Capacity of Lemna gibba L. (duckweed) for uranium and arsenic phytoremediation in mine tailing waters

The potential of Lemna gibba L. to clean uranium and arsenic contamination from mine surface waters was investigated in wetlands of two former uranium mines in eastern Germany and in laboratory hydroponic culture. Water and plants were sampled and L gibba growth and yield were monitored in tailing ponds from the field study sites. Contaminant accumulation, growth and yield experiments were conducted in the laboratory using synthetic tailing water. Mean background concentrations of the surface waters were 186.0+/-81.2 microg l(-1) uranium and 47.0+/-21.3 microg l(-1) arsenic in Site one and 293.7+/-121.3 microg l(-1) uranium and 41.37+/-24.7 microg l(-1) arsenic in Site two. The initial concentration of both uranium and arsenic in the culture solutions was 100 microg l(-1). The plant samples were either not leached, leached with deionized H2O or ethylenediaminetetracetic (EDTA). The results revealed high bioaccumulation coefficients for both uranium and arsenic. Uranium and arsenic content of L gibba dry biomass of the field samples were as follows: nonleached samples > deionized H2O leached (insignificant ANOVA p = 0.05) > EDTA leached. The difference in both arsenic and uranium enrichment were significantly high between the nonleached and the other two lead samples tested at ANOVA p > 0.001. Estimated mean L gibba density in surface water was 85,344.8+/-1843.4 fronds m(-2) (approximately 1319.7 g m(-2)). The maximum specific growth rate was 0.47+/-0.2 d(-1), which exceeded reported specific growth rates for L gibba in the literature. Average yield was estimated at 20.2+/-6.7 g m(-2) d(-1), giving approximately 73.6+/-21.4 t ha(-1) y(-1) as the annual yield. The highest accumulations observed were 896.9+/-203.8 mg kg(-1) uranium and 1021.7+/-250.8 mg kg(-1) arsenic dry biomass for a 21-d test period in the laboratory steady-state experiments. The potential extractions from surface waters with L gibba L. were estimated to be 662.7 kg uranium ha(-1) yr(-1) and 751.9 kg arsenic ha(-1) yr(-1) under the above conditions.     

Average protein density is a molecular-weight-dependent function

The mass density of proteins is a relevant basic biophysical quantity. It is also a useful input parameter, for example, for three-dimensional structure determination by protein crystallography and studies of protein oligomers in solution by analytic ultracentrifugation. We have performed a critical analysis of published, theoretical, and experimental investigations about this issue and concluded that the average density of proteins is not a constant as often assumed. For proteins with a molecular weight below 20 kDa, the average density exhibits a positive deviation that increases for decreasing molecular weight. A simple molecular-weight-depending function is proposed that provides a more accurate estimate of the average protein density.     

Analysis of part of the<Emphasis Type="Italic">Trichophyton rubrum</Emphasis> ESTs

Trichophyton rubrum (T. rubrum) is the most common of the superficial fungi. In an effort to better understand the genetic and biochemical makeup ofT. rubrum, we generated cDNA libraries from 3 growth stages and used these to isolate 4002 unique expressed sequence tags (ESTs). Sequence comparisons with the Genbank database allowed 1226 of the ESTs to be assigned putative functions or matched with homologs from other organisms. Of the remaining ESTs, 989 were only weakly similar to known sequences and 1787 had no identifiable functions, suggesting that they represent novel genes. We further analyzed the presence of several important genes involved in the growth, metabolism, signal transduction, pathogenesis and drug resistance inT. rubrum. This information was used to newly elucidate important metabolic pathways inT. rubrum. Taken together, our results should form the molecular basis for continued research on the physiological processes and pathogenic mechanisms ofT. rubrum, and may lead to a better understanding of fungal drug resistance and identification of new drug targets.     

Rapid genotyping of the osteoporosis-associated polymorphic transcription factor Sp1 binding site in the COL1A1 gene by pyrosequencing

We describe a novel polymerase chain reaction (PCR) and deoxyribonucleic acid (DNA) sequencingbased assay for rapid genotyping of the polymorphic Sp1 binding site in the COL1A1 gene (1). A single nucleotide G-->T substitution polymorphism at this GC-rich site has recently been reported to be a predictive genetic marker for low bone mineral density (BMD). To simplify screening for this marker, we optimized PCR conditions and subjected the amplicons to pyrosequencing, which is a convenient high-throughput sequence analysis technique, readily amenable to automation. The analysis of 200 deidentified convenience DNA samples extracted from blood revealed genotype frequences in Hardy-Weinberg equilibrium (SS 68.0%, Ss 28.5%, and ss 3.5%) in agreement with other studies of European populations. This study demonstrates for the first time that pyrosequencing can be used for rapid identification of the osteoporosis-associated single nucleotide polymorphism (SNP) in the COL1A1 gene.     

Effects of plant traits on ecosystem and regional processes: a conceptual framework for predicting the consequences of global change

Human activities are causing widespread changes in the species composition of natural and managed ecosystems, but the consequences of these changes are poorly understood. This paper presents a conceptual framework for predicting the ecosystem and regional consequences of changes in plant species composition. Changes in species composition have greatest ecological effects when they modify the ecological factors that directly control (and respond to) ecosystem processes. These interactive controls include: functional types of organisms present in the ecosystem; soil resources used by organisms to grow and reproduce; modulators such as microclimate that influence the activity of organisms; disturbance regime; and human activities. Plant traits related to size and growth rate are particularly important because they determine the productive capacity of vegetation and the rates of decomposition and nitrogen mineralization. Because the same plant traits affect most key processes in the cycling of carbon and nutrients, changes in plant traits tend to affect most biogeochemical cycling processes in parallel. Plant traits also have landscape and regional effects through their effects on water and energy exchange and disturbance regime.     

Differential mesowear in occluding upper and lower molars: opening mesowear analysis for lower molars and premolars in hypsodont horses

A new approach of reconstructing ungulate diet, the mesowear method, was recently introduced by Fortelius and Solounias ([2000] Am Mus Novitat 3301:1-36). Mesowear is based on facet development on the occlusal surfaces of the teeth. Restricting mesowear investigation to maxillary cheek teeth would allow mesowear investigation only in assemblages of large numbers of individuals and therefore would generally restrict this method to relatively few assemblages of recent and fossil ungulates. Most of the fossil, subfossil, and recent ungulate osteological assemblages that may be assigned to a single taxon have smaller numbers of individuals. This results in a demand to extend the mesowear method to further tooth positions in order to obtain stable dietary classifications of fossil taxa. The focus of this article is to test if a consistent mesowear classification is obtainable for mandibular as well as for maxillary teeth. For statistical testing, large assemblages of isolated cheek teeth of the Vallesian hipparionine horse Hippotherium primigenium and of the recent zebra Equus burchelli were employed as models. The upper tooth positions P4, M1, M2, and M3 as suggested by Kaiser and Solounias (2003) as the model for the "extended" mesowear method and the lower tooth positions P4-M3 were tested for their consistency in classification of the mesowear variables. We found a considerable shift of the mesowear signature towards the grazing edge of the mesowear continuum in lower cheek teeth. In order to adjust the signal of lower teeth to the signal of the upper teeth, a calibration factor was introduced which allowed incorporation of lower cheek teeth into the same model of mesowear investigation together with upper cheek teeth. We propose that this model is particularly suited for the reconstruction of paleodiets in hypsodont hipparionine and equine equids. We further investigated the functional relation between the mesowear profiles and the distribution of dental tissues along the course of the occlusal contact. We therefore correlated mesowear profiles with enamel distribution profiles and found the mesowear profile to be strongly controlled by the attritional environment encountered by a given apex area. The differential signal observed in cusp apex morphology between upper and lower cheek teeth was found to be more closely related to attrition by the antagonistic tooth than to the distribution of dental tissues in the tooth under consideration. The results suggest a general extension of the mesowear method of paleodiet reconstruction and a basic scenario for the evolution of anisodont dentitions.     

Functional-adaptive anatomy of the axial skeleton of some extant marsupials and the paleobiology of the paleocene marsupials Mayulestes ferox and Pucadelphys andinus

In this study, the axial skeletons of two Early Paleocene marsupials, Mayulestes ferox and Pucadelphys andinus, were analyzed functionally and compared to that of six South American and three Australian species of extant marsupials. In the case of the South American opossums, myological data of the epaxial musculature were collected and analyzed and osteological-myological associations were related to locomotor behavior. Various features of the vertebral column that relate to diet or to locomotor or postural patterns were pointed out. These features include: the craniocaudal development of the neural process of the axis; the position of the anticlinal vertebra; the morphology of the neural processes of the thoracolumbar vertebrae (orientation, length, and craniocaudal width); the length, orientation, and curvature of the transverse processes of the lumbar vertebrae; and the length and robustness of the caudal vertebrae. In both fossil forms the vertebral column is mobile and allows a great range of flexion and extension of the spine, more so than in most of the living didelphids. It is emphasized here that the analysis of the axial skeleton complements and improves the conclusions provided by the forelimb and hindlimb analyses. It is proposed that Mayulestes and Pucadelphys represent an ancestral morphotype suggesting that the generalized type of locomotion of Paleocene marsupials was partly terrestrial with some climbing ability.     

Efficient identification of side-chain patterns using a multidimensional index tree

Convergent evolution often produces similar functional sites in nonhomologous proteins. The identification of these sites can make it possible to infer function from structure, to pinpoint the location of a functional site, to identify enzymes with similar enzymatic mechanisms, or to discover putative functional sites. In this article, a novel method is presented that (a) queries a database of protein structures for the occurrence of a given side chain pattern and (b) identifies interesting side-chain patterns in a given structure. For efficiency and to make a robust statistical evaluation of the significance of a similarity possible, patterns of three residues (or triads) are considered. Each triad is encoded as a high-dimensional vector and stored in an SR (Sphere/Rectangle) tree, an efficient multidimensional index tree. Identifying similar triads can then be reformulated as identifying neighboring vectors. The method deals with many features that otherwise complicate the identification of meaningful patterns: shifted backbone positions, conservative substitutions, various atom label ambiguities and mirror imaged geometries. The combined treatment of these features leads to the identification of previously unidentified patterns. In particular, the identification of mirror imaged side-chain patterns is unique to the here-described method. Interesting triads in a given structure can be identified by extracting all triads and comparing them with a database of triads involved in ligand binding. The approach was tested by an all-against-all comparison of unique representatives of all SCOP superfamilies. New findings include mirror imaged metal binding and active sites, and a putative active site in bacterial luciferase.     

Comparison of (13)C(alpha)H and (15)NH backbone dynamics in protein GB1

This study presents a site-resolved experimental view of backbone C(alpha)H and NH internal motions in the 56-residue immunoglobulin-binding domain of streptococcal protein G, GB1. Using (13)C(alpha)H and (15)NH NMR relaxation data [T(1), T(2), and NOE] acquired at three resonance frequencies ((1)H frequencies of 500, 600, and 800 MHz), spectral density functions were calculated as F(omega) = 2omegaJ(omega) to provide a model-independent way to visualize and analyze internal motional correlation time distributions for backbone groups in GB1. Line broadening in F(omega) curves indicates the presence of nanosecond time scale internal motions (0.8 to 5 nsec) for all C(alpha)H and NH groups. Deconvolution of F(omega) curves effectively separates overall tumbling and internal motional correlation time distributions to yield more accurate order parameters than determined by using standard model free approaches. Compared to NH groups, C(alpha)H internal motions are more broadly distributed on the nanosecond time scale, and larger C(alpha)H order parameters are related to correlated bond rotations for C(alpha)H fluctuations. Motional parameters for NH groups are more structurally correlated, with NH order parameters, for example, being larger for residues in more structured regions of beta-sheet and helix and generally smaller for residues in the loop and turns. This is most likely related to the observation that NH order parameters are correlated to hydrogen bonding. This study contributes to the general understanding of protein dynamics and exemplifies an alternative and easier way to analyze NMR relaxation data.     

A structural-informatics approach for mining beta-sheets: locating sheets in intermediate-resolution density maps

Here, we report a new computational method, called sheetminer, for mining beta-sheets in the density maps at intermediate resolutions of 6 to 10A. The method employs a multi-step ad hoc morphological analysis of density maps to identify the unique characteristics of beta-sheets. It was tested on density maps from 12 protein crystal structures that were artificially blurred to intermediate resolutions. There are a total of 35 independent beta-sheets with a wide distribution of morphology. The method successfully located 34 of them and missed only one. The method was also applied to an experimental 9A electron cryomicroscopic structure and an 8A X-ray density map. In both cases, the sheet-searching results were found to agree very well with known high-resolution crystal structures. Collectively, these results demonstrate clearly the robustness of sheetminer in locating the regions belonging to beta-sheets in the intermediate-resolution density maps. Furthermore, sheetminer is completely complementary to all other existing computational methods, including helixhunter and threading algorithms. Their combined usage has the potential to significantly enhance the computational modeling capacity for a much more complete interpretation of structural data at intermediate resolutions, from which extraction of functional information would be more effective. This is particularly important in the field of structural genomics, in which the fast screening approach may not always yield crystals that diffract to atomic resolution. An exciting future application of sheetminer is as a valuable tool for revealing the structures of amyloid fibrils that are rich in beta-motifs.