Prokaryotic biodiversity and activity in the deep subseafloor biosphere

The deep subseafloor biosphere supports a diverse population of prokaryotes belonging to the Bacteria and Archaea. Most of the taxonomic groups identified by molecular methods contain mainly uncultured phylotypes. Despite this several cultured strains have been isolated from this habitat, but they probably do not represent the majority of the population. Evidence is starting to suggest that some of the activities measured, such as sulphate reduction and methanogenesis, reflected in geochemical profiles, are carried out by a small subset of the community detected by molecular methods. It is further possible that heterotrophy may be the most important mode of metabolism in subsurface sediments and heterotrophic microorganisms could dominate the uncultured prokaryotic population. Although, heterotrophy is limited by the increasing recalcitrance of organic matter with depth, this may be counteracted by thermal activation of buried organic matter providing additional substrates at depth.     

Pix1 and Pix2 are novel WD40 microtubule-associated proteins that colocalize with mitochondria in Xenopus germ plasm and centrosomes in human cells

In many animals, the germ line develops from a distinct mitochondria-rich region of embryonic cytoplasm called the germ plasm. However, the protein composition of germ plasm and its formation remain poorly understood, except in Drosophila. Here, we show that Xpat, a recently identified protein component of Xenopus germ plasm, interacts via its C-terminal domain with a novel protein, xPix1. Xpat and xPix1 are co-expressed in ovaries, eggs and early embryos and colocalize to the mitochondrial cloud and germ plasm in stage I and stage VI oocytes, respectively. Although Xpat appears unique to Xenopus, Pix proteins, which contain an N-terminal WD40 domain and C-terminal coiled-coil, are widely conserved. In humans, two proteins, Pix1 and Pix2, are expressed at varying levels in different cancer cell lines. Importantly, as well as localizing to mitochondria, human Pix proteins localize to centrosomes and associate with microtubules in vitro and in vivo. Although, Pix proteins are stably expressed through the cell cycle, Pix2 concentrates on microtubule structures in mitosis and microinjection of Pix antibodies interferes with cell division. Based on these data, we propose that Pix1 and Pix2 are microtubule-associated adaptor proteins that likely contribute to a range of developmental and cell division processes.     

Oxidative coupling of tyrosine and ferulic acid residues: Intra- and extra-protoplasmic occurrence,predominance of trimers and larger products,and possible role in inter-polymeric cross-linking

I discuss the range of oxidative phenolic coupling products formed from the tyrosine residues of cell wall glycoproteins and from the feruloyl residues of wall polysaccharides possibly by the action of peroxidases and/or laccases. In the cases of both tyrosine- and ferulate-coupling, the coupling products are not confined to dimers but include trimers and probably higher oligomers, which are sometimes predominant. Thus, some previous assays, in which specifically dimers were monitored, will have underestimated the extent of phenolic coupling. The possibility is discussed that some of the phenolic coupling products, in both glycoproteins and polysaccharides, are inter-polymeric and that they may therefore act as cross-links in the cell wall. The limitations in the evidence for this hypothesis are stressed. The sub-cellular site of oxidative phenolic coupling is discussed. In-vivo radiolabelling of cultured maize cells with [¹⁴C]cinnamate has shown that, especially in young, rapidly growing cultures, much oxidative coupling of feruloyl-arabinoxylans occurs within the endomembrane system, before secretion of the polysaccharides into the cell wall. Appreciable feruloyl coupling within the cell wall depended on the supply of H₂O₂ and on culture age. The situation with tyrosine coupling in glycoproteins is also debated. Although peroxidase activity has long been known to occur in the endomembrane system, the recent finding of intraprotoplasmic feruloyl coupling provided the first evidence that peroxidases (and/or laccases) may act in this sub-cellular location in vivo. I draw attention to the distinction between peroxidase action (in vivo) and activity (assayed in vitro), and to the unknown origin of H₂O₂ within the endomembrane system.     

Detection of HSV type-1 and type-2 IgG using an in vitro PCA based homogeneous immunoassay

Enzyme immunoassays (EIAs) are widely used in the clinical laboratory and research institutes for the detection of biologically relevant analytes. Almost all EIAs are heterogeneous in nature and require multiple steps of process. In contrast, homogeneous immunoassays (HA) offer a simplified one-step approach with a number of potential advantages over contemporary heterogeneous EIAs such as higher throughput and greater clinical utility. Utilizing TEM-1 β-lactamase as a reporter enzyme, we have developed HAs based on in vitro protein fragment complementation (PCA) for the detection of antibodies and potentially be used for antigens or other biomarkers. In this proof-of-principle study we demonstrate the successful in vitro differentiation of anti-herpes simplex virus (HSV) type-1 and type-2 Immunoglobulin G (IgG) in human serum with high sensitivity and specificity.     

A proposed role for copper ions in cell wall loosening

The measurement of N₂ fixation by legumes is necessary for gaining an understanding of their contributions to the N economies of agricultural and forestry systems and for their management in those systems. We report research to determine whether N₂ fixation of four of the commonly-grown ureide-producing legumes, soybean (Glycine max), cowpea (Vigna unguiculata), mungbean (V. radiata) and black gram (V. mungo), could be quantified from a single sampling and N-solute analysis of xylem sap. Data were derived from a previously-published experiment involving six genotypes of soybean at five field sites and from a second, irrigated experiment in which two genotypes of soybean, and one each of cowpea, mungbean and black gram were assessed in low- and high-nitrate soils for nodulation, yields of shoot and grain dry matter and N, and N₂ fixation using xylem solute (ureide) and ¹⁵N methods. Regression analysis of the published soybean data set indicated that the early pod-fill (R3.5 and R4) samplings for xylem sap gave estimates of percentage of plant N derived from N₂ fixation (%Ndfa) which agreed well with %Ndfa for the entire growing season obtained from ¹⁵N analysis of the shoots at R6-7. There was a marginal benefit in combining the R3.5 and R4 samplings and using the average of the two, with regression coefficients (r ²) increasing from 0.86 (R3.5 or R4 alone) to 0.92 (average of R3.5+R4). There was no additional benefit in combining R3, R3.5 and R4. In the second experiment, agreement between ¹⁵N-determined %Ndfa and either measured (R4 sampling) or calculated ureide-determined %Ndfa (R3.5 sampling) was also good (r ² of 0.73 (R4) and 0.79 (R3.5)). We conclude that seasonal %Ndfa can be accurately estimated using the xylem solute (ureide) method from a single sampling of xylem sap during early pod-fill (R3.5) and that this simplification of the protocol of the technique may encourage expanded use.     

The Influence of Landscape Grain Size on Butterfly Diversity in Grasslands

The relationship between butterfly diversity and both habitat and landscape variables was studied in two areas of southern Sweden. The habitat quality of the grasslands was similar in the two study areas but the landscape pattern differed in grain size and amount of grassland and forest. Using a transect survey method, a total of 3341 butterflies were observed and 30 taxa identified. We found that both habitat and landscape variables influenced the butterfly diversity of the investigated grasslands. Species composition differed markedly between the two study areas. A study area with a fine-grained landscape pattern, a high cover of semi-natural grassland and many forest edges had twice as many butterfly species but half the number of individuals compared with a coarser-grained study area with larger grasslands widely spread in a matrix of arable fields. The results of our study indicate that both habitat quality and landscape pattern have to be considered when developing conservation strategies for grassland butterflies.     

Plasmid transfer between Pseudomonas spp. within epilithic films in a rotating disc microcosm

Abstract A microcosm using rotating slate discs in a chemostat was used to study bacterial population dynamics and genetic interactions in river epilithon. Populations of all introduced donor and recipient Pseudomonas spp. decreased with time but all the bacteria survived better on the slate discs than in the liquid phase. Conjugal transfer of an epilithic plasmid encoding mercury resistance (pQM1) occured with transfer frequencies of 1.4 × 10⁻⁶ to 3.6 × 10⁻³ per recipient, which were about 100-fold lower than in standard membrane filter mating experiments.