Studies towards the development of chemically synthesized non-radioactive biotinylated nucleic acid hybridization probes.

Non-radioactive nucleic acid hybridization probes have been constructed in which the reporter group is long chain biotin chemically linked to a basic macromolecule (histone H1, cytochrome C or polyethyleneimine). The modified basic macromolecule which carries many biotin residues can, in turn, be covalently linked to nucleic acids (DNA) via the bifunctional cross-linking reagents, glutaraldehyde, 1,2,7,8-diepoxyoctane, bis (succinimidyl) suberate or bis (sulfonosuccinimidyl) suberate. This provides a very sensitive probe by which as little as between 10-50fg of target DNA can be visualized using dot-blot hybridization procedures in conjunction with avidin or streptavidin enzyme conjugates.     

A century of landscape disturbance and urbanization of the San Francisco Bay region affects the present-day genetic diversity of the California Ridgway’s rail (<Emphasis Type="Italic">Rallus obsoletus obsoletus</Emphasis>)

Fragmentation and loss of natural habitat have important consequences for wild populations and can negatively affect long-term viability and resilience to environmental change. Salt marsh obligate species, such as those that occupy the San Francisco Bay Estuary in western North America, occupy already impaired habitats as result of human development and modifications and are highly susceptible to increased habitat loss and fragmentation due to global climate change. We examined the genetic variation of the California Ridgway’s rail (Rallus obsoletus obsoletus), a state and federally endangered species that occurs within the fragmented salt marsh of the San Francisco Bay Estuary. We genotyped 107 rails across 11 microsatellite loci and a single mitochondrial gene to estimate genetic diversity and population structure among seven salt marsh fragments and assessed demographic connectivity by inferring patterns of gene flow and migration rates. We found pronounced genetic structuring among four geographically separate genetic clusters across the San Francisco Bay. Gene flow analyses supported a stepping stone model of gene flow from south-to-north. However, contemporary gene flow among the regional embayments was low. Genetic diversity among occupied salt marshes and genetic clusters were not significantly different. We detected low effective population sizes and significantly high relatedness among individuals within salt marshes. Preserving genetic diversity and connectivity throughout the San Francisco Bay may require attention to salt marsh restoration in the Central Bay where habitat is both most limited and most fragmented. Incorporating periodic genetic sampling into the management regime may help evaluate population trends and guide long-term management priorities.     

The error in the cryptic stereospecificity of methylmalonyl-CoA mutase. The use of carba-(dethia)-coenzyme A substrate analogues gives new insight into the enzyme mechanism

A preparation containing 80.0 +/- 0.5% (2RS)-methylmalonyl-carba-(dethia)-CoA and 20.0 +/- 0.5% propionyl-carba-(dethia)-CoA was reacted in buffered deuterium oxide with catalytic amounts of coenzyme B12, methylmalonyl-CoA mutase and methylmalonyl-CoA epimerase. The rearrangement of the methylmalonyl-carba-(dethia)-CoA to succinyl-carba-(dethia)-CoA was monitored by recording 500-MHz 1H-NMR spectra in short time intervals. After reaching equilibrium (approximately equal to 28 min) the products showed chemical stability for about 17 h, i.e. succinyl species did not undergo the spontaneous hydrolysis encountered with normal succinyl-CoA. In the pre-equilibrium stage only about 66% of the produced succinyl-CH2CoA was the expected monodeuterated species. The remainder was 15.5% unlabelled and 18.3% 3,3-dideuterated. After reaching equilibrium a continuous deuterium incorporation (washing-in) from the solvent to the products was observed and quantified. The time course of the appearance of unlabelled, mono-, di- and trideuterated succinyl-CH2CoA species was determined by assigning and integrating the isotope-shifted 1H signals from the various species. Furthermore, mutase catalyses slow deuterium incorporation into first the methylene and then the methyl group of propionyl-CH2CoA. On the basis of these data it was concluded that methylmalonyl-CoA mutase and epimerase are responsible for continuous deuterium incorporation and multiple incorporation occurs when the backward reaction (succinyl-CH2CoA----methylmalonyl-CH2CoA) becomes important. To account for all of the results obtained with dethia and natural substrates we propose a new mutase mechanism whereby the enzyme can retain full stereospecificity at C-3 of succinyl while an internal 1,2-H shift to give a C-2 succinyl radical is responsible for partial scrambling of diastereotopic protons at C-3. This mechanism successfully predicts the observed deuterium disproportionation in succinyl species and the order of appearance of di- and trideuterated products via the washing-in process.     

Identification of canine pulmonary surfactant-associated glycoprotein A precursors

Surfactant-associated glycoproteins A were identified by two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis of crude surfactant from canine alveolar lavage: an unglycosylated form (protein A1), 27,000-28,000 daltons; glycoprotein A2, 32,000-34,000 daltons; and glycoprotein A3, 37,000-38,000 daltons; pH at isoelectric point (pI) 4.5-5.0. Glycoproteins A2 and A3 were electroeluted and used to prepare a monospecific antiserum that identified proteins A1, A2, and A3 in immunoblots of crude surfactant obtained from dog lung lavage. This antiserum precipitated several proteins from in vitro translated canine lung poly(A)+ mRNA; proteins of 27,000 daltons, pI 5.0, and 28,000 daltons, pI 4.8-5.0, which precisely comigrated with proteins A1 from canine surfactant. Cotranslational processing of the primary translation products by canine pancreatic microsomal membranes resulted in larger proteins of 31,000-34,000 daltons, pI 4.8-5.0. Treatment of these processed forms of glycoprotein A with endoglycosidase F, to remove N-linked carbohydrate, resulted in proteins of 27,000-28,000 daltons which precisely comigrated with surfactant protein A1. These observations demonstrate that the polypeptide precursors to the glycoproteins A complex are extensively modified by addition of asparagine N-linked complex carbohydrate and are subsequently secreted as glycoproteins A2 and A3.     

Bacterial expression and purification of the Arabidopsis NADPH-cytochrome P450 reductase ATR2

An N-terminally modified form of the Arabidopsis NADPH-cytochrome P450 ATR2 (ATR2mod) was expressed from the tactac promoter in Escherichia coli to obtain high yields of the enzyme. The N-terminal modification eliminates the predicted chloroplast transit peptide of ATR2 allowing for more efficient expression. ATR2mod was purified from membrane extracts using a 2',5'-ADP-agarose affinity column. The specific activity of the purified ATR2mod for cytochrome c reduction was 9.4 micromol min(-1) mg(-1) and the K(m) for cytochrome c reduction was 15 +/- 2 microM. The purified NADPH-cytochrome P450 reductase was able to support function of CYP79B2.     

Rapid recovery of benthic invertebrates downstream of hyperalkaline steel slag discharges

This study assesses the physical and chemical characteristics of hyperalkaline steel slag leachate from a former steelworks on two streams in England and their impacts on benthic invertebrate communities. Using multivariate methods (CCA), we related invertebrate richness and diversity with chemical parameters along the environmental gradient from point sources to less impacted sites downstream. Point discharges are characterised by high pH (10.6–11.5), high ionic strength (dominated by Ca–CO₃–OH waters), elevated trace elements (notably Li, Sr and V) and high rates of calcium carbonate precipitation. This combination of stressors gives rise to an impoverished benthic invertebrate community in source areas. The total abundance, taxonomic richness and densities of most observed organisms were strongly negatively correlated with water pH. Analysis using biological pollution monitoring indices (e.g. BMWP and Functional Feeding Groups) shows the system to be highly impacted at source, but when pH approaches values close to aquatic life standards, some 500 m downstream, complex biological communities become established. In addition to showing the rapid recovery of invertebrate communities downstream of the discharges, this study also provides a baseline characterisation of invertebrate communities at the extreme alkaline range of the pH spectrum.     

EUROCarbDB: An open-access platform for glycoinformatics

The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb.     

beta-Hydroxy acyl-CoA inhibition of mitochondrial ATP production

beta-Hydroxypalmitoyl-CoA and beta-hydroxystearoyl-CoA were synthesized, purified and quantitated. beta-Hydroxypalmitoyl-CoA and beta-hydroxystearoyl-CoA instantly and reversibly inhibited oxidative phosphorylation by rabbit heart mitochondria oxidizing pyruvate. [8-14C]ADP uptake studies showed that the beta-hydroxy acyl-CoA species linearly inhibited the adenine nucleotide translocase system. Free beta-hydroxy fatty acids at comparable concentrations (0.005 mM) did not affect ADP uptake or state III respiration.     

An MRI-based method to align the compressive loading axis for human cadaveric knees

There is a need to align the mechanical axis of the tibia with the axis of loading for studies involving tibiofemoral compression to interpret results and to ensure repeatability of loading within and among specimens. Therefore, the objectives of this study were (1) to develop a magnetic resonance imaging (MRI)-based alignment method for use with apparatuses applying tibiofemoral joint compression, (2) to demonstrate the usefulness of the method by aligning cadaveric knees in an apparatus that could apply tibiofemoral joint compression, and (3) to quantify the error associated with the alignment method. A four degree-of-freedom adjustable device was constructed to allow determination and alignment of the mechanical axis of the tibia of cadaveric knee joints with the axis of loading of an apparatus applying tibiofemoral joint compression. MRI was used to determine the locations of bony landmarks in three dimensions defining the mechanical axis of the tibia relative to an initial orientation of the four degree-of-freedom device. Adjustment values of the device were then computed and applied to the device to align the mechanical axis of the tibia with the axis of a compressive loading apparatus. To demonstrate the usefulness of the method, four cadaveric knees were aligned in the compressive loading apparatus. The vectors describing the mechanical axis of the tibia and the loading axis of the apparatus before and after adjustment of the four degree-of-freedom device were computed for each cadaveric knee. After adjustment of the four degree-of-freedom device, the mechanical axis of the tibia was collinear with the loading axis of the apparatus for each cadaveric knee. The errors in the adjustment values introduced by inaccuracies in the MR images were quantified using the Monte Carlo technique. The precisions in the translational and rotational adjustments were 1.20 mm and 0.90 deg respectively. The MR-based alignment method will allow consistent interpretation of results obtained during tibiofemoral compressive studies conducted using the apparatus described in this paper by providing a well-defined loading axis. The alignment method can also be adapted for use with other apparatuses applying tibiofemoral compression.