low-affinity xylose transporter from Escherichia coli, in a xylose-utilizing strain of Z. mobilis. Our results show that the expression of this pentose-specific transporter improves the rate of xylose utilization in Z. mobilis; however, this enhancement is seen only at high xylose concentrations. In addition, we also found that overexpression of the promiscuous Z. mobilis transporter Glf yielded similar results, suggesting that the transport bottleneck is not due to the specificity, but rather the capacity for sugar uptake.