Differences in light interception in grass monocultures predict short-term competitive outcomes under productive conditions

Due to its inherent asymmetry, competition for light is thought to cause loss of diversity from eutrophied systems. However, most of the work on this topic in grasslands has been phenomenological and has not measured light directly. We present the results of one of the few mechanistic experiments investigating the outcome of short-term competition using measurements of light interception from monocultures of five perennial grass species grown under fertilized and irrigated conditions. We found that the level of incident light intercepted by each species in monoculture, a direct measure of resource-reduction ability, was an excellent predictor of the relative competitive effect in pairwise mixtures. Competition for light was asymmetric in relation to differences in light intercepting ability. Our results are consistent with the idea that when light is a limiting resource, competition between species for this resource can be asymmetric, contributing to high dominance and low diversity.     

The effects of 5‐azacytidine and cadmium on global 5‐methylcytosine content and secondary metabolites in the freshwater microalgae Chlamydomonas reinhardtii and Scenedesmus quadricauda

Epigenetic changes are important mechanisms in the regulation of chromatin structure and gene expression. Cytosine methylation is one of the major epigenetic modifications, mediated by DNA methyltransferases, which transfer methyl groups from S‐adenosyl‐L‐methionine (SAM) to the fifth carbon of cytosine. Various external environmental conditions can change the global hypo/hypermethylation pattern of DNA. These alterations may affect the organism's response to stress conditions. In this study, for the first time, we investigated the effects of 5‐azacytidine, a DNA methyltransferase inhibitor, and cadmium, a toxic metal and environmental pollutant, on the growth, biosynthesis of secondary metabolites (phenols, flavonoids, carotenoids), SAM, S‐adenosylhomocysteine, 5′‐methylthioadenosine and global 5‐methylcytosine (5‐mC) in the green microalgae Chlamydomonas reinhardtii and Scenedesmus quadricauda. The studied species showed major differences in 5‐mC content, secondary metabolite content, and antioxidant activity. Cadmium increased GSH (glutathione) content in C. reinhardtii by 60% whereas 5‐azacytidine did not affect GSH. The biosynthesis of GSH in S. quadricauda in response to the stressors was the opposite. Global 5‐mC content of C. reinhardtii was 1%–1.5%, and the content in S. quadricauda was 3.5%. Amount of some investigated methionine cycle metabolites (SAM, S‐adenosyl homocysteine [SAH], methionine) in S. quadricauda distinctly exceeded C. reinhardtii as well. However, chlorophylls a and b, carotenoids, total phenolic content, total flavonoid content and, antioxidant activity were significantly higher in C. reinhardtii than S. quadricauda. Therefore, in further studies it would be advisable to verify whether methylation of cytosine affects the expression of genes encoding certain secondary metabolites.     

Metallohelix vectors for efficient gene delivery via cationic DNA nanoparticles

The design of efficient and safe gene delivery vehicles remains a major challenge for the application of gene therapy. Of the many reported gene delivery systems, metal complexes with high affinity for nucleic acids are emerging as an attractive option. We have discovered that certain metallohelices—optically pure, self-assembling triple-stranded arrays of fully encapsulated Fe—act as nonviral DNA delivery vectors capable of mediating efficient gene transfection. They induce formation of globular DNA particles which protect the DNA from degradation by various restriction endonucleases, are of suitable size and electrostatic potential for efficient membrane transport and are successfully processed by cells. The activity is highly structure-dependent—compact and shorter metallohelix enantiomers are far less efficient than less compact and longer enantiomers.     

One-electron oxidation of beta-amyloid peptide: sequence modulation of reactivity

Amyloid beta peptide (Abeta) is a 39 to 43 amino-acid-long peptide implicated in Alzheimer's disease. One of its mechanisms of toxicity is related to its redox properties. Therefore we studied its one electron oxidation using azide free radicals produced in gamma and pulse radiolysis, and compared the results with those obtained with the reverse sequence Abeta(40-1). HPLC analysis combined with absorption, fluorescence, Raman spectroscopy, and MALDI-TOF MS were used for product identification. Met35 was shown to be the target in Abeta(1-40); oxidation leads to a major compound that is Abeta with methionine sulfoxide. Similarly, oxidation of fragment Abeta(29-40) also leads to methionine sulfoxide. For Abeta(40-1), Met35 is not reactive and Tyr10 is the target of azide radicals. The major products are peptide dimer linked by dityrosine and trimer. The lowering of the one-electron reduction potential of the MetS+/Met couple, which was proposed, is in agreement with our findings. To our knowledge, this is the first time that such a drastic effect of the primary sequence is observed in a small peptide. In addition, it is also the first experimental demonstration of the sensitivity of the one-electron reduction potential of methionine on neighboring groups.     

Sensitive assays for simian foamy viruses reveal a high prevalence of infection in commensal, free-ranging Asian monkeys

Foamy viruses (FV) are retroviruses that naturally infect many hosts, including most nonhuman primates (NHPs). Zoonotic infection by primate FV has been documented in people in Asia who reported contact with free-ranging macaques. FV transmission in Asia is a concern, given abundant human-NHP contact, particularly at monkey temples and in urban settings. We have developed three assays capable of detecting the presence of FV in Asian NHP species that are commensal with humans: enzyme-linked immunosorbent assay (ELISA), Western blot assays using recombinant viral Gag protein, and an indicator cell line that can detect macaque FV. The recombinant ELISA correlates very well with the presence of FV sequences detected by PCR. We have used these assays to demonstrate both that FV is highly prevalent among free-ranging NHPs and that seroconversion occurs at a young age in these animals. These assays should also prove useful for large-scale analysis of the prevalence of FV infections in human populations in Asia that are commensal with free-ranging NHPs.     

Climate and pH as determinants of vegetation succession in Central European man‐made habitats

Questions: (1) What are the most important abiotic environmental variables influencing succession in central European man‐made habitats? (2) How do these variables interact with one another and with variation in community properties? Location: Central, western and southern parts of the Czech Republic. Habitats included old fields, urban sites, spoil heaps after coal mining, sites at water reservoirs, extracted sand pit and peatland and reclaimed sites in areas deforested by air pollution. Methods: We investigated vegetation patterns on 15 succes‐sional seres, sampled by the same methods. Time of succession over which the data were available ranged from 12 to 76 years. The cover of vascular plant species (in %) was estimated in 5 m × 5 m plots. The relationships between vegetation characteristics (species composition, total cover, cover of woody species, species number and rate of dominant species turnover) and 13 abiotic site factors, including climatic and soil variables, were tested using CCA ordination and regression models. Results: Substratum pH, the only substratum characteristic, and climate were the environmental variables significantly affecting the vegetation patterns in the course of succession. The rate of succession, measured as the turnover of dominant species, was significantly more rapid in lowland than in mountain climates. On alkaline soils, species numbers in succession increased towards warmer climates. However, acid soils prevented any increase in species numbers, regardless of the climate. Surprisingly, forms of nitrogen and contents of C, P and cations did not exhibit any significant effect on the vegetation characteristics studied. Conclusions: Our approach, to compare a number of seres, can contribute not only to our understanding of succession, but also to help restoration projects to predict vegetation change because the crucial environmental variables, as identified by this study, are easy to measure.     

Tyrosine residues modification studied by MALDI-TOF mass spectrometry

Amino acid residue-specific reactivity in proteins is of great current interest in structural biology as it provides information about solvent accessibility and reactivity of the residue and, consequently, about protein structure and possible interactions. In the work presented tyrosine residues of three model proteins with known spatial structure are modified with two tyrosine-specific reagents: tetranitromethane and iodine. Modified proteins were specifically digested by proteases and the mass of resulting peptide fragments was determined using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Our results show that there are only small differences in the extent of tyrosine residues modification by tetranitromethane and iodine. However, data dealing with accessibility of reactive residues obtained by chemical modifications are not completely identical with those obtained by nuclear magnetic resonance and X-ray crystallography. These interesting discrepancies can be caused by local molecular dynamics and/or by specific chemical structure of the residues surrounding.     

Comparison of bacterial flora and enzymatic activity in faeces of infants and calves

Sixty-four breast-fed infants and 23 calves were investigated for bacteria and enzymatic activity in their faecal samples. The bacteria were measured using cultivation and fluorescence in situ hybridization. Enzymatic activity was also examined. Forty-seven (64%) infants and all the calves had high numbers of bifidobacteria (usually >9 log CFU g-1) in their faeces, but 17 infants (36%) did not have a detectable amount of the bacteria. Most of the bifidobacteria-negative infants had significant quantities of clostridia in their faecal flora. While the infants did not have significantly higher counts of bifidobacteria, the samples from calves contained significantly (P<0.05) more coliform bacteria and lactobacilli. There were also significant differences in their enzymatic activities. Bifidobacteria-positive samples had a greater alpha-glucosidase activity, while bifidobacteria-negative samples had a lower activity of alpha-galactosidase, and calf samples had the highest beta-glucuronidase activity. A significant increase in bifidobacteria in calf faeces between days 3 and 7 was accompanied by a decrease in Escherichia coli. Our results show that the faecal flora of calves is similar to that of infants with regard to the occurrence of bifidobacteria as a dominant bacterial group.     

Tissue Specific Electrochemical Fingerprinting

Background

Proteomics and metalloproteomics are rapidly developing interdisciplinary fields providing enormous amounts of data to be classified, evaluated and interpreted. Approaches offered by bioinformatics and also by biostatistical data analysis and treatment are therefore of extreme interest. Numerous methods are now available as commercial or open source tools for data processing and modelling ready to support the analysis of various datasets. The analysis of scientific data remains a big challenge, because each new task sets its specific requirements and constraints that call for the design of a targeted data pre-processing approach.

Methodology/Principal Findings

This study proposes a mathematical approach for evaluating and classifying datasets obtained by electrochemical analysis of metallothionein in rat 9 tissues (brain, heart, kidney, eye, spleen, gonad, blood, liver and femoral muscle). Tissue extracts were heated and then analysed using the differential pulse voltammetry Brdicka reaction. The voltammograms were subsequently processed. Classification models were designed making separate use of two groups of attributes, namely attributes describing local extremes, and derived attributes resulting from the level = 5 wavelet transform.

Conclusions/Significance

On the basis of our results, we were able to construct a decision tree that makes it possible to distinguish among electrochemical analysis data resulting from measurements of all the considered tissues. In other words, we found a way to classify an unknown rat tissue based on electrochemical analysis of the metallothionein in this tissue.