The carboxy-terminus of protein 4.1r resembles Beta-tubulin

The protein 4.1R is an isoform of a larger family of 4.1 proteins. It is known as a component of the plasma membrane skeleton, but it is also found at the centrosomes in interphase and mitosis. To investigate the properties of the carboxy terminal region of protein 4.1R, we raised antibodies against a peptide representing the last 14 amino acids of 4.1R. These antibodies crossreact with an epitope in beta-tubulin and stain the microtubule network by immunofluorescence. Furthermore, sequence comparison of the carboxy terminal 4.1R peptide sequence with tubulin reveals homology with a region at the end of helix 5 in beta-tubulin, but not alpha-tubulin. A potential function of the 4.1R carboxy terminus in regulating the formation of microtubule networks is discussed.     

A survey of the physiochemical characteristics and the zooplankton communities in an ephemeral karst lake

Chaney Lake State Nature Preserve is a 68 ha ephemeral karst lake in southern Warren County, Kentucky (USA). Chaney typically fills with water in the winter as groundwater levels rise and then slowly dries via evaporation and drainage back into the subsurface over the summer months. The lake contains several habitat types, identifiable by the dominant plant communities, which may have different physiochemical characteristics. Since these differences may result in an increase in habitat heterogeneity and niches available for colonization by resident zooplankton, a suite of physiochemical and nutrient parameters was monitored in these habitats from January 1997–August 1998. Zooplankton densities and community structure were assessed from January 1997 through May 1998. There were few significant differences among the habitats but there were significantly higher concentrations of NO_x and higher specific conductivities associated with some of the groundwater inlet areas in the lake. Zooplankton were abundant, but there were no differences in zooplankton densities among the areas sampled. These results suggest that the physiochemical properties in the lake are heavily influenced by the groundwater inputs and that land use patterns around Chaney Lake may be having an impact on the preserve.     

FLUXNET and modelling the global carbon cycle

Measurements of the net CO₂ flux between terrestrial ecosystems and the atmosphere using the eddy covariance technique have the potential to underpin our interpretation of regional CO₂ source–sink patterns, CO₂ flux responses to forcings, and predictions of the future terrestrial C balance. Information contained in FLUXNET eddy covariance data has multiple uses for the development and application of global carbon models, including evaluation/validation, calibration, process parameterization, and data assimilation. This paper reviews examples of these uses, compares global estimates of the dynamics of the global carbon cycle, and suggests ways of improving the utility of such data for global carbon modelling. Net ecosystem exchange of CO₂ (NEE) predicted by different terrestrial biosphere models compares favourably with FLUXNET observations at diurnal and seasonal timescales. However, complete model validation, particularly over the full annual cycle, requires information on the balance between assimilation and decomposition processes, information not readily available for most FLUXNET sites. Site history, when known, can greatly help constrain the model‐data comparison. Flux measurements made over four vegetation types were used to calibrate the land‐surface scheme of the Goddard Institute for Space Studies global climate model, significantly improving simulated climate and demonstrating the utility of diurnal FLUXNET data for climate modelling. Land‐surface temperatures in many regions cool due to higher canopy conductances and latent heat fluxes, and the spatial distribution of CO₂ uptake provides a significant additional constraint on the realism of simulated surface fluxes. FLUXNET data are used to calibrate a global production efficiency model (PEM). This model is forced by satellite‐measured absorbed radiation and suggests that global net primary production (NPP) increased 6.2% over 1982–1999. Good agreement is found between global trends in NPP estimated by the PEM and a dynamic global vegetation model (DGVM), and between the DGVM and estimates of global NEE derived from a global inversion of atmospheric CO₂ measurements. Combining the PEM, DGVM, and inversion results suggests that CO₂ fertilization is playing a major role in current increases in NPP, with lesser impacts from increasing N deposition and growing season length. Both the PEM and the inversion identify the Amazon basin as a key region for the current net terrestrial CO₂ uptake (i.e. 33% of global NEE), as well as its interannual variability. The inversion's global NEE estimate of −1.2 Pg [C] yr⁻¹ for 1982–1995 is compatible with the PEM‐ and DGVM‐predicted trends in NPP. There is, thus, a convergence in understanding derived from process‐based models, remote‐sensing‐based observations, and inversion of atmospheric data. Future advances in field measurement techniques, including eddy covariance (particularly concerning the problem of night‐time fluxes in dense canopies and of advection or flow distortion over complex terrain), will result in improved constraints on land‐atmosphere CO₂ fluxes and the rigorous attribution of mechanisms to the current terrestrial net CO₂ uptake and its spatial and temporal heterogeneity. Global ecosystem models play a fundamental role in linking information derived from FLUXNET measurements to atmospheric CO₂ variability. A number of recommendations concerning FLUXNET data are made, including a request for more comprehensive site data (particularly historical information), more measurements in undisturbed ecosystems, and the systematic provision of error estimates. The greatest value of current FLUXNET data for global carbon cycle modelling is in evaluating process representations, rather than in providing an unbiased estimate of net CO₂ exchange.     

Ecologically heterogeneous populations of the invasive ant Wasmannia auropunctata within its native and introduced ranges

Abstract 1. The biology of most invasive species in their native geographical areas remains largely unknown. Such studies are, however, crucial in shedding light on the ecological and evolutionary processes underlying biological invasions. 2. The present study focuses on the little fire ant Wasmannia auropunctata, a species native to Central and South America that has been widely introduced and which has become invasive throughout the tropics. We characterise and compare several ecological traits of native populations in French Guiana with those in one of its introduced ranges, New Caledonia. 3. We found ecologically heterogeneous populations of W. auropunctata coexisting in the species’ native geographical area. First, we found populations restricted to naturally perturbed areas (particularly floodplains) within the primary forest, and absent from the surrounding forest areas. These populations were characterised by low nest and worker densities. Second, we found dominant populations in recent anthropogenic areas (e.g. secondary forest or forest edge along road) characterised by high nest and worker densities, and associated with low ant species richness. The local dominance of W. auropunctata in such areas can be due to the displacement of other species (cause) or the filling‐up of empty habitats unsuitable to other ants (effect). With respect to their demographic features and ant species richness, the populations of native anthropogenic habitats were to a large extent similar to the invasive populations introduced into remote areas. 4. The results point to the need for greater research efforts to better understand the ecological and demographic features of invasive species within their native ranges.     

Bootstrapping phylogenies inferred from rearrangement data

ABSTRACT: Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have been designed over the last few years and have found use in comparative genomics and phylogenetic inference. However, the assessment of phylogenies built from such data has not been properly addressed to date. The standard method used in sequence-based phylogenetic inference is the bootstrap, but it relies on a large number of homologous characters that can be resampled; yet in the case of rearrangements, the entire genome is a single character. Alternatives such as the jackknife suffer from the same problem, while likelihood tests cannot be applied in the absence of well established probabilistic models. We present a new approach to the assessment of distance-based phylogenetic inference from whole-genome data; our approach combines features of the jackknife and the bootstrap and remains nonparametric. For each feature of our method, we give an equivalent feature in the sequence-based framework; we also present the results of extensive experimental testing, in both sequence-based and genome-based frameworks. Through the feature-by-feature comparison and the experimental results, we show that our bootstrapping approach is on par with the classic phylogenetic bootstrap used in sequence-based reconstruction, and we establish the clear superiority of the classic bootstrap for sequence data and of our corresponding new approach for rearrangement data over proposed variants. Finally, we test our approach on a small dataset of mammalian genomes, verifying that the support values match current thinking about the respective branches. Our method is the first to provide a standard of assessment to match that of the classic phylogenetic bootstrap for aligned sequences. Its support values follow a similar scale and its receiver-operating characteristics are nearly identical, indicating that it provides similar levels of sensitivity and specificity. Thus our assessment method makes it possible to conduct phylogenetic analyses on whole genomes with the same degree of confidence as for analyses on aligned sequences. Extensions to search-based inference methods such as maximum parsimony and maximum likelihood are possible, but remain to be thoroughly tested.     

Contribution of sucrose synthase, ADP-glucose pyrophosphorylase and starch synthase to starch synthesis in developing pea seeds

Using genetic variability existing amongst nine pea genotypes (Pisum sativum L.), the biochemical basis of sink strength in developing pea seeds was investigated. Sink strength was considered to be reflected by the rate of starch synthesis (RSS) in the embryo, and sink activity in the seed was reflected by the relative rate of starch synthesis (RRSS). These rates were compared to the activities of three enzymes of the starch biosynthetic pathway [sucrose synthase (Sus), ADP-glucose pyrophosphorylase and starch synthase] at three developmental stages during seed filling (25, 50 and 75% of the dry seed weight). Complete sets of data collected during seed filling for the nine genotypes showed that, for all enzyme activities (expressed on a protein basis), only Sus in the embryo and seed coat was linearly and significantly correlated to RRSS. The contribution of the three enzyme activities to the variability in RSS and RRSS was evaluated by multiple regression analysis for the first two developmental stages. Only Sus activity in the embryo could explain, at least in part, the significant variability observed for both the RSS and the RRSS at each developmental stage. We conclude that Sus activity is a reliable marker of sink activity in developing pea seeds.     

Sea urchin Hox genes: insights into the ancestral Hox cluster

We describe the Hox cluster in the radially symmetric sea urchin and compare our findings to what is known from clusters in bilaterally symmetric animals. Several Hox genes from the direct-developing sea urchin Heliocidaris erythrogramma are described. CHEF gel analysis shows that the Hox genes are clustered on a < or = 300 kilobase (kb) fragment of DNA, and only a single cluster is present, as in lower chordates and other nonvertebrate metazoans. Phylogenetic analyses of sea urchin, amphioxus, Drosophila, and selected vertebrate Hox genes confirm that the H. erythrogramma genes, and others previously cloned from other sea urchins, belong to anterior, central, and posterior groups. Despite their radial body plan and lack of cephalization, echinoderms retain at least one of the anterior group Hox genes, an orthologue of Hox3. The structure of the echinoderm Hox cluster suggests that the ancestral deuterostome had a Hox cluster more similar to the current chordate cluster than was expected Sea urchins have at least three Abd-B type genes, suggesting that Abd-B expansion began before the radiation of deuterostomes.      

Isozyme evidence of the parental origin and possible fertility of the hybrid Potamogeton×fluitans Roth

 The hybrid Potamogeton×fluitans Roth is thought to have resulted from hybridization between P. lucens L. and P. natans L. This hybrid has only been recorded at a few locations in the British Isles. At most of these sites the number of individuals found have been quite low. The one exception to this being a population in the Moors River, Dorset and South Hampshire, England, where a substantially larger population exists. Using seven different enzyme systems, this study provided support for the putative parental origin of this hybrid. In addition, the population in the Moors River was shown to contain numerous multi-locus phenotypes suggesting that these individuals may be partially fertile and may backcross to one of its parental species, or alternatively undergo selfing or crossing to produce an F₂ generation. Received December 1, 2000 Accepted June 20, 2001     

Formation of highly ordered cross-linked lattices between asparagine-linked oligosaccharides and lectins observed by electron microscopy

The interaction of asparagine-linked carbohydrates (N-linked) with carbohydrate binding proteins called lectins has been demonstrated to be involved in a variety of cellular recognition processes. Certain N-linked carbohydrates have been shown to be multivalent and capable of binding, cross-linking, and precipitating lectins (Bhattacharyya, L., Ceccarini, C., Lorenzoni, P., and Brewer, C. F. (1987) J. Biol. Chem. 262, 1288-1293; Bhattacharyya, L., Haraldsson, M., and Brewer, C. F. (1987) J. Biol. Chem. 262, 1294-1299; Bhattacharyya, L., Haraldsson, M., and Brewer, C. F. (1988) Biochemistry 27, 1034-1041). Recent data have further suggested that certain oligomannose and bisected hybrid-type N-linked glycopeptides form homogeneous cross-linked lattices with concanavalin A (Bhattacharyya, L., Khan, M. I., and Brewer, C. F. (1988) Biochemistry 27, 8762-8767). In the present study, evidence has been obtained from electron microscopy for the formation of highly ordered and distinct lattices for two bivalent complex type oligosaccharides cross-linked with soybean lectin (Glycine max) and isolectin A from Lotus tetragonolobus, respectively. The results indicate a new source of specificity for interactions of N-linked carbohydrates with lectins, namely their ability to form highly ordered homogeneous aggregates.