Angiotensin II and noradrenaline increase PDGF-BB receptors and potentiate PDGF-BB stimulated DNA synthesis in vascular smooth muscle

The effects of angiotensin II and noradrenaline were examined on PDGF-BB and PDGF-AB induced mitogenesis in primary cultures of rat aortic smooth muscle. Incubation of the smooth muscle with either angiotensin II or noradrenaline potentiated the submaximal but not maximal mitogenic effects of PDGF-BB but not PDGF-AB. These effects on PDGF-BB stimulated mitogenesis correlated with an increase in receptor number specific for this homodimer when the smooth muscle was incubated with either angiotensin II or noradrenaline. Mitogenic concentrations of PDGF-AB did not interact with this PDGF receptor subtype. These results indicate that the mitogenic effects of PDGF-AB and -BB are elicited via different PDGF receptor subtypes. Angiotensin II and noradrenaline potentiate the mitogenic effects of PDGF-BB by increasing the steady state concentrations of membrane receptors for this homodimer.     

Enhanced biotransformations and product recovery in a membrane bioreactor through application of a direct electric current

The simultaneous enhancement of biotransformation coupled to product recovery, purification and concentration is presented. The nitrilase of Rhodococcus rhodochrous LL100-21 catalyses the single-step hydrolytic biotransformation of benzonitrile to benzoic acid and ammonia. When a direct electric current is applied across a bioreactor containing the bacterium and benzonitrile, the charged product (benzoic acid) can be removed in situ across an anion exchange membrane and recovered in a separate compartment. Over the course of a 24-hour biotransformation, benzonitrile was converted to benzoic acid which was completely removed from the bioreactor chamber and concentrated 3-fold in a separate chamber. The rate of production of benzoic acid increased by 42% when the current was applied (0.044 mmol/min/g dry cell weight in the presence of current as compared to 0.03 mmol/min/g dry cell weight in its absence). The enhanced reaction rate was achieved irrespective of product separation and therefore appears to be a direct effect upon the bacterial cells. This process has potential for enhanced productivity from biotransformations through a simultaneous increase in metabolic activity and in situ product recovery.     

Development of an assay for the estimation of N10-propargyl-5,8-dideazafolic acid polyglutamates in tumor cells

A method is described herein for the isolation and quantitation of polyglutamates of the thymidylate synthase (TS) inhibitor N10-propargyl-5,8-dideazafolic acid (CB3717) in tumor cells exposed to the drug in vitro. Cells were incubated with 50 microM 3H-CB3717 for 12 h and then disrupted by sonication. CB3717 and its polyglutamates were extracted by boiling in 0.01 M Tris-HCl pH 10. The extract was concentrated by lyophilization and analyzed by reverse phase HPLC (10 x 0.46-cm Polygosil 5-micron C18 column) using linear gradient elution (5-16% acetonitrile in 0.1 M sodium acetate, pH 5, over 15 min, 2 ml/min). Recovery of radioactivity at each stage of the method was greater than 70%. CB3717 and its polyglutamates were identified by co-chromatography with synthetic standards and by inhibition of partially purified TS. Quantitation was by means of radiochemical analysis. The 3H-CB3717 used in these studies was prepared by catalytic tritiation of diethyl-(2-chloro-4-nitrobenzoyl)-L-glutamate followed by consecutive alkylation with propargyl bromide and 2-amino-6-bromomethyl-3,4-dihydro-4-oxoquinazoline hydrobromide. The free diacid was prepared as required by hydrolysis in sodium hydroxide and purified by HPLC. Tritiation in only one position was confirmed by 3H NMR. Following the exposure of L1210 leukemia cells to 50 microM 3H-CB3717 for 12 h the total cellular radioactivity level was approximately 7 microM, of which 27% was present as polyglutamated metabolites with four and five glutamate residues.     

Characterization of Corynebacterium group JK by whole-cell protein patterns

A total of 102 strains received as Corynebacterium 'group JK' were characterized by SDS-PAGE of their whole-cell proteins. Numerical taxonomy based on the protein pattern absorbance profiles indicated that 91 of the strains formed a cluster. Seventy strains isolated in the UK were identified as group JK, indicating the increasing detection of this group as opportunistic pathogens. Fine differences between strain patterns were visible but it was not possible to associate these with any particular clinical source.     

Long-Term Cognitive and Behavioral Outcomes following Resolution of Sleep Disordered Breathing in Preschool Children

This study aimed to determine the long term effects of resolution of SDB in preschool children, either following treatment or spontaneous recovery, on cognition and behavior. Children diagnosed with SDB at 3-5y (N = 35) and non-snoring controls (N = 25), underwent repeat polysomnography (PSG) and cognitive and behavioral assessment 3 years following a baseline study. At follow-up, children with SDB were grouped into Resolved and Unresolved. Resolution was defined as: obstructive apnea hypopnea index (OAHI) ≤1 event/h; no snoring detected on PSG; and no parental report of habitual snoring. 57% (20/35) of children with SDB received treatment, with SDB resolving in 60% (12/20). 43% (15/35) were untreated, of whom 40% (6/15) had spontaneous resolution of SDB. Cognitive reduced between baseline and follow-up, however this was not related to persistent disease, with no difference in cognitive outcomes between Resolved, Unresolved or Control groups. Behavioral functioning remained significantly worse in children originally diagnosed with SDB compared to control children, regardless of resolution. Change in OAHI did not predict cognitive or behavioral outcomes, however a reduction in nocturnal arousals, irrespective of full resolution, was associated with improvement in attention and aggressive behavior. These results suggest that resolution of SDB in preschool children has little effect on cognitive or behavioral outcomes over the long term. The association between sleep fragmentation and behavior appears independent of SDB, however may be moderated by concomitant SDB. This challenges the assumption that treatment of SDB will ameliorate associated cognitive and behavioural deficits and supports the possibility of a SDB phenotype.     

Sealer: a scalable gap-closing application for finishing draft genomes

Background

While next-generation sequencing technologies have made sequencing genomes faster and more affordable, deciphering the complete genome sequence of an organism remains a significant bioinformatics challenge, especially for large genomes. Low sequence coverage, repetitive elements and short read length make de novo genome assembly difficult, often resulting in sequence and/or fragment “gaps” – uncharacterized nucleotide (N) stretches of unknown or estimated lengths. Some of these gaps can be closed by re-processing latent information in the raw reads. Even though there are several tools for closing gaps, they do not easily scale up to processing billion base pair genomes.

Results

Here we describe Sealer, a tool designed to close gaps within assembly scaffolds by navigating de Bruijn graphs represented by space-efficient Bloom filter data structures. We demonstrate how it scales to successfully close 50.8 % and 13.8 % of gaps in human (3 Gbp) and white spruce (20 Gbp) draft assemblies in under 30 and 27 h, respectively – a feat that is not possible with other leading tools with the breadth of data used in our study.

Conclusion

Sealer is an automated finishing application that uses the succinct Bloom filter representation of a de Bruijn graph to close gaps in draft assemblies, including that of very large genomes. We expect Sealer to have broad utility for finishing genomes across the tree of life, from bacterial genomes to large plant genomes and beyond. Sealer is available for download at https://github.com/bcgsc/abyss/tree/sealer-release.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0663-4) contains supplementary material, which is available to authorized users.     

RCL hydrolyzes 2'-deoxyribonucleoside 5'-monophosphate via formation of a reaction intermediate

RCL is an enzyme that catalyzes the N-glycosidic bond cleavage of purine 2'-deoxyribonucleoside 5'-monophosphates. Recently, the structures of both free wild type and GMP-bound mutant complex have been determined by multidimensional NMR, revealing a doubly wound α/β protein existing in a symmetric homodimer. In this work, we investigated the catalytic mechanism by rational site-directed mutagenesis, steady-state and pre-steady-state kinetics, ITC binding analysis, methanolysis, and NMR study. First, we provide kinetic evidence in support of the structural studies that RCL functions in a dimeric form, with an apparent dissociation constant around 0.5 μM in the presence of substrate dGMP. Second, among the eight residues under investigation, the highly conserved Glu93 is absolutely critical and Tyr13 is also important likely contributing to the chemical step, whereas Ser117 from the neighboring subunit and Ser87 could be the key residues for the phosphate group recognition. Lastly, we demonstrate by methanolysis study that the catalytic reaction proceeds via the formation of a reaction intermediate, which is subsequently hydrolyzed by solvent nucleophile resulting in the formation of normal product deoxyribose monophosphate (dR5P) or methoylated-dR5P. In conclusion, the current study provides mechanistic insights into a new class of nucleotide hydrolase, which resembles nucleoside 2'-deoxyribosyltransferases structurally and functionally but also possesses clear distinction.