DNA recognition by the EcoK methyltransferase. The influence of DNA methylation and the cofactor S-adenosyl-L-methionine

The methyltransferase of the EcoK type I restriction/modification system is trimeric, M2S1, where the S subunit determines the sequence specificity of the enzyme. The methyltransferase has a strong preference for hemimethylated substrate DNA and, therefore, we have investigated the effect of the methylation state of DNA on binding by the enzyme, together with the effects on binding of the cofactor S-adenosyl-L-methionine. Our results indicate that the methyltransferase has two non-interacting S-adenosyl-L-methionine binding sites, each with a dissociation constant of 3.60 (+/- 0.42) microM determined by equilibrium dialysis, or 2.21 (+/- 0.29) microM determined by the displacement of a fluorescent probe. Ultraviolet light-induced crosslinking showed that S-adenosyl-L-methionine binds strongly only to the modification (M) subunits. Changes in the sedimentation velocity of the methyltransferase imply a protein conformational change due to S-adenosyl-L-methionine binding. Gel retardation results show that the binding of S-adenosyl-L-methionine to the methyltransferase enhances binding to both specific and non-specific DNAs, but the enhancement is greater for the specific DNA. Differences in binding affinities contribute to the recognition of the specific nucleotide sequence AAC(N)6GTGC by the methyltransferase in preference to a non-specific sequence. In contrast, although the complexes of unmodified and hemimethylated DNAs with the methyltransferase have different mobilities in non-denaturing gels, there appears to be no contribution of binding affinity to the distinction between these two substrates. Therefore, the preference for a hemimethylated substrate must be due to a difference in catalysis.     

Detection of Fibre Waviness Using Ultrasonic Array Scattering Data

Composite materials owe their success to the ability to favour mechanical properties in specific directions whilst minimising the weight of components. Although the composite manufacturing process has been progressively improved, subtle defects such as fibre waviness are still commonplace. Any localised departure of a ply from the desired lay-up direction is known to adversely affect strength. Therefore, manufacturers and end users are interested in detecting defects such as fibre waviness at various stages during prototyping and as part of the manufacturing process. In this paper, an ultrasonic array is used to both image the composite and extract information that characterises the scattering of the interior structure. The scattering information is encoded in the scattering matrix: defined as the far field amplitude of scattered signals from a defect as a function of the incident and scattering angles. A method for extracting the scattering matrix from experimental array data over a spatially localised region is presented. Ultimately this could lead to the ability to map the distribution of scattering behaviour within the composite. The method is demonstrated on composite samples containing various levels of waviness. It is also shown that use of the differences in the scattering matrices can offer the possibility to statistically differentiate wavinesses of different nature and severity.     

A finite element formulation to model the flow of flotation foams

In this paper, a numerical model for the flow of foams in flotation cells in up to three dimensions is described. By using finite elements to solve Laplace's equation for a potential scalar, the flow pattern and velocity of the foam can be obtained. This has allowed, for the first time, the carrying out of numerical investigations of foam flow patterns regardless of the symmetry of the system. The numerical model has been implemented in Fluidity, a general purpose finite element method code that allows simulations to be carried out on anisotropic unstructured meshes. Such a model is of particular interest since other phenomena occurring in flotation depend on the foam velocity. Convergence tests that verify the numerical model are presented, and simulation results that showcase important features of the present implementation are discussed.     

GeSe4 glass fibres with low optical losses in the mid-IR

This study proposes the realisation of low-loss fibres in the Ge–Se system. Ge–Se chalcogenide fibres are transparent in the near and middle infrared and show a high non linear refractive index. So, such fibres are of high interest for new optical applications like all optical telecommunication provided that optical losses be sufficiently low. To decrease the optical losses of fibres, several GeSe₄ glasses have been prepared with different chemical and physical purification steps and thorough distillation of selenium under dynamic vacuum. The lowest the optical losses of GeSe₄ fibre are lower than 0.5 dB/m between 1.7 and 7.5 μm except at 4.5 μm where losses are equal to 2.8 dB/m because of Se–H absorption.     

Isotopic identification of the sources of lead contamination for white storks (Ciconia ciconia) in a marshland ecosystem (Doñana,S.W. Spain)

White storks (Ciconia ciconia) fed in contaminated waters resulting from the Aznacollar acid mining-sludge spillage into the R. Guadiamar, which feeds the eastern flank of the Guadalquivir marshes (Do?ana), S.W. Spain. The sludge was rich in a range of toxic elements, and in organic pollutants such as the aromatic amines. Storks did not exhibit elevated metals in their blood immediately following the accident, but chick blood collected the year following the accident showed genotoxic damage compared to the controls. In this study lead isotope analysis was used to assess if the storks had ingested sludge-derived contaminants. The sludge lead isotope ratio was distinct from that of the Do?ana sediments. The stork blood lead isotope ratios exactly matched that of the sludge. It was concluded that the storks had ingested sludge-derived contaminants. A detailed study of the lead contamination along the R. Guadiamar and the R. Guadalquivir (of which the Guadiamar is a tributary) was also conducted to place the white stork colony lead exposure in the context of the spatial contamination of the storks' habitat.     

The existence of a precursor of cathepsin D: evidence from autolysis, denaturation and activation studies

This report evidences that the single polypeptide chain of cathepsin D undergoes in vitro autolysis resulting in heavy (Mr about 30000) and light (Mr about 15000) polypeptide chains. These two chains are held together through non-covalent interaction, thus constituting a stable active conformation. Fluorescence and circular dichroism measurements demonstrate the irreversible denaturation of cathepsin D. The existence of cathepsin D precursor, cathepsinogen D, of about 50000 molecular weight was proved. Cathepsinogen D is converted to the active enzyme by intramolecular activation, releasing activation-inhibitory peptide(s).     

Characterization of Early Enzymes Involved in TDP‐Aminodideoxypentose Biosynthesis en Route to Indolocarbazole AT2433

The characterization of TDP‐α‐d ‐glucose dehydrogenase (AtmS8), TDP‐α‐d ‐glucuronic acid decarboxylase (AtmS9), and TDP‐4‐keto‐α‐d ‐xylose 2,3‐dehydratase (AtmS14), involved in Actinomadura melliaura AT2433 aminodideoxypentose biosynthesis, is reported. This study provides the first biochemical evidence that both deoxypentose and deoxyhexose biosynthetic pathways share common strategies for sugar 2,3‐dehydration/reduction and implicates the sugar nucleotide base specificity of AtmS14 as a potential mechanism for sugar nucleotide commitment to secondary metabolism. In addition, a re‐evaluation of the AtmS9 homologue involved in calicheamicin aminodeoxypentose biosynthesis (CalS9) reveals that CalS9 catalyzes UDP‐4‐keto‐α‐d ‐xylose as the predominant product, rather than UDP‐α‐d ‐xylose as previously reported. Cumulatively, this work provides additional fundamental insights regarding the biosynthesis of novel pentoses attached to complex bacterial secondary metabolites.     

Lead contamination and associated disease in captive and reintroduced red kites Milvus milvus in England

Since 1989, a red kite Milvus milvus reintroduction programme has been underway in the United Kingdom, with 4-6 week old nestlings brought into captivity and held for 6-8 weeks before reintroduction. As scavengers, red kites may consume unretrieved game, and ingest shot or lead (Pb) fragments in their prey's flesh. We evaluated exposure to Pb in captive and wild red kites by taking blood samples from 125 captive young red kites prior to release, through analysing 264 pellets (regurgitated by wild birds) collected from under a roost site, and analysing Pb concentrations in livers and/or bones of 87 red kites found dead between 1995 and 2003. Lead isotope analyses of livers were also conducted in an effort to identify Pb exposure routes. Forty-six (36.8%) kites sampled prior to release had elevated blood Pb concentrations (201-3340 microg l(-1)). The source of this Pb was probably small fragments of lead ammunition in the carcasses of birds or mammals either fed to the nestlings by their parents or, more likely, subsequently whilst in captivity. Once released, kites were also exposed to lead shot in their food, and a minimum of 1.5-2.3% of regurgitated pellets contained Pb gunshot. Seven of 44 red kites found dead or that were captured sick and died within a few days had elevated (>6 mg kg(-1) dry weight [d.w.]) liver Pb concentrations, and six of these (14%) had concentrations of >15 mg kg(-1) d.w., compatible with fatal Pb poisoning. Post-mortem analyses indicated that two of these birds had died of other causes (poisoning by rodenticide and a banned agricultural pesticide); the remaining four (9%) probably died of Pb poisoning. Bone samples from 86 red kites showed a skewed distribution of Pb concentration, and 18 samples (21%) had Pb concentrations >20 mg kg(-1) d.w., indicating elevated exposure to Pb at some stage in the birds' life. Lead isotopic signatures (Pb (208/206); Pb (206/207)) in liver samples of the majority of kites were compatible with those found in lead shot extracted from regurgitated pellets. Lead isotope ratios found in the livers of kites with very low Pb concentrations were distinct from UK petrol Pb isotopic signatures, indicating that birds were exposed to little residual petrol Pb. We conclude that the primary source of Pb to which red kites are exposed is lead ammunition (shotgun pellets or rifle bullets), or fragments thereof, in their food sources; in some cases exposure appears sufficient to be fatal. We make recommendations to reduce Pb poisoning in both captive and wild red kites and other scavenging species.