Further studies on the GS element. A novel mycobacterial insertion sequence (IS1612), inserted into an acetylase gene (mpa) in Mycobacterium avium subsp. silvaticum but not in Mycobacterium avium subsp. paratuberculosis

We have recently described the GS element, found in Mycobacterium avium subsp. paratuberculosis (MAP), Mycobacterium avium subsp. silvaticum (MAS) and some isolates of Mycobacterium avium subsp. avium serotype 2 (MAAs2), which contains a set of genes of low GC% content, putatively associated with the biosynthesis, modification and transference of fucose to cell wall glycopeptidolipids. Here we describe a further gene of low GC% content (mpa), within the GS element in MAP. mpa is a putative acetyltransferase with homology to genes directly responsible for host specificity and virulence in Salmonella typhimurium and Shigella flexneri. Unlike other GS genes, strong homologues of mpa have not been found in related species, including Mycobacterium tuberculosis (MTB). In MAP, mpa encodes an ORF of 445aa, however, in MAS and MAAs2 mpa contains a single inserted copy of a novel insertion sequence. This element (IS1612) has two sets of inverted repeats at each terminus and encodes two ORFs with good homologies to transposase and helper proteins of IS21 (E. coli) and IS1415 (R. erythropolis). Sequence comparisons between mpa in MAP and MAS indicate the target site for IS1612 is duplicated on insertion to give a direct repeat at each end of the element. Immediately, downstream of the mpa gene in both MAP and MAS are a group of three genes with good homology to the daunorubicin resistance cluster. This cluster has a high GC% content which suggests a 'border' for the GS element. A short motif present at the beginning of this cluster matches with an inverted repeat of this motif at the beginning of the first gene in the GS element. This encapsulates the whole of this group of low GC% genes in MAP and further suggests its cassette-like nature. Homologues of the GS element in MTB show a marked similarity of organisation, suggesting a parallel role for these genes in both pathogens.     

Large-cage zeolite structures with multidimensional 12-ring channels

Zeolite type structures with large cages interconnected by multidimensional 12-ring (rings of 12 tetrahedrally coordinated atoms) channels have been synthesized; more than a dozen large-pore materials were created in three different topologies with aluminum (or gallium), cobalt (or manganese, magnesium, or zinc), and phosphorus at the tetrahedral coordination sites. Tetragonal UCSB-8 has an unusually large cage built from 64 tetrahedral atoms and connected by an orthogonal channel system with 12-ring apertures in two dimensions and 8-ring apertures in the third. Rhombohedral UCSB-10 and hexagonal UCSB-6 are structurally related to faujasite and its hexagonal polymorph, respectively, and have large cages connected by 12-ring channels in all three dimensions.     

Fatty acid composition and change in Collembola fed differing diets: identification of trophic biomarkers

To assess the potential of fatty acid (FA) compositions to act as biomarkers in the soil food web, two species of Collembola, Folsomia candida and Proisotoma minuta, were switched to four possible diets: Cladosporium cladosporioides (a common soil fungus), Panagrellus redivivus (a bacteria feeding nematode), Zea mays (maize) and Alnus glutinosa (alder). The change in FA content of the Collembola was observed over the following 39 days. The four diets produced significant shifts in the FA compositions of the Collembola, with P. redivivus causing the most extreme changes; Collembola fed P. redivivus gained complex FA compositions similar to those of the nematode diet. Changes in the relative abundances of some FAs were found to follow negative exponential curves, as the components either accumulated in, or were removed from, the FA pool in the Collembola; abundance half-lives varied between 0.5 and 22.4 days, indicating that Collembolan FA compositions changed readily with the input of new exogenous components. The results demonstrate that Collembolan FA compositions are influenced by diet, and that the abundances of FAs such as i15:0, i17:0 and 18:1(n-7) may be used as biomarkers of nematode consumption by Collembola. In contrast, the C₂₀ polyunsaturated FAs cannot be used as biomarkers for nematode predation as Collembola possess the ability to biosynthesise high abundances of these compounds when not provided by the diet.     

Collembolan trophic preferences determined using fatty acid distributions and compound-specific stable carbon isotope values

The trophic preferences of soil invertebrates such as Collembola are often determined by the analysis of gut contents, or through visual observations of the location of individuals. As an alternative approach, two species of Collembola, Folsomia candida and Proisotoma minuta, were offered a choice of the soil fungus Cladosporium cladosporioides or the bacterial feeding nematode Panagrellus redivivus; each exhibited distinct fatty acid profiles and stable carbon isotopic compositions. Over 21 days, the fatty acids i15:0, i17:0, 18:1(n-7) and 18:2(n-6) all increased in abundance in both collembolan species consistent with direct routing from the nematode dietary choice which contained a high concentration of these components. Collembolan fatty acid δ¹³C values increased by between 5.7 and 21.6‰ over 21 days reflecting those of the nematode diet. Therefore, both fatty acid profiles and δ¹³C values were consistent with a strong feeding preference of F. candida and P. minuta for the nematodes over the offered fungi. In fact, neither collembolan species consumed any detectable amount of C. cladosporioides. Comparison of the δ¹³C values of the 16:0 and 18:0 fatty acids (which are biosynthesised by the Collembola as well as directly incorporated from the diet) and the 16:1(n-7) and 18:2(n-6) components (which are not biosynthesised by the Collembola) demonstrated that the input of distinct pools of C can lead to large shifts in δ¹³C values between diet and consumer. The fatty acids that were not biosynthesised by Collembola better reflected the δ¹³C values of the diet helping to differentiate between biosynthesised and directly incorporated compounds; an important prerequisite in the interpretation of compound-specific δ¹³C values in trophic behaviour tests. The combination of fatty acid distributions and δ¹³C values is a significant improvement on traditional methods of examining feeding preferences, since it determines directly the assimilated dietary carbon rather than relying on indirect observations, such as the proximity of individuals to a defined food source.     

Critical loads for nitrogen deposition for Great Britain

There is currently much interest in mapping critical loads for nitrogen deposition as part of a strategy for controlling nitrogen emissions. While nitrogen deposition may cause acidification and excess nutrient effects, the former were considered previously in studies of sulphur deposition. In the UK, work on developing nutrient nitrogen critical loads maps has used several methods and databases. Two approaches are described here, one a steady state calculation using a nitrogen saturation limit for soil systems, the other an empirical estimate of critical loads set to prevent changes to vegetation communities. The empirical method uses national species records and land cover data derived from satellite imagery. Maps drawn from the available data are dependent upon a number of factors which reflect the approach used. To apply the nutrient critical loads to a strategy for future abatement measures, the nutrient nitrogen values for soils have been incorporated within a “critical loads function” which takes into account both acidity and nutrient effects as related to deposition loads for sulphur and nitrogen. This function may be used with deposition data to identify the need for sulphur and nitrogen emission reductions.     

Polymorphic expression in the CD8alpha chain surface receptor of African lions (Panthera leo).

Free-ranging African lion (Panthera leo) peripheral blood mononuclear cells (PBMC) were examined using flow cytometry and antibodies developed for use in the domestic cat to determine if phenotypic changes occurred in lion lymphocytes as a result of feline immunodeficiency virus (FIV) infection. The percentage of CD8 cells from lion peripheral blood was considerably lower than in the domestic cat. Lions with elevated levels of CD8+ cells were typically infected with FIV, similar to observations in the domestic cat. Antibodies against the alpha chain of the CD8 receptor (monoclonal antibody (mAb) 3.357) did not react consistently in all lions examined. Flow cytometric analysis determined that approximately 82 and 80% of the animals from Kruger and Hluhluwe-Umfolozi National Parks in South Africa reacted with the monoclonal antibody against the alpha chain of CD8 receptor, while only 17% of the lions in Etosha National Park in Namibia cross-reacted with the CD8alpha chain. There was no apparent correlation between FIV status and CD8alpha chain reactivity. The relative isolation of Etosha from the other two parks could explain the marked difference in CD8alpha chain expression and suggests that lions similar to other mammalian species demonstrate polymorphic expression of the CD8alpha chain (197).     

The use of resource patches by earthworms

A field experiment was established to assess the effects of additional organic matter on earthworm populations. Bags of soil (15 cm deep) were placed in a pasture at Balhannah, South Australia, at the beginning of autumn 1991. The bags were initially seeded with five individuals ofAporrectodea trapezoides, and 250 g dried sheep manure was added to most bags. Manure was added either in pellet or milled form, and applied either on the surface, in the 5–10 cm layer, or evenly dispersed over 15 cm. In harvests during weeks 7,9, and 11 after the start of the experiment,A. trapezoides and three other species,A. caliginosa, A. rosea, andMicroscolex dubius, were recovered from the bags. Bags with added manure had significantly higher numbers of each species than bags with no manure. During the 4-week sampling period (weeks 7–11) the numbers ofM. dubius recovered per bag decreased, whileA. rosea increased. Total earthworm numbers were not influenced by either the form or the location of application of the manure. Earthworms were sampled from three depths, 0–5, 5–10, and 10–15 cm. Both numbers and biomass of earthworms were positively correlated with the location of the manure. Cocoons ofAporrectodea spp. were more abundant when the manure was milled and evenly dispersed, and were consistently located in the lower soil layers, regardless of the form or location of manure.