Investigating the community consequences of competition among clonal plants

Although clonal plants comprise most of the biomass of several widespread ecosystems, including many grasslands, wetlands, and tundra, our understanding of the effects of clonal attributes on community patterns and processes is weak. Here we present the conceptual basis for experiments focused on manipulating clonal attributes in a community context to determine how clonal characteristics affect interactions among plants at both the individual and community levels. All treatments are replicated at low and high density in a community density series to compare plant responses in environments of different competitive intensity. We examine clonal integration, the sharing of resources among ramets, by severing ramets from one another and comparing their response to ramets with intact connections. Ramet aggregation, the spacing of ramets relative to each other, is investigated by comparing species that differ in their natural aggregation (either clumped growth forms, with ramets tightly packed together, or runner growth forms, with ramets loosely spread) and by planting individual ramets of all species evenly spaced throughout a mesocosm. We illustrate how to test predictions to examine the influence of these two clonal traits on competitive interactions at the individual and community levels. To evaluate the effect of clonal integration on competition, we test two predictions: at the individual level, species with greater clonal integration will be better individual-level competitors, and at the community level, competition will cause a greater change in community composition when ramets are integrated (connected) than when they are not. For aggregation we test at the individual level: clumped growth forms are better competitors than runner growth forms because of their ability to resist invasion, and at the community level: competition will have a greater effect on community structure when ramets are evenly planted. An additional prediction connects the individual- and community-level effects of competition: resistance ability better predicts the effects of competition on relative abundance in a community than does invasion ability. We discuss additional experimental design considerations as revealed by our ongoing studies. Examining how clonal attributes affect both the individual- and community-level effects of competition requires new methods and metrics such as those presented here, and is vital to understanding the role of clonality in community structure of many ecosystems.     

Biogeochemistry of platelet ice: its influence on particle flux under fast ice in the Weddell Sea, Antarctica

An array of four sediment traps and one current meter was deployed under a well-developed platelet layer for 15 days in the Drescher Inlet in the Riiser Larsen ice shelf, in February 1998. Traps were deployed at 10 m (just under the platelet layer), 112 m (above the thermocline), 230 m (below thermocline) and 360 m (close to sea floor). There was a substantial flux of particulate organic material out of the platelet layer, although higher amounts were collected in the traps either side of the thermocline. Material collected was predominantly composed of faecal pellets containing diatom species growing within the platelet layer. The size classes of these pellets suggest they derive from protists grazing rather than from larger metazoans. Sediment trap material was analysed for particulate organic carbon/nitrogen/phosphorus (POC/PON/POP) and '¹³C_POC (carbon isotopic composition of POC). These were compared with organic matter in the overlying platelet layer and the water column. In turn, the biogeochemistry of the platelet layer and water column was investigated and the organic matter characteristics related to inorganic nutrients (nitrate, nitrite, ammonium, silicate, phosphate), dissolved organic carbon/nitrogen (DOC/DON), pH, dissolved inorganic carbon (DIC), oxygen and '¹³C_DIC (carbon isotopic composition dissolved inorganic carbon).     

Small-molecule metabolism: an enzyme mosaic

Escherichia coli has been a popular organism for studying metabolic pathways. In an attempt to find out more about how these pathways are constructed, the enzymes were analysed by defining their protein domains. Structural assignments and sequence comparisons were used to show that 213 domain families constitute 90% of the enzymes in the small-molecule metabolic pathways. Catalytic or cofactor-binding properties between family members are often conserved, while recognition of the main substrate with change in catalytic mechanism is only observed in a few cases of consecutive enzymes in a pathway. Recruitment of domains across pathways is very common, but there is little regularity in the pattern of domains in metabolic pathways. This is analogous to a mosaic in which a stone of a certain colour is selected to fill a position in the picture.     

Terrestrial biosphere model performance for inter‐annual variability of land‐atmosphere CO2 exchange

Interannual variability in biosphere‐atmosphere exchange of CO₂ is driven by a diverse range of biotic and abiotic factors. Replicating this variability thus represents the ‘acid test’ for terrestrial biosphere models. Although such models are commonly used to project responses to both normal and anomalous variability in climate, they are rarely tested explicitly against inter‐annual variability in observations. Herein, using standardized data from the North American Carbon Program, we assess the performance of 16 terrestrial biosphere models and 3 remote sensing products against long‐term measurements of biosphere‐atmosphere CO₂ exchange made with eddy‐covariance flux towers at 11 forested sites in North America. Instead of focusing on model‐data agreement we take a systematic, variability‐oriented approach and show that although the models tend to reproduce the mean magnitude of the observed annual flux variability, they fail to reproduce the timing. Large biases in modeled annual means are evident for all models. Observed interannual variability is found to commonly be on the order of magnitude of the mean fluxes. None of the models consistently reproduce observed interannual variability within measurement uncertainty. Underrepresentation of variability in spring phenology, soil thaw and snowpack melting, and difficulties in reproducing the lagged response to extreme climatic events are identified as systematic errors, common to all models included in this study.     

Different Steady State Subcellular Distributions of the Three Splice Variants of Lysosome-associated Membrane Protein LAMP-2 Are Determined Largely by the COOH-terminal Amino Acid Residue

The extensively glycosylated lysosome-associated membrane proteins (LAMP)-2a, b, and c are derived from a single gene by alternative splicing that produces proteins with differences in the transmembrane and cytosolic domains. The lysosomal targeting signals reside in the cytosolic domain of these proteins. LAMPs are not restricted to lysosomes but can also be found in endosomes and at the cell surface. We investigated the subcellular distribution of chimeras comprised of the lumenal domain of avian LAMP-1 and the alternatively spliced domains of avian LAMP-2. Chimeras with the LAMP-2c cytosolic domain showed predominantly lysosomal distribution, while higher levels of chimeras with the LAMP-2a or b cytosolic domain were present at the cell surface. The increase in cell surface expression was due to differences in the recognition of the targeting signals and not saturation of intracellular trafficking machinery. Site-directed mutagenesis defined the COOH-terminal residue of the cytosolic tail as critical in governing the distributions of LAMP-2a, b, and c between intracellular compartments and the cell surface.     

Interactions of rhizobia with rice and wheat

Recently, evidence has been obtained that naturally occurring rhizobia, isolated from the nodules of non-legume Parasponia species and from some tropical legumes, are able to enter the roots of rice, wheat and maize at emerging lateral roots by crack entry. We have now investigated whether Azorhizobium caulinodans strain ORS571, which induces root and stem nodules on the tropical legume Sesbania rostrata as a result of crack entry invasion of emerging lateral roots, might also enter rice and wheat by a similar route. Following inoculation with ORS571 carrying a lacZ reporter gene, azorhizobia were observed microscopically within the cracks associated with emerging lateral roots of rice and wheat. A high proportion of inoculated rice and wheat plants had colonized lateral root cracks. The flavanone naringenin at 10 and 10 M stimulated significantly the colonization of lateral root cracks and also intercellular colonization of wheat roots. Naringenin does not appear to be acting as a carbon source and may act as a signal molecule for intercellular colonization of rice and wheat by ORS571 by a mechanism which is nod gene-independent, unlike nodule formation in Sesbania rostrata. The opportunity now arises to compare and to contrast the ability of Azorhizobium caulinodans with that of other rhizobia, such as Parasponia rhizobia, to intercellularly colonize the roots of non-legume crops.     

Molecular cloning of protease gene(s) from Xanthomanas campestris pv. campestris: Expression in Escherichia coli and role in pathogenicity

Summary The recombinant plasmid pIJ3070 isolated from a genomic library of Xanthomonas campestris pv. campestris constructed in the conjugal cosmid pLAFR3 contains protease gene(s) which can be expressed in Escherichia coli. Tn5 mutagenesis and subcloning revealed that the protease structural gene(s) is(are) located in a ca. 10 kb EcoRI fragment. Several protease-minus mutants of X. c. campestris were obtained by Tn5 mutagenesis of pIJ3070 and marker exchange techniques. Studies of pathogenicity of these Tn5 mutants showed that the protease is not critically important for the pathogenicity of X. c. campestris on turnip plants but may play a minor role in disease development.Abbreviations Gm gentamicin - Km kanamycin - Rif rifampicin - Spc spectinomycin - Sm streptomycin - Tc tetracycline     

Evolution of eukaryotic genome architecture: Insights from the study of a rapidly evolving metazoan, Oikopleura dioica: Non-adaptive forces such as elevated mutation rates may influence the evolution of genome architecture

Recent sequencing of the metazoan Oikopleura dioica genome has provided important insights, which challenges the current understanding of eukaryotic genome evolution. Many genomic features of O. dioica show deviation from the commonly observed trends in other eukaryotic genomes. For instance, O. dioica has a rapidly evolving, highly compact genome with a divergent intron-exon organization. Additionally, O. dioica lacks the minor spliceosome and key DNA repair pathway genes. Even with a compact genome, O. dioica contains tandem repeats, comparable to other eukaryotes, and shows lineage-specific expansion of certain protein domains. Here, we review its genomic features in the context of current knowledge, discuss implications for contemporary biology and identify areas for further research. Analysis of the O. dioica genome suggests that non-adaptive forces such as elevated mutation rates might influence the evolution of genome architecture. The knowledge of unique genomic features and splicing mechanisms in O. dioica may be exploited for synthetic biology applications, such as generation of orthogonal splicing systems.     

The use of CD 34(+) mobilized peripheral blood as a donor cell source does not improve chimerism after in utero hematopoietic stem cell transplantation in non-human primates

In utero hematopoietic stem cell transplantation is a therapeutic procedure that could potentially cure many developmental diseases affecting the immune and hematopoietic systems. In most clinical and experimental settings of fetal hematopoietic transplantation the level of donor cell engraftment has been low, suggesting that even in the fetus there are significant barriers to donor cell engraftment. In postnatal hematopoietic transplantation donor cells obtained from mobilized peripheral blood engraft more rapidly than cells derived from marrow. We tested the hypothesis that use of donor hematopoietic/stem cells obtained from mobilized peripheral blood would improve engraftment and the level of chimerism after in utero transplantation in non-human primates. Despite the potential competitive advantage from the use of CD 34(+) from mobilized peripheral blood, the level of chimerism was not appreciably different from a group of animals receiving marrow-derived CD 34(+) donor cells. Based on these results, it is unlikely that this single change in cell source will influence the clinical outcome of fetal hematopoietic transplantation.