Coastal Forest in Eastern Southern Africa has Savanna Bush-clump Origins

Ecosystems - The extensive coastal forests in eastern southern Africa persist as a putative alternative stable state in an open ecosystem mosaic that includes grassland and savanna. We examine two...     

The molecular basis for inhibition of BphD, a C-C bond hydrolase involved in polychlorinated biphenyls degradation: large 3-substituents prevent tautomerization

The microbial degradation of polychlorinated biphenyls (PCBs) by the biphenyl catabolic (Bph) pathway is limited in part by the pathway's fourth enzyme, BphD. BphD catalyzes an unusual carbon-carbon bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA), in which the substrate is subject to histidine-mediated enol-keto tautomerization prior to hydrolysis. Chlorinated HOPDAs such as 3-Cl HOPDA inhibit BphD. Here we report that BphD preferentially hydrolyzed a series of 3-substituted HOPDAs in the order H>F>Cl>Me, suggesting that catalysis is affected by steric, not electronic, determinants. Transient state kinetic studies performed using wild-type BphD and the hydrolysis-defective S112A variant indicated that large 3-substituents inhibited His-265-catalyzed tautomerization by 5 orders of magnitude. Structural analyses of S112A.3-Cl HOPDA and S112A.3,10-diF HOPDA complexes revealed a non-productive binding mode in which the plane defined by the carbon atoms of the dienoate moiety of HOPDA is nearly orthogonal to that of the proposed keto tautomer observed in the S112A.HOPDA complex. Moreover, in the 3-Cl HOPDA complex, the 2-hydroxo group is moved by 3.6 A from its position near the catalytic His-265 to hydrogen bond with Arg-190 and access of His-265 is blocked by the 3-Cl substituent. Nonproductive binding may be stabilized by interactions involving the 3-substituent with non-polar side chains. Solvent molecules have poor access to C6 in the S112A.3-Cl HOPDA structure, more consistent with hydrolysis occurring via an acyl-enzyme than a gem-diol intermediate. These results provide insight into engineering BphD for PCB degradation.     

High cell density cultivation of a novel Aurantiochytrium sp. strain TC 20 in a fed-batch system using glycerol to produce feedstock for biodiesel and omega-3 oils

A recently isolated Australian Aurantiochytrium sp. strain TC 20 was investigated using small-scale (2 L) bioreactors for the potential of co-producing biodiesel and high-value omega-3 long-chain polyunsaturated fatty acids. Higher initial glucose concentration (100 g/L compared to 40 g/L) did not result in markedly different biomass (48 g/L) or fatty acid (12–14 g/L) yields by 69 h. This comparison suggests factors other than carbon source were limiting biomass production. The effect of both glucose and glycerol as carbon sources for Aurantiochytrium sp. strain TC 20 was evaluated in a fed-batch process. Both glucose and glycerol resulted in similar biomass yields (57 and 56 g/L, respectively) by 69 h. The agro-industrial waste from biodiesel production—glycerol—is a suitable carbon source for Aurantiochytrium sp. strain TC 20. Approximately half the fatty acids from Aurantiochytrium sp. strain TC 20 are suitable for development of sustainable, low emission sources of transportation fuels and bioproducts. To further improve biomass and oil production, fortification of the feed with additional nutrients (nitrogen sources, trace metals and vitamins) improved the biomass yield from 56 g/L (34 % total fatty acids) to 71 g/L (52 % total fatty acids, cell dry weight) at 69 h; these yields are to our knowledge around 70 % of the biomass yields achieved, however, in less than half of the time by other researchers using glycerol and markedly greater than achieved using other industrial wastes. The fast growth and suitable fatty acid profile of this newly isolated Aurantiochytrium sp. strain TC 20 highlights the potential of co-producing the drop-in biodiesel and high value omega-3 oils.     

Computer-aided studies of vision in crabs

A system for the back projection of computer-generated visual images onto a screen or screens that cover 240° of the horizontal visual field is described. Its applicability for the study of crab vision is tested by comparing the frequency response of the optokinetic response of the land crab, Cardisoma guanhumi , to sinusoidal oscillation of computer-generated striped patterns and a real striped drum. Significant differences were observed only at the low end of the frequency spectrum. The flexibility of computer-generated visual stimulation and its advantages for the study of optic flow are illustrated by experiments that: (a) demonstrate how well crabs separate the translational and rotational components of optic flow by showing compensatory eye movements to only the latter; (b) show that the ability to compensate for rotation is not impaired by combinations of rotation and translation; (c) show that motion parallax cues are used in addition to previously-described global cues for making the distinction between rotation and translation. Finally, the use of these methods in a successful search for visual interneurones sensitive to optic flow stimuli is demonstrated for the shore crab, Carcinus maenas .     

Variation in stress resistance patterns among stx genotypes and genetic lineages of shiga toxin-producing Escherichia coli O157

To evaluate the relationship between bacterial genotypes and stress resistance patterns, we exposed 57 strains of Shiga toxin-producing Escherichia coli (STEC) O157 to acid, freeze-thaw, heat, osmotic, oxidative, and starvation stresses. Inactivation rates were calculated in each assay and subjected to univariate and multivariate analyses, including principal component analysis (PCA) and cluster analysis. The stx genotype was determined for each strain as was the lineage-specific polymorphism assay (LSPA6) genotype. In univariate analyses, strains of the stx(1) stx(2) genotype showed greater resistance to heat than strains of the stx(1) stx(2c) genotype; moreover, strains of the stx(1) stx(2) genotype showed greater resistance to starvation than strains of the stx(2) or stx(2c) genotypes. LSPA6 lineage I (LI) strains showed greater resistance to heat and starvation than LSPA6 lineage II (LII) strains. PCA revealed a general trend that a strain with greater resistance to one type of stress tended to have greater resistance to other types of stresses. In cluster analysis, STEC O157 strains were grouped into stress-resistant, stress-sensitive, and intermediate clusters. In stx genotypes, all strains of the stx(1) stx(2) genotype were grouped with the stress-resistant cluster, whereas 72.7% (8/11) of strains of the stx(1) stx(2c) genotype grouped with the stress-sensitive cluster. In LI strains, 77.8% (14/18) of the strains were grouped with the stress-resistant cluster, whereas 64.7% (11/17) of LII strains were grouped with the stress-sensitive cluster. These results indicate that the genotypes of STEC O157 that are frequently associated with human illness, i.e., LI or the stx(1) stx(2) genotype, have greater multiple stress resistance than do strains of other genotypes.     

Neurogenesis and neuronal communication on micropatterned neurochips

Neural networks are formed by accurate connectivity of neurons and glial cells in the brain. These networks employ a three-dimensional bio-surface that both assigns precise coordinates to cells during development and facilitates their connectivity and functionality throughout life. Using specific topographic and chemical features, we have taken steps towards the development of poly(dimethylsiloxane; PDMS) neurochips that can be used to generate and study synthetic neural networks. These neurochips have micropatterned structures that permit adequate cell positioning and support cell survival. Within days of plating, cells differentiate into neurons displaying excitability and communication, as evidenced by intracellular calcium oscillations and action potentials. The structural and functional capacities of such simple neural networks open up new opportunities to study synaptic communication and plasticity.     

Modelling population redistribution in a leaf beetle: an evaluation of alternative dispersal functions

1. Dispersal is a fundamental ecological process, so spatial models require realistic dispersal kernels. We compare five different forms for the dispersal kernel of the tansy beetle Chrysolina graminis moving between patches of its host-plant (tansy Tanacetum vulgare) in a riparian landscape. 2. Multi-patch mark-recapture data were collected every 2 weeks over 2 years within a large network of patches and from 2226 beetles. Dispersal was common (28.4% of 880 recaptures after a fortnight) and was more likely over longer intervals, out of small patches, for females and during flooding. Interpatch movement rates did not differ between years and exhibited no density dependence. Dispersal distances were similar for males and females, in both years and over all intervals, with a median dispersal distance of just 9.8 m, although a maximum of 856 m was recorded. 3. A model of dispersal, where patches competed for dispersers based on their size and distance from the beetle's source patch (scaled by the dispersal kernel) was fitted to the field data with a maximum likelihood procedure and each of five alternative kernels. The best fitting had relatively extended tails of long-distance dispersal, while Gaussian and negative exponential kernels performed worst. 4. The model suggests that females disperse more commonly than males and that both are strongly attracted to large patches but do not differ between years, which are consistent with the empirical results. Model-predicted emigration and immigration rates and dispersal phenologies match those observed, suggesting that the model captured the major drivers of tansy beetle dispersal. 5. Although negative exponential and Gaussian kernels are widely used for their simplicity, we suggest that these should not be the models of automatic choice, and that fat-tailed kernels with relatively higher proportions of long-distance dispersal may be more realistic.     

Flyway population delineation in Taiga Bean Geese Anser fabalis fabalis revealed by multi‐element feather stable isotope analysis

Fundamental to effective management of migratory waterbird populations is an understanding of their flyway delineation. Taiga Bean Geese Anser fabalis fabalis wintering in NW Denmark, Scotland and England are considered to originate from northern and central Sweden, southern and central Norway (‘Western flyway’), those wintering in southern Sweden, NE and southern Denmark are considered to originate from northern Fennoscandia and western Russia (‘Central flyway’), and those wintering in eastern Germany and Poland (which show far less favourable conservation status) are thought to come from western Siberia (‘Eastern 1 flyway’), although evidence to demonstrate this has largely been lacking. Evidence for different natal and moult origins of Taiga Bean Geese was investigated using stable isotope analyses of feathers of four elements (δ²H, δ¹³C, δ¹⁵N and δ³⁴S). There were significant differences in isotopic composition of feathers from Swedish (Central) and German (Eastern 1) wintering populations and those moulting in Sweden in late summer (Western), which validated the three proposed major management flyway units above. The strong continental gradient in the stable hydrogen isotope ratios in precipitation (δ²H_p) across the region was used to assign wintering birds geospatially to natal and moulting origin, indicating separate natal and moulting areas for German (n = 37, from western Siberia) and Swedish (n = 20, Fennoscandia and more western Russia) wintering birds. These results confirm the largely discrete nature of these three flyways and contribute significantly to our ability to deliver effective targeted and appropriate research, monitoring and management actions throughout the ranges of these flyways.