Indications of species status from total protein signatures in Callithamnion (Ceramiaceae)

Lead mining in Wales originated before the Roman Occupation. The main active period was from 1750–1900 when zinc and copper were also mined and during this period only simple and inefficient ore processing methods were available. Consequently large amounts of copper, lead and zinc compounds were lost to the environment and have since become incorporated in sediments and soils. Locally, pollution may still occur from drainage from abandoned mines and by mobilization of mine tailings. This paper describes the present state of Welsh rivers and reviews the distribution of contaminants in sediments and soils. The uptake of heavy metals by plants and the consequences for human health are alto discussed.     

Fitting a sinusoid to biological rhythm data using ranks

Biological data are frequently collected with small numbers of observations from several subjects. Often a linear model is fitted to the data by averaging over subjects. Frequently there are considerable between-subject differences, and due allowance should be made for these when the model is fitted by parametric techniques. In this paper it is proposed that the model should be fitted by using the within-subject ranks of the observations. The technique is applied to the problem of estimating the 'cosinor' diagram for biological rhythm data. An example involving melatonin levels, in which there are considerable between-subject differences, is considered. The results obtained by use of the ranks are compared with those of a parametric analysis which makes allowance for the between-subject differences. The results are very similar, but the rank analysis requires much less computation.     

Developmental mechanisms in heterospory

The megasporangium of Selaginella sulcata (Desv.) Spring contains approximately equal numbers of megasporocytes of two kinds that can be distinguished on size and ultrastructure. These are called viable and non-viable. During the prophase of meiosis the non-viable megasporocytes degenerate by a process corresponding to cellular autophagy. One viable megasporocyte completes the meiotic cycle and the others persist, presumably as diploid cells, in the post-meiotic megasporangium; and it is shown that in S. plana (Desv.) Hieron an exine is formed on these. The possible significance of the particular disposition of the mitochondria and of intranuclear vesicles in the viable megasporocytes is discussed.     

The complete primary structure of a nematode alpha 2(IV) collagen and the partial structural organization of its gene.

We have isolated and characterized cDNA and genomic DNA clones which encode an alpha 2(IV) collagen chain from the parasitic nematode Ascaris suum. In addition we have determined, by nucleic acid sequence analysis, the structural organization of approximately two-thirds of the gene. This analysis has shown that the gene contains at least 15 introns, and those that have been characterized range in size from 141 to 854 base pairs. The derived protein sequence contains 1763 amino acids and includes a putative 26-amino acid signal sequence. The collagenous triple-helical region contains 17 interruptions, many of which occur in the same positions as those in the human alpha 1(IV) and alpha 2(IV) chains. Comparison of the genomic DNA sequence with the cDNA sequence has revealed the presence of a sequence within the gene which appears to be an intact and normal exon that is not represented in our cDNA sequence. The presence of this putative exon raises the possibility that the A. suum alpha 2(IV) collagen gene may undergo alternative splicing.     

Monoclonal antibodies specific for the core protein of the beta-subunit of the gastric proton pump (H+/K+ ATPase). An autoantigen targetted in pernicious anaemia.

The gastric H+/K(+)-transporting adenosine triphosphatase (H+/K+ ATPase) (proton pump) consists of a catalytic alpha-subunit and a recently proposed 60-90-kDa glycoprotein beta-subunit. Using dog gastric membranes as the antigen, we have produced two murine monoclonal antibodies, 4F11 (IgG1) and 3A6 (IgA), which are specific for the 60-90-kDa glycoprotein. The monoclonal antibodies (1) specifically stained the cytoplasm of unfixed and formalin-fixed dog gastric parietal cells; (2) specifically reacted by ELISA with gastric tubulovesicular membranes; (3) recognised epitopes located on the luminal face of parietal cell tubulovesicular membranes, the site of the proton pump, by immunogold electron microscopy; (4) immunoblotted a 60-90-kDa molecule from tubulovesicular membranes and a 35-kDa component from peptide N-glycosidase-F-treated membrane extracts; (5) immunoblotted the 60-90-kDa parietal cell autoantigen associated with autoimmune gastritis and pernicious anemia, purified by chromatography on parietal cell autoantibody- or tomato-lectin-Sepharose 4B affinity columns, and the 35-kDa protein core of this autoantigen; this autoantigen has amino acid sequence similarity to the beta-subunit of the related Na+/K(+)-transporting adenosine triphosphatase (Na+/K+ ATPase) [Toh et al. (1990) Proc. Natl Acad. Sci. 87, 6418-6422]; (6) co-precipitated a molecule of 95 kDa with the 60-90-kDa molecule from 125I-labelled detergent extracts of dog tubulovesicular membranes; and (7) co-purified the catalytic alpha-subunit of the H+/K+ ATPase with the 60-90-kDa molecule by immunoaffinity chromatography of tubulovesicular membrane extracts on a monoclonal antibody 3A6-Sepharose 4B column, indicating a physical association between the two molecules. These results provide further evidence that the 60-90-kDa glycoprotein is the beta-subunit of the gastric H+/K+ ATPase. We conclude that the monoclonal antibodies specifically recognise luminal epitopes on the 35-kDa core protein of the 60-90-kDa beta-subunit of the gastric proton pump, a major target molecule in autoimmune gastritis and pernicious anaemia. These monoclonal antibodies will be valuable probes to study the structure and function of this associated beta-subunit, as well as the ontogeny of the gastric proton pump.     

Human autoantibodies as reagents to conserved Golgi components. Characterization of a peripheral, 230-kDa compartment-specific Golgi protein.

We have used a serum from a patient with Sj?gren's syndrome containing high titer (100,000) anti-Golgi autoantibodies and lower titer (20,000) anti-nuclear autoantibodies to characterize the Golgi complex. The Sj?gren's syndrome serum immunoprecipitated a number of components of molecular mass 35-230 kDa from detergent extracts of [35S]methionine-labeled HeLa cells; at high dilution, the serum precipitated one major 230-kDa component. Using the Sj?gren's syndrome serum, cDNA clones encoding the Golgi autoantigen were isolated from a lambda gt11 HeLa cell cDNA library. Autoantibodies from the Sj?gren's syndrome serum, affinity purified from a recombinant bacterial fusion protein generated from one of the cDNA clones, showed Golgi staining of human, mouse, and chicken cells by immunofluorescence. The purified autoantibodies immunoprecipitated and immunoblotted a 230-kDa component. A rabbit antiserum raised to the recombinant fusion protein specifically stained the Golgi complex by immunofluorescence and reacted with a 230-kDa protein by immunoprecipitation and immunoblotting. The 230-kDa protein was recovered in both the 100,000 x g sedimentable and soluble fractions in cell lysates and in the aqueous phase of Triton X-114 extracts. The 230-kDa autoantigen was dissociated from the Golgi complex by 15-min brefeldin A treatment, dissociation kinetics similar to that of mannosidase II. However, unlike mannosidase II, autoantigen staining was markedly reduced after drug treatment. Removal of brefeldin A resulted in reassociation of the autoantigen with the Golgi complex. The epitopes recognized by the affinity purified human and rabbit antibodies were ultrastructurally localized to the cytosolic face of one side of the Golgi stack, probably the trans-face. Taken together, the 230-kDa protein is a conserved, peripheral membrane component specifically associated with one Golgi compartment. We suggest that this peripheral Golgi protein may have a role in the compartment-specific structural organization of the Golgi or in sorting and transport of proteins.     

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized.     

Activity of Commercial Enzymes on Settlement and Adhesion of Cypris Larvae of the Barnacle Balanus amphitrite,Spores of the Green Alga Ulva linza,and the Diatom Navicula perminuta

Fouling species produce adhesive polymers during the settlement, adhesion and colonization of new surfaces in the marine environment. The present paper tests the hypothesis that enzymes of the appropriate specificity may prevent biofouling by hydrolysing these adhesive polymers. Seventeen commercially available enzyme preparations designed originally for bulk use in a range of end-use applications were tested for their effects on the settlement and/or adhesion of three major fouling species, viz. the green alga Ulva linza, the diatom Navicula perminuta and the barnacle Balanus amphitrite. The serine-proteases were found to have the broadest antifouling potential reducing the adhesion strength of spores and sporelings of U. linza, cells of N. perminuta and inhibiting settlement of cypris larvae of B. amphitrite. Mode-of-action studies on the serine-protease, Alcalase, indicated that this enzyme reduced adhesion of U. linza in a concentration-dependent manner, that spores of the species could recover their adhesive strength if the enzyme was removed and that the adhesive of U. linza and juvenile cement of B. amphitrite became progressively less sensitive to hydrolysis as they cured.     

Conditioning of surfaces by macromolecules and its implication for the settlement of zoospores of the green alga Ulva linza

Conditioning, ie the adsorption of proteins and other macromolecules, is the first process that occurs in the natural environment once a surface is immersed in seawater, but no information is available either regarding the conditioning of surfaces by artificial seawater or whether conditioning affects data obtained from laboratory assays. A range of self-assembled monolayers (SAMs) with different chemical terminations was used to investigate the time-dependent formation of conditioning layers in commercial and self-prepared artificial seawaters. Subsequently, these results were compared with conditioning by solutions in which zoospores of the green alga Ulva linza had been swimming. Spectral ellipsometry and contact angle measurements as well as infrared reflection absorption spectroscopy (IRRAS) were used to reveal the thickness and chemical composition of the conditioning layers. The extent that surface preconditioning affected the settlement of zoospores of U. linza was also investigated. The results showed that in standard spore settlement bioassays (45–60 min), the influence of a molecular conditioning layer is likely to be small, although more substantial effects are possible at longer settlement times.     

Amphiphilic block copolymer/poly(dimethylsiloxane) (PDMS) blends and nanocomposites for improved fouling-release

Amphiphilic diblock copolymers, Sz6 and Sz12, consisting of a poly(dimethylsiloxane) block (average degree of polymerisation = 132) and a PEGylated-fluoroalkyl modified polystyrene block (Sz, average degree of polymerisation = 6, 12) were prepared by atom transfer radical polymerization (ATRP). Coatings were obtained from blends of either block copolymer (1–10 wt%) with a poly(dimethylsiloxane) (PDMS) matrix. The coating surface presented a simultaneous hydrophobic and lipophobic character, owing to the strong surface segregation of the lowest surface energy fluoroalkyl chains of the block copolymer. Surface chemical composition and wettability of the films were affected by exposure to water. Block copolymer Sz6 was also blended with PDMS and a 0.1 wt% amount of multiwall carbon nanotubes (CNT). The excellent fouling-release (FR) properties of these new coatings against the macroalga Ulva linza essentially resulted from the inclusion of the amphiphilic block copolymer, while the addition of CNT did not appear to improve the FR properties.