Analysis of Chlorophyll Fluorescence by Means of Noisy Light

Linearization is an efficient means of detecting individualcomponents in complex fluorescence induction curves. In a previousinvestigation based on sine-waves (Hansen, Kolbowski, and Dau,1987) the components related to the plastoquinone pool, thehigh-energy state of the thylakoid membrane and the state 1-state2 transition controller could be identified. In this paper,binary noise is used as an alternative input signal which canalso allow linearization by mathematical tools. Comparison withexperiments using sine-waves shows that curve-fitting of thenoise experiments yields the same data as the sine-wave analysis.Further, some additional components were revealed as labelledby the related time-constants whose values depended on lightintensity (e.g. 5, 15, 20, 70, 85, 550 s for spinach at 2.5W m^–2). The advantages of noise analysis are a shorter measuring time and the availability ofan on-line criterion which indicates when a sufficient signal-to-noiseratio is reached. Key words: Chlorophyll fluorescence, correlation functions, linearization, noise, spinach, time-constants     

Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities

High-throughput Structural Genomics yields many new protein structures without known molecular function. This study aims to uncover these missing annotations by globally comparing select functional residues across the structural proteome. First, Evolutionary Trace Annotation, or ETA, identifies which proteins have local evolutionary and structural features in common; next, these proteins are linked together into a proteomic network of ETA similarities; then, starting from proteins with known functions, competing functional labels diffuse link-by-link over the entire network. Every node is thus assigned a likelihood z-score for every function, and the most significant one at each node wins and defines its annotation. In high-throughput controls, this competitive diffusion process recovered enzyme activity annotations with 99% and 97% accuracy at half-coverage for the third and fourth Enzyme Commission (EC) levels, respectively. This corresponds to false positive rates 4-fold lower than nearest-neighbor and 5-fold lower than sequence-based annotations. In practice, experimental validation of the predicted carboxylesterase activity in a protein from Staphylococcus aureus illustrated the effectiveness of this approach in the context of an increasingly drug-resistant microbe. This study further links molecular function to a small number of evolutionarily important residues recognizable by Evolutionary Tracing and it points to the specificity and sensitivity of functional annotation by competitive global network diffusion. A web server is at http://mammoth.bcm.tmc.edu/networks.     

Late Cretaceous follicular fruits from southern Sweden with systematic affinities to early diverging eudicots

Eight new species in seven new genera of follicular fruits are described from the Late Cretaceous of southern Sweden. They are Agapitocarpus emisxus , Chontrocarpus pachytoichus , Maiandrocarpus moirasmenus , Malliocarpus batrachoides , Mitocarpus elegans , Xylocarpus rhitidoides , Zeugarocarpus adroagathus and Z. leptoagathus . The fossil follicles are borne along infructescence axes or more commonly occur as isolated, dispersed fruits. Three genera, Maiandrocarpus , Mitocarpus and Zeugarocarpus , have follicles in distinct pairs borne spirally on an infructescence axis. Each follicle of a pair faces the axis with its ventral slit, which strongly indicates that the paired follicles were derived from two separate, monocarpellate flowers rather than from a single, bicarpellate flower. One genus ( Malliocarpus ) has follicles borne individually in the infructescence and three others ( Agapitocarpus , Chontrocarpus and Xylocarpus ) are known only as dispersed follicles. The paired follicles share many features with most of the dispersed follicles, including a sessile stigmatic area, a three-layered simple follicle wall, a simple vascular system composed of one dorsal and two lateral bundles, as well as a marginal-linear placentation bearing several anatropous ovules. Accordingly they are thought to belong to the same complex of taxa. The general structure of the fossils and comparison with modern angiosperms suggest that the fossils might represent an extinct lineage within or close to basal eudicots and many characters are shared with members of extant Proteaceae.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 148 , 377–407.     

Effect of ambient temperature on mechanosensory host location in two parasitic wasps of different climatic origin

Abstract.  Several parasitic wasps of the Pimplinae (Ichneumonidae) use self-produced vibrations transmitted through plant substrate to locate their concealed immobile hosts (lepidopteran pupae) by reflected signals. This mechanosensory mechanism of host location, called vibrational sounding, depends on the physical characteristics of the plant substrate and the wasp's body and is postulated to depend on ambient temperature. Adaptations of two parasitoid species to thermal conditions of their habitats and the influence of temperature on the trophic interaction during host location are investigated in the tropical Xanthopimpla stemmator (Thunberg) and compared with the temperate Pimpla turionellae (L.). Plant-stem models with hidden host mimics are offered to individual wasps under defined temperature treatments and scored for the number and location of ovipositor insertions. Significant effects of temperature are found on host-location activity and its success. The tropical species possesses an optimum temperature range for vibrational sounding between 26 and 32 °C, whereas the performance decreases both at low and high temperatures. The temperate species reveals substantial differences with respect to performance at the same thermal conditions. With increasing temperature, P. turionellae shows a reduced response to the host mimic, reduced numbers of ovipositor insertions, and decreased precision of mechanosensory host location. In the tropical X. stemmator , the female wasps are able to locate their host with high precision over a broad range of ambient temperatures, which suggests endothermic thermoregulation during vibrational sounding. Environmental physiology may therefore play a key role in adaptation of the host location mechanism to climatic conditions of the species' origin.     

THE MIDDLE ORDOVICIAN PROVENTOCITUM PROCERULUM RADIOLARIAN ASSEMBLAGE OF SPITSBERGEN AND ITS BIOSTRATIGRAPHIC CORRELATION

Abstract: The Proventocitum procerulum radiolarian assemblage from the Valhallfonna Formation of Spitsbergen is described for the first time in some detail from material investigated in transmitted light. A number of species are recognized in the well‐preserved material, showing unexpected diversity. The age of the fauna is restricted to the early Darriwilian (Da1‐2), based on comparison with precisely dated radiolarian assemblages from the Cow Head and Table Head Groups of western Newfoundland. Most species, however, are left in open nomenclature until additional material is available for SEM investigation. Inanigutta magnifica n. sp. is described as new.     

Survey and prioritisation of potential biological control agents for prickly acacia (Acacia nilotica subsp. indica) in southern India

Prickly acacia, Acacia nilotica subsp. indica (Benth.) Brenan (Mimosaceae), a multi-purpose tree native to the Indian subcontinent, is a weed of national significance, widespread throughout the grazing areas of western Queensland and has the potential to spread throughout northern Australia. Biological control of prickly acacia has been in progress since the early 1980s, but with limited success to date. Based on genetic and climate matching studies, native surveys for potential biological control agents were conducted in 64 sites in Tamil Nadu state and eight sites in Karnataka state from November 2008 to December 2011. Surveys yielded 33 species of phytophagous insects (16 species of leaf-feeders, eight species of stem feeders, four species with leaf-feeding adults and root-feeding larvae, two stem-borers and bark-feeders and three flower-feeders) and two rust fungi. The number of species recorded at survey sites increased with the number of times the sites were surveyed. Using a scoring system based on field host range, geographic range, seasonal incidence and damage levels, we prioritised a scale insect (Anomalococcus indicus Ramakrishna Ayyar), two leaf-webbing caterpillars (Phycita sp. A and Phycita sp. B), a leaf weevil (Dereodus denticollis Boheman), a leaf beetle (Pachnephorus sp.), a gall-inducing rust (Ravenelia acacia-arabica Mundk. & Thirumalachari) and a leaf rust (Ravenelia evansii Syd. & P.) for detailed host specificity tests. The two rusts were sent to CABI-UK for preliminary host-specificity testing. Three insects (A. indicus, D. denticollis and Phycita sp. A) were imported into a quarantine facility in Brisbane, Australia where host-specificity tests are in progress.     

A substrate ambiguous enzyme facilitates genome reduction in an intracellular symbiont

Background

Genome evolution in intracellular microbial symbionts is characterized by gene loss, generating some of the smallest and most gene-poor genomes known. As a result of gene loss these genomes commonly contain metabolic pathways that are fragmented relative to their free-living relatives. The evolutionary retention of fragmented metabolic pathways in the gene-poor genomes of endosymbionts suggests that they are functional. However, it is not always clear how they maintain functionality. To date, the fragmented metabolic pathways of endosymbionts have been shown to maintain functionality through complementation by host genes, complementation by genes of another endosymbiont and complementation by genes in host genomes that have been horizontally acquired from a microbial source that is not the endosymbiont. Here, we demonstrate a fourth mechanism.

Results

We investigate the evolutionary retention of a fragmented pathway for the essential nutrient pantothenate (vitamin B5) in the pea aphid, Acyrthosiphon pisum endosymbiosis with Buchnera aphidicola. Using quantitative analysis of gene expression we present evidence for complementation of the Buchnera pantothenate biosynthesis pathway by host genes. Further, using complementation assays in an Escherichia coli mutant we demonstrate functional replacement of a pantothenate biosynthesis enzyme, 2-dehydropantoate 2-reductase (E.C. 1.1.1.169), by an endosymbiont gene, ilvC, encoding a substrate ambiguous enzyme.

Conclusions

Earlier studies have speculated that missing enzyme steps in fragmented endosymbiont metabolic pathways are completed by adaptable endosymbiont enzymes from other pathways. Here, we experimentally demonstrate completion of a fragmented endosymbiont vitamin biosynthesis pathway by recruitment of a substrate ambiguous enzyme from another pathway. In addition, this work extends host/symbiont metabolic collaboration in the aphid/Buchnera symbiosis from amino acid metabolism to include vitamin biosynthesis.

     

Towards a universal barcode of oomycetes – a comparison of the cox1 and cox2 loci

Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide and include several devastating plant pathogens, for example Phytophthora infestans (potato late blight). The cytochrome c oxidase subunit 2 gene (cox2) has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. The cox1 locus has been used in some studies of Pythium and Phytophthora, but has rarely been used for other oomycetes, as amplification success of cox1 varies with different lineages and sample ages. To determine which out of cox1 or cox2 is best suited as a universal oomycete barcode, we compared these two genes in terms of (i) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (ii) sequence polymorphism, intra‐ and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding‐type material. Sequence data for several historic type specimens exist for cox2, but there are none for cox1. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. The cox2‐1 spacer could be a useful marker below species level. Improved protocols and universal primers are presented for all genes to facilitate future barcoding efforts.     

Host genotype affects the relative success of competing lines of aphid parasitoids under superparasitism

1. In solitary parasitoids, only one individual can complete development in a given host. Therefore, solitary parasitoids tend to prefer unparasitised hosts for oviposition, yet under high parasitoid densities, superparasitism is frequent and results in fierce competition for the host's limited resources. This may lead to selection for the best intra‐host competitors. 2. Increased intra‐host competitive ability may evolve under a high risk of superparasitism if this trait exhibits genetic variation, and if competitive differences among parasitoid genotypes are consistent across environments, e.g. different host genotypes. 3. These assumptions were addressed in the aphid parasitoid Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae) and its main host, the black bean aphid, Aphis fabae (Scopoli) (Hemiptera: Aphididae). Three parthenogenetic lines of L. fabarum were allowed to parasitise three aphid clones singly and in all pairwise combinations (superparasitism). The winning parasitoid in superparasitised aphids was determined by microsatellite analysis. 4. The proportions of singly parasitised aphids that were mummified were similar for the three parasitoid lines and did not differ significantly among host clones. 5. Under superparasitism, significant biases in favour of one parasitoid line were observed for some combinations, indicating that there is genetic variation for intra‐host competitive ability. However, the outcome of superparasitism was inconsistent across aphid clones and thus influenced significantly by the host clone in which parasitoids competed. 6. Overall, this study shows that the fitness of aphid parasitoids under superparasitism is determined by complex interactions with competitors as well as hosts, possibly hampering the evolution of improved intra‐host competitive ability.     

Soil water repellency and its implications for organic matter decomposition – is there a link to extreme climatic events?

Earth system models associate the ongoing global warming with increasing frequency and intensity of extreme events such as droughts and heat waves. The carbon balance of soils may be more sensitive to the impact of such extremes than to homogeneously distributed changes in soil temperature (T_s) or soil water content (θ_s). One parameter influenced by more pronounced drying/rewetting cycles or increases in T_s is the wettability of soils. Results from laboratory and field studies showed that low θ_s, particularly in combination with high T_s can increase soil water repellency (SWR). Recent studies have provided evidence that the stability of soil organic matter (SOM) against microbial decomposition is substantially enhanced in water repellent soils. This review hypothesizes that SWR is an important SOM stabilization mechanism that could become more important because of the increase in extreme events. We discuss wettability‐induced changes in soil moisture distribution and in soil aggregate turnover as the main mechanisms explaining the reduced mineralization of SOM with increasing SWR. The creation of preferential flow paths and subsequent uneven penetration of rainwater may cause a long‐term reduction of soil water availability, affecting both microorganisms and plants. We conclude that climate change‐induced SWR may intensify the effects of climatic drought and thus affects ecosystem processes such as SOM decomposition and plant productivity, as well as changes in vegetation and microbial community structure. Future research on biosphere–climate interactions should consider the effects of increasing SWR on soil moisture and subsequently on both microbial activity and plant productivity, which ultimately determine the overall carbon balance.