Assessing biodiversity with species accumulation curves; inventories of small reptiles by pit‐trapping in Western Australia

Abstract We examined 11 non‐linear regression models to determine which of them best fitted curvilinear species accumulation curves based on pit‐trapping data for reptiles in a range of heterogeneous and homogenous sites in mesic, semi‐arid and arid regions of Western Australia. A well‐defined plateau in a species accumulation curve is required for any of the models accurately to estimate species richness. Two different measures of effort (pit‐trapping days and number of individuals caught) were used to determine if the measure of effort influenced the choice of the best model(s). We used species accumulation curves to predict species richness, determined the trapping effort required to catch a nominated percentage (e.g. 95%) of the predicted number of species in an area, and examined the relationship between species accumulation curves with diversity and rarity. Species richness, diversity and the proportion of rare species in a community influenced the shape of species accumulation curves. The Beta‐P model provided the best overall fit (highest r²) for heterogeneous and homogeneous sites. For heterogeneous sites, Hill, Rational, Clench, Exponential and Weibull models were the next best. For homogeneous habitats, Hill, Weibull and Chapman–Richards were the next best models. There was very little difference between Beta‐P and Hill models in fitting the data to accumulation curves, although the Hill model generally over‐estimated species richness. Most models worked equally well for both measures of trapping effort. Because the number of individuals caught was influenced by both pit‐trapping effort and the abundance of individuals, both measures of effort must be considered if species accumulation curves are to be used as a planning tool. Trapping effort to catch a nominated percentage of the total predicted species in homogeneous and heterogeneous habitats varied among sites, but even for only 75% of the predicted number of species it was generally much higher than the typical effort currently being used for terrestrial vertebrate fauna surveys in Australia. It was not possible to provide a general indication of the effort required to predict species richness for a site, or to capture a nominated proportion of species at a site, because species accumulation curves are heavily influenced by the characteristics of particular sites.     

Lithiation‐Induced Dilation Mapping in a Lithium‐Ion Battery Electrode by 3D X‐Ray Microscopy and Digital Volume Correlation

Recent advances in high‐resolution 3D X‐ray computed tomography (CT) allow detailed, non‐destructive 3D structural mapping of a complete lithium‐ion battery. By repeated 3D image acquisition (time lapse CT imaging) these investigations of material microstructure are extended into the fourth dimension (time) to study structural changes of the device in operando. By digital volume correlation (DVC) of successive 3D images the dimensional changes taking place during charge cycling are quantified at the electrode level and at the Mn₂O₄ particle scale. After battery discharging, the extent of lithiation of the manganese (III/IV) oxide grains in the electrode is found to be a function of the distance from the battery terminal with grains closest to the electrode/current collector interface having the greatest expansion (≈30%) and grains furthest from the current collector and closest to the counter electrode showing negligible dilation. This implies that the discharge is limited by electrical conductivity. This new CT+DVC technique is widely applicable to the 3D exploration of the microstructural degradation processes for a range of energy materials including fuel cells, capacitors, catalysts, and ceramics.     

The crystal structure of a 2-fluorocellotriosyl complex of the Streptomyces lividans endoglucanase CelB2 at 1.2 A resolution

Glycoside hydrolases have been classified into over 66 families on the basis of amino acid sequence. Recently a number of these families have been grouped into "clans" which share a common fold and catalytic mechanism [Henrissat, B., and Bairoch, A. (1996) Biochem. J. 316, 695-696]. Glycoside hydrolase Clan GH-C groups family 11 xylanases and family 12 cellulases, which share the same jellyroll topology, with two predominantly antiparallel beta-sheets forming a long substrate-binding cleft, and act with net retention of anomeric configuration. Here we present the three-dimensional structure of a family 12 endoglucanase, Streptomyces lividans CelB2, in complex with a 2-deoxy-2-fluorocellotrioside. Atomic resolution (1.2 A) data allow clear identification of two distinct species in the crystal. One is the glycosyl-enzyme intermediate, with the mechanism-based inhibitor covalently linked to the nucleophile Glu 120, and the other a complex with the reaction product, 2-deoxy-2-fluoro-beta-D-cellotriose. The active site architecture of the complex provides insight into the double-displacement mechanism of retaining glycoside hydrolases and also sheds light on the basis of the differences in specificity between family 12 cellulases and family 11 xylanases.     

Development of an assay and determination of kinetic parameters for chondroitin AC lyase using defined synthetic substrates

Many techniques have been developed for the assay of polysaccharide lyases; however, none have allowed the measurement of defined and reproducible k(cat) and K(m) values due to the inhomogeneous nature of the polymeric substrates. We have designed three different substrates for chondroitin AC lyase from Flavobacterium heparinum that can be monitored by three different techniques: UV/Vis spectroscopy, fluorescence spectroscopy, and use of a fluoride ion-selective electrode. Each is a continuous assay, free from interferences caused by other components present in crude enzyme preparations, and allows meaningful and reproducible kinetic parameters to be determined. The development of these defined synthetic substrates has opened up a wide variety of mechanistic studies that can be performed to elucidate the detailed catalytic mechanism of this, and other, polysaccharide lyases. The application of these techniques, which include kinetic isotope effects and linear free energy analyses, was not possible with the previous polymeric substrates and will allow this relatively poorly understood class of polysaccharide-degrading enzymes to be studied mechanistically.     

Mechanistic studies of a retaining alpha-galactosyltransferase from Neisseria meningitidis

Lipopolysaccharyl alpha-galactosyltransferase from Neisseria meningitidis catalyzes the transfer of a galactosyl moiety from the activated donor UDP-Gal to glycoconjugates to yield an elongated saccharide product with net retention of anomeric configuration relative to the donor substrate. Through kinetic analyses in which the concentrations of both substrates are independently varied and through inhibition studies with dead-end analogues of both substrates and with the oligosaccharide product, we have demonstrated that this enzyme follows an ordered bi-bi kinetic mechanism. Various aspects of the chemical mechanism including the possible formation of a covalent glycosyl-enzyme intermediate were also probed using an assortment of strategies. While the results of these investigations were unable to clearly delineate the chemical mechanism of this enzyme, they provide important insights into the catalytic machinery surrounding the events involved in catalysis.     

Oxygen consumption, carbon dioxide excretion and respiratory quotient of larval lampreys (Mordacia mordax) in air

The standard rates of O2 consumption of larval Mordacia mordax (weight range 1.3-2.3 g), after these ammocetes had been in humidified air for 18 hr, were 26.8, 46.3 and 71.2 microL x g(-1) x hr(-1) at 10, 15 and 20 degrees C, respectively. The corresponding rates of CO2 excretion were 20.7, 35.6 and 54.1 microL x g(-1) x hr(-1). The RQs at the three temperatures were essentially identical (0.76 or 0.77) and similar to that of adults of the lamprey Geotria australis in air at 15 degrees C. The above RQs for ammocoetes, which are probably similar to those that would be recorded in water, are consistent with the view that the aerobic respiration of these animals relies predominantly on lipid as an energy source, but that some energy is derived from carbohydrate and/or protein. The RQs for larval and adult lampreys in air lie well within the range recorded for amphibious fishes in air.     

Comparison of the gastrointestinal syndrome after total-body or total-abdominal irradiation

In pathogen-free mice, but not standard conventionally housed laboratory rodents, two distinctly different modes of early radiation lethality can be identified by modifying the irradiation technique (total-body versus abdominal irradiation) or by therapeutic intervention such as rescue of total-body-irradiated mice with syngeneic bone marrow or spleen. While damage to the gastrointestinal tract is usually designated as the predominant cause of death occurring within 10 days of radiation exposure, it was demonstrated that damage to the hematopoietic/lymphopoietic system can result in animal lethality over the same period as the gastrointestinal syndrome and that this target cell population is more radiation-sensitive than the gastrointestinal epithelium.     

Th17 Effector Cells Support B Cell Responses Outside of Germinal Centres

Th17 cells are pro-inflammatory CD4⁺T cells, which are important in immune responses against fungal pathogens and extracellular bacteria and have also been implicated in various autoimmune syndromes. However, their role in supporting B cell responses in these scenarios remains unclear, representing a significant lapse in our understanding of the role Th17 play in vaccine responses and the regulation of autoimmunity. We employed T cell and B cell receptor transgenic mice specific for model antigens, and adoptive transfer approaches that allowed the tracking of cognate B and T cells in situ and ex vivo using immunological methods. We have found that T cells activated under Th17 polarising conditions have a greater capacity to provide cognate B cell help compared with Th1 polarised populations, supporting higher expansion of antigen specific B cells and enhanced antibody titres. This advantage is associated with the increased persistence of Th17 polarised cells in areas of the lymph nodes where they can provide help (i.e. the B cell follicles). Also the Th17 cells are characterised by their higher expression of ICOS, a costimulatory molecule important for B cell help. Surprisingly, contrary to published reports, Th17 cells were not detected inside germinal centres, although they were found in close proximity to cognate B cells in the follicle early in the genesis of the humoral immune response. These data indicate that, Th17 cells have a more significant role earlier in the initiation/development of the germinal centre response and/or germinal centre-independent events, consistent with their early effector status.